LRRK2 gene, encoding leucine-rich repeat kinase 2, are a common risk factor for Parkinson’s disease. How LRRK2 alterations lead to cell pathology is an area of ongoing investigation, however, multiple lines of evidence suggest a role for LRRK2 in lipid pathways. It is increasingly recognized that in addition to being energy reservoirs and structural entities, some lipids, including neural lipids, participate in signaling cascades. Early investigations revealed that LRRK2 localized to membranous and vesicular structures, suggesting an interaction of LRRK2 and lipids or lipid-associated proteins. LRRK2 substrates from the Rab GTPase family play a critical role in vesicle trafficking, lipid metabolism and lipid storage, all processes which rely on lipid dynamics. In addition, LRRK2 is associated with the phosphorylation and activity of enzymes that catabolize plasma membrane and lysosomal lipids. Furthermore, LRRK2 knockout studies have revealed that blood, brain and urine exhibit lipid level changes, including alterations to sterols, sphingolipids and phospholipids, respectively. In human LRRK2 mutation carriers, changes to sterols, sphingolipids, phospholipids, fatty acyls and glycerolipids are reported in multiple tissues. This review summarizes the evidence regarding associations between LRRK2 and lipids, and the functional consequences of LRRK2-associated lipid changes are discussed.Genetic alterations in the  LRRK2 are also associated with an increased risk of the more common sporadic form of PD  to form phosphatidylinositol (PI) [2 hydrolysis and clathrin uncoating, as studies in cell lines indicate that a PIP2-generating enzyme appears to inhibit the recycling of GLUT-1 from the endosome to the membrane [In vitro kinase assays demonstrate that LRRK2 can also phosphorylate synaptojanin-1 and in vivo, LRRK2 has been associated with increased synaptojanin-1 phosphorylation ,81. Synaor both) ,83,84. Sor both) . Synaptoor both) . Synaptotol (PI) . It is smembrane . Therefo2+, which ultimately affects oxidation rates [Interestingly, overexpression of WT LRRK2 in hepatic cell lines results in increased fatty acid oxidation, whereas LRRK2 knockdown decreases fatty acid oxidation. The effect on oxidation appears to be through LRRK2 regulation of the mitochondrial fatty acid transporter carnitine palmitoyltransferase 1A and the β-oxidation proteins peroxisome proliferator-activated receptor α and AMP-activated protein kinase. This suggests that LRRK2 plays a role in fatty acid catabolism . In a reon rates . As phos-/- rodents exhibit more lipid droplets in the kidney and liver than WT animals [Lipids can be stored in the form of lipid droplets, organelles comprising mainly of triacylglycerols and cholesterol esters, surrounded by a phospholipid monolayer. Lipid droplets are a reservoir of lipids for energy metabolism and membrane synthesis . Multipl animals . In huma animals . Whether animals ,94, whic animals . Another animals ,96, is n animals ,98. Rab1 animals . Therefo animals . Therefo3 from PIP2 and subsequently its dephosphorylation to PIP2 by 5-phosphatase and PI(3)P by 4-phosphatase [The regulation of lipid composition at synaptic membranes is essential for the proper functioning of the synaptic vesicle cycle, a process that relies heavily on lipid membrane dynamics. Although several candidate protein partners are reported for LRRK2 at pre- and post-synaptic sites (reviewed in ), those sphatase ,107,108.sphatase .2 to PI at the presynaptic membrane appears to control vesicle recycling [2 is necessary for the recruitment of several endocytic proteins, including clathrin adaptors, and PIP2 dephosphorylation to PI triggers the release of such clathrin adaptors, which is crucial for the presynaptic vesicle recycling [Additional putative substrates subject to phosphorylation by LRRK2 are synaptojanin-1  and endoecycling . Specifiecycling ,113,114.ecycling  and synaecycling  show a s2 can also be hydrolyzed by phospholipase C to form inositol 1,4,5-trisphosphate (IP3) and diacylglycerol [PIPglycerol . Primingglycerol ,119,120.glycerol . Diacylgglycerol . HoweverPLA2G6, are linked to Parkinsonism and PD [PLA2G6 homolog in Drosophila reveals smaller synaptic vesicles than WT, suggesting an important role for these phospholipids in the synaptic vesicle cycle [Serum lysophosphatidylcholine and phosphatidylcholine species from LRRK2 G2019S mutation carriers differ from those without a LRRK2 mutation . These tm and PD ,123,124.le cycle . Interesle cycle ,126. To LRRK2 are associated with altered levels of blood cholesterol in rodents [As presented in  rodents ,16 and h rodents . How exa rodents ,50 and G rodents , respect rodents ,131,132. rodents ,133,134. rodents ,96,135,  rodents ). Anothe rodents ,147,148. rodents ,152,153. rodents . Studies rodents . This su rodents ,157, howIn summary, the LRRK2 substrates or putative substrates Rab5 and synaptojanin-1 affect the metabolism of PI, either indirectly or directly, respectively, to mediate endocytosis. Lysophosphatidylcholine, diacylglycerol, ceramide and cholesterol are altered in LRRK2 mutation carriers and may be involved in exocytosis, however, the diverse functions of these lipids mean that further studies are required to elucidate possible mechanisms of involvement in LRRK2-associated PD. The effects of LRRK2 involving lipid pathways are summarized in Given that gain-of-function mutations in LRRK2 are associated with PD and altered lipid homeostasis, pharmacological inhibition of LRRK2 kinase activity holds therapeutic potential. For example, the endolysosomal phospholipid di-22:6-BMP, thought to be a biomarker of lysosomal dysregulation, is increased in urine from LRRK2 G2019S mutation carriers and is reduced in nonhuman primates treated with brain-penetrating LRRK2 kinase inhibitors (GNE-7915 and GNE-0877/DNL201) . In phasIn a study that utilized a Food and Drug Administration (FDA)-approved drug library to screen for compounds that could rescue LRRK2 G2019S neurite degeneration in mice and flies, the statin lovastatin was found to prevent dopaminergic neuron loss. In addition, lovastatin rescued motor deficits in LRRK2 G2019S flies . StatinsIn summary, a collection of evidence indicates that LRRK2 phosphorylates substrates that either directly metabolize phospholipids in the synaptic membrane (synaptojanin-1) or recruit enzymes that do (Rab5). These effects appear essential for the proper functioning of the synaptic vesicle cycle. In addition, LRRK2 appears to affect GCase, which metabolizes sphingolipids in the lysosome. Furthermore, the LRRK2 substrates Rab5, Rab8 and Rab10 are involved in lipid trafficking, lipid droplet fusion and lipophagy, respectively. Rabs are additionally involved in trafficking receptors such as GLUT-4, critical in insulin and glucose pathways. Future investigations should address the variability encountered in LRRK2-GCase interaction studies and clarify the potential mechanisms by which this occurs. Although the LRRK2 knockout models have been informative regarding potential LRRK2-associated lipid alterations, future investigations on LRRK2 mutation knock-in models may provide a more comparative model of human LRRK2 mutation changes. In addition, further studies in brains from humans that carry LRRK2 mutations will help clarify whether peripheral and CSF lipid changes are reflected in the brain. LRRK2 kinase inhibitors and statins have lipid-altering effects, however, whether and how this benefits PD patients are an area of active investigation. In addition, whether the unique lipid signature of LRRK2 mutation carriers has diagnostic and prognostic biomarker potential is of interest.


FGFRs activation modulates intracellular responses in various cell types under metabolic stress. FGF21, in particular is considered as the key regulator for mediating systemic metabolic effects by binding to receptors FGFR1, FGFR3, and FGFR4. The complex of FGFR1 and beta Klotho (β-KL) facilitates endocrine and paracrine communication networks that physiologically regulate global metabolism. This review will discuss FGF21-mediated FGFR1/β-KL signaling pathways in the liver, adipose, and cardiovascular systems, as well as how this signaling is involved in the interplay of these organs during the metabolic syndrome. Furthermore, the clinical implications and therapeutic strategies for preventing metabolic syndrome and its complications by targeting FGFR1/β-KL are also discussed.Metabolic syndrome is a chronic systemic disease that is particularly manifested by obesity, diabetes, and hypertension, affecting multiple organs. The increasing prevalence of metabolic syndrome poses a threat to public health due to its complications, such as liver dysfunction and cardiovascular disease. Impaired adipose tissue plasticity is another factor contributing to metabolic syndrome. Emerging evidence demonstrates that fibroblast growth factors (FGFs) are critical players in organ crosstalk  FGFR (Fibroblast Growth Factor Receptor) signaling is involved in various stages of human development and metabolic health. In humans, there are 23 distinct fibroblast growth factors (FGFs), 18 of which (FGF1-10 and 16-23) are mitogenic signaling molecules that bind to four high-affinity cell surface receptors, named FGFR1, FGFR2, FGFR3, and FGFR4  or ketogenic diets, thereby mediating hepatic response to nutritive stimuli –15. Morevia uncoupling protein 1 (Ucp1) activation  and ERK signaling (via hepatic adiponectin secretion in a paracrine manner (Adipocytes express both β-KL and FGFRs (mainly FGFR1 and FGFR2) and are important targets for FGFs . White ativation . Thus, Btivation , mediatetivation , 35. BATignaling , 28, 36.e manner , 37, 38.e manner , indicate manner . Therefovia paracrine and endocrine FGFs and exhibits anti-hypertrophic, anti-oxidative and anti-apoptotic properties under physiological and pathological conditions (via anti-oxidative mechanisms and recovery of energy homeostasis in cardiac cells (via ERK 1/2 and AMP-activated protein kinase (AMPK) in an acute manner and via Phosphoinositide 3-kinases (PI3K)/ protein kinase B (Akt) in a sustained fashion  upregulation owing to decreased lipid oxidation, and impaired glucose oxidation. Conversely, using genetic or pharmacological modulation, FGF21 displays cardioprotective properties under dysregulated glucose and lipid metabolism (In streptozotocin (STZ)-induced diabetes, cardiac FGF21 mRNA level is increased significantly . FGF21 mtabolism –57 FGF21tabolism . In additabolism .via reduction of ATF4-C/EBP homologous protein (CHOP) pathway  stress is invoked by oxidative stress, lipid deposition, and abnormal proteins synthesis in cardiomyocytes . Maladap pathway . Althoug pathway .via AMPK activation in endothelial cells under diabetic stress , a prolyl peptidase related to the dipeptidyl peptidase IV (DPP-IV) enzyme. Increased circulating FAP levels are associated with decreased levels of bioactive to total FGF21, thus impairing its metabolic regulation potential . Hence, Because pharmacokinetic properties of FGF21 analogs remain the most challenging for balancing therapeutic benefits and mechanism-related toxicity, further research on targeting FGFR1/β-KL signaling is crucial to identify novel therapeutic potentials . For insFGF21 is an endocrine and cell-autonomous autocrine regulator displaying a varied response across different organs in a stress- and time-dependent manner , 98. MosNK, SG, and JS collected references, generated, drafted, did revisions, and proofread the manuscript. NK and RR generated the figure. OF proofread the manuscript. NK and WL designed the manuscript. All authors contributed to the article and approved the submitted version.This work was supported by grants FS/15/16/31477, FS/18/73/33973, PG/19/66/34600, and FS/19/70/34650 to WL from the British Heart Foundation.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.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


PKP2 gene that causes biventricular arrhythmogenic cardiomyopathy and affects a family, of which the only member with the positive phenotype is a competitive endurance athlete.Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) is a hereditary condition that can cause sudden cardiac death in young, frequently athletic individuals under the age of 35 due to malignant arrhythmias. Competitive and endurance exercise may hasten the onset and progression of ARVC, leading to right ventricular dysfunction and potentially fatal ventricular arrhythmias earlier in life. In this article, we present a novel, pathogenic, early truncating heterozygous variant in the  Human c09040 is A thorough medical and family history covering three generations was obtained from the index patient. We also performed a 12-lead electrocardiogram (ECG), exercise stress testing, transthoracic echocardiography (TTE), flourine-18 fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT), 48 h Holter ECG, and cardiac magnetic resonance imaging (MRI). His first-degree relatives are asymptomatic and their cardiologic workup including exercise test, TTE and genetic cascade screening was carried out.CTNNA3, DES, DSC2, DSG2, DSP, JUP, LDB3, LMNA, PKP2, PLN, RYR2, SCN5A, TGFB3, TMEM43, TP63, and TTN) according to the evidence-based evaluation of gene validity for ARVC by the most recent 2022 European Society of Cardiology guidelines [The Prepito  DNA Blood250 kit was used to extract DNA from an ethylenediaminetetraacetic acid (EDTA) blood sample. For molecular genetic analyses, the SwissDNAlysis Cardiopanel  was used, and high-throughput sequencing (Illumina MiSeq) was performed, with 92.3% of bases sequenced with a Q-score ≥ Q30. 98.8% of the analyzed gene segments had a coverage of ≥20×. The average sequencing depth of the analyzed gene segments was 270.7×. The patient was examined for 173 genes related with inherited heart disease, of which 16 are associated with ARVC (RYR2 (Exon 3 und 97), DSP , PKP2 , TGFB3 , JUP , DSC2  und DSG2  genes ). Data analysis was performed with Coffalyser.Net .The sequences were aligned and realigned locally against the human reference genome (GRCh37hg19) using lllumina alignment software version 2.5.42.7 . Variants with an allele frequency <5% in the coding regions including the flanking intronic regions (±8 bp) were scored. Data interpretation was performed using Variant Studio 3.0, Varsome Clinical, dbSNP153, the gnomAD database, PubMed, and ClinVar. Using standard Sanger sequencing, all variations in this study were confirmed. Multiplex Ligation dependent Probe Amplification (MLPA) was used for relative copy number analysis to detect deletions and duplications  in the PKP2-gene  was performed using a plasma polymerase chain reaction (PCR) followed by direct Sanger sequencing. The primers were as follows: Forward, 5′-CATACCACAGACAGTACCAGCA-3′ and reverse, 5′-CCAGAAGTGCCAGCTCAT GC-3′.For the genetic testing of the family members, genetic analysis of exon 3 of the 2) parasternal short axis RV outflow tract = 38 mm (18.5 mm/m2) with reduced area of shortening (fac = 27%) and normal longitudinal function . On the RV inflow view, a subtricuspid aneurysm and multiple sacculations of the RV free wall were noticeable  in exon 3) that causes an early truncation of the protein, which was confirmed by Sanger sequencing. It was classified as pathogenic (class V) according to the 2015 American College of Medical Genetics Criteria [PKP-2 variant. Both did not report a history of participating in competitive sports, and thorough cardiac evaluation of these two genotype positive family members showed normal findings.Genetic testing revealed a novel heterozygous nonsense variant in the Criteria . CascadePKP2 [PKP2 cardiomyopathy is inherited autosomally dominantly and is thought to affect primarily the RV, making it specifically associated with ARVC. Competitive and endurance exercise may accelerate the onset and progression of ARVC, resulting in potentially life-threatening ventricular arrhythmias and RV dysfunction at a younger age. Although it has been shown in previous studies that early truncation of the PKP2 C-terminus likely causes ARVC irrespective of transcript position [The most frequent gene linked to ARVC is PKP2 . The PKPposition , desmosoposition  and it iposition . In thisposition . Based oPKP2 variant provides a genetic risk, it is insufficient to cause an ARVC phenotype on its own. It is important to consider that other genetic and environmental factors can modify the individual threshold for disease penetration. The altered proteins in the intercalated discs interfere with normal cell adhesion, mechanical stability, cell-to-cell communication, and electrical connection. It has been hypothesized that mechanical stress, such as that caused by exercise, leads to instability, inflammation and fibro-fatty infiltration. [PKP-2 cardiomyopathies [As a marathon runner, the index patient was the only one to develop ARVC in his family, indicating that while the novel tration. . Exercistration.  but biveopathies . Thanks PKP2 gene causing biventricular arrhythmogenic cardiomyopathy and affecting a family, in which the only phenotype-positive member is a competitive endurance athlete. This highlights the importance of environmental factors such as endurance exercise for disease penetrance and progression in patients with classical right-dominant ARVC associated with (likely) pathogenic variants in PKP-2.Taken together, we describe a novel, pathogenic, heterozygous early truncating variant in the


LOX, LOXL1, and LOXL3 expression correlated with matrisome gene expressions. LOXL1 correlations were detected in LGG with IDH mutation (IDHmut), LOXL3 correlations in LGG with IDH wild type (IDHwt) and strong LOX correlations in glioblastoma (GBM) were found. These increasing correlations may explain the increment of ECM stiffness and tumor aggressiveness from LGG-IDHmut and LGG-IDHwt through to GBM. The expression of the mechanosensitive transcription factor, β-catenin, also increased with malignancy grade and was correlated with LOXL1 and LOXL3 expression, suggesting involvement of this factor in the outside–in signaling pathway.Tumor cell infiltrative ability into surrounding brain tissue is a characteristic of diffusely infiltrative astrocytoma and is strongly associated with extracellular matrix (ECM) stiffness. Collagens are the most abundant ECM scaffolding proteins and contribute to matrix organization and stiffness. LOX family members, copper-dependent amine oxidases, participate in the collagen and elastin crosslinking that determine ECM tensile strength. Common IDH mutations in lower-grade gliomas (LGG) impact prognosis and have been associated with ECM stiffness. We analyzed the expression levels of LOX family members and matrisome-associated genes in astrocytoma stratified by malignancy grade and IDH mutation status. A progressive increase in expression of all five LOX family members according to malignancy grade was found.  Invasiveness, the infiltrative capacity of tumor cells into surrounding tissue, is a major characteristic of gliomas that prevents complete tumor resection, leads to inexorable tumor recurrence, and confers poor clinical outcome. Tumor extracellular matrix (ECM) stiffness has emerged as a physical hallmark of cancer that, contributes to cancer initiation, progression, metastasis and metabolic reprogramming ,2, and rmut) to LGG with IDH wild type (LGG-IDHwt), through to GBM. Tumor recurrence occurs independently of other factors, but time to recurrence varies according to malignancy grade and IDH mutational status, proving shorter in IDHwt than IDHmut tumors [Astrocytomas, or astrocytic gliomas, are the most common brain tumor. These tumors are classified according to their histologic and molecular characteristics and, more recently, according to isocitrate dehydrogenase (IDH) mutation status, where the presence of this mutation confers a more favorable prognosis . Low-grat tumors . A growit tumors .IDH1 mutation status [mut, LGG-IDHwt, and GBM groups. Additionally, a search for mechanosensitive transcriptional factors, whose expression correlated with the group of differentially expressed genes, was performed. The study objective was to identify the LOX family members, along with matrisome components, that impact astrocytoma ECM stiffness. This knowledge can help identify LGG-IDHwt that are more prone to tumor progression, together with new candidates for interventions aimed at reducing tumor invasiveness.Our group has previously reported a correlation between increased LOX expression and higher malignancy grade in human astrocytomas, and also a correlation of LOX expression with n status . In the LOX, LOXL1, LOXL2, LOXL3, and LOXL4 showed increased expression levels in astrocytoma samples compared to non-neoplastic (NN) samples. Moreover, these expressions increased with malignancy, proving the highest in GBM. Pairwise comparisons of NN samples and diffusely infiltrative astrocytoma grades 2, 3, and 4  were significant (p < 0.0001) for all five LOX family genes. The paired comparisons relative to GBM were also significant, except for the LOXL3-AG3 comparison (p < 0.0001), with the highest significance found in the paired comparisons with GBM , encompassing AG2 and AG3, according to IDH mutation status and for GBM cases  for mparison A. The rewith GBM B. ExpresBM cases C. Gene emut, LGG-IDHwt, GBM-IDHmut, and GBM-IDHwt. A progressive increase in expression of these proteins was observed from LGG-IDHmut, LGG-IDHwt, and through to GBM, proving highest in GBM and confirming the results of the gene expression analyses  and LOXL1 (p = 0.002) expression had shorter OS than patients with lower expression (LOX expression had OS of 49.91 ± 7.38 months and 57.89 ± 10.59 months (p = 0.033), respectively. LGG with the highest and lowest levels of LOXL1 expression had OS of 19.87 ± 5.25 months and 57.89 ± 8.06 months (p = 0.0034), respectively. Similarly, OS of GBM patients was analyzed using Kaplan–Meier curves. Only LOXL1 expression levels impacted the prognosis of GBM, where patients with high expression had shorter OS . Multivariate Cox regression analysis with age at diagnosis identified only LOXL1 expression as an independent variable for predicting prognosis in LGG (p = 0.027) (p = 0.032)  indications among 111 LGG patients with high LOXL1 expression. Nevertheless, the survival time was shorter for those with high LOXL1 expression (The impacts of pression A. LGG wiorter OS B. GBM pa= 0.027) C and GBM= 0.032) D. In addpression .p ≤ 0.05 in any of the comparisons were selected, resulting in 439 upregulated genes and 233 downregulated genes, including LOX, LOXL1, and LOXL3. Expression of LOXL2 and LOXL4 did no differ significantly on any of the comparisons. Subsequently, a total of 672 up and downregulated genes in LGG-IDHmut, LGG-IDHwt, and GBM groups were analyzed using Kruskal–Wallis and Dunn’s post hoc tests (LGG-IDHwt vs. LGG-IDHmut and LGG-IDHwt vs. GBM). This analysis led to the identification of 70 differentially expressed genes, comprising 9 genes coding for collagens, 17 for ECM glycoproteins, 23 for ECM regulators, 5 for ECM-affiliated proteins, 3 for proteoglycans, 10 for secreted factors, and 3 LOX genes   . The wormut, 22 genes exhibited a moderate correlation , 1 gene, CTHRC1, had strong correlation  with LOXL1, and only 2 genes were moderately correlated with LOXL3. None of the genes showed a significant correlation with LOX. In LGG-IDHwt, 15, 21, and 2 genes had moderate correlations with LOXL1, LOXL3, and LOX, respectively, while S100A11 and CTSB showed strong correlations with LOXL3 . In GBM, 28, 28, and 43 genes showed moderate correlations with LOXL1, LOXL3, and LOX, respectively, while SERPINE1 and PLOD2 displayed strong correlations with LOX . The levels of expression of the matrisome-associated genes correlated (in increasing complexity) with LOXL1 in LGG-IDHmut, LOXL3 in LGG-IDHwt and with the three LOXs, but most strongly with LOX in GBM  in the observed expression profiles was investigated by analyzing the correlation of these TFs with LOXL1, LOXL3, and LOX expressions. NFKB1 and SOX2 were differentially expressed across the groups analyzed  but correlated only with LOXL3 and LOX expression levels in LGG-IDHwt and GBM, respectively (data not shown). Interestingly, the level of CTNNB1 expression was significantly higher in LGG-IDHwt than in LGG-IDHmut (p < 0.0001), and also higher in GBM related to LGG-IDHwt (p = 0.0081)  ( 0.0081) A, correlGG-IDHwt B.LOXL1, LOXL2, LOXL3, and LOXL4 expression levels were also found to increase progressively in astrocytomas from grades 2 to 4, proving highest in GBM, and significantly higher relative to non-neoplastic brain tissue. These results were subsequently confirmed in silico for the TCGA glioma RNAseq dataset. Similar results have been observed for other tumors, suggesting a key role of the LOX family members in tumor progression [mut has been shown to restrict tumor aggression by decreasing HIF1α-dependent tenascin C expression, thereby decreasing ECM stiffness and mechanosignaling [mut than in IDHwt tumors [wt has a poorer prognosis than LGG-IDHmut [LOX [LOXL1, and LOXL3 [LOX expression with epithelial mesenchymal transition (EMT) and IDH1 mutation status have also been described [LOXL1 has been associated with tumor invasion, metastasis, and extracellular accumulation of lactate [LOXL3 expression with EMT (through E-cadherin transcription repression by SNAIL) [wt [ECM stiffness contributes significantly to cancer progression by promoting tumor cell proliferation, invasion, and drug resistance. In fact, the matrix stiffness of glioma is higher than that of normal brain tissue and increases with malignancy ,29. The gression ,38,39,40gression . Similargression , an oncogression  and decrgression . Moreovegression . Given αgression . Thus, igression  and upregression . Glioma ignaling . In factt tumors  and, cliG-IDHmut . Moreovemut [LOX , LOXL1, nd LOXL3  expressind LOXL3 , and LOXnd LOXL3 . Correlaescribed . Similar lactate , linked  lactate . Associay SNAIL) ,56, celly SNAIL) , and wity SNAIL)  have beeAIL) [wt .LOX, LOXL1, and LOXL3 expression was observed for LGG-IDHmut, LGG-IDHwt, and GBM in the TCGA glioma RNAseq dataset, suggesting their role in determining ECM composition and stiffness enhancement in these phenotypes.In the present study, a progressive increase in levels of COL1A1, COL1A2, COL3A1, and COL5A1 expression levels were correlated with all three LOXs in GBM, whereas COL6A1-3 expression levels correlated with LOXL1 and LOXL3 in LGG, and with all three LOXs in GBM. Fibrillar collagen deposition was described in the adventitia of remodeled large vessels and glomeruloid vascular structures of GBM [COL6A1 expression levels were observed in astrocytoma of different malignancy grades, especially in higher grade tumors associated with poor prognosis [ECM stiffness is related to matrix composition, matrix contraction, and matrix crosslinking, where LOX family members play a major role . Concerns of GBM . High COrognosis . COL6A1 rognosis  and VEGFrognosis .PLOD1, and PLOD2, involved in collagen biosynthesis and crosslinking [wt and GBM. Similar results were recently reported by other authors [SERPINH1), which was significantly correlated with LOXL1 in LGG-IDHwt and GBM, and with LOX in GBM. SERPINH1 encodes a heat shock protein (HSP47) localized in the endoplasmic reticulum, participates in the correct folding of collagen [Results showed overexpression of two genes coding for lysyl hydroxylases, procollagen-lysine, and 2-oxoglutarate 5-dioxygenase (PLOD) , PLOD1, slinking ,67 in LG authors ,69 and i authors . We alsocollagen , and faccollagen . Increascollagen . Transfocollagen , and thecollagen  and has collagen , the molLUM), a class II leucine rich proteoglycan. The ECM organization process assembles adhesion plaque complexes and allows integrins to transduce cues from the ECM by activating a signaling cascade that induces cytoskeletal remodeling and regulates cell behavior [LUM and FN1 were upregulated and showed significant correlation with LOX in GBM. A high abundance of FN1 protein in the ECM of GBM was previously demonstrated by our group [The organization of collagen fibrils, including modulation of their diameters and interfibrillar spacing , is perfbehavior . Thus, Lbehavior . Fibronebehavior  also indbehavior . In addibehavior . Previoubehavior . In the ur group .wt possesses a cytosolic substrate composition that is better suited for collagen biosynthesis. Proline (Pro) constitutes about 10% of total amino acids in collagen [mut in glioma leads to a significant reduction in Gln and Glu levels, whereas IDHwt gliomas contain high levels of intracellular Glu [ALDH18A1, and pyrroline-5-carbohydrate reductase 1, coded by PYCR1. These two enzymes synthesize Glu to glutamate ϒ-semialdehyde and then to Pro, respectively. Interestingly, both these genes were upregulated in both LGG and GBM (data not shown).Metabolically, IDHcollagen , and cancollagen . The preular Glu ,88, provwt due to the Warburg effect, with a shift of the oxidative tricarboxylic acid cycle towards glycolysis [CSTB upregulation has been described in GBM [wt, and has been strongly associated with the mesenchymal subtype and immunosuppressive conditions in gliomas [CTSB was highly correlated with LOXL3 in LGG-IDHwt and with LOX in GBM. The 2-HG generated in IDHmut enhances angiogenesis through HIF1α stabilization, partially by decreasing levels of endostatin, an HIF1α antagonist, which in turn increases vascular VEGF signaling [LOX in GBM. Additionally, the expression level of the collagen triple helix repeat containing-1 gene (CTHRC1), an ECM glycoprotein inducer of angiogenesis, migration, and cell invasion, showed the highest correlation with LOXL1 in LGG-IDHmut. FN1, significantly correlated with LOX expression in GBM in the present analysis, may also promote angiogenesis in cancer by providing a ridged structure for vessel development and signaling for endothelial cell migration [In addition to Glu accumulation, an increase in lactate level can be observed in IDHycolysis . Glycolyycolysis . The aciycolysis , throughycolysis  and MMP9ycolysis . Moreoveycolysis , is secrycolysis  and partycolysis ,97,98. Iycolysis ,100. CSTd in GBM  and GBM d in GBM , particu gliomas . Interesignaling . VEGFA wigration .CTNNB1, which codes for β-catenin, according to astrocytoma malignancy grade, and its expression correlated significantly with LOXL1 and LOXL3 expression in both LGG-IDHmut and LGG-IDHwt. Collagen deposition and crosslinking promote ECM stiffness and clustering of integrins, leading to FAK activation with subsequent PI3K/AKT activation, inhibition of GSK-3β, and stabilization of β-catenin [LOXL3 with β-catenin expression level in cancer. Recently, our group identified upregulation of LOXL1 and involvement of Wnt/β-catenin signaling in the malignant transformation of normal astrocytes by anoikis [LOXL1, and its interactions with the matrisome-related genes, may be involved in this first step of transformation towards an astrocytic tumor. Additionally, elements of TCF/LEF transcription factors were identified in the promoter region of LOXL1, suggesting that the β-catenin signaling pathway may regulate positively LOXL1 expression [Lastly, the ways in which ECM stiffness can trigger mechanotransduction were analyzed by searching for correlations between the differentially expressed genes and mechanosensitive transcription factors. Interestingly, there was a progressive increase in -catenin . Nuclear-catenin . LOXL1 h-catenin . However anoikis . We specpression .LOXL1, LOXL3 and LOX with matrisome-related gene expression, possibly explaining the progressive increase in ECM stiffness from LGG-IDHwt, LGG-IDHwt, and through to GBM. LOXL1 correlation net was detected in less malignant astrocytomas. Connectivity with LOXL3 was prominent among more aggressive LGG-IDHwt, and strong connectivity with LOX was detected in GBM, demonstrating the complexity of ECM components involved in astrocytoma progression. More specifically, level of LOXL1 expression impacted the outcome of LGG and GBM patients, with shorter OS in individuals exhibiting higher expression. In addition, radiotherapy was indicated more frequently in LGG patients with high LOXL1 expression, yet this group had shorter survival than LGG patients with low LOXL1 expression.Overall, the results showed a significant correlation of increased gene expression of The casuistic samples consisted of 130 diffusely infiltrative astrocytomas (grades II to IV). Tumors were graded according to the WHO classification AG2 , AG3 , and GBM . The non-neoplastic control group consisted of samples from individuals undergoing temporal lobe resection during epilepsy surgery . All samples were collected during surgical procedures by the Neurosurgery Group of the Department of Neurology at the Hospital das Clinicas of the School of Medicine of University of Sao Paulo. Fresh surgical samples were immediately snap-frozen in liquid nitrogen upon surgical removal. Before RNA extraction, a 4-μm-thick section of each sample was obtained for histological assessment using a cryostat at −25 °C. Sections were stained with hematoxylin and eosin and examined under light microscope. Necrotic and non-neoplastic areas were removed from the frozen block of tumoral tissue by microdissection prior to RNA extraction. Grey matter was avoided in the control samples. Written informed consent was obtained from all patients according to the ethical guidelines approved by the Ethical Committee of the School of Medicine, University of São Paulo (0599/10).Total RNA was extracted from frozen tissues using the RNeasy Mini kit . RNA concentration and purity were determined by measuring absorbance at 260 and 280 nm. Ratios of 260/280 measures ranging from 1.8 to 2.0 were considered acceptable for purity standards. Denaturing agarose gel electrophoresis was used to evaluate the integrity of samples. A conventional reverse transcription reaction was performed to yield single-stranded cDNA. The first strand of cDNA was synthesized from 1000 ng of total RNA previously treated with one unit of DNase I  using random and oligo (dT) primers, RNase inhibitor, and SuperScript III reverse transcriptase according to the recommendations of the manufacturer . The resulting cDNA was subsequently treated with one unit of RNase H , diluted with TE buffer, and stored at −20 °C until later use.Analysis of relative expression levels of LOXL1, LOXL2, LOXL3, and LOXL4 were performed by RT-qPCR using the Sybr Green I approach. Quantitative data were normalized in relation to the geometric mean of three reference genes: glucuronidase beta (GUSB), hypoxanthine phosphoribosyltransferase (HPRT), and TATA box binding protein (TBP). The immunohistochemical procedures for LOX, LOXL1, and LOXL3 expression analyses were performed on 4-μm slices of paraffin-embedded tissues of 6 cases each of AG2, AG3, and GBM. Tissue sections were first subjected to antigen retrieval in 10 mM citrate buffer, pH 6.0, and incubated at 122 °C for 3 min using an electric Pascal . Specimens were then blocked and further incubated with primary antibodies against human LOX , LOXL1 , and LOXL3  at 16–20 °C for 16 h. Slices were then incubated for endogenous peroxidase blocking  at 16–20 °C for 16 h. Antibodies localization was visualized using diaminobenzidine and Harris hematoxylin. http://www.cbioportal.org, accessed on 1 May 2022) [https://gtexportal.org/, accessed on 1 May 2022) [mut, 58 IDHwt), and 160 samples of GBM . Matrisome gene lists were based on the Matrisome Project  [In silico analysis of gene expression was performed in TCGA database (ay 2022) ,110. Genay 2022) . Data waay 2022) . Data coay 2022) . Normalimut and IDHwt, and for GBM samples, the cases were divided into proneural and mesenchymal subtype. Limma package with voom method in R package was used for differentially expressed gene analysis. Correlation analyses between gene expression values were assessed by the non-parametric Pearson’s correlation test. Correlation coefficient R value used was R > 0.5. Statistical significances were considered when p ≤ 0.05. All analyses were performed using SPSS version 20.0 , R software, and plots were made using the program GraphPad Prism version 8.0 .The distribution of gene expression data was analyzed by the normality test of Kolmogorov–Smirnov and Shapiro–Wilk test. For gene expression, non-parametric Kruskal–Wallis test was used to compare multiple groups, followed by Dunn’s post-hoc test. Kaplan–Meier survival curves were analyzed using the log-rank test. Multivariate Cox proportional regression analysis was performed using age as a covariate with gene expression level. Receiver Operating Characteristic curves were used to determine the high and low expression groups to Kaplan–Meier analysis for OS of LGG and GBM cases. The cut off of the expression values for ROC analysis was determined for the LGG cases were divided into IDHmut, LGG-IDHwt, and through to GBM, reinforce the impact of ECM components contributing for matrix stiffness on the malignant progression and prognosis of astrocytoma.The LOX family was increasingly expressed according to malignancy of astrocytoma, exhibiting the highest expression in GBM. The progressive gene expression connectivity among LOX, LOXL1, and LOXL3 and matrisome-related genes from LGG-IDH


Camellia sinensis under shade in winter remain unclear. In our study, tea leaves were utilized for physiological attributes and transcriptome analysis in November and December in three shading groups and no-shade control plants. When compared to the no-shade control plants, the shading group protected tea leaves from cold damage, increased photochemical efficiency (Fv/Fm) and soil plant analysis development (SPAD), and sustained chlorophyll a, chlorophyll b, chlorophyll, and carotenoid contents by physiological mean. Then, transcriptome analysis revealed 20,807 differentially expressed genes (DEGs) and transcription factors (TFs) in November and December. A comparative study of transcriptome resulted in 3,523 DEGs and many TFs under SD0% vs. SD30%, SD0% vs. SD60%, and SD0% vs. SD75% of shading in November and December. Statistically, 114 DEGs were downregulated and 72 were upregulated under SD0% vs. SD30%. SD0% vs. SD60% resulted in 154 DEGs, with 60 downregulated and 94 upregulated. Similarly, there were 505 DEGs of which 244 were downregulated and 263 were upregulated under SD0% vs. SD75% of shading throughout November. However, 279 DEGs were downregulated and 105 were upregulated under SD0% vs. SD30%. SD0% vs. SD60% resulted in 296 DEGs, with 172 downregulated and 124 upregulated. Finally, 2,173 DEGs were regulated in December, with 1,428 downregulated and 745 upregulated under SD0% vs. SD75%. These indicate that the number of downregulated DEGs in December was higher than the number of upregulated DEGs in November during low temperatures. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of differentially expressed genes were highly regulated in the photosynthesis, plant hormone signal transduction, and mitogen-activated protein kinase (MAPK) signaling pathways. However, qRT-PCR and RNA-seq relative expression of photosynthetic (DEGs) Lhcb2 in both November and December, plant hormone (DEGs) BRI1 and JAZ in November and IAA and ERF1 in December, and key DEGs of MAPK signal transduction FLS2, CHIB, and MPK4 in November and RBOH, MKK4_5, and MEKK1 in December in three shading groups and no-shade control plants responded to tea cold tolerance. The enhanced expression of light-harvesting photosystem I gene Lhca5, light-harvesting photosystem II gene Lhcb2, and mitogen-activated protein kinases MEKK1 and MPK4/6 enhance the cold-tolerance mechanism of C. sinensis. These comprehensive transcriptomic findings are significant for furthering our understanding of the genes and underlying regulatory mechanisms of shade-mediated low-temperature stress tolerance in horticultural crops.Tea is a vital beverage crop all over the world, including in China. Low temperatures restrict its growth, development, and terrestrial distribution, and cold event variability worsens cold damage. However, the physiological and molecular mechanisms of  The tea tree thrives in 10°C–30°C warm, humid climates (zone 8 climate or warmer). Due to climatic changes, tea plants undergo environmental and abiotic stresses such as cold, chilling, and hot and low temperatures, damaging plant development, quality, and yield  and metabolism (food utilization). Each plant species has a temperature range in which it grows best based on its origin . The temperature has an enormous impact on plant resilience, fall color, and senescence . The capability of a plant to tolerate the average minimum temperature of a region without damage or death is determined by its hardiness. Even cold-hardy plants are vulnerable to the devastating effects of a rapid temperature drop to freezing . Plants thaliana . Tea plathaliana . Many sivia energy partitioning, as well as contemporaneous changes in chloroplast carbon metabolism, allocation, and partitioning, are mechanisms for overcoming the restrictions of short-term and long-term exposure to low temperatures. Thus, the mechanisms involved in photosynthetic acclimation to low temperatures arise from thylakoid membrane system alterations that affect photosynthetic electron transport. The genes and transcription factors that trigger the signals in the photosynthesis pathway regulate these photosynthetic processes during low temperatures, as well as post-transcriptional activation, increase the expression of sucrose synthesis enzymes, alter the expression of Calvin cycle enzymes, change the leaf protein content, and affect plant photosynthesis process. Plant hormones and their derivatives play a role in how plants react to cold temperatures  have been found in horticultural plants, including tomatoes and apples, based on whole-genome sequencing and transcriptome analysis. Recent research has shown that the MAPK cascade is also important in the biotic and abiotic stress responses of horticulture plants, including low temperatures. The genes and transcription factors are triggered in plant hormone signal transduction and mitogen-activated protein kinase signaling pathways , 30% of shading (SD2), 60% of shading (SD3), and 75% shading (SD4) were used . In this experiment, we tested the 5-year-old Zhong Cha 102 Cere used Table 1.2.22.2.1Cold plant injuries in three shading groups and no-shade control plants were recorded. Browning symptoms (on leaf tissue) were confirmed to be a cold-damage indication , and the2.2.2A portable photosynthesis system  was used to measure chlorophyll fluorescence. The photochemical efficiency of photosystem II (Fv/Fm) was also measured. In brief, the fourth developed leaf from the shoot tip was acclimated in the dark for 30 min in three shading groups compared with no-shade control plants during low temperatures. As mentioned in our previous work, soil plant analysis development (SPAD) values in three shading groups and no-shade control plants were also recorded .2.2.3For measuring the chlorophyll and carotenoid concentrations in three shading groups in comparison with no-shade control plants during low temperatures, 50 g of fresh tea leaves was cut into small pieces and kept in the dark at 25°C for 48 h in acetone–anhydrous ethanol solution (1:1) with minor modifications, and data were recorded according to our previous work .2.3C. sinensis ‘Shuchazao’. Feature Counts program tallied the genes . |log2 (fold change)|2 or FDR = 0.05 was used to screen DEGs. After adjustment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways with p = 0.05 were considered enriched. Transcriptome analysis was completed at Wuhan Metware Biotechnology Co., Ltd.Tea leaf total RNA was extracted using RNAprep Pure, and the library was constructed following the RNA detection method. After quality control, 150-bp paired-end reads were generated using Illumina HiSeq. HISAT2 software utilized the aligned reference genome of he genes . FPKM quhe genes . The Ben2.4® Green master mix . Three biological replicates were analyzed, with glyceraldehyde 3-phosphate dehydrogenase (CsGAPDH) gene used as the internal reference gene.To verify the accuracy of the transcriptome data, 11 DEGs were selected for expression-level validation. Primers were designed using Beacon Designer 8, and the primer sequences are shown in 2.5p-values < 0.05) were used to analyze physiological and gene expression data under shading group and no-shade control plants during low temperatures. GraphPad Prism software was used for making figures. Graphics were formatted using Adobe Photoshop CC 2019.Statistix 8.1 software was used to determine significant differences between groups, and one-way analysis of variance (ANOVA) and Duncan’s multiple-range tests  slightly increased as compared to no-shade control plants. The carotenoid (Cx) content increased in the no-shade control plants compared to the three shading groups. Similarly, chlorophyll a and b and chlorophyll (Chll) increased in the shading group, but there were no significant differences between SD30%, SD60%, and no-shade control plants during November. However, under SD75% of shading, the levels of chlorophyll a and b and chlorophyll (Chll) and carotenoid (Cx) were significantly reduced in comparison with no-shade control plants in December during winters  and the KEGG pathway to identify the genes associated with tea leaves in three shading groups compared with no-shade control plants in November and December during low temperatures. These genes are mainly involved in cellular processes, metabolic processes, signaling, response to stimulus, growth, and regulation of biological processes in the biological process (BP) category. In the cellular component (CC) process category, the enriched genes were involved in protein-containing complex cellular, anatomical entities. Similarly, genes related to catalytic activity, binding, transcriptional regulator activity, molecular transducer activity, and molecular function regulator enriched in the molecular function (MF) category under SD0% 3.6vs. SD30%  proteins that constitute the antenna system of the photosynthetic apparatus , CA, abscisic acid (AB), GBs, ethylene (ET), BRs, JA, and SA, as shown in vs. SD30%, nine DEGs and transcription factors were activated under SD0% vs. SD60%, and 27 DEGs and transcription factors were triggered under SD0% vs. SD75% of shading  “Plant hormone signal transduction” and map (ko04016) “mitogen-activated protein kinase signaling pathway” activated and enriched the key DEGs and transcription factors in three shading groups in comparison with no-shade control plants during low temperatures ( shading Table 3.44.1C. sinensis leaves in three shading groups compared with no-shade control plants in November and December during low temperatures. The results demonstrate that shaded tea leaves were shielded from leaf injury in November and December during low temperatures compared to no-shade control plants. It means that shading protected tea leaves from cold damage due to stopping ice accumulation in extracellular tissues (−2 s−1) rate was significantly lower in three shading groups compared to no-shade control plants in November and December during low temperatures. Our results are like those of the previous study, which reported a higher PAR rate in the controlled group than in the shading groups (a and b, chlorophyll, and carotenoid contents in November. A lower amount of chlorophyll a and b and a higher chlorophyll concentration were beneficial for photosynthesis under different shades, consistent with an earlier study (a and b, chlorophyll, and carotenoid were degraded under SD75% of shading in December during low temperatures. The reasons are unknown. Moving forward, under SD30% and SD60% of shade conditions, the concentrations of chlorophyll a and b and chlorophyll were higher as compared to no-shade control plants in December during low temperatures. This indicates that under different shade groups, the higher chlorophyll concentration and more pigment-binding proteins are associated with their photons collected by photosystem II per unit. The light-harvesting complex of photosystem II is mainly composed of chlorophyll b (Temperature changes are among the most common abiotic stressors encountered by plants. Low-temperature stress affects plants’ various morphological, physiological, biochemical, and molecular characteristics, ultimately inhibiting plant growth and development . Therefo tissues . Therefo tissues . Our stug groups . We alsog groups . Increasg groups , includig groups . In thiser study . The degophyll b . In cont4.2According to various transcriptome data, several genes and transcription factors play an essential role in photosynthesis, plant hormone signal transduction, and mitogen-activated protein kinase signal cascades under different abiotic stresses . In this4.3via the cytochrome complex and the electron transport chain (PsbB, PsbC, PsbR, PsbO, PsbP, and PsbQ, are essential components of the oxygen-evolving complex (PsaA and PsaB; binding subunits PsaG, PsaK, PsaH, PsaL, PsaO, and PsaP; ferredoxin docking subunits PsaD and PsaE; plastocyanin docking subunits PsaF and PsaN; and FeS apoprotein (Lhca5 in photosystem under SD0% vs. SD75%, may be a key DEG for coping with cold stress in November and December during low temperatures. LHCII-related DEG Lhcb2 was increased under low temperatures. This suggests that shade promoted the regulation of LHC-related genes under low temperatures and improved the photosystem machinery of tea leaves during low temperatures. Our findings are congruent with those of a previous study in which authors discovered that the high expression of light-harvesting chlorophyll Lhca2 in the photosystem is an important contributor to cold tolerance in tea leaves (PsbR and PsbQ were highly expressed under SD0% vs. SD75% in December during low temperatures, and the photosystem I core complex contains reaction center subunits PsaK and PsaO, which were also highly expressed under SD0% vs. SD75% during low temperatures. At the same time, psaK was found to be downregulated under SD0% vs. SD75% in November during low temperatures. We validated the highly regulated key DEG Lhcb2 expressed in November and December under shading and no-shade control plants, respectively. The relative expression level was satisfactory between RNA-seq and qRT-PCR analysis of Lhcb2.Photosynthesis is the essential process that drives the growth and development of a plant. In the photosynthesis process, photosystem I and II pigment–protein complexes are related rt chain  from plart chain . In thisrt chain . Oxygen- complex . Photosyoprotein . In the a leaves . In addi4.4BRI1 and MYC2 were upregulated and JAZ was downregulated under SD0% vs. SD30%, and under SD0% vs. SD60%, BRI1, JAZ, and PR-1 were expressed highly. AA-R, GIDI1, CTRI1, MPK6, ERF1/2, BAK1, and BRI1 were also expressed highly and PP2C, BIN2, BZR1/2, TCH4, JAZ, and MYC2 were downregulated in November during low temperatures. In contrast, BRI1 was upregulated and JAZ and MYC2 were downregulated under SD0% vs. SD30%. Under SD0% vs. SD60%, AUX/AA, GIDI, SIMKK, BAK1, BRI1, and MYC2 were found to be expressed highly. However, AUX/AA, ARF, SAUR, B-AAR, A-AAR, GIDI, DELLA, PPC2, CTRI, SIMKK, EBF1/2, ERF1/2, BAK1, BRI1, BSK, BZR1/2, TCH4, CYCD3, JAR1, JAZ, MYC2, TGA, and PR-1 were differentially regulated in December during low temperatures. This indicates that several important DEGs and transcription factors are associated with hormone signal transduction playing an essential role in three shading groups in comparison with no-shade control plants in November and December during low temperatures in C. sinensis, and the molecular mechanism of these DEGs is illustrated in AUX/IAA family, response factor ARF family, and the short auxin RNA-SAUR family (AUX1, ARF, and SAUR. Moreover, most known reactions of plant cytokinin metabolism or signaling systems to low temperatures are inhibitory (ARR expression in a cytokinin- and ethylene-dependent way (B-ARR and type A ARR were expressed highly in three shading groups compared with no-shade control plants in November and December during low temperatures. Our results demonstrate that these two cytokinins interact to manage cold stress signals and alleviate the harmful effects of low temperatures in tea leaves. These findings align with earlier research, in which the author stated that mutations in cytokinin-type genes increase cold tolerance in A. thaliana during cold temperatures (GID1 controls plant growth and development by interacting with DELLA protein in the gibberellic signaling pathway. The involvement of these DEGs in signaling pathways improved cold tolerance, and the overexpression of GID1 and DELLA was regulated during low temperatures in three shading groups compared with no-shade control plants during low temperatures. The enzymes involved in ABA synthesis are zeaxanthin epoxidase, 9-cis-epoxycarotenoid dioxygenase, and abscisic aldehyde oxidase (NCDE 1 gene and SnRKs, were identified and expressed differentially under cold stress (PYR/PYL, PP2C, and SnRK2. In our study, we found that PPC2 regulated differentially in three shading groups in contrast with no-shade control plants in November and December during low temperatures might play an important role during cold stress. BRs are a class of steroid hormones that play an important role in plant growth and development (A. thaliana and mostly used in in-depth investigations under different abiotic stress, plays a regulatory role by establishing the COI1/JAZs/MYC2 complex (MYC2, JAZ1, JAZ2, JAZ3, and JAZ12 are involved in the jasmonic signal transduction pathway and were significantly upregulated in Phoebe bournei under shade (C. sinensis under low temperatures. However, we validated the high expression of key DEGs BRI1 and JAZ under shading and no-shade control plants in November and IAA and ERF1 in December. The relative expression level was reasonable between RNA-seq and qRT-PCR analysis of confirmed DEGs enriched in plant hormone signal transduction pathway (In order to survive in low-temperature environments, plants have evolved a set of complex signaling pathways . Among tR family  are all hibitory , but thehibitory . Interesdent way . In our eratures . The cla oxidase . In a prd stress , which felopment . Both BRelopment , includielopment . Among t complex . In thiser shade . We assuer shade . In facter shade . Therefo4.5A. thaliana cold stress response via regulating the ICE1 pathway (FLS2, CHIB, and MPK4 expressed in November and RBOH, MKK4_5, and MEKK1 in December under shading and no-shade control plants, and the relative expression level was similar between RNA-seq and qRT-PCR analysis (MEKK1 and MPK4/6, enriched in the mitogen-activated protein kinase signaling pathway, a novel discovery for our tea cultivar Zong Cha 102. Both DEGs were highly regulated under shading groups compared with no-shade control plants in November and December during low temperatures. These DEGs are positive indicators for cold tolerance in C. sinensis (MEKK1 directly mediates MPK4 and MPK6 and that the regulation of these two key genes in the mitogen-activated protein kinase signaling pathway in model plant A. thaliana is mainly responsible for cold stress tolerance (Mitogen-activated protein kinase cascades are essential in regulating many distinct biological processes, including cell function, proliferation, and response to various abiotic stresses , includi pathway . Moreoveolerance .5Lhca5 and light-harvesting photosystem II gene Lhcb2 synthesized the CO2 fixation and maintained photosynthetic machinery, sustaining chlorophyll concentration. Finally, DEGs involved in plant hormone signaling and mitogen-activated protein kinase signaling cascades were activated, and shading might protect the tea plants from cold injury due by retaining the ice accumulation and maintaining membrane fluidity in cellular compartments of leaf tissues under low temperatures. Mitogen-activated protein kinase signal transduction DEGs MEKK1 and MPK4/6 are key players in this study for strengthening the cold-tolerance mechanisms in C. sinensis. Taking it all together, in this study, we confirm that different shading groups compared to no-shade conditions played a substantial role as a cover for sheltering tea cultivar Zhong Cha 102 on physiological and molecular levels during low temperatures. Also, shading is a fast and reliable technique for enhancing the cold-tolerance mechanism in C. sinensis. This study paves the way for researchers to better understand the protective approach for shielding horticultural crops under low-temperature scenarios.In summary, we revealed some novel physiological and transcriptomic information from the tea plant at low temperatures in three shading groups and no-shade control plants. We discovered that the adaptive regulation of tea leaves under shading conditions is primarily related to physiological characteristics such as photochemical machinery, photochemical efficiency of soil plant development, and chlorophyll content and gene expression analysis. In comparison to no-shade control plants, the shading group performed a main role in the protection mechanism of tea leaves against cold damage. Furthermore, DEGs and transcription factors associated with photosynthesis, plant hormone signaling, and mitogen-activated protein kinase signaling pathways played an important role in shading and no-shade control plants. The light-harvesting photosystem I gene The original contributions presented in the study are included in the article/Conceptualization of work and evaluation by SZ and ZD. Methodology and investigation by SW and DS. Physiological analysis performed by HW, XP, and MW. Physiological data analysis performed by JS, DS, and SD. Manipulation of transcriptome data and manuscript written by SZ. The article was revised and organized by IS. Project direction, resources, and funding achieved by YW and ZD. All authors contributed to the article and approved the submitted version.


Emerging respiratory viruses are major health threats due to their potential to cause massive outbreaks. Over the past 2 years, the coronavirus disease 2019 (COVID-19) pandemic has caused millions of cases of severe infection and deaths worldwide. Although natural and vaccine-induced protective immune mechanisms against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been increasingly identified, the factors that determine morbimortality are less clear. Comparing the immune signatures of COVID-19 and other severe respiratory infections such as the pandemic influenza might help dissipate current controversies about the origin of their severe manifestations. As such, identifying homologies in the immunopathology of both diseases could provide targets for immunotherapy directed to block shared pathogenic mechanisms. Meanwhile, finding unique characteristics that differentiate each infection could shed light on specific immune alterations exploitable for diagnostic and individualized therapeutics for each case. In this study, we summarize immunopathological aspects of COVID-19 and pandemic influenza from the perspective of cytokine storms as the driving force underlying morbidity. Thereby, we analyze similarities and differences in the cytokine profiles of both infections, aiming to bring forward those molecules more attractive for translational medicine and drug development. Outbreaks of viral pneumonia have occurred all along human history. Although the mechanism behind morbidity remained unclear for decades, current paradigms indicate that besides the microorganisms' virulence, an overdriven host immune response mediates devastating manifestations of infections. This idea has gained further notoriety after the coronavirus disease 2019 (COVID-19) pandemic. Thus, it is now accepted that the critical forms of the disease are frequently accompanied by excessive cytokine release into the circulation (hypercytokinemia)  subtype (Centers for Disease and Prevention This review compares cytokine storm syndromes (CSS) observed during COVID-19 and influenza to detect conserved immunopathogenic mechanisms underlying severe disease. Moreover, by highlighting unique immune profiles in critical COVID-19, we provide the theoretical bases for future research on specific cytokine networks implicated in pathogenesis that could be targeted through immunotherapy.Cytokines coordinate the immune response activation, regulation, and amplification. They have short half-life times, and their production is very regulated to prevent systemic damage , also named hemophagocytic lymphohistiocytosis (HLH), is characterized by immune overstimulation. This condition can be primary and secondary according to its cause , ferritin and D-dimer levels, prolonged prothrombin time, decreased erythrocyte sedimentation rate, hypertriglyceridemia, and hypoalbuminemia  and interleukin 1 beta (IL-1β). TNFα is expressed as a membrane-bound heterotrimer and is released after shedding by a disintegrin and metalloproteinase 17 (ADAM17) in macrophages, lymphocytes, and fibroblasts. Meanwhile, IL-1β is secreted by monocytes, macrophages, and dendritic cells (DCs) is found at high concentrations in patients with sepsis (MERA and others IL-12 and interferon-gamma (IFNγ). IL-12 and IL-18 act synergistically to elicit the release of IFNγ from type 1 T helper (Th1) cells  production contribute to microcirculatory dysfunction, inadequate oxygen delivery, and tissue hypoxia  cells suppress the activity of CD4+ T cells, and follicular DCs , from which only A and B infect humans. The structure of the influenza virions has a multisegmented, negative-sense, single-strand (ss) RNA genome of 12–15 kb, with a rounded shape of 80–120 nm in diameter. Inside the capsid, the RNA and the polymerase form a viral ribonucleoprotein (vRNP) complex. The genome is segmented into 8 parts in A and B virus types (7 in C and D), which encode 8 structural proteins , neuraminidase (NA), M1, M2, NP), and 2 nonstructural proteins (NS1 and NEP).HA and NA are the major glycoprotein antigens, the first facilitating the entry into the target cell, while NA mediates the release and dissemination of virions from infected cells  are the first protective antiviral barrier  and activates serine-threonine kinases (IKKɛ) and TBK1, which phosphorylates IRF3 for subsequent expression of IFN-β , IL-6, CXCL8, CCL2, CCL3, CCL4, and CCL5 are produced at the site of infection  that binds to IgG antibodies, leading to antibody-mediated cellular cytotoxicity (ADCC). NK cells can also release granular granzyme and perforin to induce cell lysis and secrete cytokines such as TNFα and IFNy , and ROS production. Excessive neutrophil recruitment and degranulation destroy the lung extracellular matrix and induce epithelial apoptosis and alveolar lesions , and lung specimens of severely ill influenza patients is characterized by large concentrations of TNFα, IFNy, IL-1β, IL-2, IL-6, CXCL8, CCL2, CCL3, CXCL10, G-CSF, FGF, VEGF, and anti-inflammatory mediators such as TGF-β, IL-10, and IL-1RA , antibody neutralization of IFNy reduces lung tissue inflammation and BAL cytokine levels, and improves survival , IL-1R , IL-6 , and IL-6R  is being tested in clinical trials, showing promising benefits by reducing symptomatic burden, need for invasive respiratory support, and death, thus warranting further investigation, as revised elsewhere  and activating molecules (G-CSF) acting on monocytes and neutrophils. As mentioned above, a range of monocyte and neutrophil subsets with inflammatory and degranulating phenotypes mediate lung inflammation and disease progression in influenza and COVID-19 , eosinophil chemokines (CCL11), growth factors, and vasoactive molecules . Hence, the lack of balance of the effector response might be another determinant of the host defensive collapse observed in some critical COVID-19 patients. Specifically, the Th2 component of this response might inhibit antiviral responses in specific subgroups of patients and generate interstitial infiltrates of neutrophils, eosinophils, and type 2 innate lymphoid cells (ILC2s), mediating lung inflammation and tissue damage. In fact, evidence exists that Th2 mediators and eosinophilia are associated with worse outcomes in a subset of individuals with severe COVID-19  have been used in patients with atopic dermatitis and COVID-19 without increasing the risk of severe complications and even apparently reducing respiratory symptoms , inflammatory , regulatory (IL-10), chemoattractant , angiogenic , and growth factor  properties. Hence, pathogenic mechanisms such as excessive innate immune activation, monocyte/neutrophil chemotaxis, and microvascular dysfunction might be important during the 2 diseases. Conversely, discrepancies in the immune signature of these infections include higher levels of Th1 cytokines along with IL-2, APRIL, sTNF-R1, sTNF-R2, SP-D, and CXCL17 in severe influenza patients, with COVID-19 displaying a polyfunctional Th1/Th2/Th17 immune activation profile in some patients with severe manifestations. Hence, reestablishing a balanced immune reaction might be a good objective for host-directed therapies directed to certain subgroups of COVID-19 patients.Nonetheless, additional research is warranted to validate these immune profiles and clarify the best timing for administering specific immunotherapies according to the cytokine dynamics of these infections.


Rhizoctonia solani using a quantitative LC-MS/MS-based proteomic approach to identify the differentially expressed proteins promoting higher virulence. Across several rice-growing regions in Odisha, Eastern India, 58 Rhizoctonia isolates were obtained. All the isolates varied in their pathogenicity. The isolate RS15 was found to be the most virulent and RS22 was identified as the least virulent. The PCR amplification confirmed that the RS15 and RS22 belonged to the Rhizoctonia subgroup of AG1-IA with a specific primer. The proteomic information generated has been deposited in the PRIDE database with PXD023430. The virulent isolate consisted of 48 differentially abundant proteins, out of which 27 proteins had higher abundance, while 21 proteins had lower abundance. The analyzed proteins acquired functionality in fungal development, sporulation, morphology, pathogenicity, detoxification, antifungal activity, essential metabolism and transcriptional activities, protein biosynthesis, glycolysis, phosphorylation and catalytic activities in fungi. A Quantitative Real-Time PCR (qRT-PCR) was used to validate changes in differentially expressed proteins at the mRNA level for selected genes. The abundances of proteins and transcripts were positively correlated. This study provides the role of the proteome in the pathogenicity of R. solani AG1-IA in rice and underpins the mechanism behind the pathogen’s virulence in causing sheath blight disease.Sheath blight of rice is a destructive disease that could be calamitous to rice cultivation. The significant objective of this study is to contemplate the proteomic analysis of the high virulent and less virulent isolate of  Rhizoctonia solani Kuhn (Teleomorph: Thanatephorus cucumeris (Frank) Donk) is a soil-borne necrotrophic fungal pathogen that affects many food crops that are important to humankind. Fourteen anastomosis groups (AG1–AG13 and AGBI) have been assigned based on hyphal fusion  (Q4P763), glycylpeptide N-tetradecanoyltransferase (P34809), sulfate adenylyltransferase (Q4P460), glyceraldehyde-3-phosphate dehydrogenase 1 (P32635) and pentafunctional AROM polypeptide (P0CM22), were randomly selected for gene expression analysis. The relative mRNA levels of each transcript were checked in RS15 and RS22. Each gene’s mRNA levels were normalized to the expression of Rhi-18S rRNA as a control gene in each sample. The qRT–PCR results demonstrated a positive correlation of the mRNA expression level with the changes in protein abundance levels for all eleven genes .r = 0.95) that indicated a strong agreement between the qRT-PCR analysis and the proteomic data. This result confirmed our proteomics data and implied that the proteomics results were reliable.The relative fold changes of mRNA and protein level were positively correlated for eleven genes with a 95% correlation .Several researchers have well documented the morphological and genetic diversity of isolates ,46,47. Hisolates . In thisisolates  reportedg et al.  reportedAspergillus nidulans and phytopathogenic fungus Fusarium graminearum [Magnaporthe oryzae. The fungal development requires MoJMJ1-encoding JmjC histone demethylase, especially in the pre-penetration phase of M. grisea [In our study, the proteins P0CO40 and P0CO41 were identified as the histone demethylation protein 1 containing the JmjC domain. These play a vital role in histone demethylation and transcriptional regulation of secondary metabolite gene clusters in minearum ,51. Huh minearum  conducte. grisea . From thUstilago maydis is imperative for pathogenicity and was characterized as part of a conserved cellular response to ER stress [MoSsb1, MoSsz1 and MoZuo1 and their functional mechanisms are involved in regulating the conidiation, pathogenicity, vegetative growth and mating of rice blast fungus. Similarly, FgHsp90 is required for the virulence sexual and asexual development of the plant pathogenic fungus, Fusarium graminearum [FpHsp70 genes were up-regulated when infected with F. pseudograminearum, implying their significance in the virulence of F. pseudograminearum. This supporting information suggested an up-regulation of Hsp70 in virulent isolates that plays a significant role in sexual development, sporulation and virulence.The protein P18694 was identified as Heat shock 70 kDa (Hsp70) protein 2, which was overexpressed in RS15. Hsp70 is highly conserved and has a prominent role in the fungal system for growth, morphogenesis and various stress conditions ,54. Dnj1R stress . Yang etR stress  revealedminearum . Chen ettop1 mutants of F. graminearum and F. culmorum demonstrated exceptionally reduced virulence. The particularly mutated strain F. graminearum negatively affected the pathogenicity and conidia formation of the fungi [Ustilago maydis demonstrated that vegetative growth did not require it, but a pigmentation defect was exhibited by its mutant [R. solani [Another up-regulated protein was P0CR92, Topoisomerase 1, which relaxes the supercoiled DNA and enables numerous basic cellular processes, including transcription, replication and recombination . In wheahe fungi . When fus mutant . From ths mutant ,62. Thiss mutant . Primaris mutant . Numerous mutant . The sec. solani ,67,68. MThermomyces lanuginosus demonstrated the presence of cyanase (Tl-Cyn), and the overexpressed Tl-Cyn gene was evaluated for cyanate detoxification activity [R. solani had overexpressed cyanases and hypothesized that virulent R. solani could tolerate plant-produced and another microbial cyanate in the soil environment. The protein Q6QWR1 is linked with pyranose 2-oxidase (Pox2), a flavin-dependent oxidoreductase [D-glucose as well as other monosaccharide substrates of hydrogen peroxide. Pox is typically found in basidiomycetes fungi, where it is associated extracellularly with membrane-bound vesicles or other membrane structures in the periplasmic space of hyphae [2O2) secreted by the fruiting bodies of Tricholoma matsutake, produced by pyranose oxidase, strongly inhibited mycelial growth of the phytopathological fungus R. solani. This data suggested a high-level expression of pyranose oxidase that plays a significant role in the antifungal activity, thereby dominating the microbial communities [R. solani, is unknown.The protein A8NV38, cyanate hydratase, is over-expressed in virulent isolate, which plays a vital role in nitrogen assimilation or cyanate detoxification in bacteria, fungi and plants ,70,71. Cactivity ,74,75,76eductase . It oxidf hyphae ,79. The munities . The rolA total of 21 proteins were under-expressed in RS15 when compared to RS22. For instance, Elongation factor G (Q4P257), Sulfate adenylyltransferase (Q4P460), 5′-3′ exoribonuclease 2(Q4P149), Glyceraldehyde-3-phosphate dehydrogenase 1 (P32635), Inositol-pentakisphosphate 2-kinase (Q4P4C1) and Pentafunctional AROM polypeptide (P0CM22 and P0CM23) were responsible for translation, biosynthesis of sulfur-containing amino acids, protein biosynthesis, glycolysis, phosphorylation and catalytic activities in fungi, respectively ,82,83,84R. solani isolates were obtained from rice-growing areas of Odisha, Eastern India. They displayed differences in virulence on the rice cultivar, Tapaswini. The isolate RS15 was found to be the most virulent and RS22 was identified as the least virulent. The virulence of RS15 and RS22 was further confirmed on other rice genotypes viz., Pusa Basmati-1, Vanaprabha, Hazaridhan, Swarna, Lunishree, Savitri, Sadabahar and TN1. Further, we employed an LC-MS/MS-based proteomic approach to profile the proteomic differences between the virulent RS15 isolate and less virulent RS22 isolate. A total of 48 differentially expressed proteins were identified, of which 27 proteins were up-regulated in virulent isolate. These up-regulated proteins were more responsible for pathogenicity, detoxification, antifungal activity, sporulation, fungal development, morphology, essential metabolism and transcriptional activities. The important proteins, such as sorting nexin-4, JmjC domain-containing histone demethylation protein 1, topoisomerase 1, squalene synthase, pyranose 2-oxidase, Hsp70 and cyanate hydratase, may have major roles in the pathogenicity and virulence of R. solani RS15. The proteomic information generated in this study contributes knowledge on the virulence mechanism responsible for the sheath blight of rice disease. Further research is required to explore the importance of these proteins and their possible roles during sheath blight disease establishment.A total of 58


The construction of a competing endogenous RNA (ceRNA) network is an important step in the identification of the role of differentially expressed genes in cancers. In the current research, we used a number of bioinformatics tools to construct the ceRNA network in prostate cancer and identify the importance of these modules in predicting the survival of patients with this type of cancer. An assessment of microarray data of prostate cancer and normal samples using the Limma package led to the identification of differential expressed (DE) RNAs that we stratified into mRNA, lncRNA, and miRNAs, resulting in 684 DEmRNAs, including 437 downregulated DEmRNAs (such as TGM4 and SCGB1A1) and 241 upregulated DEmRNAs (such as TDRD1 and CRISP3); 6 DElncRNAs, including 1 downregulated DElncRNA (H19) and 5 upregulated DElncRNAs (such as PCA3 and PCGEM1); and 59 DEmiRNAs, including 30 downregulated DEmiRNAs (such as hsa-miR-1274a and hsa-miR-1274b) and 29 upregulated DEmiRNAs (such as hsa-miR-1268 and hsa-miR-1207-5p). The ceRNA network contained a total of 5 miRNAs, 5 lncRNAs, and 17 mRNAs. We identified hsa-miR-17, hsa-miR-93, hsa-miR-150, hsa-miR-25, PART1, hsa-miR-125b, PCA3, H19, RND3, and ITGB8 as the 10 hub genes in the ceRNA network. According to the ROC analysis, the expression levels of 19 hub genes showed a high diagnostic value. Taken together, we introduce a number of novel promising diagnostic biomarkers for prostate cancer. Prostate cancer is the most frequent malignancy in males worldwide, accounting for 27% of all cancer diagnoses . During It is also important to mention that high-grade prostate cancer is likely on a genetic basis, whereas low-grade disease is more likely to be associated with environmental factors. In fact, the vivid alteration in stage from the time when PSA was introduced as a screening test has been accompanied by a more modest shift in Gleason grade, suggesting that grade may be established in the early phases of tumor pathogenesis . MeanwhiThe recent decade has witnessed a revolution in the application of high throughput data analysis tools, leading to the construction of several interaction networks between different types of biomolecules including RNA, DNA, and protein in different disease contexts, particularly cancer. This type of study has led to the identification of promising biomarkers for the early detection of cancer. In the field of prostate cancer, several efforts have been made. For instance, the re-analysis of high throughput expression data has led to the identification of several differentially expressed genes (DEGs) between cancerous and normal tissues. Further functional enrichment analyses have shown the relationship between these genes and clinical outcomes of patients . SimilarThe competing endogenous RNA (ceRNA) network being constructed between long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs has been shown to contribute to the pathoetiology of different cancers and regulate fundamental processes, both within cancer cells and inside the tumor microenvironment ,9. Identhttp://www.ncbi.nlm.nih.gov/geo/) (accessed on 12 September 2022) was used to obtain the human expression data for GSE88808 , Duarte, CA, USA), GSE200879 ((HTA-2_0) Affymetrix Human Transcriptome Array 2.0 (Genosplice), Créteil, France), and GSE60117 (Agilent-021827 Human miRNA Microarray (V3), Palo Alto, CA, USA). There were 98, 137, and 77 samples in each of these datasets, respectively. For further analysis, we chose 113 prostate cancers and 9 normal tissues from GSE200879, 49 prostate tumors and 49 adjacent normal samples from GSE88808, and 56 prostate tumors and 21 normal tissues from GSE60117 . Next, data from both platforms were combined using the R software. The ComBat function from the R Package Surrogate Variable Analysis (SVA) was utilized to exclude batch effects  [Normalization is a crucial stage in the integration of heterogeneous data since the described datasets contain various and trendy platforms. The statistical programming language R was used for the processing and integration of microarray data. Data were initially normalized independently for pre-processing using the preprocessCore package’s normalizeQuantiles function (erences) . The batp value) < 0.05. Following that, we used the HUGO gene nomenclature committee to identify DElncRNAs.We used the Limma package in R language  to identWe determined the gene expression levels of significant DEGs. We used this data in the pheatmap package in R language  to complp value) < 0.05 and |log2 fold Change (FC)| > 0.5. Finally, we identified the genes that were present in both the TCGA and GEO datasets.We included a total of 500 PRAD samples and 52 control samples for further analysis. We used the TCGAbiolinks package to download the transcriptome profiling data (TCGA-PRAD), and limma and edgeR packages to analyze the data. As a result, DEGs were evaluated with the cut-off criteria of the false discovery rate  (accessed on 30 September 2022). (2) Applying miRDB (http://www.mirdb.org/) (accessed on 30 September 2022) [https://mirtarbase.cuhk.edu.cn/) (accessed on 30 September 2022) [http://www.targetscan.org/) (accessed on 30 September 2022) [http://129.206.7.150/) (accessed on 30 September 2022) [We created a ceRNA network by carrying out the following steps: (1) Evaluating the interactions between lncRNAs and miRNAs based on the PC-related miRNAs using miRcode er 2022) , miRTarB22 , miRTer 2022)  and miRWThe expression value of hub genes was assessed using the Gepia database . The hubThe boxplot of unprocessed raw data and normalized data after batch effect removal is shown in The Limma package (version 3.52.3) was used to analyze microarray data from prostate cancer and normal samples. This analysis resulted in the identification of 684 DEmRNAs, including 437 downregulated DEmRNAs (such as TGM4 and SCGB1A1) and 241 upregulated DEmRNAs (such as TDRD1 and CRISP3); 6 DElncRNAs, including 1 downregulated DElncRNA (H19) and 5 upregulated DElncRNAs (such as PCA3 and PCGEM1); and 59 DEmiRNAs, including 30 downregulated DEmiRNAs (such as hsa-miR-1274a and hsa-miR-1274b) and 29 upregulated DEmiRNAs (such as hsa-miR-1268 and hsa-miR-1207-5p). In order to compare the variation in miRNA, lncRNA, and mRNA expressions between prostate cancer and normal samples, we utilized the volcano plot using the EnhancedVolcano package  in R Fi. In addip value) < 0.05 and |log2 fold Change (FC)| > 0.5. Finally, we identified the genes that exist in both GEO datasets and the TCGA dataset , followed by cellular component (CC) and molecular function (MF). The first 30 entries are collagen-containing extracellular matrix (CC), sarcolemma (CC), cell-substrate junction (CC), focal adhesion (CC), basement membrane (CC), extracellular matrix binding (MF), muscle system process (BP), muscle contraction (BP), muscle tissue development (BP), urogenital system development (BP), ear development (BP), membrane raft (CC), membrane microdomain (CC), gland development (BP), muscle cell differentiation (BP), contractile fiber (CC), regulation of epithelial cell proliferation (BP), cell-substrate adhesion (BP), epithelial cell proliferation (CC), response to xenobiotic stimulus (BP), mesenchyme development (BP), regulation of smooth muscle cell proliferation (BP), smooth muscle cell proliferation (BP), laminin binding (MF), cell junction assembly (BP), extracellular matrix structural constituent (MF), collagen binding (MF), inner ear development (BP), mesenchymal cell differentiation (BP), and muscle organ development (BP). For the analysis, the clusterProfiler package (version 4.4.4) was employed. In GO functional enrichment analysis, 604 GO entries reached an adjusted The dot plot of the top 10 enriched functions and the enriched GO-induced graph are, respectively, visualized in In Using Pathview  and gagehttps://genomics.senescence.info/cells/ (accessed on 24 September 2022) to find the genes associated with cell senescence. A total of 279 genes associated with cell senescence were found in this database. As a result, 21 DEGs, including TP63, ID4, ITGB4, CAV1, ID1, TLR3, TGFB1I1, MYLK, NTN4, ETS2, LGALS3, GNG11, IGFBP3, SIK1, VEGFA, EZH2, MATK, HJURP, NOX4, MYC, and MMP9 were discovered to be involved in cell senescence  (accessed on 30 September 2022). Additionally, we used CancerMIRNome  (accessed on 30 September 2022) to evaluate the hub miRNA gene expression value. As a result, CAMK2B, CAV1, GPC1, H19, ITGA3, ITGA8, ITGB4, LAMA3, MMP9, MYH11, PCA3, PRKCA, RND3, VEGFA, hsa-miR-25, hsa-miR-93, hsa-miR-125b, and hsa-miR-17 indicated good statistical significance (The expression value of hub genes was assessed using the Gepia (ificance .We used graphpad prism 9.0 and CancerMIRNome to construct ROC curves. The ROC curve was used to evaluate how accurately the hub genes predicted outcomes. AUC was used to compare the diagnostic values of these hub genes. ROC curves and AUC values of the dataset are shown in In order to find novel biomarkers for prostate cancer, we used a bioinformatics approach and constructed the ceRNA network in this context. We also valued the importance of the identified hub genes in the pathogenesis of prostate cancer and found their association with signaling pathways. TGM4 gene codes for transglutaminase 4, a protein with a restricted pattern of expression toward prostate. The encoded protein has been shown to regulate the interactions between prostate cancer cells and vascular endothelial cells through bypassing the ROCK pathway [TDRD1 is responsible for coding a protein containing a tumor domain that suppresses transposable elements during spermatogenesis. The encoded protein has been shown to be expressed in most human prostate tumors, in spite of its absence in normal prostate tissues [In the first step, we identified several DEGS. TGM4 and SCGB1A1 have been among down-regulated mRNAs in this type of cancer.  pathway . Moreove tissues . CRISP3  tissues . We also tissues .Key factors known to be involved in prostate cancer tumorigenesis were identified with this approach. However, there are limitations. Importantly, the bioinformatic prediction is strongly dependent on the patient-derived data sets and number of data sets. We have used here a large number of data sets and from different original sources to minimize off-target finings. Still, it may be possible that using other patient-derived data sets will provide results that do not show a complete overlap of the ceRNA network.KEGG pathway analysis has revealed glutathione metabolism and the regulation of actin cytoskeleton as the mostly down-regulated pathways. DEmiRNAs have also been reported to participate in a number of critical signaling pathways that affect prostate carcinogenesis. The ceRNA network contained a total of 5 miRNAs, 5 lncRNAs, and 17 mRNAs. We identified hsa-miR-17, hsa-miR-93, hsa-miR-150, hsa-miR-25, PART1, hsa-miR-125b, PCA3, H19, RND3, and ITGB8 as the 10 hub genes in the ceRNA network. According to the ROC analysis, the expression levels of 19 hub genes showed a high diagnostic value. Therefore, the constructed ceRNA network has been shown to affect important cellular pathways in prostate carcinogenesis and influence the prognosis of patients with this type of cancer. Taken together, we introduce a number of novel, promising diagnostic biomarkers for prostate cancer. This ceRNA-based panel can be applied as a second-level test to patients with certain PSA levels. This level should be identified in future studies.


Blumeria graminis f. sp. tritici (Bgt), is a devastating fungal disease that seriously damages the yield and quality of wheat in many regions of the world. Identifying new resistance genes and breeding new resistant varieties are effective methods to control this disease. The breeding line SN15218 shows good resistance against powdery mildew. We, therefore, developed an F2 population and 287 F2:3 families crossed between SN15218 and the powdery mildew susceptible cultivar Huixianhong (HXH). Genetic analysis indicated that a single dominant gene, designated herein PmSN15218, conferred resistance to the Bgt isolate E09 in SN15218. Bulked segregant RNA-Seq (BSR-Seq) analysis revealed that PmSN15218 is located in a ∼25-Mb interval on chromosome 2AL. Using the polymorphism information between SN15218 and HXH, we developed 13 polymerase chain reaction (PCR) markers and mapped this gene to a 0.5-cM genetic interval between the two flanking markers PmM12 and PmM14, corresponding to a 6.01-Mb physical region in the Chinese Spring reference genome. The results of molecular marker analysis, allelic tests of resistance spectrum, and DNA resequencing indicated that PmSN15218 is distinct from the known resistance gene Pm4b on 2AL.Powdery mildew, caused by  Triticum aestivum L.) is an important food crop worldwide, providing about 20% of human calories (Blumeria graminis f. sp. tritici (Bgt), is a devastating wheat foliar disease. In recent decades, powdery mildew has led to severe yield losses of 5–8% during the years of average infection, and as high as 40% in some years, in China and other parts of the world  have been reported, with the loci Pm1, Pm3, Pm4, Pm5, and Pm24 having 5, 17, 8, 5, and 2 alleles, respectively , and the common wheat variety Marne  comes from the common wheat line 81-7241, which exhibits high resistance to powdery mildew and has a broad resistance spectrum. Pm4c is located at a 4.9-cM genetic interval between Xbarc122 and Xgwm356 on chromosome 2AL , respectively, and identified multiple resistant or susceptible haplotypes of Pm4-Fed simultaneously  newly identified in recent years, only Pm52, Pm54, and Pm65 originated from adapted cultivars   .PmSN15218, through genetic analysis, molecular mapping, spectrum analysis, and allelic relationship comparison.SN15218 is derived from a natural mutant plant of the cultivar Yannong 19 (YN19) in the seed production field. It shows a high level of resistance to powdery mildew at both seedling and adult stages, suggesting that it harbors a powdery mildew resistance gene that could be valuable for wheat breeding. In this study, we characterized the resistance gene in SN15218, temporarily named Bgt isolates. SN15218 is a breeding line with a YN19 background. It is similar to common wheat and shows resistance to many powdery mildew races. To analyze the inheritance of powdery mildew resistance, SN15218 was crossed with HXH to construct a segregating population, and F1, F2, and F2:3 materials were tested for resistance to the Bgt isolate E09, which is avirulent on SN15218 but virulent on HXH.The materials used in this study included the winter wheat cultivars YN19 and Huixianhong (HXH) and powdery mildew resistant line, SN15218. YN19 and HXH are widely planted commercial cultivars and are susceptible to most 1 hybrids, F2 populations, and F2:3 families (25 seedlings for each line), as well as YN19 as a susceptible control, were tested for powdery mildew resistance using the Bgt isolate E09. Meanwhile, 23 single-spore-derived Bgt isolates and several wheat lines carrying known Pm genes were grown in a greenhouse at the Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, to compare the reaction patterns of SN15218 and the other wheat lines with the different Bgt isolates. At the two-leaf stage, seedlings were inoculated with fresh spores and then transferred to a plant growth chamber at 15–18°C with 60% relative humidity and a 12 h light/12 h dark cycle to allow symptom development. Two weeks after the susceptible control materials HXH and YN19 were heavily infected, the plants were scored into infection types (ITs) according to a 0–4 scale (2) test for goodness of fit.SN15218, HXH, and their F–4 scale . We clas2:3 families with contrasting resistance phenotypes against isolate Bgt E09 (30 homozygous resistant and 30 susceptible families) were used to construct sample pools. Leaves of similar quality were collected from five plants of each family. Resistant and susceptible leaves were pooled for RNA isolation. Two parents, SN15218 and HXH, were also processed as parental checks. Total RNA was extracted using TRIzol reagent  according to the manufacturer’s protocol. Library construction, high-throughput sequencing (Illumina NovaSeq 6000), and sequencing data qualification were performed by Berry Genomics Company . Adapter sequences and low-quality bases were trimmed using fastp v0.19 with default paraments  markers were newly developed  using the Kosambi mapping function.Leaf tissue was collected from 2-week-old plants, and total genomic DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method . Accordieveloped  for furtTriticeae repeat database mipsREdat 9.3p (PGSB Repeat Database) using BWA-mem v0.7.17 in order to filter out repeat noises. Non-mapped reads (which come from the genome region of non-repeat sequences) were fished using Samtools v1.93 and then used for de novo assembly using SPAdes v3.134 with default parameters.DNA resequencing reads of the powdery mildew resistant line SN15218 were first aligned to the Bgt isolate E09, SN15218 was highly resistant (IT = 0) and HXH was highly susceptible to the fungus (IT = 4)  and 69 individuals showed susceptibility (IT = 3–4), indicating segregation of a single resistance gene . All the 285 F2:3 families derived from these two parents were also tested using the same Bgt isolate E09 in the climate chamber at the seedling stage. A total of 82 and 69 families were homozygous-resistant and homozygous-susceptible, respectively, and the remaining 134 families were segregated, confirming that the powdery mildew resistance of SN15218 was inherited as a single gene . We temporarily named this resistance gene PmSN15218.When inoculated with (IT = 4) . F1 planWe sequenced the two parents (SN15218 and HXH) and two resistant and susceptible descendant pools in 150-bp paired-end mode, generating 58.9–63.7 million clean paired reads; the average read depth was more than 60 for each SNP after filtration . ApproxiPmM1, PmM4, PmM5, and PmM7) or an InDel marker (PmM6)  /derived cleaved amplified polymorphic sequences (dCAPSs) markers (r (PmM6) . Using 9 markers  using th770.104) .PmSN15218 from SN15218, several powdery mildew resistance genes, Pm4a, Pm4b, and Pm4c, that were previously identified from different wheat varieties or lines  were also mapped on chromosome 2AL. We evaluated the disease reactions of SN15218 and the above resistant landraces to 23 Bgt isolates. Line 81-7241, carrying Pm4c, showed high resistance to all of the isolates. Khapli, carrying Pm4a, showed resistance to most powdery mildew isolates but was susceptible to seven isolates. Armada, carrying Pm4b, showed a similar resistance spectrum to Khapli except for two isolates, E05 and E15   , Pm4d, Pm4e, Pm65, and PmSN15218 were located in the physical interval of Mb 760–770. Among them, the Pm4b-Fed gene, originating from tetraploid T. carthlicum, is not in the “Chinese Spring” genome reference but is most closely related to the gene TraesCS2A01G557900 near Mb 761 of chromosome 2AL, the ancestor of which was duplicated and fused to form the kinase structural domain of Pm4b-Fed , and the results showed that SN15218 did not contain Pm4. We also performed de novo assembly using DNA resequencing data of SN15218 and found no Pm4b-Fed gene or fragment in the assembly database. In addition, we compared five other Pm genes, PmX  , Pm4d (S3)  . These sPm4b-Fed . To furtnes, PmX , PmLK906 near the Pm4 loci derived from the resistant mutant SN15218 through genetic analysis, molecular mapping, resistance spectrum investigation, and allelic relationship analysis. We tested different wheat genotypes against 23 Bgt isolates. The SN15218, carrying PmSN15218, displayed a different resistance pattern from wheat carrying Pm4a, Pm4b, or Pm4c. SN15218 was highly resistant to powdery mildew in fields and has the genetic background of common wheat. Therefore, it could serve as a good intermediate material for powdery mildew resistance breeding.Powdery mildew is a widespread fungal disease of wheat, which can infect wheat at both the seedling stage and adult stage and causes significant yield losses. Loss of resistance in wheat cultivars caused by the rapid evolution of this pathogenic fungus has prompted a continuing search for new sources of resistance. Here, we identified a single dominant resistance gene , wild emmer wheat Zavitan  variety Marne (Pm4b-Fed is derived from three wheat lines, Weihenstephan M1, ELS, and TP229, and was first named Mle, which was identified as an allele of Pm4a and then transferred to the Australian spring wheat variety Federation by backcrossing (SN15218Pm and Pm4b-Fed, we tested JS717 × JS718 and Pm4.1, two specific markers for Pm4b-Fed (Pm4b-Fed-S (Pm genes, including PmX, Pm65, PmLK906, PmPS5A, and PmMl92145E8-9, on chromosome 2AL using in silico PCR (de novo assembly database of SN15218. Combining the results of the genetic map, resistance spectra, allelic relationship, and DNA resequencing data, we speculate that SN15218Pm may be a potential new powdery mildew resistance gene, distinct from Pm4, on chromosome 2AL.The osome 2A . Howeverty Marne . It was crossing . Since tPm4b-Fed , and a n4b-Fed-S , and foulico PCR . These mPmSN15218, located on chromosome 2AL. It is distinct from the previously cloned Pm4b. This gene was derived from the breeding line SN15218 and could serve as a valuable genetic resource for wheat powdery mildew resistance breeding without any adverse factors or linkage drag of undesirable genes.Herein, we identified a wheat powdery mildew resistance gene, The original contributions presented in this study are included in the article/YB, FN, and JW designed the project. MS, QL, YH, GL, and JQ performed the experiments. YB, FN, and JQ analyzed the data and wrote the manuscript. All authors discussed the results and reviewed 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.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. 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