Major birth defects are inborn structural or functional anomalies with long-term disability and adverseimpacts on individuals, families, health-care systems, and societies. Approximately 20% of birth defects are dueto chromosomal and genetic conditions. Inspired by the fact that neonatal deaths are caused by birth defects inabout 20 and 10% of cases in Iran and worldwide respectively, we conducted the present study to unravel the roleof chromosome abnormalities, including microdeletion/microduplication(s), in multiple congenital abnormalitiesin a number of Iranian patients. In this descriptive cross-sectional study, 50 sporadic patients with Multiple CongenitalAnomalies (MCA) were selected. The techniques employed included conventional karyotyping, fluorescence insitu hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA), and array comparative genomichybridisation (array-CGH), according to the clinical diagnosis for each patient. Chromosomal abnormalities and microdeletion/microduplication(s) were observed in eight out of fifty patients(16%). The abnormalities proved to result from the imbalances in chromosomes 1, 3, 12, and 18 in four of the patients.However, the other four patients were diagnosed to suffer from the known microdeletions of 22q11.21, 16p13.3, 5q35.3,and 7q11.23.In the present study, we report a patient with 46,XY, der(18)[12]/46,XY, der(18), +mar[8] dn presentedwith MCA associated with hypogammaglobulinemia. Given the patient’s seemingly rare and highly complexchromosomal abnormality and the lack of any concise mechanism presented in the literature to justify the case,we hereby propose a novel mechanism for the formation of both derivative and ring chromosome 18. In addition,we introduce a new 12q abnormality and a novel association of an Xp22.33 duplication with 1q43q44 deletionsyndrome. The phenotype analysis of the patients with chromosome abnormality would be beneficial for furtherphenotype-genotype correlation studies. Major birth defects are considered to be inbornstructural or functional abnormalities which couldbe diagnosed prenatally, at birth, or later in infancy,or even in adulthood. Their consequence will bea long-term disability with major adverse effectson individuals, families, health-care systems, andsocieties . ApproxiGenetic factors are regarded as one of the mostprominent etiologies of MCA . Also, cIn this descriptive cross-sectional study conductedduring the three past years from April 2015 to May2018, clinical evaluation was performed for 50 selectedsporadic patients suffering from MCA preferably bornto unrelated parents and referred to us by experiencedclinical specialists for genetic investigation from allover the country. All of the patients had ID/DD withat least one major anomaly and additional minordysmorphic features. All of the steps taken for testingand procedures were fully explained for all of theprobands’ parents, and signed informed consent formsfrom all of the participants were obtained for publishingany information or accompanying photographs. Thisstudy was approved by the Ethics Committee of theUniversity of Social Welfare and RehabilitationSciences (IR.USWR.REC.1394.186).A conventional cytogenetic study was carried out onperipheral blood lymphocytes using GTG high-resolutionbanding technique according to standard protocols forall patients . Twenty Metaphase FISH was done only for patient 9 usingthe centromeric probe of chromosome 18  according to Kreatech protocol for the patients suspected of microdeletion/microduplication syndromes. MLPA protocol wasperformed based on the instructions provided by themanufacturer, MRC Holland, and the data were analyzedutilizing capillary electrophoresis in the 3130XL DNAAnalyzer, Coffalyser. Net software  and Gene Marker softwareversion 2.7.0 .Abnormal results obtained with MLPA assay wererepeated and if different, further investigations werecarried out with array-CGH. MLPA studies were donefor the patients’ parents with abnormal results in orderto determine the causal role (de novo or inherited) ofmicrodeletions.The analysis of oligonucleotide array-CGHfor Genomic DNA was carried out. To do so, theBlueGnome CytoChip ISCA 8×60 K v2.0 wholegenomeoligo array was utilized for patients 1, 5,9, 13, and 41. This array included intragenic andintergenic probe spacings of about 48 kb and 70 kb,respectively and high probe density in 500 clinicallyimportant regions. CytoSNP-850K v1.1 BeadChipoverall effective resolution of about 18 Kb was usedfor patient 27. The tests were performed based onthe manufacturer’s protocol. INNOPSYS 910 laserscanner was utilized for scanning according to therecommended protocol of the manufacturer. Imageanalysis and base calling were carried out employingthe BlueFuse Multi-version 3 analysis software foroligo array and Multi-version 4.4 analysis softwarefor SNP array. The analysis of the samples was carriedout two times against two non-identical controlsand representation of minimum three clones on theplatform in both of the experiments was consideredto approve the imbalances. To evaluate the calledCNVs, we utilized the standards and guidelines ofAmerican College of Medical Genetics and Genomicsto interpret the postnatal constitutional CNVs ,craniofacial dysmorphic features in 31 patients (62%),musculoskeletal, ear and genitourinary abnormalities,each one in 19 patients (38%), eye abnormalities in16 patients (32%), gastrointestinal abnormalities in5 patients (10%), and endocrine abnormalities in 3patients (6%) .In patient 9, a 31-month-old boy fromconsanguineous parents  and bornto a 27-year-old G1P1L1A0  mother, the clinical featureswere global DD, PDA, PFO, optic nerve hypoplasia,hypogammaglobulinemia, facial dysmorphic features,microcephaly, and mild ventriculomegaly in frontalhorns in the axial spiral CT-scan of the brain withoutcontrast, and benign extra-axial hydrocephalus andatrophic changes in the brain magnetic resonanceimaging (MRI). The karyotype analysis by highresolutionGTG banding showed 46,XY, der[12]/46,http://www.ecaruca.net) , epilepsy, abnormal EEG, hypotonia, andtrigonocephaly , carriedThe karyotype of patient 27, an 18-year-old boy fromnon-consanguineous parents and born to a 31-year-oldG7P6L6A1 mother at term, had been reported as a normalmale in his medical documents. The result of furtherinvestigation using P245 Microdeletion Syndromes-1kit was negative for the microdeletion/microduplicationsyndromes. The clinical features were ID, tetralogy offallot (TOF), microcephaly, severe scoliosis, short stature,speech delay, and facial dysmorphic features .In the Patient 1 was a 14-month-old girl from healthyand young non-consanguineous parents born throughnormal vaginal delivery to a G1P1L1A0 mother atterm. The clinical characteristics were ID, intrauterinegrowth restriction (IUGR), hypotonia, hypothyroidism,supravalvular aortic stenosis, supravalvular pulmonarystenosis, left visual defect, attention deficit/hyperactivitydisorder, strabismus, long philtrum, and thick lips.Conventional cytogenetic analysis was normal. MLPAscreening demonstrated a deletion of 7q11.23 consistentwith Williams-Beuren syndrome. Further assays usingarray-CGH confirmed about 1.37 Mb deletion including22 OMIM genes. Array-CGH analyses of the parentswere normal.Patient 5 was a 5.5-year-old girl, born through normalvaginal delivery to healthy and young non-consanguineousparents following a full-term pregnancy. Her mother wasG2P1L1A1. She had suffered constipation for the firstsix months after birth. At the age of 14 months, the renalcortical scan revealed lesser activity in the lower pole ofthe left kidney because of pyelonephritis. During voidingcystourethrogram, severe urinary tract reflux was presentin the left kidney. She also had a large ASD, ID, seizureattacks, autistic behavior, macrocephaly, dolicocephaly,frontal bossing, fish-shaped mouth, sparse hair, and jointlaxity. She can say up to 5 words. The karyotype analysiswas normal. MLPA assay revealed a deletion of 5q35.3consistent with Sotos syndrome. Further investigationsusing array-CGH confirmed 1.86 Mb deletion including25 OMIM genes. Array-CGH analyses of the parentswere normal.Patient 13 was a 3-year-old boy who was theproduct of the first pregnancy and cesarean delivery ofnonconsanguineous parents. The clinical features werewidow’s pick hair, down-slanting palpebral fissures, longeyelashes, deep set eyes, malformed, posteriorly rotatedand low set ears, upward nose and nares, long philtrum,small mouth, high arched palate, high pitched cry, wheezingrespiratory sounds, cardiac surgery scar, simian crease, 5thtoe clinodactyly, umbilical hernia, sacral mongolian spot,overriding of 1st toe with 2nd toe, right lower limb paresis,joint contractures, right sided tippy-toed walking andbilateral undescended testes. Axial spiral CT-scan of thebrain without contrast media showed bilateral pachygyriaat frontotemporoparietal lobes due to abnormal neuronalmigration. The karyotype analysis was normal. MLPAassay detected a deletion of 22q11.21 consistent withDiGeorge syndrome. Further investigations using array-CGH confirmed 2.86 Mb deletion including 41 OMIMgenes, arr 22q11.21  x1 dn.Array-CGH analyses of the parents were normal.Patient 35 was a 7-month-old girl born through cesareansection to a healthy consanguineous (first cousin) couple.Her mother was G1P1L1A0. She had bilateral cataracts,hypertelorism, left ptosis, frontal bossing, low set ears, longphiltrum, broad nasal bridge, micrognathia, a borderline lacticacid and normal creatinine in urine, ascending aorta dilatation,peripheral pulmonary stenosis, and small ASD. Conventionalcytogenetic analysis showed a normal female karyotype. TheMLPA technique indicated a deletion of 16p13.3 consistentwith Rubinstein-Taybi syndrome. The sample assay wascarried out twice. The parents’ karyotype analyses and MLPAassays were normal.Based on several studies, the diagnostic yields ofconventional cytogenetic studies in patients with MCA,global DD, and autism spectrum disorders, barring theknown trisomy syndromes, have been reported to beabout 3% . In thisWell-defined microdeletion syndromes were the mostcommon cause of MCA in this study, consistent withthe results of previously reported studies . ThecliAccording to a hypothesis, two critical regions arewithin the long arm of chromosome 18 (18q), including18q12.1-q21.2 and 18q22.3-qter. Duplication occurrenceis essential in both proximal and distal regions in orderto cause the typical clinical features of a trisomy 18 tobe manifested , previously introduced as astrong candidate gene associated with autism spectrumdisorders (SLC6A1 and SLC6A11encoding GABA transporter proteins have been proposedas possible candidates for seizures/EEG abnormalities,ataxia, and ID (The autistic behavior of patient 41 may be becauseof isorders . Two gen, and ID .AKT3 gene haploinsufficiency has been linkedwith microcephaly in previously reported cases with1q43q44 deletion syndrome (AKT3 gene, the other candidate genes such as NLRP3,HNRNPU, SMYD3, and KIF26B have been suggestedto cause microcephaly (AKT3 deletionmay explain the severity of microcephaly in patient 27.1q43q44 deletion in patient 27 with the size of 7.2Mb included 126 HGNC and 19 OMIM genes. Of thesegenes, syndrome . Howeverocephaly . NonetheZBTB18 and HNRNPUgenes in the patients with 1q43q44 deletion syndrome,respectively (ZBTB18 andHNRNPU disruptions. Recent studies have suggestedthat modifier genes or two-hit hypothesis may explainvariable expressions among some patients with identicalmicrodeletions. Another CNV is a disruptive singlebase-pair mutation in a related gene or an environmentalevent which influences the phenotype. These are all theexamples of the second hit (Corpus callosum agenesis/hypoplasia and epilepsy aremostly associated with deletions of ectively . Howevercond hit .PLCXD1, GTPBP6 and PPP2R3Bgenes as well as exons 1-3 and part of exon 4 of SHOX gene.PPP2R3B is one of the four major Ser/Thr phosphatasesand negatively affects cell growth and division. PPP2R3Bperforms a regulatory control over the starting of DNAreplication and its overexpression results in G1 phase cellcycle arrest (Patient 27 also had a duplication of about 541 Kb inXp22.33 containing e arrest .SHOXgene. Although some studies point to a correlationbetween SHOX gene deletions and short stature and Leri-Weill dyschondrosteosis, others have found some patientswith the same clinical features who had partial or fullduplications of SHOX gene. Bunyan et al. (SHOX gene in apatient who had only short stature with no other clinicalfindings inherited from the proband’s affected mother.Co-overexpression of PPP2R3B and SHOX genes seemsto have a synergistic effect on our proband’s short statureseverity.There has been a variable impact on stature due toduplications of the region PAR1 containing the n et al.  reportedIn this study, 50 patients with MCA were studied interms of chromosomal abnormalities and microdeletion/microduplication syndromes. A patient was introduced with46,XY, der[12]/46,X


Plants constantly suffer from simultaneous infection by multiple pathogens, which can be divided into biotrophic, hemibiotrophic, and necrotrophic pathogens, according to their lifestyles. Many studies have contributed to improving our knowledge of how plants can defend against pathogens, involving different layers of defense mechanisms. In this sense, the review discusses: (1) the functions of PAMP (pathogen-associated molecular pattern)-triggered immunity (PTI) and effector-triggered immunity (ETI), (2) evidence highlighting the functions of salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET)-mediated signaling pathways downstream of PTI and ETI, and (3) other defense aspects, including many novel small molecules that are involved in defense and phenomena, including systemic acquired resistance (SAR) and priming. In particular, we mainly focus on SA and (JA)/ET-mediated signaling pathways. Interactions among them, including synergistic effects and antagonistic effects, are intensively explored. This might be critical to understanding dynamic disease regulation. Phytophthora parasitica, Erysiphe orontii, and Erysiphe cichoracearum [Botrytis cinerea, Alternaria brassicicola, and Sclerotinia sclerotiorum are taken as general examples of necrotrophic infections that kill hosts using toxic metabolites, enzymes, or microRNAs [B.cinerea small RNAs hijack the host RNA interference machinery to achieve virulence [Pseudomonas syringae is often taken as a hemibiotroph [Since they exposed to challenging environments, plants face great threats from pathogen infections. Pathogens can be classified into three categories—biotrophic, necrotrophic, and hemibiotrophic pathogens—according to their different infection strategies . Biotropracearum . NecrotricroRNAs ,3,4. Forirulence . Hemibiobiotroph .Arabidopsis; however, examples from other species are introduced as well, where appropriate.During the long-term battle with pathogens, plants have developed sophisticated defense mechanisms to fight pathogen attacks. ,7,8. HerPlants are sessile, and thus, they have developed effective methods to fight against pathogens. Once pathogens have overcome physical barriers such as the cell wall, the most important issue for defense will be the pathogen’s perception. A “zigzag” model of plant immunity was given by Jones and Dangl to describe the evolutionary development of the plant immune system . SimilarPseudomonas syringae [Botryosphaeria dothidea, which is an apple disease [Arabidopsis SG2-type R2R3-MYB transcription factor, MYB15 [Arabidopsis, can be regulated by two major enzymes: Arabidopsis cytochrome P450 monooxygenase 71A13 (CYP71A13), and Arabidopsis cytochrome P450 monooxygenase 71B15/ phytoalexin-deficient 3 (PAD3). The increased susceptibility of the mutant pad3 toward Alternaria brassicicola was caused by camalexin biosynthesis impairment [Arabidopsis, and their biosynthesis is regulated by the basic helix–loop–helix (bHLH) transcription factors (TFs): MYC2, MYC3, and MYC4 [Arabidopsis [Solanum lycopersicum (tomato) [Nicotiana tabacum [Due to the constant exposure to a broad range of pathogens, plants have evolved complicated immune systems, including different aspects of defense mechanisms, to protect against pathogen colonization ,12,13,14syringae . Lentice disease . The imp disease . Recentlr, MYB15 . Secondlr, MYB15 . The synpairment . Phytoanpairment . Glucosipairment ,24. Glucand MYC4 . Plant dand MYC4 ,27,28. Tbidopsis , Solanum(tomato) , and Nic tabacum .Physical and chemical defenses play significant roles in defending pathogens. However, in the future, the signals from pathogens that direct these responses should receive more research attention.Arabidopsis [PTI takes the main role in the combat against pathogens as a basal resistance for susceptible hosts, and in non-host resistance . PAMPs cbidopsis . Similarbidopsis ,40. EF-Tbidopsis . EFR phybidopsis ,43. Endobidopsis ,45,46. Sbidopsis . Botrytibidopsis . In addibidopsis . Interesbidopsis .Arabidopsis, more than 600 RLKs exist [Solanum pimpinellifolium (tomato) [Oryza sativa (rice), kinase XA21 mediates the resistance of Xanthomonas [Solanum pimpinellifolium (tomato), Gossypium barbadense (cotton), and Brassica napus [Arabidopsis [Fusarium oxysporum in tomato [Arabidopsis [RLP20, RLP21, RLP22, and RLP40 are responsive to Pseudomonas syringae infection [In Ks exist , formingKs exist . They plKs exist . The aboKs exist . FLS3, a(tomato) . In Oryzthomonas . Receptoca napus ,56,57. Fbidopsis ; RLP23 sbidopsis . The RLPbidopsis . RLP20, nfection . HoweverPseudomonas syringae type III effector can suppress PTI by the downregulation of the putative secreted cell wall and defense proteins [Pseudomonas syringae, can target the FLS2 receptor for degradation in Arabidopsis and mitogen-activated protein kinase 2 in N. benthamiana [P. syringae virulence protein, was found to interact with Arabidopsis HopM interactor 7 (AtMIN7), which is an immunity-related vesicle traffic regulator, and interfere with its stability via proteasome degradation to suppress PTI [During the long-term battle between pathogens and plants, pathogens have evolved a mechanism involving a type III secretion system that is used to inject effectors to interfere with an unspecific PTI, in order to achieve a successful infection. Many virulent effectors are known to suppress PTI ,63. It hproteins . Avirulethamiana . In addiress PTI . Recentlress PTI . Generalress PTI ,69,70. Tress PTI ,72. The ress PTI . Howeverress PTI . Conversress PTI .Future research studies will reveal more novel strategies that are employed by pathogen effectors, which can be exploited to control plant disease.cis element (GAAGAAGAA) in the promoter regions to upregulate defense genes [Pseudomonas syringae 4 and 6 (RPS4 and RPS6). Interestingly, EDS1 was found to interact with the bacterial effector AvrRPS4 and HopA1 [Although PTI and ETI recognize different pathogen patterns, generally, they trigger quite similar responses with mostly overlapping genes expression that suggests their synergistic effects in PTI and ETI . The nonse genes . Enhancese genes . Furthernd HopA1 ,79. Thussid2 mutants; the level of SA is only 5–10% of control values after infection or UV stress [Arabidopsis [npr1-inducible 1 (SNI1). These NIMINs play roles in inhibiting the promoter activity of defense genes, which is likely via influencing TGACG sequence-specific binding protein (TGA) transcriptional factors. The binding partner and regulation mechanism of SNI1 by far is still unclear. The sni1 mutant was screened to rescue the SA response in npr1 mutants, suggesting an NPR1-independent response. In addition, the constitutively enhanced SA response in suppressor of SA insensitivity 2 (ssi2) was confirmed to be partially dependent on SA, but not on NPR1. Moreover, the transcriptional factor glutaredoxin C9 (GRXC9) is another example that regulates a SA-dependent, although NPR1-independent, defense response [npr1 mutant, DCA-induced resistance was only mildly affected [npr1 [PR1 could be further induced in the npr1 mutant by the infection of different accessions of Botrytis cinerea indicating other unknown signals bypassing NPR1 [WRKY70, since TGAs could play a negative role in mediating the defense response [Downstream of PTI and ETI, the crucial role of signaling pathways such as the SA pathway, JA pathway, and ET pathway in pathogen defense responses is well-established . BiotropV stress ,81. Mostbidopsis ,82. EDS1bidopsis . NPR1 isbidopsis . In non-bidopsis  , accelerated cell death (acd), lesions simulating disease (lsd), constitutive expression of PR genes (cpr), mildew resistance locus o (mlo), hypersensitive response-like lesions 1 (hrl1), HR-like lesion mimic (hlm1), suppressor of NPR1-1 (sni1) and suppressor of salicylic acid insensitivity (ssi1) mutants [WRKY transcription factors are induced after the nuclear translocation of NPR1 monomers [Many loss-of-function mutants leading to retarded SA response and accompanied by a reduced resistance to biotrophic pathogens were thus identified to positively regulate the SA pathway. For instance, genes in involved in kinase-activated signaling such as enhanced disease resistance 1 (EDR1), mitogen-activated protein kinase 3 (MPK3), and MPK6, probably act upstream of SA synthesis ,99,100.  mutants ,109,110. mutants ,113,114.monomers .l-isoleucine (JA-Ile), methyl jasmonate (MeJA), jasmonoyl -1-aminocyclopropane-1-carboxylic acid (JA-ACC), jasmonoyl-1-O-β-glucose (JA-Glc), and 12-hydroxyjasmonic acid sulphate (12-HSO4-JA). However, there is evidence showing that only MeJA and JA-Ile are the active forms [COI1 and directs the degradation of JAZs, causing the activation of the JA response. In Arabidopsis, there are 12 JAZ members (JAZ1–JAZ12). Under normal conditions, JAZ proteins repress the activity of positive transcriptional regulators by binding to them. Co-repressors are recruited to coordinate the suppression with JAZ proteins. The recruitment of Topless (TPL) is achieved through the novel interactor of JAZ (NINJA), containing an ethylene response factor (ERF)-associated amphiphilic repression (EAR) motif (Vegetative storage protein 2 (VSP2), which is the JA-responsive marker gene. MYC2 recruits MED25, which is one subunit of the plant mediator complex to initiate transcription [JAZ2, which is regulated by MYC2. The ERF branch, containing the ethylene response factor 1 (ERF1) and octadecanoid-responsive Arabidopsis AP2 59 (ORA59), controls the JA-responsive marker gene plant defensin 1.2 (PDF1.2), which is usually regulated by the ET pathway in response to necrotrophic pathogen infection  genes, but negatively regulate PDF1.2 [EIN3 and EIL1 are activated by the release of repression from JAZ and HDA6 in the JA pathway; however, they are positively regulated by the essential regulator ethylene insensitive 2 (EIN2) in the ET pathway. EIN2 can stabilize EIN3 and EIL1, via preventing them from being degraded by EIN3-binding F box protein 1 and 2 (EBF1 and EBF2). EBF1 and EBF2 are two F-box proteins mediating the proteasome degradation [The JA pathway mainly protects plants against necrotrophic pathogens and wounding. The plant hormone JA is a lipid-derived compound, and it is synthesized through the oxylipin biosynthetic pathway. The JA synthesis starts with the precursor α-linolenic acid, which is released from membrane lipids in chloroplast. The key synthetic enzymes include a 13-lipoxygenase (13-LOX), a 13-allene oxide synthase (13-AOS), an allene oxide cyclase (AOC), and an OPDA-specific reductase (OPR3). There are many conjugation forms of JA, including jasmonoyl-ve forms . Upon stve forms . COI1 fuR) motif . TPL hasR) motif . There aR) motif . The MYCcription . The actcription ,121. MYCcription . MYC2 prnfection . Interesesponses . When thresponse . MYC2 ne unclear . Interese PDF1.2 . Recentlradation   constitutively activates JA and ET signaling, suggesting a common regulation of both pathways [PR3 and PR4 are the marker genes of the ET response. PDF1.2 requires both the JA and ET pathways to be induced, and therefore is a marker gene for both pathways.The plant hormone ET is a gaseous hormone, playing key roles in many physiological processes. The biosynthesis of ET originates from S-adenosyl methionine (SAM), which is produced by SAM synthetase from methionine and ATP. 1-Aminocyclopropane-1-carboxylic acid (ACC), the precursor of ET, can be synthesized by ACC oxidase from SAM and converted to ET. It induces the ripening of the fruits or leaf abscission. However, ET also plays an active role in plant defense. For example, in echanism  , TGAs, and WRKYs [PDF1.2 in the mutant npr1, after the pharmacological application of SA and MeJA, showed that SA suppression on the JA pathway is dependent on NPR1 [The mutually antagonistic effect between the SA and JA pathways are quite well-known. The suppression of the SA pathway on the JA pathway has been extensively studied ,77. NPR1nd WRKYs ,136,137 nd WRKYs . Additio on NPR1 .ORA59 expression and protein stability, which targets GCC-box motifs in JA-responsive promoters [Many other regulators have been reported to play roles in the cross-talk of SA and JA pathways, such as the WRKY TFs including WRKY70, WRKY50, WRKY51, WRKY33, and WRKY75, which exert antagonistic influences on SA–JA communication ,140,141.romoters . Howeverromoters .ANAC019, ANAC055, and ANAC072 , which transforms SA into the inactive SA ester  double mutant, SA and JA marker genes were synergistically activated, although the single gene mutations edr1 and gsl5 only prime the SA response [The influence of the JA pathway on the SA pathway is less clear. The inhibition of the SA pathway by the JA pathway is through the activation of three homologous NAC TF genes:  ANAC072 . These cSA ester . Despite aphidis . A low l unclear . In the response . Exogenoresponse .GLB1), encoding hemoglobin, led to the enhanced resistance to both biotrophs and necrotrophs, which is concomitant with elevated NO accumulation after both infections [Reactive oxygen species (ROS), NO, and Mediator, which is a multi-protein complex that functions as a transcriptional co-activator in all of the eukaryotes, are believed to positively regulate both SA and JA pathways. NO was established to have a positive influence on the defense against both biotrophic and necrotrophic pathogens. Ozone exposure to plants generated reactive oxygen species (ROS), and this could trigger all of the SA, JA, and ET responses. ET synthesis preceded both SA and JA production . The losfections . The mutfections . Furtherfections ,153. TheIn addition to the major roles of the SA, JA, and ET pathways in plant defense, other hormone pathways can mediate plant defense as well. The pathogen entry is facilitated by stomatal opening; in turn, for defense, the plant will close the stomata . It is wS-methyl benzo  thiadiazole-7-carbothioic acid S-methyl ester (BTH) are external molecules. The defense genes’ expressions have been shown to be highly induced by the exogenous application of INA and BTH [Arabidopsis plants overexpressing a salicylate hydroxylase gene (NahG), which are unable to accumulate SA. INA and BTH function independently from SA biosynthesis and perception [Arabidopsis. However, upon infection, pretreatment of BABA can induce stronger SA accumulation and the expression of defense genes such as PR1 compared to control without BABA treatment [Pseudomonas infection [Arabidopsis leaves upon infection. Furthermore, AzA can protect plants against infection in both local and systemic leaves. These results strongly suggest a key role of AzA in the defense response [ald1, the loss of function of aminotransferase aberrant growth and death 2 (AGD2)-like defense response protein 1 (ALD1) could be rescued by the application of Pip. This indicates that ALD1 might be involved in the synthesis of Pip [N-hydroxypipecolic acid was found to be the product of FMO1 from Pip, and it can accumulate upon infection. Furthermore, it can restore the resistance against infection for the FMO1 mutant. Thus, a novel internal molecule, N-hydroxypipecolic acid, was revealed to regulate defense, suggesting a close connection between amino acids and defense [The good establishment of high-throughput chemical screening methods allows for the identification of many novel small molecules, protecting plants against infection. The compounds can be generally classified into external and internal compounds according to whether they exist in plants. The external group does not exist in plants. 2,6-Dichloroisonicotinic acid (INA) and acibenzolar- and BTH . INA andrception ,157. Witreatment . Recentlreatment . In addinfection ,161. Azeresponse . Pipcolis of Pip ,164. Inds of Pip ,166. How defense ,168.PR1, PR2, and PR5. Although SA is required for SAR, it is not a mobile signal. Instead, other signals such as methyl salicylic acid (MeSA), AzA, glycerol-3-phosphate (G3P) and dehydroabietinal (DA), an abietane diterpenoid, are mobile, and they could induce SA accumulation and trigger the expression of pathogen-related genes in systemic leaves [N-hydroxy-pipecolic acid, indicating the role of Pip and its product in transducing SAR through FMO1 [Arabidopsis mediator subunit 16 (MED16) was compromised in SAR, and it probably acts as the bridge between NPR1 and RNA polymerase II transcription machinery [Systemic acquired resistance (SAR) is a broad-spectrum resistance that occurs at systemically in leaves following ETI. Due to the activation of SAR, plants will stay alarmed and be prepared for further infections for a time over weeks to months. Some signals are obviously passed from locally-infected tissues to systemic leaves. The initiation of SAR in systemic leaves is accompanied by the massive transcriptional programming of SA-related genes, such as c leaves . FMO1 isugh FMO1 ,169,170.achinery .Pseudomonas is somehow compromised in salicylate hydroxylase gene (NahG) and npr1, suggesting a dependence on the SA pathway. BABA-induced priming was shown to be partially dependent on abscisic acid (ABA) in Arabidopsis, since BABA-primed resistance was impaired in aba1-5 and abi4-1 mutants, which are deficient in ABA signaling. In addition, in the gsl5 mutant of a callose synthase gene glucan synthase-like 5 (the same as powdery mildew resistant 4), BABA-induced callose accumulation and resistance to Alternaria brassicicola and Plectosphaerella cucumerina is blocked [Arabidopsis. In Arabidopsis, priming for potentiated PALs expression could be mimicked by pretreatment with low dosages of the synthetic SAR inducer BTH, which resulted in the augmented accumulation of messenger RNA (mRNA) of PALs after infection with virulent Pseudomonas syringae pv.tomato DC 3000 [Arabidopsis, in order to protect against B.cinerea [edr1 mutant led to the enhanced resistance to Pseudomonas syringae and powdery mildew, suggesting a negative role in plant defense. However, unchallenged by pathogens, edr1 did not show significantly elevated SA levels and PR1 expression, instead resembling the primed state in BABA-treated plants [Defense priming is a status in plants without the obvious induction of defense; however, it can activate defense mechanisms more rapidly and robustly upon the pathogen infection. The intensity of the defense response is usually at the cost of plant health. The resistance effect in primed plants can be comparable as in constitutively defense-elevated plants; however, it does not have a fitness cost. Thus, defense priming has a more practical use in agriculture without influence on yields. Defense priming is believed to be relevant to ROS production, transcription programming, and modification on an epigenetic level, which can facilitate the switch-on defense response very rapidly upon infection . For ins blocked . Additio blocked . BABA wa blocked . It is s blocked . Interes DC 3000 . Hexanoi.cinerea . The prid plants .Arabidopsis has significantly elaborated upon its different defense mechanisms. In this review, different layers of defense mechanisms are revealed. The classical hormone pathways against defense are intensely discussed. Extensive studies have demonstrated that these different layers of plant defense are linked to hormone pathways, especially for the SA and JA/ET pathways. However, the connections between the hormone pathways and other above-mentioned defense aspects will need further investigation. For physical defense, the stomata rapidly close less than one hour after infection, in order to prevent pathogen entry [Researches in en entry . The horen entry ,180,181.Pseudomonas syringae [We also need to know how hormone pathways participate in plant immunity. The bridges of how PRRs mediate hormone pathways are still missing, although some connections are revealed for the SA pathway. For instance, some PRRs, such as pattern-triggered immunity compromised receptor-like cytoplasmic kinase 1 (PCRK1) and PCRK2, are required for SA biosynthesis upon infection . Howeversyringae . This wasyringae ,184. ThiPseudomonas syringae, is the functional mimic of JA-Ile, and therefore induces the JA pathway to suppress the SA pathway for bacterial infection [Streptomyces scabies and Xanthomonas campestris pv. Phormiicola [During the co-evolution of pathogens and plant hosts, hormone pathways cannot only protect against pathogens invasion, they can also be utilized by pathogens to facilitate disease. Coronatine (COR), which is produced by nfection . Other Crmiicola ,186. Howrmiicola . Recentlrmiicola . This surmiicola . It is pN-hydroxypipecolic acid [Other defense mechanisms, such as SAR and priming, might be manipulated to improve plant defense without the loss of yield . Recentllic acid ,167. SARlic acid ,171,188.lic acid . The rol


Epinephelus akaara) is one of the most commercially important aquatic species in China. However, its seedstock has low larval survival rates, and its stability is confronted with the danger of overexploitation. In this study, a high-density genetic map was constructed using 3435 single nucleotide polymorphisms (SNPs) from 142 first generation (F1) full-sib offspring and two parents of a red-spotted grouper population. The total genetic length of the map was 2300.12 cM with an average intermarker distance of 0.67 cM. Seventeen genome-wide significant quantitative trait loci (QTLs) for growth-related traits were detected on 24 linkage groups, including 5 QTLs for full length, 7 QTLs for body length, and 5 QTLs for body weight. The contribution values of explained phenotypic variance ranged from 10.7% to 12.9%. Moreover, 13 potential candidate genes for growth-related traits were identified. Collectively, these findings will be useful for conducting marker-assisted selection of the red-spotted grouper in future studies. The red-spotted grouper ( Epinephelus akaara) is a popular, edible aquatic species in many Asian countries [The red-spotted grouper  [Paralichthys olivaceus) [Oncorhynchus mykiss) [Eriocheir sinensis) [Silurus meridionalis) [Crassostrea gigas) [Chrysophrys auratus) [Channa argus) [Epinephelus coioides) was constructed previously [Epinephelus aeneus) [Epinephelus bruneus) have been published [With the development of next-generation sequencing (NGS) technology, the construction of high-quality linkage maps for various economically important fish species has been facilitated. Several methods have been simultaneously developed for high-throughput marker discovery and genotyping using restriction enzymes, including restriction site-associated DNA sequencing (RAD-Seq) . Thus, do salar) , Japanesivaceus) , rainbow mykiss) ,8, Chineinensis) , southerionalis) , Pacifica gigas) , snapperauratus) , and nora argus) . The fireviously , which reviously . Additioeviously , white g aeneus) , and kelublished . Recentlublished . HoweverDanio rerio) [Computational tools provide a promising alternative for helping identify biologically significant QTLs and SNPs. In this study, two open software packages were used to study the red-spotted grouper in RAD analysis data. STRING (a database of known and predicted protein-protein interactions) collects and integrates this information by consolidating known and predicted protein–protein association data for a large number of organisms . Cytoscao rerio) , orange-o rerio) , and raio rerio) .In this study, we constructed a high-quality genetic linkage map and developed QTLs for growth-related traits in the red-spotted grouper. In total, 17 growth-related QTLs were identified, and 13 related genes were discovered. These findings will be beneficial for MAS with regard to growth traits in the red-spotted grouper.1) full-sib family was collected from a large seawater farm in Xiaodeng Island, Fujian Province, China, during July 2016. The fish were acclimatized for one month under controlled conditions. Approximately 15,000 progenies were stocked into a 600-m2 (30 m × 20 m × 1.5 m) pond at an initial density of 17 fish per m3. All fish were fed at 08:00 h and 16:00 h every day. During this period, the water quality parameters were monitored as follows: water temperature 27.5 ± 1.5 °C, salinity 29 ± 1‰, dissolved oxygen 10 ± 0.5 mg/L, pH 8.0 ± 0.2, and un-ionized ammonia 0.02 ± 0.1 mg/L. After 50 days of culturing, 144 individuals were randomly selected for phenotypic measurements, and the average weight of the fish was 4.2 g. Three growth-related traits, body weight (BW), full length (FL), and body length (BL), were recorded as phenotypic data  following the phenol-chloroform protocol . DNA quaTen RAD-Seq libraries were prepared for the 142 offspring and two parents following standard protocol . BrieflyAll RAD sequence analyses and genotyping were conducted using the non-reference genomes software program Stacks v2.4 . First, 1 red-spotted grouper population using the following process: (1) linkage analysis was performed for at least 80% of the markers; (2) the default value of data tolerance  was used to filter out highly segregated markers ; (3) markers were assigned to LGs and executed with a logarithm of odds (LOD) score ranging from 2 to 10; and (4) markers within each LG were ordered. The error parameters were also calculated.JoinMap v4.1 software was used to assign linkage groups (LGs) based on the cross population (CP) algorithm . The genp < 0.05) of the whole genome was determined based on the threshold level of LOD. The genes located in the QTL regions were supposedly growth-related genes, which were identified by QTL mapping. First, markers in the red-spotted grouper QTL regions were identified, and the corresponding marker sequences were selected from the reference parents based on their SNP ID. Second, sequences were mapped based on the position of the orange-spotted grouper genome scaffolds. Lastly, upstream and downstream coding gene functions were identified by a BLASTX  search in the National Biotechnology Information Center. The sequencing reads of the orange-spotted grouper genome were deposited in the ENA Public Database .The MapQTL v6 software was used to perform the QTL analyses . ComposiDanio rerio) can be selected by clicking on the arrow or directly typing the name into the related input field. Two criteria were applied for detecting important nodes: high confidence with score = 0.15 and no more than 10 interactors. Then the network images were generated; clicking on a node provides details about the protein. Lastly, Cytoscape v3.7.1 software was used to visualize and analyze the molecular and interaction networks [Genes in the connection groups were determined using the STRING online software by inputting SNP ID sequences ; the orgnetworks .n = 2373), <lm × ll> (n = 7430), and <nn × np> . In total, 114 Gb of raw data were generated from 10 RAD libraries, and 98 Gb of clean data were retained after data trimming by removing low-quality raw reads. Clean reads of separated individuals were stored in the CNSA (CNGB Nucleotide Sequence Archive) public database (CNP0000564). Then, loci in a set of individuals were identified, and the genotype of each locus was determined. Collectively, 20,798 SNPs were obtained, including four segregation types: <ef × eg> (n = 740), <hk × hk> (n = 48) [A high-resolution genetic map of the red-spotted grouper was constructed using JoinMap and Lep-MAP for the first time. The successful mapping of 3435 SNPs in 24 LGs was consistent with the haploid chromosome number of the red-spotted grouper (2n = 48) . The totIn total, 17 QTLs for growth-related traits were distributed on LG1, LG6, LG8, LG10, LG11, LG16, LG18, and LG19, including 5 QTLs for BW, 5 QTLs for FL, and 7 QTLs for BL. There were 9 SNPs located on FL-related QTLs with LOD values ranging from 3.52 to 3.98, accounting for 10.7–11.9% of the phenotypic variation. Twelve SNPs were located on BL-related QTLs with LOD values ranging from 3.54 to 4.32, accounting for 10.7–12.9% of the phenotypic variation. Nine SNPs were located on BW-related QTLs with LOD values ranging from 3.55 to 4.21, accounting for 10.7–12.2% of the phenotypic variation. The LOD value of qTLG10_BL for BL was the highest value (4.32) recorded, and accounted for 12.9% of the phenotypic variation. Interestingly, markers 21190 (LG6), 449098 (LG6), 858434 (LG10), 17495 (LG10), and 343730 (qTLG18) all appeared for the BL and FL traits ; Table 2Anguilla anguilla) [Carassius auratus) [Ctenopharyngodon idella) [Clarias macrocephalus), the transcriptome data indicated that spermidine synthase (srm) was related to growth. It was demonstrated that cytochrome c (cyc1), NADH-ubiquinone oxidoreductase, and ubiquinol-cytochrome c reductase complex subunits were associated with the coordinated expression of related functional genes during muscle recovery and growth [Larimichthys crocea) by influencing dietary lipid levels. Sialidase-4 (neu4) is an enzyme encoded by the neu4 gene and was found to regulate mammal neuronal functions by degrading polySia, thereby affecting neurological function including synaptic plasticity, neurite growth, and cell migration [Additionally, 13 potential candidate genes were identified by the BLAST search of the orange-spotted grouper genomic region . Among tnguilla) , goldfisauratus) , rainbowauratus) , and gra idella) . The sst idella) . In bighd growth . In a prigration . Other gp < 0.05) based on the false discovery rate correction in this network, including mitochondrial electron transport, the ATP metabolic process, and the purine ribonucleoside monophosphate metabolic process  populations could meet the needs of most aquatic animals, according to previous studies [Molecular marker technology has revolutionized research on aquaculture genetic studies. In the past, many molecular markers were used to study the genetic diversity of different aquatic organisms, including allozymes, mitochondrial DNA, restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), microsatellite DNA, and SNP markers . To date studies . ClearlyIn groupers, eight genetic maps have been published previously: 5 maps were constructed using SSR markers and 3 were developed using SNP markers . Dor et Lates calcarijer)  [In this study, a linkage map of the red-spotted grouper using RAD-Seq was constructed for the first time using 3,435 RAD markers genotyped from 144 individuals. The length of the consensus map was 2300.12 cM with an average inter-location space of 0.67 cM. The total lengths of the female and male maps were 1370.9 and 1335.5 cM, respectively, indicating a substantial female bias in recombination with a female-to-male recombination ratio of 1.47:1. Sex-specific differences in recombination rates are common and have been reported in both vertebrates and invertebrates. In organisms with chromosomal sex determination, the meiotic recombination rate of males is substantially lower than females . This pa 1.12:1) , common  1.12:1) , Atlanti 1.12:1) ,65. Ther 1.12:1) ; and (3)Lctalurus punctatus) [Nibea albiflora) [Siniperca chuatsi) [Thunnus orientalis) [Sander lucioperca) [Megalobrama amblycephala) [Mapping QTLs contributes to our understanding of the underlying genetic mechanisms of economic traits. Like most economic traits, growth is a quantitative trait regulated by multiple genes from different genomic regions. Mainly, growth traits include full length, body length, body weight, and head length. QTL mapping is a practical approach for identifying these regions. Recently, along with the successful construction of high-density genetic linkage maps, a multitude of QTLs related to growth traits have been detected in snapper , channelnctatus) , yellow biflora) , golden biflora) , Mandarichuatsi) , Pacificentalis) , pikeperioperca) , blunt scephala) , Atlanticephala) , large ycephala) , and crucephala) . No QTLsPenaeus vannamei) [In this study, based on the high-density genetic linkage map of the red-spotted grouper, 17 growth trait-related QTLs with a LOD ≥3.5 were identified on eight LGs. Many QTLs exhibited pleiotropy. Namely, qTLG6-FL  and qTLG6_BL  were identified in a 32.24–32.59 cM interval on LG6; qTLG10-FL  and qTLG10_BL  were identified in the same genetic position (93.08–96.14 cM) on LG10; and qTLG11-FL (755146) and qTLG11-BW (755146) were identified in a 14.33–15.33 cM interval on LG11. The clustering of QTLs indicates that the same chromosome region is shared by various QTLs, which may be due to the high correlation between the full length and body length phenotypic traits. Identification of these pleiotropic QTLs could increase the efficiency of MAS and accelerate breeding progress. A similar result has also been reported in whiteleg shrimp (annamei) . CollectPolychloride miticide [uqcrh, uqcrc2b, uqcrc1, cyc1, cytb, ENSDARG00000007745, uqcrq, uqcrb, uqcrfs1, cycsb, ndufs2, grid1, gabra5, alkbh8, kbtbd3, srm, gabra6b, raly, zfp36, and mb21d2b. The red-spotted grouper candidate gene with the greatest number of node networks (n = 11) was cyc1. Cytochrome c is a key protein involved in the process of energy utilization, which is the terminal step of the electron transport system. In animals, cytochrome c activity is closely related to actual oxygen consumption rates of different tissues. It is also sensitive to energy demands of exercise activity and various nutritional states [Micropterus salmoides) [Progress has been made in “omics” research , which has led to vast amounts of biological data. Visualization is the easiest way to represent large biological datasets. STRING and Cytoscape software are commonly used in bioinformatic visualization studies. For example, the virulence gene prediction and construction of the protein interaction network of the orange-spotted grouper were determined using STRING and Cytoscape software, which suggested that the spleen of the orange-spotted grouper is an excellent target for studying the immune response of grouper to miticide . In thislmoides) . TherefoA high-density genetic linkage map of the red-spotted grouper was constructed in this study. The map comprised 3435 SNPs on 24 LGs. Seventeen growth-related QTLs were identified in a genomic region. A protein–protein interaction network was also constructed. These findings provide a pivotal interactions network and will serve as a valuable resource for future investigations on the underlying molecular mechanisms of the red-spotted grouper.


BRCA genes account for a small proportion of the familial risk of breast cancer. Low-penetrance alleles are expected to underlie the remaining heritability. By now, there are about 180 genetic polymorphisms that are associated with risk, most of them of modest effect. In combination, they can be used to identify women at the lowest or highest ends of the risk spectrum, which might lead to more efficient cancer prevention strategies. Most of these variants were discovered in populations of European descent. As a result, we might be failing to discover additional polymorphisms that could explain risk in other groups. This review highlights breast cancer genetic epidemiology studies conducted in Latin America, and summarizes the information that they provide, with special attention to similarities and differences with studies in other populations. It includes studies of common variants, as well as moderate- and high-penetrance variants. In addition, it addresses the gaps that need to be bridged in order to better understand breast cancer genetic risk in Latin America.The last 10 years witnessed an acceleration of our understanding of what genetic factors underpin the risk of breast cancer. Rare high- and moderate-penetrance variants such as those in the  Breast cancer is the most common cancer in women, and a major public health concern worldwide . ImproveBRCA1 and BRCA2 genes [ATM, BARD1, PALB2, and CHECK2, explain ~20–25% of breast cancer risk [Only a relatively small proportion of breast cancers can be explained by the presence of high-penetrance genetic mutations, such as those in the A2 genes ,17,18,19cer risk ,22,23 ancer risk ,49,50,51cer risk . HoweverLatin American populations are diverse, not only culturally, but also in their genetic ancestry composition ,53. ThisBRCA), “case–control study” , and “Latinas”  in the PubMed database (https://www.ncbi.nlm.nih.gov/pubmed/). We also added to these terms the name of each Latin American country. We complemented the search by reviewing manuscripts cited in the selected papers. We focused on studies with case series, cohorts, or case/control design, conducted in Latin America and that included genetic factors as main predictors. In some instances, we make reference to studies conducted in or including US Latinas. We only included studies published in the English language. We did not narrow the search by date; the selected studies were published between 2008 and 2018.For paper retrieval, we combined search terms such as “breast cancer” (breast cancer subtypes), “genetics”  in the US; this includes Brazil [BRCA1 to BRCA2 carriers were also observed. While most countries report higher frequencies of BRCA1 mutations, in Costa Rica, Cuba, Puerto Rico, and Uruguay, BRCA2 mutations are predominant [The Hereditary Breast and Ovarian Cancer (HBOC) syndrome is caused by loss-of-function mutations in the  cancers . Despite cancers ,58,59,60s Brazil , Colombis Brazil , Cuba [6s Brazil , Mexico s Brazil ,65, Perus Brazil , and Pues Brazil , for whidominant . This isdominant ,69.BRCA1/BRCA2 carriers in the Ashkenazi Jewish population [BRCA1 185delAG  is the most common pathogenic variant with the largest geographical span as it was shown to be recurrent in Argentina, Brazil, Mexico, and Peru [BRCA pathogenic variants reported in the literature were observed in more than one country of Latin America and the Caribbean [BRCA mutation spectrum and to provide adequate recommendations and treatment in women from Latin America. A previous review by Dutil et al. provided additional information regarding specific BRCA mutations in Latin American women [BRCA genes, there are other high-penetrance mutations that are uncommon in the population , which are associated with well-known familial syndromes [TP53 gene, best known as R337H, was found in 2–7% of Brazilian breast cancer patients [Three founder mutations were shown to account for 79% of the pulation . In Latipulation . The BRCand Peru . In Mexiand Peru . Founderand Peru ,72,74,75aribbean ,77. In aaribbean . In Coloyndromes ,82. For patients ,84,85.Polymorphisms in moderate- and low-penetrance genes may be relatively common in the population, and collectively confer a small to moderate increased relative risk for breast cancer . Common ATM gene in Chile and Mexico [DNA repair is crucial for normal cell function, and common polymorphisms in DNA repair genes or genes that play a role in DNA repair pathways are potential candidates for association with breast cancer risk. Several studies in Latin America assessed the association between DNA repair gene variants and breast cancer risk ,122,123.d Mexico ,100,112.The BARD1 protein heterodimerizes with BRCA1 and induces translocation and retention of BRCA1 into the nucleus . The c.1BRCA1/2 mutations and found two variants, c.1676A>G (rs152451) and c.2993C>T (rs45551636), that were associated with breast cancer risk in a subsequent case–control study [CHEK2 c.1100delC truncating mutation, which increases the risk of breast cancer twofold, was widely analyzed. This mutation has a frequency of 0.3–1.2% in European populations [AKT1 is frequently mutated in mammary tumors [AKT1 and its association with breast cancer risk, as well as histopathological and immunohistochemical characteristics, in 276 Ecuadorian mestizo women. They found that the intronic SNP rs3803304 was associated with breast cancer risk. Moreover, they found that the heterozygous genotype CG of that SNP had a significantly different frequency between intrinsic subtypes (p ≤ 0.05), with luminal B showing the highest frequency (63.6%). This result suggests that the SNP rs3803304 may affect DNA transcription, acting as a risk factor for breast cancer in Ecuadorian mestizo population living in high altitudes.Three other BRCA1 and BRCA2 functionally related genes were screened in Latin American populations. PALB2 binds BRCA2 and recruits it to BRCA1 foci on damaged DNA . Leyton ol study . CHEK2 pol study . The CHEulations  and caseulations ,136,137.y tumors . Activaty tumors . Lopez-Cy tumors  analysedXRCC3 c.722C>T (rs861539) and RAD51D c.698A>G (rs28363284), were assessed for their association with breast cancer risk in high-risk families in Chile without known BRCA1/2 mutations [XRCC3 gene yielded a statistically significant result [XPC and XPD) and ultraviolet (UV) excision repair protein (RAD23B) genes and breast cancer risk [RAD23B and breast cancer risk, and between XPC and RAD23B and DNA repair capacity in the cases [XRCC1 gene and breast cancer risk [TP53, which is an important gene in DNA-repair related pathways [Polymorphisms within two DNA double-strand break repair genes, cer risk . They hyhe cases . Similarcer risk . Variantpathways , were re98A>G rs263284, wepathways ,144,145.pathways ,143,144.pathways . Three o98A>G rs263284, wepathways .TS) gene produces an enzyme that is involved in one-carbon metabolism and is crucial for DNA synthesis. A study in Mexico explored the association between polymorphisms in the TS gene and breast cancer risk and reported negative results [MTHFR) and cystathionine β synthase (CBS) genes, which are involved in the processing of amino acids, and breast cancer risk. Four out of five studies found a positive association [MTHFR messenger RNA (mRNA) expression in triple-negative breast cancer (TNBC) tumors. The 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) gene, also involved in the amino-acid synthesis pathway, was tested in a Brazilian population with no significant results [The thymidylate synthase , androgen (AR), and progesterone receptors (PGR)) yielded mostly negative results except in secondary stratified analyses (by body mass index or use of hormone replacement therapy) [ESR1, PGR, COMT, CYP19A1, and CYP1A1 genes [PGR gene and breast cancer risk [CYP1A1 gene [Sex hormones, their receptors, and other relevant components within their pathways, are thought to be involved in breast cancer development because of their role in cell growth and proliferation. Analyses of a limited number of candidate variants in hormone receptor genes (estrogen (therapy) ,151,152.A1 genes ,150,153.cer risk , while o1A1 gene ,115.MMP-1, MMP-2, MMP-3, and MMP-9 genes and breast cancer risk [MMP-1 , MMP-3 , and MMP-9  genes among women with high Native-American ancestry [MMP-2 c.-1586C>T polymorphism (rs243865) and breast cancer risk [ITGA6) gene and the c.-1562 C>T (rs3918242) polymorphism in the MMP-9 gene, respectively [Matrix metalloproteinases (MMPs) are enzymes that can degrade the extracellular matrix and basement membrane and are thought to play an important role in cell proliferation, migration, differentiation, apoptosis, and angiogenesis . A largecer risk . Signifiancestry . A studycer risk . Other sectively ,158.TNF-α, RETN, CAP1, and PTGS2 genes). No association was detected for nine SNPs evaluated within the PTGS2 gene [TNF-α c.-308G>A (rs1800629) polymorphism was found to be associated with breast cancer risk in a study conducted in Mexico [RETN c.-225C>G (rs1862513) and CAP1 c.881G>A (rs35749351) polymorphisms and breast cancer risk [Different analyses conducted in the Breast Cancer Health Disparities Study samples analyzed tag SNPs in genes related to inflammation and energy balance, taking into account possible interactions with body mass index ,163,164.GS2 gene . The TNFn Mexico , and anocer risk .HER2-overexpressing breast cancer patients [IL-18 gene, c.-838C>A(rs1946518) and c.-368G>T (rs187238), and breast cancer risk [Two studies assessed polymorphisms related to tumor immune response in Brazilian populations, and both of them found statistically significant associations with breast cancer risk ,90. Tumopatients . Banin Hpatients , suggestcer risk ,170. Precer risk ,172.GPX1, GPX2, GPX3, GPX4, SELS, SEP15, SEPN1, SEPP1, SEPW1, TXNRD1, and TXNRD2) and breast cancer risk in US Latinas, finding mostly negative results except when analyses were stratified by genetic ancestry and by tumor subtype [CYP2W1, CYP4F11, CYP8A1, and CYP1B1 [ABCB1, which encodes the MDR1 protein, [GSTM1 and GSTP1, members of the glutathione S-transferase (GST) gene family [eNOS, which can react with other free radicals and damage DNA [CYP genes were mostly negative, except for CYP1B1 [GSTM1 deletion (tagged by rs366631), and ABCB1 c.3435C>T (rs1045642), GSTP1 c.313A>G (rs1695), and eNOS polymorphisms [ABCB1 gene was an important risk factor for breast cancer in premenopausal women and specifically for the TNBC subtype [ABCB1 function, and reduced mRNA and/or protein expression, which might impact the metabolism and posterior elimination of toxic and carcinogenic compounds inducing cellular accumulation leading to cancer development [Selenoproteins were shown to have a redox function and to decrease oxidative stress. One study tested the association between SNPs in different selenoprotein-related genes . These SNPs have a frequency of between 5% and 23% in Latin American populations and are practically absent in all other groups. The minor allele was protective, with an associated odds ratio (OR) of 0.60 : 0.53–0.67) and was more protective for estrogen-receptor-negative (ER−)  than for estrogen-receptor-positive disease  [The first GWAS on Latina women was published in 2014 , reporti49-0.80) .FGFR2, TOX3, and MAP3K1 genes and the 2q35 and 8q24 loci, that were replicated in different populations [FGFR2 (c.109+906T>C (rs2981582), c.109+1899A>G (rs2420946), 109+7033T>A (rs1219648), MAP3K1 (rs889312), TOX3 (rs3803662), 2q35 (rs13387042), and 8q24 (rs13281615) and breast cancer risk in Chilean patients [FGFR2, MAP3K1, TOX3, and 2q35, but not for 8q24 [FGFR2 rs2981582 polymorphism in the Mexican population reported an interaction between the FGFR2 polymorphism and alcohol intake [Some studies conducted in Latin America replicated selected loci that were discovered in breast cancer GWAS conducted in samples of European origin: two in Chile and one in Mexico ,96,116. ulations ,183,184.ulations ,186,187.patients ,96. Theyfor 8q24 ,96. Anotl intake .ESR1 gene mostly observed in women of Indigenous American ancestry.There is a heterogeneous genetic background in Latin American populations, with regional variation in the relative proportions of the three main ancestral continental influences: Indigenous American, European, and African. A study conducted in US Hispanic/Latinas from the Bay Area first reported the association between genetic ancestry and breast cancer risk . Women wA large proportion of the case/control studies described in In this review, we presented a summary of genetic association studies in Latin American women, including studies of relatively rare high-penetrance mutations and those discovered using candidate gene approaches or GWAS, which tend to be of moderate or small effects but are more common.BRCA1- and BRCA2-associated hereditary breast cancers in Latin America emerged. While still incomplete, available evidence points to a unique genetic make-up characterized by remarkable diversity across and within countries [BRCA1 and BRCA2 analysis to extended panels of genes including high- and moderate-penetrance risk genes. Although this approach became standard of care in the US, the data on the use of these panels in Latin American populations are sparse. In parallel to emerging efforts aimed at describing the molecular characteristics of hereditary breast cancers in Latin America, there is a need to improve access to genetic testing and for the development of supporting infrastructures in cancer risk assessment, education, and genetic counseling [In recent years, a picture of the ountries ,75,196. unseling ,198.Risk prediction models that combine non-genetic and genetic risk factors were developed and are constantly being improved ,201,202.Progress in the discovery of population-specific breast cancer genetic risk variants in this region is limited by different factors, such as the slower incorporation of new genotyping and sequencing technologies, and the relatively small samples sizes partly due to the paucity of National Cancer Registries and the inconsistent collection of biospecimens  for research . On averThere are ongoing efforts to improve homogeneity of study design and increase sample size in studies in Latin America. In 2009, the Center for Global Health of the US National Cancer Institute (NCI) created the US-Latin America Cancer Research Network (LACRN), a collaborative management structure that includes Argentina, Brazil, Chile, Mexico, and Uruguay . In 2011To conclude, large collaborative international efforts that include knowledge and technology exchange and transfer will lead to studies with appropriate sample sizes and approaches to discover rare high-penetrance polymorphisms, as well as low-penetrance variants in Latin American women from different regions and with different ancestral proportions. Only then will we be able to provide appropriate genetic risk estimates and care to women of Latin American origin worldwide.


Recent advances in the field of cancer genome analysis revolutionized the picture we have of acute myeloid leukemia (AML). Pan-genomic studies, using either single nucleotide polymorphism arrays or whole genome/exome next generation sequencing, uncovered alterations in dozens of new genes or pathways, intimately connected with the development of leukemia. From a simple two-hit model in the late nineties, we are now building clonal stories that involve multiple unexpected cellular functions, leading to full-blown AML. In this review, we will address several seminal concepts that result from these new findings. We will describe the genetic landscape of AML, the association and order of events that define multiple sub-entities, both in terms of pathogenesis and in terms of clinical practice. Finally, we will discuss the use of this knowledge in the settings of new strategies for the evaluation of measurable residual diseases (MRD), using clone-specific multiple molecular targets. This clinical classification does not reflect the high heterogeneity of AML, as each clinical category encompasses many different types of diseases with distinct prognosis and molecular features.From a clinical ontogeny point of view, three different kinds of acute myeloid leukemia (AML) can be defined as follows: The 2016 WHO classification [(PML-RARA), AML with t (RUNX1-RUNX1T1), AML with inv(16)(p13.1q22) or t (CBFB-MYH11), AML with t (MLLT3-KMT2A), AML with t (DEK-NUP214), AML with inv(3)(q21.3q26.2) or t (RPN1-MECOM), and AML with t (RBM15-MKL1). They were clearly characterized in a large cohort as having a strong prognostic value. On the other side, some gene mutations, such as RUNX1, CEBPA, and NPM1 define specific subgroups. All these subgroups and variegated genetic landscapes were unraveled over the past 10 years, thanks to the development of high throughput sequencing technologies, which allowed the characterization of the most frequently-mutated genes in AML [FLT3, NPM1, and DNMT3A, which are especially found in de novo AML with normal karyotype. Some other genes, such as SRSF2, SF3B1, U2AF1 or BCOR are often found mutated in s-AML. Mutations in TP53, almost always associated with a complex karyotype, are mainly found in t-AML. Some mutations, including those in DNMT3A, TET2, and ASXL1, have been shown to appear years before the occurrence of AML [The WHO classification  and larg with t8;1q22;q22;9)p23;q3.1 (DEK-N3.3) RBM1-MKL1. Thwith inv1, only if DNMT3A and NPM1, are both mutated. However, when neither DNMT3A nor NPM1 are mutated, or when only one of them is mutated, the occurrence of an ITDFLT3 mutation does not alter the prognosis. Conversely, when G12/13NRAS mutations co-occur with DNMT3A and NPM1 mutations, the OS is statistically improved. Then again, if neither DNMT3A nor NPM1 are mutated or if only one of them is mutated, the occurrence of a G12/13NRAS mutation does not change the prognosis. These results reveal the complex network of gene-gene interaction as prognostic modifiers. Moreover, it is tempting to consider that these specific interactions confer particular functionalities to the mutated clone.A large study of one thousand five hundred and forty patients  with AMLNPM1, transcription factors, tumor suppressors, and the signaling pathways , followed by a mutation in NPM1 or in a classically-mutated transcription factor in AML , then the last mutation arises in a gene involved in the signaling pathways  [de novo AMLs with normal karyotype, of which DNMT3A and NPM1 mutations represent the most classical association. In the cohort of one thousand five hundred and forty AML analyzed by Papaemmanuil and colleagues [NPM1, the most frequently-associated mutated genes were CHIP mutations—DNMT3A which was found mutated 54% of the time and TET2 in 16% of cases—, and mutations in tyrosine-kinase and RAS pathways genes, which were found in 39% of cases for FLT3, in 19% for NRAS, and 15% for PTPN11. Through variant allele frequency (VAF) analysis, the order of mutations showed that CHIP mutations appeared first, followed by NPM1, and then by mutations in signaling pathway genes. These data established this kind of clonal hierarchy as the archetype of CHIP-derived AML. Taken together, NPM1 mutations were associated, in 75% of cases, with one or more CHIP mutations [IDH1 and IDH2 mutations, which are known to be mutually exclusive with TET2 and WT1, because of their similar consequences on DNA hydroxymethylation and similar role in leukemogenesis [R172 mutations, the least frequent mutations of IDH2, have been shown to be mutually exclusive with NPM1 [Among rarchies B. The fiy genes) . Single-y genes) ,11. Of nutations , or IDH1ogenesis ,15,16. Cde novo-type AMLs follows almost the same pattern as the first group but lacks the CHIP-associated mutations. Indeed, the first mutation occurs in NPM1 or in transcriptions factors , followed by mutation in genes involved in proliferative pathways [CEBPA , which is not associated with mutations in CHIP-related genes, in more than 80% of cases, but is associated with NRAS mutations in 30% of cases [GATA2 (20–30%), WT1 (20%), and CSF3R (20%) [CEBPAbi-allelic is a recognized AML subgroup by the 2016 WHO classification of myeloid neoplasms and acute leukemia. From a development point of view, CEBPAbi-allelic must occur in later stages, during the hematopoietic development, as opposed to the CHIP mutations which occur in early hematopoietic stem cells (HSC), because CEBPA plays a fundamental role in the maintenance of HSC pool and in the priming of myeloid differentiation [Cebpa-knockout mouse models [Cebpa leads to an exhaustion of HSC pool and abortion of myeloid commitment. As opposed to CEBPAbi-allelic, mono-allelic mutations of CEBPA  rarely occur alone in AML and are often found associated with NPM1, FLT3, or ASXL1 mutations [CEBPAmono-allelic mutation to drive AML, by either cooperating with mutations involving genes from other functional subgroups  or with a second mutation in CEBPA. As the first category, this type of clonal hierarchy is mainly found in de novo AML with normal karyotype.The second type of clonal hierarchy in pathways . This is3R 20%) ,17. CEBPntiation ,19,20. S% ,17. CEe models  show thautations ,23. Thesde novo-type AML is designated by specific chromosomal aberrations as the initiating event, often followed by mutations in tyrosine-kinase or RAS pathways, but never associated with the NPM1, CEBPA, RUNX1, or GATA2 mutations. These chromosomal aberrations correspond to the recurrent rearrangements included in the WHO category “AML with recurrent genetic abnormalities”, such as t, inv(16)(p13.1q22) or t, and MLL  fusion genes. Amongst the two hundred AMLs of the cancer genome atlas [NPM1, CEBPA, or RUNX1 mutations. By contrast, they are frequently associated with FLT3, KIT, or RAS mutations. The very large cohort of Papaemmanuil et al. [NPM1 or in the previously cited transcription factor genes, and shows an association between t and KIT in 38% of cases. This association has been shown to have poorer outcomes [in situ hybridization), we analyzed the clonal hierarchy of four AMLs with MLL fusion genes [The third clonal hierarchy encountered in me atlas  cohort, outcomes . An evenon genes . For eacon genes ,26,27.de novo AML  and SRSF2 (20%), which also correspond to the most frequent association, between the eight genes. Indeed, 63% of SRSF2 mutated s-AML are also mutated for ASXL1. The latter is also frequently associated with EZH2, ZRSR2, STAG2, and U2AF1. Being one of the most commonly CHIP-associated gene [ASXL1-repeated association with the other genes makes sense from a statistical point of view, but also, from a clinical perspective, because MDS principally occurs in elderly patients who are mostly affected by CHIP. DNA methylation-associated genes, such as TET2 and DNMT3A, extremely frequent CHIP-associated genes, or IDH1/2, are found to be mutated in forty-four out of the ninety-three s-AML in this cohort, and are more than half the time, associated with one of the eight s-AML specific mutations. The second overall most frequently mutated gene in this s-AML cohort is RUNX1. Out of the ninety-three s-AML, twenty-nine (31%) carry RUNX1 mutations and twenty-five co-occur with one or more of the eight specific mutations, especially with ASXL1 and SRSF2. RUNX1 cannot be categorized as s-AML-specific mutated gene because of its high prevalence in de novo AML. Likewise, signaling pathway genes are also mutated in more than 50% of s-AML.In secondary AML (s-AML), which is a particularly frequent complication of myelodysplastic syndrome, as more than 20% of MDS transform into s-AML , the assnovo AML C. LindslTET2, SF3B1, ASXL1, SRSF2, DNMT3A, and RUNX1. Other recurrently mutated genes (found mutated in 2–10% of cases) were U2AF1, ZRSR2, STAG2, TP53, EZH2, CBL, JAK2, BCOR, IDH2, NRAS, MPL, NF1, ATM, IDH1, KRAS, PHF6, BRCC3, ETV6, and LAMB4. The same mutational landscape was observed by numerous other smaller scale studies [STAG2, IDH2, ASXL1, RUNX1, and BCOR. ASXL1 mutations were the most frequent associated mutations. The SF3B1 and DNMT3A mutations were less likely associated with ASXL1. TET2 mutations showed positive correlations with SRSF2 and ZRSR2 mutations. The TET2/SRSF2 association was also pointed in the context of CMML [SRSF2 mutations and those in the DNMT3A and EZH2. Regarding SF3B1 mutations, they were less associated to the other lesions, apart from DNMT3A and JAK2, and occurred mainly in MDS with ring sideroblasts (MDS-RS). The link between SF3B1 mutations and MDS-RS was confirmed later on by another large-scale study, showing that SF3B1 mutations occurred in 83% of MDS-RS cases [SF3B1 and DNMT3A mutations was confirmed more recently [To assess the question of order of appearance of mutations, one must look backwards and investigate mutational profiles of MDS. Haferlach et al.  analyzed studies ,33,34,35 of CMML . InteresRS cases . The sigrecently . Concernrecently ,34,36,38recently ,32. Concrecently ,34.JAK2, CALR, and MPL, are the unique lesions found in 45% of patients, but in the remaining 55% other mutations can be found, during the chronic phase of the disease. A 2018 study by Grinfeld et al. [JAK2 homozygosity, and mutations in the three most frequently encountered CHIP genes, TET2, ASXL1, and DNMT3A. Alterations in EZH2, IDH1, IDH2, PHF6, CUX1, ZRSR2, SRSF2, U2AF1, KRAS, NRAS, GNAS, CBL, RUNX1, STAG2, BCOR, PPM1D, TP53, and chr4q and chr7/7q LOH were less frequent, as each of them account for less than 5% of cases. Concerning the order of occurrence, CALR and MPL are usually the first event, but for JAK2 mutations, this study confirmed the previous results [JAK2 mutations were shown to appear first, followed by mutations in chromatin modifiers, such as ASXL1 or EZH2, especially in the PMF cases. Conversely, when JAK2 appeared to be sub-clonal to TET2, DNMT3A or SF3B1 mutations, it occurred in the ET cases. These data highlight the fact that the order of occurrence of mutations has an impact, as well as the type of mutations in the pathophysiology and, thereby, in the phenotype induction. The risk of leukemic and myelofibrotic transformation, in line with other studies [IDH1/2, chromatin modifier (EZH2 and ASXL1) splicing factors (SRSF2), RAS signaling, and in TP53, which were more likely to appear as second or later event, in the course of the disease. In order to identify mutations in the blast-phase, compared to the chronic-phase MPN, Lasho et al. [ASXL1 (47%), TET2 (19%), RUNX1 (17%), TP53 (16%), EZH2(15%), SRSF2 (13%), and IDH1 (12%). A relative mutual exclusivity for TP53, NRAS/KRAS, EZH2, SH2B3, RUNX1, and SRSF2 was observed. Interestingly, associations were seen between CEBPA and MPL, and between NRAS and triple-negative diseases . Nineteen cases of paired chronic-blast phase samples were analyzed. The following mutations have appeared in the blast-phase: EZH2 and PTPN11 in 67% of cases, SH2B3 in 60%, TET2 in 50%, and ASXL1 in 33%. Two cases of TP53 mutations were only found in the blast-phase samples. These data confirmed the results of a previous study, which reported increased prevalence of the TP53 (27%), PTPN11 (7%), ASXL1 (47%), IDH2 (31%), and SRSF2 (22%) mutations in blast-phase [TP53 mutations is increased in s-AML, as compared to de novo AML, this partially explains the dismal prognosis of s-AML.BCR-ABL-negative myeloproliferative neoplasms (MPN), represented by polycythaemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), can evolve during the course of the natural history of the disease to what is called blast-phase, which is namely, s-AML to MPN C. The ind et al.  analyzed results ,43 showi studies , was assst-phase . It is wTP53 mutated AML account for 12–13% of all AML cases, they are associated with complex karyotype and display particular dismal outcomes [TP53 mutations in t-AML has recently been demonstrated by Wong and collaborators [TP53. These pre-existing TP53 mutations correspond to CHIP and are resistant to chemotherapy or radiation regimen, thereby, giving a selective advantage to the mutated-clone over the normal chemo-sensitive HSC, which could expand after treatment. Of note, no difference between chemotherapy and radiation regimen concerning the development of t-AML, has ever been shown. T-AML represent around 7% of all AML cases [TP53, either display de novo-type mutation association or s-AML-type pattern of mutations [TP53 mutations, complex karyotype, and chromosomal copy-number alterations, such as −5/5q, −7/7q, −17/17p, −12/12p, +8/8q for the most frequent and the most repeatedly associated with TP53 mutations  [SBDS and CSF3R) [GATA2 [CEBPA [SRP72 [ATG2B/GSKIP [DDX41 [TP53 [BRCA1 or BRCA2 mutations [RUNX1, CEBPA, DDX41, or TP53 predisposition syndromes will frequently involve the alteration of the respective wild-type allele as an important step towards transformation. Conversely, other AMLs can occur after a process where hematopoietic stem and progenitor cells are positively selected as they manage, through acquired mutations, to escape from their inherited dysfunction. One example may be AMLs in the context of Shwachman-Diamond syndrome, where frequent complex karyotype and TP53 mutations are found [Among AMLs in children and young adults, there is an increased proportion of cases originating from familial AML predisposition syndromes when compared to adult or elderly AMLs. Several types of inherited forms of AMLs exist, involving multiple predisposition alleles that affect distinct cellular pathways . Most caANKRD26) ,55,56,57d CSF3R) ,59, and ) [GATA2 . AML occ2 [CEBPA , SRP72 [A [SRP72 , ATG2B/G2B/GSKIP  duplicatP [DDX41  mutant c41 [TP53 , BRCA1 outations . One canre found ,67. The molecular alterations described above, shape the pathophysiology and the prognosis of AMLs. This wide genetic landscape offers us powerful tools to follow the course of the disease after treatment, at a deep molecular level, in order to detect an early relapse and a poor response to therapy, which is not seen by the morphological and immunophenotypical evaluation of the residual disease. Indeed, one can anticipate four general outcomes when one starts an AML treatment . The firThe ensemble of tools that are used to evaluate the residual disease, after the treatment of leukemia, is called measurable residual disease (MRD). It was previously termed minimal residual disease, because it was defined by the ability to detect diseases below the morphology-based threshold of 5% of blasts in the bone marrow . MRD is −4 to 10−5. According to the different targets and treatments schedules, MRD detection after one, two, or more courses, is associated with a worse outcome (higher CIR (cumulative incidence of relapse) and lower EFS  and OS  rates). NPM1 mutations can also be used for the MRD evaluation by allele-specific PCR, with a sensitivity of 10−5  technologies, it seems that at least one molecular mutation can be identified in more than 90% of adult AML patients [Molecular MRD have first been developed and evaluated for fusion transcript quantification, including mainly RUNX1-RUNX1T1, CBFB-MYH11 ,75,76, a of 10−5 . Detectipatients ,5,85. InMulti target NGS MRD evaluation and ddPCR evaluation have been tested in a few studies and seems to be able to predict prognosis. The first survey using NGS targeted resequencing for MRD analysis, demonstrated in a cohort of 50 patients, that all mutations found at diagnosis can be searched for in post-induction samples . The detDNMT3A, ASXL1, and TET2) from the analysis. Persistent mutations in these isolated genes was not associated with prognosis. In line with these results, persistence or emergence of DNMT3A mutations after chemotherapy, have already been described, and was not associated with short term prognosis [TP53, IDH2, IDH1, STAG2, and others [Other recently published series ,88,89 harognosis ,90,91, bd others ,93,94. Td others  and are,d others ,94, as tKMT2A/MLL translocation), all patients were good responders. As specific PCR MRD evaluation is already well-validated for these recurrent translocations, such strategies should be restricted to the other patients. This strategy seems to be useful in all other categories of AML, including de novo AML, s-AML, and TP53 AML, even if multiple molecular or chromosomal events are often detected in CR, in this last category. Technical progress, based on error-corrected NGS (using molecular barcodes) could allow a more sensitive detection of targets [−3 or 10−4, for multi-target MRD remains not proven, yet.An evaluation of clone specific MRD could be useful to overcome the problem of choosing the best target . In a re targets ,96. HoweThe use of similar NGS-based strategies at other time points  has not been well studied, yet. One recent study  evaluateAML is an exquisitely complex and heterogeneous type of blood cancer. The outstanding progresses of sequencing techniques from the last decades led us to a precise view of how each kind of AML occur in children, young and old adults, in patients with germline defects, or in patients simply predisposed by aging, or by a toxic exposure. All of this new information allows us to refine our practical classifications, which are now relying not only on the prognostic value of each sub-entity, but also on its precise clonal composition. The multiple genetic hierarchies found in AML can be considered as a double signature. On one hand, although we do not fully understand the mechanisms that underlie the development of AMLs, the history of the clone is the signature of the multiple events that made a hematopoietic stem or progenitor cell become a true leukemic cell. On the other hand, each genetic hierarchy is also the signature of the expected outcome of the disease. Some sub-entities are considered to be good prognosis, and others to be bad prognosis. Along with this static picture at the time of diagnosis, one can also predict the AML outcome by using MRD tools, which gives a dynamic view of the clonal evolution. Thanks to the implementation of new molecular tools, we are now able to back-track the AML clone in a comprehensive manner. In the future, we will be able to delineate what are the key lesions that must be evaluated in an MRD setting, to propose unprecedented personalized treatments.


The isolation of graphene in 2004 has initiated much interest in two-dimensional (2D) materials. With decades of development, solution processing of 2D materials has becoming very promising due to its large-scale production capability, and it is therefore necessary to examine progress on solution-processed 2D materials and their applications. In this review, we highlight recent advances in the assembly of solution-processed 2D materials into thin films and the use of them for electronics and optoelectronics. We first present an overview about typical approaches to assemble solution-processed 2D materials into desired structures, including layer-by-layer assembly, Langmuir–Blodgett assembly, spin coating, electrophoretic deposition, inkjet printing, and vacuum filtration. Then, electronic and optoelectronic applications of such assembly films are presented, such as thin-film transistors, transparent conductive films, mechanical and chemical sensors, photodetectors and optoelectronic devices, as well as flexible and printed electronics. Finally, our perspectives on challenges and future opportunities in this important field are proposed.  Importantly, these different kinds of 2D materials can be metallic , semiconducting  or insulating , and possess very different optical properties . T. T2. Bes~3 × 105 . This Ioin films . The sub in TFTs . The carown in 2 ) with a nosheets . Besides2V−1s−1 can be used to drive liquid crystal displays (LCDs), which do not need rather high carrier mobilities like OLEDs (>10 cm2 V−1s−1) ..2V−1s−1,. It i2, MoS2, h-BN, and graphene printable inks with a Z value between 20 and 22. Despite Z > 14, the drop in this work was stable. Further, all printable inks can be fabricated as flexible heterostructures and logic memory devices as shown in For example, McManus et al. demonstrated a general method and achieved water-based, biocompatible, inkjet-printable 2D materials formulations ,f) 45]..45]. In However, inks from solution-processed 2D materials usually suffer from the problem that they are difficult to achieve controlled and stable pattern. The reported Z, which is larger than 14, still limits its further applications, especially when it was used in long printing sessions. To address this challenge, ink formulations using some polymeric binders were reported ,113. Thi4.In this review, we highlight the importance of solution-processed 2D materials and the corresponding electronics-related applications. We first summarize six typical assembly methods for 2D films preparation, including layer-by-layer method, Langmuir–Blodgett technique, spin coating, electrophoretic deposition method, inkjet printing, and vacuum filtration. In this section, the assembly methods as well as their advantages and disadvantages are carefully discussed. Then, solution-processed 2D materials-based TFTs, TCFs, different sensors, photodetectors, flexible and printed electronics, are discussed. Though they hold significant potential for future electronics development, there still need some efforts to address several key issues. One issue is the imperfection of existing assembly methods. There is no single assembly method which can meet all requirements including cost-effectiveness, simplicity, controllability, scalability and high-quality of assembled film. Thus, the existing assembly processes may need to be reassessed and analyzed. In addition, exploring suitable electrical applications for solution-processed 2D materials and improving the devices performance is another important issue. In the following part, we will propose several directions to which researchers should pay particular attention for further advancing the solution-processed 2D materials and their applications .10.1080/The large-area and continuous film assembly is the most important goal for solution-processed 2D materials. Among all assembly methods discussed in this review, we think Langmuir–Blodgett assembly with high controllability is of great promise. To address the large-area production issue, a roll-to-roll dip-coating technique has been developed in the Langmuir–Blodgett process for nanoparticle assembly , which i2 flakes and [2 can be slowly hydrolyzed in aqueous solutions without adverse biological effects [2 is thickness-dependent [For applications, solution-processed 2D materials may not compete with bottom up grown ones in terms of device performance. Thus, special functions or features of devices using solution-processed 2D materials should be explored and maximized. For example, various heterostructures and patterned structures can be readily made via solution process, which is not feasible in bottom up growth. Grand breakthrough might be achieved to make incorporation of functional thin-films based on solution-processed 2D materials to achieve different functions within one device. Furthermore, it is envisioned that wearable, personal health-care devices will be one of the promising applications for solution-processed 2D materials, since 2D flakes possess good mechanical properties, for example, they have high Young modulus of 0.33 ± 0.07 TPa for thin MoSakes and  and 1.0 akes and . In addi effects . Compareependent , which m


Gastrointestinal (GI) homeostasis is strongly dependent on nuclear receptor (NR) functions. They play a variety of roles ranging from nutrient uptake, sensing of microbial metabolites, regulation of epithelial intestinal cell integrity to shaping of the intestinal immune cell repertoire. Several NRs are associated with GI pathologies; therefore, systematic analysis of NR biology, the underlying molecular mechanisms, and regulation of target genes can be expected to help greatly in uncovering the course of GI diseases. Recently, an increasing number of NRs has been validated as potential drug targets for therapeutic intervention in patients with inflammatory bowel disease (IBD). Besides the classical glucocorticoids, especially PPARγ, VDR, or PXR-selective ligands are currently being tested with promising results in clinical IBD trials. Also, several pre-clinical animal studies are being performed with NRs. This review focuses on the complex biology of NRs and their context-dependent anti- or pro-inflammatory activities in the regulation of gastrointestinal barrier with special attention to NRs already pharmacologically targeted in clinic and pre-clinical IBD treatment regimens. This review is based on the most recent advances in our understanding of the complex biology of nuclear receptors (NRs) within both the healthy and inflamed intestinal tract –3 and th2+ or the MAPK signaling cascade , rosiglitazone, pioglitazone, bezafibrate, and curcumin (targeting PPARγ), and 1,25-di-hydroxyvitamin, calcitriol, and cholecalciferol (targeting VDR) , 4 Tabl.Current strategies to treat IBD include anti-inflammatory drugs, immunosuppressives, biological agents, antibiotics, and changes in dietary habits in combination with pain medication . These tNutrient uptake and elimination of toxic dietary components or xenobiotics within gut epithelium are dependent on the dietary lipid-activated NRs such as CAR (NR1I3), FXR, PXR, and VDR. Also, glucose, fatty acid, triglycerides, and lipoprotein metabolism in intestinal epithelial cells (IECs) are regulated by the PPAR family , whereas cholesterol transport and absorption and bile acid metabolism are dependent on LXR and LRH (NR5A2) .Furthermore, NRs such as ERβ, RARα, HNF4α, and NR2F6 regulate essential aspects of intestinal barrier functions such as mucus secretion, goblet and paneth cell numbers, autophagy and expression of tight junction proteins , 2 11–1, 22.Microbiota, and their metabolites such as butyrate, propionate, or indole, influence NR biology directly, functioning as ligands to target FXR, PPARγ, or PXR  5). Dep. Dep5). Within the intestinal epithelium, NRs such as VDR, HNF4α, LXR, PPARγ, LRH1, and NR2F6 play protective roles in intestinal epithelial integrity , 2; decrThe microbiota-NR axis influences not only metabolism of the intestinal epithelium, but also the components of the circadian clock; in particular, RORα (NR1F1) and RevErbα (NR1D1) influence corticosterone synthesis in IEC whereas PPAR and LXR families can alter the hepatic circadian clock , 29 Fig.NRs contribute especially to gut homeostasis by shaping intestinal immune cells; on one side, they are constantly challenged in the face of stimulatory signals from nutrients and gut microbiota, and on the other, they shape the composition of the microbiota themselves , 2 5, 1, 28, 29.+ T cells into either pro-inflammatory Th17 or tolerance-inducing regulatory T cells is dependent on several NRs such as RORγ, RORα, LXR, NR4A2 (NURR1), PPARγ, RAR, or VDR , PPARγ, or RARα are essential for gut immune homeostasis –34 Figu. Especia, or VDR   clearance from the nd CCL20 . LXR red pathway . NR2F6 d by RORc . It is sNRs, such as VDR or PPAR also regulate intestinal CD8 T cell responses –44. In pInnate lymphoid cells are tissue-resident immune cells that play essential roles in maintaining and protecting the gastrointestinal barrier against invading pathogens. In particular, ILCs themselves mediate immune responses but are controlled by dietary components and microbial metabolites. ILCs also directly regulate host metabolism and glucose tolerance . NR of tThus, whereas on one side, microbiota and their metabolites shape the homeostasis of the gut immune system, innate and adaptive lymphocytes sequentially shape gut microbiota and lipid metabolism on the other. Thus, NRs occupy a center stage of gut immune homeostasis .The two major forms of chronic inflammatory disorders within the gastrointestinal tract are Crohn's disease (CD) and ulcerative colitis (UC), characterized by clinical symptoms like severe diarrhea, pain, fatigue and weight loss . UC primSeveral members of the NR family have a protective role during disease progression, and their loss in different IBD animal models  leads to exacerbated colitis symptoms –3 Figur. In humaThe characterization of NRs that either promote or suppress intestinal inflammation has led to efficacious therapeutics for IBD. One classic anti-inflammatory drug, namely 5-ASAs, augments PPARγ expression and promotes its translocation from the cytoplasm to the nucleus resulting in activation of peroxisome-proliferator hormone response element-driven genes to suppress colitis activity , 75. RegRegulating the glucocorticoid receptor (GR), glucocorticoids play an important role in inducing remission in IBD . UnfortuThere is strong evidence in support of vitamin D that targets the VDR having protective effects in IBD-related inflammatory responses . TreatmeRifaximin, an intestine-specific human PXR agonist, appears to have more antimicrobial efficacy in the therapy of CD than traditional medications like metronidazole or ciprofloxacin; it decreases intestinal permeability and targets (NFκB), regulating anti-inflammatory effects in IBD patients –90 Tabl.Besides clinical data on nuclear receptor therapy targets, so far, several NRs have only been tested pre-clinically in animal models.ERα and ERβ gene expression levels are comparable between male and female UC colon samples, suggesting that sex-based differences in ER-mediated effects are most likely not caused by differences in gene expression ..ERα and ERβ expression has been found markedly decreased in colonic mucosa of CD/UC patients with active disease; specifically, ERβ expression in female mice protected against DSS colitis, whereas it failed to protect male mice , members of the signal transducer and activator of transcription (STAT), CCAT/enhancer-binding protein (C/EBP), and nuclear factor of activated T cells (NFAT) families , 107. ThWithin the immune system, glucocorticoids are circadian mediators  and reguGCs have a long history in IBD therapy and are well-known immune suppressants. Nevertheless, the expression of the GR itself does not appear to predict steroid treatment responses in IBD patients although conflicting data exist . GCs areThe role of the GR in IBD has been reviewed recently . Human tThe role of other steroid hormone receptors such as the androgen receptor (AR) and the progesterone receptor (PR) during colitis progression have been investigated only poorly. Pre-diagnostic circulating testosterone is associated with a lower risk of CD but not UC in women . ProgestDespite a wide range of pre-clinical IBD trials with compounds specifically targeting NR family members, the following NRs have not yet reached UC or CD patients in clinical trials.The xenobiotic NR CAR can be regulated by xenobiotics and endobiotics but also by steroid hormones . One of Car-deficient mice whereas activation of CAR using a selective CAR agonist 3,3',5,5'-tetrachloro-1,4-bis(pyridyloxy)benzene (TCPOBOP) enhances mucosal healing . FFXR mRNA  and its em cells   reside, and where it contributes to epithelial renewal by potentiating WNT/β-catenin signaling –138. GWA tissues , 139. Bo colitis  69). On. OnLRH-1 colitis . Apart f colitis , 2 140)LRH-1 andrganoids . Therebyrganoids . As prelLXRs control lipid and glucose homeostasis and respond to physiological concentrations of sterols. Whereas, LXRα is mainly expressed in the liver, intestine, kidney, and immune cells, LXRβ is more ubiquitously expressed –143. WitLxr-deficient mice are more susceptible to DSS colitis, show slower recovery and decreased survival . W. WLxr-deed colon , LXRβ haed colon . Additioed colon .The orphan NR4A subfamily includes three members, which are expressed in a wide variety of tissues, especially innate and adaptive immune cells .NUR77 gene locus are associated with increased risk for both UC and CD, and NUR77 expression is significantly reduced in colon tissues from patients with UC or CD and mice treated with DSS .+ T cells and subsequent exacerbation of colitis . T. T+ T ce colitis .PPARs are involved in the control of energy metabolism, inflammation and immune responses activated by natural ligands such as fatty acids, eicosanoids, and phospholipids , 152. PPExpression and activity of PPARγ are directly induced by microbial metabolites such as butyrate or propionate , 154.Direct targeting of the activity of PPARγ to enhance anti-inflammatory effects via its agonistic ligand rosiglitazone is efficacious in the treatment of mild to moderately active UC , 156 Ta. In combIn addition to PPARγ, the two other family members, PPARα (NR1C1) and PPARδ (NR1C2) are used for therapeutic IBD intervention. Each PPAR isotype has a specific expression pattern within the gut, but all of them mediate the effects of the microbiota . AgonistPXR protects the body from harmful foreign toxicants and endogenous toxic substances as it induces genes involved in drug transport and metabolism . PregnanPXR agonists reduce the mRNA expression of several pro-inflammatory cytokines in a PXR-dependent manner such as TNF-α and IL-1β in a rat DSS colitis model . PXR hasRARs usually form heterodimers and function as ligand-dependent transcription factors but also play extra-nuclear and non-genomic roles. The vitamin A metabolite all-trans-retinoic acid (atRA) acts as a ligand for RAR and is involved in the regulation of both the intestinal barrier function as well as immune homeostasis , 180.In general, the NRs of the RAR family play important pleiotropic roles in the regulation of innate immune cells such as dendritic cells, macrophages, and ILCs, and are especially important in the regulation of T cell homing to the gut as well as IgA class switching in B cells  19). Th. Th19). Rorc or Il22 loci, promoting maturation of LTi-like ILC3s, and regulating ILC3 proliferation (The vitamin A metabolite retinoic acid (RA) can also enhance ILC3 responses in mice through multiple mechanisms, including direct binding to the feration , 51, 181feration , 51, 182+ T cell responses highlighting the relevance of NRs as a potential therapeutic option to treat colon cancer patients  and accumulation of Th1/Th17 cells . I. IRxra+/nduction  . T. T203). IL-22 production is dependent on vitamin D and in the absence of vitamin D, mice develop a more severe enteric infection that takes longer to resolve  206)..206).In contrast Chen et al., report that VDR KO mice have more interleukin-22 (IL-22)-producing ILCs and more antibacterial peptides than WT mice. The increased ILCs in the VDR KO mice was a cell-autonomous effect of VDR deficiency on ILC frequencies .A double-blind, randomized placebo-controlled study of the effect of vitamin D supplementation over 3 months showed significantly increased 25(OH)D levels in patients in remission accompanied by maintenance of the intestinal permeability  Table 4Table 4. NR1D2 expression in UC patients is downregulated  and RORα (NR1F1), data only from human patient biopsy is available. Whereas, egulated , NR1F1 ec mucosa  . P. PMuc ge+ Th17 T cell responses and autoimmunity , RXR , PPARα (fibrates), and PPARγ (thiazolidinediones) have already been successfully targeted by approved drugs for treating autoimmunity, cancer, hyperlipidemia, or type 2 diabetes, respectively. Understanding the molecular mechanism of NRs in other human diseases will hopefully provide important insights into how to optimize NR-targeting therapies in IBD.VK and NH-K wrote the manuscript. ARM, HT, and GB contributed to the colitis and nuclear receptor biology aspects and helped with writing the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.