SOD1), chromosome 9 open reading frame 72 (c9orf72), TAR DNA Binding Protein (TARDBP), and Fused In Sarcoma (FUS); additional ALS-related genes including Charged Multivesicular Body Protein 2B (CHMP2B), Senataxin (SETX), Sequestosome 1 (SQSTM1), TANK Binding Kinase 1 (TBK1) and NIMA Related Kinase 1 (NEK1), have been identified. Mutations in these genes could impair different mechanisms, including vesicle transport, autophagy, and cytoskeletal or mitochondrial functions. So far, there is no effective therapy against ALS. Thus, early diagnosis and disease risk predictions remain one of the best options against ALS symptomologies. Proteomic biomarkers, microRNAs, and extracellular vehicles (EVs) serve as promising tools for disease diagnosis or progression assessment. These markers are relatively easy to obtain from blood or cerebrospinal fluids and can be used to identify potential genetic causative and risk factors even in the preclinical stage before symptoms appear. In addition, antisense oligonucleotides and RNA gene therapies have successfully been employed against other diseases, such as childhood-onset spinal muscular atrophy (SMA), which could also give hope to ALS patients. Therefore, an effective gene and biomarker panel should be generated for potentially “at risk” individuals to provide timely interventions and better treatment outcomes for ALS patients as soon as possible.Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease affecting the upper and lower motor neurons, leading to muscle weakness, motor impairments, disabilities and death. Approximately 5–10% of ALS cases are associated with positive family history , whilst the remainder are sporadic . At least 50 genes have been identified as causative or risk factors for ALS. Established pathogenic variants include superoxide dismutase type 1 ( Amyotrophic lateral sclerosis (ALS), or “Lou Gehrig’s disease”, is a neurodegenerative disorder resulting in the degeneration of motor neurons inside the brain and spinal cord. The disease affects lower motor neurons (LMNs) in the brainstem and spinal cord and upper motor neurons (UMNs) in the motor cortex ,2. ALS pc9orf72), TAR DNA Binding Protein (TARDBP), Sequestosome 1 (SQSTM1), Valosin Containing Protein (VCP), Fused In Sarcoma (FUS), TANK Binding Kinase 1 (TBK1), or Cyclin F (CCNF) [C9orf72; p = 0.03 for rs13302855 and p = 0.005 for rs3849942) [OPTN) [PRPH) [TAF15) [Several genes have been identified which could impact both FTD and ALS, including chromosome 9 open reading frame 72 (3849942)  with the3849942) ,12. Furt) [PRPH) , leukemi [TAF15) . The aboSOD1), TAR DNA Binding Protein (TARDBP), Fused in Sarcoma (FUS) gene and Chromosome 9 Open Reading Frame 72 (c9orf72) . Finally, the c9orf72 gene is common in European familial ALS cases (more than 30%), while it may be a rare causative factor among Asian fALS cases (less than 3%). However, these genes are rarely encountered in either European or Asian  sporadic ALS (sALS) cases [To date, there are four mendelian genes that cause ALS: The Cu–Zn superoxide dismutase (c9orf72) . Since iLS cases . The TARS) cases .SOD1 gene is located on chromosome 21, producing a 153 conserved-amino-acid-long protein in the cytoplasm, nucleus and mitochondria. In the active configuration, the protein exists as a homodimer enzyme containing eight antiparallel beta strands housing copper and zinc ions, which play a role in the dimerization and disulfide bond stabilization (between Cys57 and Cys146). SOD1 protein functions as an antioxidant enzyme, which protects the cells from oxidative stress by the conversion of catalyzing toxic superoxide anions into hydrogen peroxide and oxygen molecules, lowering the steady state of radical ions , regulating apoptosis [SOD1 mutations are heterozygous with autosomal dominant inheritance, but homozygous variants with autosomal recessive inheritance have been reported in rare cases [SOD1 mutations increase protein instability and the capacity to misfold due to metal ion and disulfide bond deficiencies. Collectively, such deficits can result in oligomerization, abnormal protein aggregation, and the formation of amyloid-like aggregates [SOD1 can lead to nuclear and mitochondrial DNA damage [SOD1 variants disrupt cytosolic and mitochondrial calcium homeostasis, leading to abnormal cell functions and alterations of glial cell-motor and skeletal muscle-motor neuronal crosstalk, triggering apoptosis [The poptosis ,19,20,21poptosis . Most SOre cases . SOD1 mugregates ,25,26. IA damage . SOD1 vapoptosis .SOD1; for example, A4V is a common mutation in American populations, which is thought to accelerate progressive familial ALS, reducing disease duration to 2 years or less. The disease initially presents with limb and bulbar muscle weakness, primarily affecting the lower motor neurons [SOD1 [SOD1 G93A. Transgenic mice carrying this variant are frequently used in ALS drug screening [SOD1 mutations (including A4V or H46R) in ALS.Several geographical mutations are associated with  neurons ,29. Commns [SOD1 ,31,32. Acreening ,34. FiguTARDBP gene and deemed causal for autosomal dominant ALS and associated TDP43 proteinopathy. The TARDBP gene contains six exons on chromosome 1, expressed ubiquitously, residing mainly in the nucleus [TARDBP transcription and RNA splicing through homodimer formation [TARDBP mutations are associated with the misfolding aggregation of TDP43  protein [TARDBP may result in impaired protein–protein interactions between TARDBP protein and its binding partners, such as FUS or ataxin. The TDP-43 aggregations may disturb the autophagic mechanisms and proteosome formation. Furthermore, mutations in TARDBP could impact the processing of miRNAs and lncRNAs  [FUS mutations may present TDP43 inclusions in their brain, but TDP43 proteinopathy can also be absent in ALS patients with FUS, particularly when the abnormal transcript utilizes TDP43-independent pathways [FUS mutations are thought to exercise their toxicity by reducing ion channel expression and synaptic activity, inhibiting intra-axonal translation [FUS transcript and autoregulation of FUS levels [FUS immunoreactive cytoplasmatic inclusions inside neurons and glial cells. The inclusions usually occur in the nucleus [FUS mutations may down-regulate genes  essential to oxidative phosphorylation, impacting skeletal muscle functions [A significant ratio of  of age) ,52, manypathways . For exapathways . Moreovenslation . FurtherS levels . As a reS levels . Additio nucleus , but can nucleus . Other m nucleus . In addiunctions .c9orf72 gene. DeJesus Hernandez et al. (2011) revealed that c9orf72 was present in 11.7% of familial FTD and 23.5% of familial ALS patients. In healthy individuals, repeat expansions typically range from 3 to 30. G4C2 is the abbreviation of hexanucleotide repeat expansion mutation (HREMs) and ranges from 30 to 100 in ALS patients, although G4C2 expansions in the hundreds or thousands have been reported in sALS patients [c9orf72 variant 1 is often undetectable. An initial study suggested that the repeat expansion could limit the expression of c9orf72 variant 1, significantly impacting brain development and function [c9orf72 gene and its promoter activity. Repeat expansions were associated with a more significant degree of methylation, leading to reduced transcriptional activity and haploinsufficiency, resulting in dipeptide repeat protein (DPR) and glutamate receptor elevations. Furthermore, intermediate repeats, ranging between 7 and 24 G4C2 units, showed a slight increase in methylation compared to a low number of repeats (2–6), suggesting that “intermediate alleles “may also act as risk alleles [c9orf72 participates in loss-of-function (LOF) mechanisms and has the potential for gain-of-function toxicity (GOF) . The abnormal translation of G4C2 repeats could result in DPR, such as poly-(Gly-Ala or polyGA), poly-(Gly-Pro or polyGP) and poly-(Gly-Arg or polyGR) proteins, which have a strong tendency to aggregate due to their high degree of hydrophobicity. DPR aggregates are moderately neurotoxic, whilst poly-GA aggregates are highly neurotoxic [c9orf72 repeat expansion could impair the function of master DNA repair kinases, contributing to ataxia telangiectasia (AT). In addition, perturbation of kinase functions due to C9orf72 repeat expansion might lead to heterochromatin formation and an increase in the frequency of double-strand DNA breaks [The next causative pathogenic variant is the hexanucleotide repeat expansion mutation ) located between the non-coding exons 1a and 1b of the patients . In a nofunction ,64,65. M alleles . Even thty (GOF) , the varurotoxic ,69,70,71A breaks . SOD1, TARDBP, c9orf72, and FUS mutations are relatively common in familial ALS, several additional genes were identified which could play a role in ALS onset. In addition, approximately 44.5% of European and ~60% of Asian fALS cases are associated with rare genetic factors. More than 50 genes (Even though 50 genes  have beeCHMP2B) is on chromosome 3 and encodes the 213 amino-acid-long protein. This essential protein plays multiple roles in the Endosomal Sorting Complex Required For Transport III (ESCRT-III), from the biogenesis and sorting of endosomes to the trafficking of multivesicular bodies (MVBs), proteostasis, and neuronal homeostasis. CHMP2B mutations are not unique to ALS and have been associated with numerous diseases, including FTD and progressive muscular atrophy (PMA) [CHMP2B intron5 was recently implicated in the hyperphosphorylation of TDP-43 via the ubiquitin-proteasome system (UPS), decreasing ubiquitination and turnover of casein kinase 1 (CK1), highlighting a genetic link between TARDBP and CHMP2B and the associated ALS pathology [Charged multivesicular body protein 2 (hy (PMA) ,76. Howeathology . VCP) which exhibits chaperon-like properties that regulate the ubiquitin-proteasome system (UPS) and autophagic processes. VCP mutations are rare causative factors for ALS [VCP plays a crucial role in UPS-mediated protein degradation processes, and its impairment leads to the accumulation of ubiquitinated proteins. However, the specific role of VCP in autophagy remains unclear, as the protein has been implicated in several processes, including autophagy activation, autophagic complex maturation, autophagosome, and lysosome fusion and homeostasis [VCP, the vesicle-associated membrane-protein-associated protein B (VAPB) gene plays a role [VAPB mutants (P56S) includes disorganized endoplasmic reticulum (ER) structures and an enhanced propensity of a cell to form aggregates [FIG4), which regulates endosomal/lysosomal vesicle transport [FIG4 has a potential role in Charcot–Marie–Tooth disease, ALS, primary lateral sclerosis (PLS), recessively inherited hereditary motor and sensory neuropathy, or Yunis–Varón syndrome [SPG11) is a primary causative factor for autosomal recessive hereditary spastic paraplegia (HSP). Still, it may also play a role in other neurodegenerative diseases, including autosomal recessive juvenile ALS and CMT. SPG11 could play a role in multiple processes, including lysosome trafficking, cholesterol transport, autophagy, and calcium homeostasis. ALS’s SPG11 mutations (such as c.704_705delAT and c.5199delA) may be associated with a lack of thinned corpus callosum and cognitive and ocular abnormalities [NIPA1) was initially associated with Prader–Willi/Angelman syndrome 1 or Type 6 HSP, but it may also impact ALS [NIPA1 impacts magnesium metabolism inside the cells. It may also affect endosome regulation inside neurons and epithelial cells [NIPA1 was suggested to impact ALS risk. ALS patients with NIPA1 CGG repeat expansions may be associated with increased ALS risk, earlier disease onset, and reduced survival [NIPA1 in ALS was verified by a large-scale replication analysis performed by Tazelaar et al. in 2019. The pathogenic mechanism of CGG repeat expansion remained unclear. The polyalanine repeats may result in abnormal protein conformation, protein–protein interactions, and aggregation [Another gene implicated in ALS is the Valosin-containing protein  gene encodes the cyclin F, which functions as ubiquitin-protein ligase. Cyclin F could regulate proteosome degradation by recruiting substrates fort polyubiquitination. CCNF mutations  could limit proteosome turnover and the post-translational modification of CCNF protein and E3 ligase activity [Cyclin F  is a member of the ubiquitin proteosome system and plays a role in the homeostasis of different proteins and the quality control of mitochondrial proteins. Also, UBQLN2 participates in the degradation of ubiquitinated proteins through proteosome and autophagic pathways. Different mutations have been linked to FTD and ALS [UBQLN2 mutations  could restrict proteosome-mediated degradation due to their reduced binding ability, leading to aggregation and neurotoxicity [UBQLN2 may decrease the expression of ATPase H+ Transporting V1 Subunit G1 (ATP6v1g1), leading to impaired autophagy due to failed acidification and maturation [Ubiquilin-2  mutations are thought to impact CMT and distal hereditary motor neuropathy and, therefore, considered a potential risk factor for ALS. HSPB1 mutations are suspected to enhance protein misfolding and aggregation. For example, HSPB1 mutations reported in sporadic ALS cases, such as Q190H and A204Gfs* 6, were assumed to reduce the protein stability and chaperon activity, rendering motor neurons more sensitive to stress. HSPB1 mutations may also be associated with impaired autophagy by reducing the ability of Sequestosome 1 (SQSTM1)/p62 body formation [The chaperon small heat-shock protein family B member 1  gene encodes the sequestosome 1/p62 protein, with suspected roles in FTD, Paget bone disease, or familial and sporadic forms of ALS. The SQSTM1 mutations could impact the turnover of p62, promoting aggregation or autophagy, and impair its interaction with the Kelch-like ECH-associated protein 1 (KEAP1) [Sequestosome 1 ( (KEAP1) . For exa (KEAP1) . Another (KEAP1) . TBK1) is an NF-κB activator kinase protein that could impact ALS and FTD. TBK1 protein consists of a kinase, a ubiquitin-like, and two scaffold dimerization domains, permitting its participation in several pathways, including mitophagy  and autophagy by phosphorylating several adaptor proteins, such as optineurin (OPTN) or Parkin (PRKN). In addition, TBK1 may be involved in T-cell activation and autoimmunity [TBK1 mutations could potentially generate a variety of disease phenotypes via several mechanisms. For example, R47H, D135N, G217R, or R228H expression could result in lower autophosphorylation. Specifically, G217R could decrease mitochondrial fragmentation and the interaction between TBK1 and PRKN. Other mutations, such as G217R, R357Q, and M559R, could disrupt TBK1 assembly and mitophagy events. In addition, D135N or D559N mutations could impair mitophagy by inhibiting LC3 recruitment, increasing the likelihood of accumulation of damaged mitochondria. Moreover, these mutations could also elevate mitochondrial reactive oxygen species (ROS), promoting aggregate formations and neuronal cell death and neuroinflammation [TANK-binding kinase 1  was initially reported as a causative gene for glaucoma and was later found to contribute to ALS pathology. The gene is expressed in several human organs, such as the brain, skeletal muscles, liver, kidney, or placenta muscle [OPTN mutation-associated ALS could be either autosomal dominant or autosomal recessive. However, the disease-related mechanisms can vary between these two traits. For example, a homozygous STOP codon mutation, Q398X, could reduce gene expression by nonsense-mediated decay, whilst the heterozygous mutation, E478G, could result in OPTN-immunoreactive cytoplasmic inclusions [OPTN mutations were observed in ALS, including R69L, Q165X, I451T or E516Q [Optineurin  encodes the p150Glued protein, a member of the dynactin protein complex. DCTN1 protein directly binds microtubules via the highly conserved N-terminal glycine-rich and cytoskeleton-associated protein (CAP-Gly) domain and plays a role in retrograde vesicle transport. DCTN1 can interact with TDP43 forming co-aggregates in the cytoplasm. Most disease-related mutations of DCTN1 (such as G71A) are located in the glycine-rich domain [NEK1) is a serine/threonine kinase and a mitotic checkpoint protein, which could control cell cycle progression and mitosis. It could also be involved in DNA repair. NEK1 was also suggested to regulate the cilia formation, microtubule stability, and dynamics [NEK1 dysfunctions are associated with brain diseases such as hydrocephalus and mental retardation. In 2016, NEK1 was initially associated with ALS since a loss-of-function mutation, R261H, was observed as a risk factor for the disease [NEK1 expression and haploinsufficiency [Dynactin 1  is a 140 amino acid actin-binding protein that promotes nucleotide exchange on actin, resulting in the conversion of monomeric ADP-actin to ATP-actin [PFN1 binds to phosphoinositides and an extensive network of proteins with poly–L-proline stretches. Some mutations, such as G118V or M114T, could result in disturbances in the polyproline-binding region of PFN1, leading to abnormal actin assembly. Another variant, PFN1 C71G, potentially reduces PFN1 expression [Profilin-1  is a type III intermediate filament, a multifunctional protein implicated in neuronal processes, cytoskeletal dynamics, axonal progressions, transport and myelination, neurite stability, and growth, with possible roles in processing DNA/RNA, mitochondrial functions, and vesicle transport. In addition, PRPH is considered a risk factor for diseases such as ALS, Charcot–Marie–Tooth Type 2B, diabetes, or enterovirus-A71 infection [PRPH is overexpressed in injured neurons and promotes axon regeneration. Mutations in PRPH, such as R133P and D141Y [NEFH) or Neurofilament Modest Chain (NEFM) expression via a small group of ALS-linked miRNAs is shown to perturb cytoskeleton composition and disrupt axon structure and transport exhibiting impaired N-methyl-D-aspartate (NMDA)-mediated calcium influx [Peripherin  gene is a rare risk gene for FTD and ALS. It encodes a subunit for alpha-tubulin, which forms a heterodimer with beta-tubulin and is involved in microtubule formation [TUBA4A gene, such as W407X, could disrupt the assembly of alpha and beta tubulins, leading to reduced assembly of microtubules. ALS cases with TUBA4A were spinal onset, but upper motor neurons can also be involved. Cognitive dysfunctions and frontal involvement may also be involved [ALS2) is a Rho Guanine Nucleotide Exchange Factor, which could impact young onset autosomal recessive ALS or hereditary spastic paraplegia [ALS2 can be either missense, such as I94V, E159K, M368V or affecting RNA splicing, such as IVS7 + 3A>G [ALS2 remains unclear, but ALS2 may impact cytoskeletal dynamics [ALS2 could significantly damage postsynaptic subsynaptic reticulum (SSR) functions. ALS2 defects may also impair late endosome trafficking, synaptic development, and neuroprotection [The Tubulin Alpha 4a ormation ,133. Mutinvolved . Alsin  is a helicase for DNAs and RNAs and is involved in different processes, including DNA repair, replication or recombination, RNA processing, and translation [SETX mutations  have been implicated in impaired DNA repair and gene expression [In addition to nslation . Severalpression  associatpression  and rareTAF15) protein is closely related to FUS, since they have similar structures and both belong to heterogeneous nuclear ribonucleoparticle (hnRNP) proteins. TAF15 was verified to regulate RNA synthesis and also protein splicing. Mutations in TAF15  may be related to familial and sporadic ALS [The TATA box-binding protein (TBP)-associated factor 15  was suggested as a rare risk factor for Alzheimer’s disease (AD), Parkinson’s disease (PD), and ALS. ANG is a ribonuclease A protein which activates ribosomal RNA regulating its transcription. Moreover, its involvement could also extend to angiogenesis, cell survival, and neuronal growth [ANG mutants  have been associated with impaired RNase activity, leading to a lower rate of cell proliferation and angiogenesis [Angiogenin (l growth . For exaogenesis .ATXN2) gene are reported to cause spinocerebellar ataxia type 2, whereas intermediate (24–34) CAG repeats are considered a risk factor for ALS [TARDBP, ATXN2 may also impact RNA processing control [Polyglutamine (polyQ) expansions in the neuronal stress protein Ataxin 2 ( for ALS . Along w control . In addi control .HNRNPA1) is a member of a heterogeneous nuclear ribonucleoprotein, which could impact mRNA processing, including splicing and RNA assembly, regulating the stability of RNA and gene expression. Mutations in the prion-like domain of HNRNPA1, such as P288A, G264R, or D262V, were identified in ALS cases but could also impact other diseases, such as FTD, multisystem proteinopathy (MSP), or inclusion body myopathy (IBM) [HNRNPA1, leading to alternative splicing and aggregation [Heterogeneous Nuclear Ribonucleoprotein A1 (hy (IBM) . In ALS hy (IBM) . TDP43 cregation ,149.MATR3) is a conserved DNA–RNA binding protein, which may play a role in several mechanisms, such as mRNA stabilization, DNA repair and transport or splicing. Mutations in MATR3 could impact ALS, FTD, and distal myopathy [MATR3 mutations were identified in ALS, such as S85C, F115C, P154S, or T622A, which were associated with impaired RNA processing, such as abnormal mRNA export, especially the mRNA for TDP43 or FUS [Matrin3  mutations, S59L, R15L, or G66V, was suggested to impact FTD and ALS [CHCHD10 S59L mutation is thought to evoke dysfunction through gain-of-function mechanisms via irregular oxidative phosphorylation, cristae destabilization, organelle defragmentation, abnormal protein aggregation, and heightened mitochondrial stress response, inhibiting biogenesis and leading to neurodegeneration [The Coiled-coil-helix-coiled-coil-helix domain containing 10  gene plays a role in neuroprotection, neuroplasticity, and mitochondrial calcium transport through the inositol trisphosphate receptor (IP3) receptor, which impacts both FTD and ALS [SIGMAR1 mutants may contribute to TDP43 mislocalization and ubiquitinoylation, leading to additional mitochondrial and autophagosome impairment in motor neurons [SIGMAR1 could result in abnormal autophagy and stress granule aggregation. Furthermore, mutant SIGMAR1 expression may result in abnormal cytoplasmic RNA binding protein assemblies involving TDP43, FUS or MATR3 proteins [The Sigma Non-Opioid Intracellular Receptor 1  belongs to the tyrosine kinase family and is member of the epidermal growth factor receptor subfamily. ERBB4 could bind to neuregulin proteins (NRGs), leading to ERBB4 activation and elevated tyrosine kinase activity. Activated ERBB4 may be associated with multiple cellular pathways, including neurodevelopment. ERBB4 gene was established to impact cancers, but it may also play a role in ALS. Mutations, such as R927Q or R1275W, may disrupt the tyrosine kinase activity of ERBB4, resulting in reduced neuregulin downstream signaling. These mutations were associated with slow progressive ALS, where both upper and lower motor neurons were involved, but cognitive function was spared [ANXA11) is a calcium-dependent phospholipid-binding protein that could impact ALS and FTD onset. Mutations in ANXA11, such as D40G, G228Lfs*29, H390P, or R456H, could be associated with both gain- and loss-of-function mechanisms, including abnormal protein aggregation and loss of intracellular calcium responses, respectively. Also, the mutations may result in abnormal stress granule dynamics. ANXA11 protein could co-aggregate with other ALS-related RNA-binding proteins, such as FUS or hnRNPA1, inside lower motor neurons or the brain [CREST or SS18L1) is a calcium-dependent transcription activator involved in dendrite growth. It was established to impact cancer onset, but its role in ALS is also investigated. The exact mechanisms of how CREST mutations may be related to ALS remained unclear. Mouse studies revealed that an ALS-related CREST mutation, Q388X, could repress the cytokine expression  inside neurons [DAO) could cause ALS and bipolar diseases. DAO protein regulates brain D-serine, which could act as a neuromodulating factor. Also, DAO may have a neuroprotective role in the brain by protecting against D-amino acid aggregation by modulating their degradation. Furthermore, DAO may also impact dopamine synthesis. ALS-related DAO mutations like R199W may be associated with elevated D-serine levels. The D-serine could accumulate in the spinal cord, leading to motor neuron degradation [Erb-B2 Receptor Tyrosine Kinase 4  are associated with the gain (multiplication) or loss (deletion) of a certain sequence into the genome, which could result in abnormal protein expression. The CNVs were suggested to impact different disorders, including CMT, autism, schizophrenia, and epilepsy, but they could also play a role in ALS [SMNs, SMN1 and SMN2). SMN proteins may impact several cellular functions, including RNA splicing, recycling, and axonal transport. SMN gene mutations could impact motor diseases, including spinal muscular atrophy (SMA). SMN1 duplications were suggested to play a role in sporadic ALS, but they failed to find an association between SMN2 and ALS. However, further studies are needed on the mechanism of SMN1 duplication in ALS onset [SMN1 or SMN2. Also, this study suggested that SMN genes may not impact the ALS disease course or disease severity [CRYBB3, Crystallin Beta B2-CRYBB2, LDL Receptor Related Protein 5 Like-LRP5L, Crystallin Beta B2 Pseudogene 1-CRYBB2P1), which were more common in ALS patients, compared to controls, suggesting CNVs as possibly ALS susceptibility factors [DPP6) and NIPA1 CNVs may be possibly promising candidates for ALS association [Besides the repeat expansions in e in ALS . For exaLS onset ,174. A sseverity . Blauw e factors . An addiociation .ALS is a complex disease that shares similar phenotypes with other diseases, such as FTD or PD. To limit misdiagnosis, a battery of comprehensive tests, including brain-and spine imaging, biofluid analysis, and neuropsychological tests, are routinely employed . CurrentGiven the diversity of pathological mechanisms related to ALS  , a biomaA novel set of ALS-specific biomarkers might include a combination of multiple biomarkers, including neurophysiological and neuroimaging and markers from biological fluids and tissues, which could effectively diagnose and monitor the disease progression . Alteredn = 429) further highlighted the potential of serum NFL to distinguish ALS from other diseases, implying that the routine examination of serum NFL can improve survival prediction and diagnostic accuracy [n = 234), ALS mimics (n = 44), as well as non-neurological disorder controls (n = 9), SF NFL, CSF pNFH, and plasma NFL levels were significantly increased in ALS patients, with authors concluding pNFH had diagnostic value capable of differentiating ALS from clinically relevant mimics [Neurofilaments are part of the cytoskeleton; their level could be higher in biological fluids in case of axonal damage. NFs have three subunits: light (NFLs), medium (NFMs), and heavy (NFHs) chains. It was suggested that their fluid levels potentially reflect the degree of axonal injury in the case of neurodegenerative diseases . Multiplaccuracy . In addiaccuracy ,189. Best mimics . Higher t mimics . In addit mimics . Behzadit mimics .Multiple studies have confirmed that inflammatory cytokines and T-cell-related immune response are elevated in body fluids of ALS patients, compared to unaffected age-and gender-matched controls ,195,196,Early studies showed CSF-Tau could be a reliable marker for several neurogenerative diseases, including ALS ,201. HowGaiani et al. (2017) investigated a study on NFL levels in the blood and CSF of ALS patients. This study revealed that NFLs can potentially support disease diagnosis and prognosis in ALS patients. High early-stage NFL levels may be associated with poorer disease outcomes . VacchiaTDP43 is a neurodegenerative marker frequently used to confirm AD and FTD ,208 and,Other inflammatory markers in a potential ALS panel are the metalloproteases (MMPs) MMP-2 and MMP-9, and their tissue inhibitors (TIMPs), essential in regulating enzyme activity. TIMPs, specifically TIMP-1, could inhibit the proteinase activity of several MMPs, impacting ALS progression ,211,212.n = 105), researchers evaluated the potential of secreted macrophage and epithelial proteins, Chitotriosidase-1 (CHIT1), chitinase-3-like protein 1 (YKL-40), and monocyte chemoattractant protein-1 (MCP-1) as ALS prognostic biomarkers. CSF levels of these markers were elevated in ALS patients compared to the controls; however, they may not be effective as discriminatory markers between ALS and ALS mimics. A correlation was observed between CHIT1, YKL-40, and disease progression rate. The CSF CHIT1 levels were higher in the ALS patients, who presented more regions with motor neuron degeneration. The YKL-40 and MCP-1 in CSF could predict the disease survival of ALS patients. Furthermore, CHIT1 and YKL40 were weakly correlated with disease progression rate [In another study, using larger sample (CSF and serum) sizes  [SOD1 have exhibited [Predicting the impairment of regulatory processes and the formation of abnormal DPR proteins  due to ees (ASO) , suggestxhibited  similar xhibited ,218. Abnxhibited . NFL mayxhibited . The CHIxhibited .The aberrant expression of microRNAs (miRNAs) and extracellular vesicle contents are potential indicators of neurodegeneration and disease progression ,229,230.The potential outlook regarding the clinical application of miRNA signatures for SALS is somewhat limited, given the lack of multi-center studies and serum miRNAs. In an attempt to address this issue, a recent study examined miR-181 levels in 252 ALS patients and found an association between higher levels in the plasma and a higher risk of mortality. Moreover, when miR-181 was paired with NFLs, the combination offered superior prognostication capacity for ALS, leading to improved patient stratification .Other potential serum biomarkers include miR-206, 143-3p, and 374b-5p, which may also improve ALS diagnosis and prognosis. For example, the expression of miR-206 and miR-143-3p was higher in ALS patients, and miR-374b-5p expression decreased compared to controls, suggesting miRNAs may have a role in monitoring patients . In addiThe contents of EVs can potentially be employed to diagnose different stages of ALS and other neurodegenerative diseases. The vehicles are involved in the transport and exchange of RNAs, lipids, and proteins between recipient cells. Since they can cross the BBB, they may accurately reflect the disease-specific changes inside the brain. Also, they may be sufficiently present in peripheral areas, making them easy to obtain from several sources, including plasma, whole blood, CSF, or saliva. Alterations in the protein/RNA contents were suggested as promising markers that may reflect the disease-related changes ,240,241.Regarding storage, EVs have a double membrane, which could preserve and protect RNAs and protein content ,244,245,Elevated TDP43 and hyperphosphorylated TDP43 levels have been reported in plasma EVs ,243. TDPSOD1, c9orf72, TARDBP, and FUS, many other rare disease-causing genes were discovered, which may impact either familial or sporadic forms of ALS. With the availability of next-generation sequencing technologies, the cost and time of sequencing has been reduced. With novel sequencing technologies, more and more novel genes were discovered, not only in the coding but also in the non-coding regions. The discovery of new genetic variants revealed that multiple pathways might be involved in ALS progression, including regulation of gene expression, protein trafficking, or autophagy [ALS is a motor neuron disease which could affect the neurons responsible for muscle movement control. The phenotypes of ALS may overlap with other disorders, including FTD or PD, which may make the diagnosis more difficult . ALS is utophagy ,18. Receutophagy ,249. Undutophagy . In the utophagy .MiRNAs have multiple roles, from regulating gene expression (mRNAs inhibition) to impacting several neurological processes, including neurodevelopment, neuroprotection, or maturation of brain cells. Impairment in miRNA functions may be associated with neurodegenerative processes, including dysfunctions of motor neurons. Dysregulation of miRNAs may be a common hallmark in ALS. Several miRNAs were dysregulated in ALS , but further studies are needed to understand how the miRNAs could impact ALS diagnosis, prognosis and therapies ,251,252.ALS is clinically recognized as a heterogenic  disease with a complex molecular background. As mentioned previously, novel genetic factors continue to be identified, whose functional role in ALS involving endosome composition, autophagy, or cytoskeletal system is yet to be determined. In addition, several biomarkers (proteomic markers or miRNAs) in the biological fluids could play a role in ALS diagnosis, prognosis, or prediction . Moreover, these markers’ timely presence may indicate a patient’s responses to therapies ,254. As SOD1, FUS, TARDBP, or c9orf72, was suggested to be helpful in disease therapy. The gene therapy methods may be helpful in patients positive for ALS-causing mutations. For example, ALS patients who received ASO-Tofersen were associated with reduced SOD1 and NFL levels in CSF and plasma of ALS patients, respectively. However, the drug did not improve the clinical symptoms of patients [c9orf72 repeat expansion is C9orf72-631 or BIIB078. BIIB078 may protect the neurons from gain-of-function toxicity of repeat expansion and may prevent glutamate-related toxicity, and is in phase I of clinical trials [FUS mutations, an ASO-related drug called Jacifusen (NCT04768972 or ION363) is also in phase III of clinical trials [Similar to most neurodegenerative diseases, no successful therapy is currently available for ALS. However, promising strategies are available through gene therapy. In other motor neuron diseases, spinal muscular atrophy (SMA), and several gene therapeutic approaches, such as Nusinersen, Zolgensma, or Risdiplam, have been approved, which could lead to improved life quality of patients. The gene therapy strategy may also be promising for ALS drug development ,259. Antpatients . Tofersepatients . Anotherl trials ,263,264.l trials .SOD1 mutant mice showed reduced SOD1 expression and improved motor skills [SOD1 was tested in two ALS patients with SOD1 mutants. A slight improvement was observed in one of the patients in leg strength, while the other patient’s condition remained stable. These findings suggested that AAV-related gene silencing may slow down the disease progression. However, AAV therapy may need immunosuppression to avoid side effects, such as meningoradiculitis [c9orf72 repeat expansion in ALS mouse models (AAV5-miC). These mice showed reduced RNA aggregation with repeat expansion in nerve cells, leading to reduced neurotoxicity [c9orf72 mRNA in both plasma and cytoplasm of the cells. In addition, RNA foci were reduced in the nucleus [SOD1, C9orf72, FUS, ATXN2, and TARDP mutations. These studies showed promising data in iPSC cell lines derived from ALS patients, such as increased survival and reduced mutant protein-related toxicity [Research is ongoing on viral-based strategies of gene therapy as well. For example, adeno-associated virus (AAV)-related gene therapies may also be promising approaches in ALS mutants. AAV-related gene silencing in r skills . AAV-miRiculitis ,268. AAVtoxicity . The AAV nucleus . StudiesSOD1, c9orf72) may not define all ALS cases. Several biomarkers, such as elevated NFL in the serum and CSF, may be present years before the disease symptoms appear. As well as the lack of definitive markers or ratios, pre-symptomatic ALS diagnoses face many other challenges. One of the most significant is a patient’s psychological readiness before pre-symptomatic testing, comprehension of a positive result, their legal protections regarding information disclosure, and potential discrimination based on genetic results, particularly if a mutation or risk factor is present; counseling should be tailored. The other issue with pre-ALS testing is the logistical complexity. For example, potential pre-ALS individuals may live remotely and are inexperienced with telemedicine. Moreover, if trained personnel are unavailable, monitoring the initial stages of the disease may go undetected, particularly given the overlap of FTD with ALS, leading to further complications [Treatment of neurodegenerative diseases may be more effective in the early disease stage or even in the pre-symptomatic phase. Studies are needed regarding pre-symptomatic ALS to identify the individuals who may develop disease phenotypes. Genetic analysis may effectively identify at-risk individuals; however, the known genetic factors  occur in early childhood, but most ALS cases are adult onset. Therefore, the gene therapies for SMA may be given before the second year of age, but the treatment may not be efficient later, especially after the clinical symptoms appear . The othALS is a complex disease, since many diseases associated genes were identified, including SOD1, c9orf72, TARDBP, or FUS. Emerging studies are also discovering new genetic factors, which could cause disease or contribute to disease progression. Also, several proteomic  and microRNAs were discovered, which could play a role in disease diagnosis, prognosis, and prediction. Diagnosing ALS in early or even pre-clinical stages should be important. Currently, there are no therapies available for ALS. However, gene therapies were successfully adapted against other motor diseases, such as SMA. Also, ASO-based gene therapies (such as Tofersen or Jacifusen) are currently in clinical trial phases, but AAV-based therapies are also under development. Finding the possible genetic and proteomic markers for ALS diagnosis, prognosis, and prediction should be essential for gene therapies against the disease.


Cunninghamia lanceolata), namely, ClMDH-1, -2, -3, …, and -12. Chinese fir is one of the most abundant commercial timber trees in China, and low phosphorus has limited its growth and production due to the acidic soil of southern China. According to the phylogenetic analysis, MDH genes were classified into five groups, and Group 2 genes  were only found to be present in Chinese fir but not in Arabidopsis thaliana and Populus trichocarpa. In particular, the Group 2 MDHs also had specific functional domains—Ldh_1_N  and Ldh_1_C —indicating a specific function of ClMDHs in the accumulation of malate. All ClMDH genes contained the conserved MDH gene characteristic functional domains Ldh_1_N and Ldh_1_C, and all ClMDH proteins exhibited similar structures. Twelve ClMDH genes were identified from eight chromosomes, involving fifteen ClMDH homologous gene pairs, each with a Ka/Ks ratio of <1. The analysis of cis-elements, protein interactions, and transcription factor interactions of MDHs showed that the ClMDH gene might play a role in plant growth and development, and in response to stress mechanisms. The results of transcriptome data and qRT-PCR validation based on low-phosphorus stress showed that ClMDH1, ClMDH6, ClMDH7, ClMDH2, ClMDH4, ClMDH5, ClMDH10 and ClMDH11 were upregulated under low-phosphorus stress and played a role in the response of fir to low-phosphorus stress. In conclusion, these findings lay a foundation for further improving the genetic mechanism of the ClMDH gene family in response to low-phosphorus stress, exploring the potential function of this gene, promoting the improvement of fir genetics and breeding, and improving production efficiency.Malate dehydrogenase (MDH) genes play vital roles in developmental control and environmental stress tolerance in sessile plants by modulating the organic acid–malic acid level. However, MDH genes have not yet been characterized in gymnosperm, and their roles in nutrient deficiency are largely unexplored. In this study, 12 MDH genes were identified in Chinese fir ( Malate dehydrogenase (MDH) is a class A dehydrogenase that catalyzes the reversible transformation between malic acid and oxaloacetate and participates in the tricarboxylic acid cycle (TCA) process in plants, animals and microorganisms. MDH can be divided into NAD-MDH, containing coenzyme NAD+, and NADP-MDH, containing coenzyme NADP+ . NADP-deArabidopsis thaliana [Arabidopsis tolerance to salt stress by overexpressing plastid maize NADP-malate dehydrogenase (ZmNADP-MDH) in Arabidopsis [To date, multiple MDHs have been identified from different plants, such as 12 MDH have been identified in rice , 12 in tthaliana , and 16 thaliana , tobaccothaliana , column thaliana , and oththaliana , leaf rethaliana , and morthaliana ,23. Functhaliana . Over-exthaliana , and Kanbidopsis . Twenty bidopsis . Mitochobidopsis . In addibidopsis . AlthougCunninghamia lanceolata) is the most critical fast-growing afforestation tree species in southern China [GmMDH12 was found to enhance malic acid synthesis while inhibiting soybean nodule size under low-phosphorus stress [GhmMDH1 had the ability to catalyze the mutual conversion of oxaloacetic acid and malic acid. Under low-phosphorus stress, GhmMDH1 overexpression significantly increases the content of malic acid in roots, leaves, and root secretions in plants compared with wild-type controls, indicating that GhmMDH1 is involved in response to low-phosphorus stress [Phosphorus is an essential nutrient for plant growth and is involved in a range of physiological and biochemical processes such as photosynthesis, respiration, carbon (C) and nitrogen (N) assimilation, energy metabolism, and cell growth ,27,28,29rn China , which hrn China . Due to rn China , as wellrn China . Phosphorn China ,39,40. Nrn China ,42,43, arn China ,45,46,47rn China ,49. Sixts stress . Lü Jun s stress . MDH enzs stress . These sWith the development of molecular biology, more and more studies are being conducted on transcriptome sequencing and gene cloning of Chinese fir, and research on the MDH gene family of Chinese fir can improve the biogenic mechanism of the Chinese fir MDH gene family, explore the stress resistance of the gene, and improve the production efficiency of forest trees. The recently published whole Chinese fir genome provides an excellent opportunity to explore MDH family members in the Chinese fir genome . The ideClMDH were analyzed in detail. Subcellular localization, protein–protein interactions, and cis-elements analysis of MDH genes in Chinese fir were speculated. In addition, the existing Chinese fir RNA-seq data were used to analyze the expression of the ClMDH gene in different tissues and low-phosphorus stress. In addition, the expression of 12 ClMDH genes under low-phosphorus stress was detected by qRT-PCR  under low-phosphorus stress conditions, to better understand the function of the MDH gene in gymnosperm. The results of this study lay a foundation for understanding the regulatory mechanism of the MDH gene, which is conducive to further study of the function of the MDH gene, promoting the growth and development of Chinese fir and the genetic improvement of stress resistance.In this study, a comprehensive genome-wide identification and analysis of MDH family members of the Chinese fir genome was performed. In addition, the physicochemical properties, phylogenetic relationships, gene structure, chromosome position, conserved motifs and domain of ClMDHs were identified in Chinese fir, namely, ClMDH-1, -2, -3, …, and -12 ), and it was found that the total amino acid numbers of ClMDHs ranged from 229aa (ClMDH5) to 441aa (ClMDH11). The predicted molecular weight of ClMDHs was from 24.65 kDa (ClMDH5) to 48.14 kDa (ClMDH11), and the theoretical isoelectric point (pl) range was from 4.99 (ClMDH5) to 9.47 (ClMDH2). In addition, all ClMDHs except ClMDH4 were stable proteins according to the instability index. The secondary structure of ClMDH protein was predicted by PRABI (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html (accessed on 2 November 2022)), and the α-helix rate was 36.44~46.08%, the β-angle rate was 3.85~10.32%, the extension chain was 13.78~23.27%, and the rest were irregularly curled , Arabidopsis (9 AtMDHs), and Populus trichocarpa (16 PtMDHs)  . Accordir plants . The MDHClMDH gene family, the function of proteins was both conserved and differentiated, and their sequence similarity was 35.72%. To further reveal the unique regional characteristics of ClMDHs, the amino acid residues in the conserved functional domain were comparatively analyzed   A. The reGroup 5) A. In addGroup 5) B. The reGroup 5) B.The groups comprised almost similar motifs. Group 1 differed from the other groups containing motif1 and motif2 , in containing the peculiar motif10, motif13, motif14, and motif20. In addition, motif9, motif12, motif15, motif18, and motif19 only appeared in Group 2. Thus, members with similar conserved motifs were classified in the same phylogenetic branch, and the results of conserved motifs were consistent with phylogenetic relationships, indicating that ClMDH members of the same group may have similar functions A,B. Analcis-elements analysis of the ClMDH genes from the 2000 bp upstream promoter region was conducted to further understand the possible role of ClMDH genes in response to plant growth and development, phytohormone, and light and stress responsiveness , followed by ClMDH8 (34 members), while ClMDH10 had only 13 members of cis-elements. Among the 12 ClMDH genes, light-responsive cis-elements were the most common at 35% (104/301), followed by the hormone-responsive elements at 31% (98/301), and the growth and development response elements were the smallest at 10% (30/301).A siveness . The maiThe light-responsive cis-elements included AE-box, AT1-motif, ATCT-motif, Box 4, chs-CMA1a/2a/2b/2c, G-Box, GA-motif, GATA-motif, GT1-motif, I-box, Sp1, and TCCC-motif IIB. Of tClMDH genes were classified according to the cis-elements involved in each category, and it was found that all 12 ClMDH genes were involved in light, hormone  and stress  responsiveness, and 11 genes were involved in plant growth and development response  indicating that all duplicated genes underwent purifying selection  and 16.7% (2/12) of ClMDH proteins were modeled with the clsmkD, c8ldhA, and c5nufA reference templates. However, only single proteins including ClMDH5, ClMDH6, ClMDH7, ClMDH10 and ClMDH11 were predicted to be modeled with the clsevA, c5nufA, c6k12A,c6or9B and c7MDHA reference templates B. All 12ClMDH genes and a TF regulatory network was constructed using Cytoscape. The results showed that among all 12 ClMDH genes, a total of 460 TFs were identified, belonging to 35 different TF families including AP2, ARF, B3, BBR-BPC, BES1, bHLH, bZIP, C2H2, C3H, CAMTA, CPP, Dof, E2F/DP, EIL, ERF family, G2-like, GATA, GeBP, GRAS, HD-ZIP, HSF, LBD, MIKC_MADS, MYB, MYB_related, NAC, Nin-like, RAV, SBP, TCP, Trihelix, VOZ and WRKY  was highly enriched followed by ERF (82), BBR-BPC (32), MYB (31), Dof (28), TCP (22), MIKC_MADS (15), bHLH (14), C2H2 (12), HD-ZIP (10), bZIP (10), GATA (10), MYB_related (9), B3 (9), LBD (8 members), and GRAS (5 members) . The leaClMDH genes, ClMDH7 was the most targeted by 146 TFs followed by ClMDH9 (113 TFs), ClMDH4 (50 TFs), ClMDH8 (37 TFs), and ClMDH12 (26 TFs), whereas ClMDH3 was targeted least, by only 4 TFs , ERF (32), and BBR-BPC (27) family members, and ClMDH9 was enriched in NAC (62) and ERF (28) family members. The TF interaction networks of all 12 ClMDH genes are shown in ClMDH genes with TFs were ClMDH7, ClMDH9, ClMDH10, and ClMDH12  under different treatments of the two clones  and 25% (3/12) of the o clones . In addiP stress .ClMDH (7/12), 50% of ClMDH (6/12), and 59% of ClMDH (6/12) genes were expressed in roots, stems, and leaves, respectively. The highest expression in the root was 2.51FC (ClMDH11), followed by 2.26FC (ClMDH6) in the stem, and 1.60FC (ClMDH11) in the leaf. ClMDH11 was positively expressed in different tissue sites of 061, whereas ClMDH4 was negatively expressed in different tissue sites of 061. The ClMDH7, ClMDH8, ClMDH9, and ClMDH10 genes were not expressed at different tissue sites of fir clone 061, suggesting that they may not function during plant growth  under different P conditions, indicating that these genes may play an important role in the root development of Chinese fir. ClMDH1, ClMDH8, ClMDH9, and ClMDH10 genes were upregulated under low-phosphorus stress, and ClMDH4 and ClMDH12 genes were downregulated under low-phosphorus stress, indicating that these genes may play an important role in responding to low-P stress and can be used for further functional research.In summary, most of the ClMDH gene in response to low-phosphorus stress in different P-sensitive Chinese fir, we completed the qRT-PCR expression profiles of all 12 ClMDH genes in the root and leaf tissues of clones 34 and 41 under low-phosphorus stress  conditions in Chinese fir. Genes such as ClMDH1, ClMDH6, ClMDH7, ClMDH2, ClMDH4, ClMDH5, ClMDH10, and ClMDH11 were highly upregulated  [Populus (16MDH) [Arabidopsis (9MDH) [All 12 es, at 3 . It was  (12MDH) , tomato  (12MDH) , Populus (16MDH) , Arabidos (9MDH) , and cots (9MDH) .ClMDH genes have different subcellular localization   , which sa, etc.) , consista, etc.) B, indicainghamia . Membersinghamia A,B. ClMDinghamia , and MDHnese fir . A ClMDHn cotton  and popln cotton , which iClMDH cis-regulatory element analysis identified different plant development and stress response elements  (accessed on 1 November 2022). The Chinese fir protein sequences, CDS, genome and gff files were kindly provided by Prof. Zhong-jian Liu from Fujian Agriculture and Forestry University [Arabidopsis MDH amino acid was blasted to Chinese fir genome using Basic Local Alignment Search Tool for proteins (BLASTp) with default parameters. These analyses were performed to identify orthologous genes. The ClMDH candidates were then scanned to the Pfam files downloaded from Pfam Protein Family Database (https://pfam.xfam.org/) (accessed 1 November 2022) using Hidden Markov Model (HMM) by TBtools version 1.0984735 (https://github.com/CJ-Chen/TBtools/releases) (accessed on 1 November 2022) [https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi) (accessed 1 November 2022), SMART tool (http://smart.embl-heidelberg.de/) (accessed 1 November 2022), and an internal search tool (http://www.ebi.ac.uk/Tools/pfa/iprscan/) (accessed 1 November 2022). Further analysis confirmed the domains in which MDH was present in each gene.To identify the MDH genes in Chinese fir, the iversity  (accesseer 2022) , with thClMDH genes including molecular weight (MW), number of amino acids (aa), ORF length (bp) and isoelectric point (pI) were calculated using the ExPASy online program (https://web.expasy.org/protparam/)  (accessed on 2 November 2022) with default parameters. The protein secondary structures were predicted using PRABI (https://npsa-prabi.ibcp.fr/cgi-bin/) (accessed on 2 November 2022). The ClMDH proteins’ subcellular localization were predicted using WoLF PSORT (https://wolfpsort.hgc.jp/) (accessed on 2 November 2022). The MDH protein sequences of Cunninghamia (ClMDH), Arabidopsis (AtMDH) and Populus (PtMDH) were aligned by MEGA  software version 11 (https://www.megasoftware.net/) (accessed on 2 November 2022) [https://itol.embl.de/) (accessed on 2 November 2022) online tool along with Adobe Photoshop CC 2018 software.The physicochemical properties of er 2022) , and a nClMDH genes were shown by gene Structure Display Server 2.0 (http://gsds.cbi.pku.edu.cn/ (accessed on 2 November 2022)), based on the alignment of its coding sequence with the corresponding genomic sequence. The conserved motifs in ClMDH proteins were predicted by MEME (Multiple Expectation Maximization for Motif Elicitation) web tool version 5.4.1 (https://meme-suite.org/meme/tools/meme) [ClMDH phylogenetic tree, intron/exon structure and conserved motifs. Finally, the figure was further optimized by Adobe Photoshop CC 2018 software.The structural characteristics of the ls/meme)   of the ClMDH genes was extracted and submitted to the Plant CARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) (accessed on 5 November 2022). The cis-elements figure was drawn by TBtools software [ClMDH genes were summarized. The figures were further optimized and integrated by Adobe Photoshop CC 2018 and Excel software.For the prediction of cis-acting elements in the software . FurtherClMDH genes were mapped at their respective chromosomal locations according to the GFF annotation information and visualized using TBtools software [ClMDH genes with only one intervening gene on the same Chinese fir chromosome were considered to be tandem duplicated, while on other chromosomes were segmentally duplicated. The ClMDH gene duplication, synteny analysis, and Ka (non-synonymous)/Ks (synonymous) value calculations were performed by TBtools software. The TBtools software was used to annotate the Ka, Ks nucleotide substitution rates and Ka/Ks ratios of duplicated ClMDH genes. The divergence time  of ClMDH genes was calculated using following formula: T = Ks/2x (x = 6.38 × 10−9) [software . Gene du × 10−9) .https://string-db.org) (accessed on 6 November 2022) was used. The STRING parameters were set as follows: network type—full STRING network; the meaning of network edges —evidence; the minimum required interaction score—medium confidence parameter (0.4); and the max number of interaction display was no more than 10 interactors. Furthermore, the three-dimensional (3D) models of all 12 ClMDH proteins were predicted using online Phyre2 tool (http://www.sbg.bio.ic.ac.uk/phyre2/html/ (accessed on 9 November 2022)) with the confidence level set as 100% [To predict and generate protein-to-protein interaction networks between ClMDH proteins based on known Arabidopsis homologous proteins, the STRING database ) [p ≤ 1 × 10−5. The predicted TFs were visualized into a network using Cytoscape software version 3.9 (https://cytoscape.org/download.html (accessed on 9 November 2022)) [The plant TF prediction, and regulatory network analysis, were performed as described by Rizwan et al. (2022). The online tool Plant Transcriptional Regulatory Map (PTRM) (r 2022))  was usedr 2022)) .ClMDH in different Chinese fir tissues and different conditions using the available transcriptional expression data was performed, as described in our previous publication [The expression analysis of lication . The samlication .−1 KH2PO4), and low phosphorus supply , pH 5.6. Other nutrient content was supplemented according to the formula of 1/3 Hoagland Nutrient Solution 2·H2O, l mL·L−1 Fe-EDTA) and Arnon trace elements .The test materials were selected from the Chinese fir Yang 036 and 041 clone 1 annual container seedlings with good growth and consistency for the sand culture pot planting test, and the test process was carried out in the research greenhouse of Fujian Agriculture and Forestry University. The sand test was based on river sand that had passed through a 2 mm pore sieve after washing, and the effective phosphorus content of river sand was traced. After the roots of the seedlings were washed with pure water, they were transplanted into round pots filled with river sand, and the low-phosphorus stress culture test was carried out after 7 days of sowing the seedlings. Different phosphorus supply treatments were set up using 1/3 Hoagland nutrient solution formula: normal phosphorus supply (0.33 mmol·Lhttps://porimer3.ut.eel (accessed on 7 November 2022)) and NCBI (https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi) (accessed 7 November 2022) based on the CDS sequence of the selected gene  using the Tiangen mini-RNA extraction kit  following the manufacturer’s instructions. The quality and concentration of the RNA samples were assessed by Thermo Scientific NanoDrop 2000 UV-Vis Spectrophotometer . For cDNA synthesis, 1 µg of total RNA was used and the first strand of cDNA (complementary DNA) was synthesized using Maxima H Minus First Strand cDNA Synthesis Kit, with dsDNase , and the cDNAs were diluted to 5x with deionized distilled water. Gene-specific primers were designed using the Primer3 online web tool  (accessed 9 November 2022).Statistical analysis was performed with one-way analysis of variance (ANOVA) between treated and controlled samples using Student’s t-test and were considered statistically significant if ClMDH genes in the Chinese fir genome were identified by comprehensive analysis. The physicochemical properties, gene structure, evolution and expression patterns of ClMDH genes were determined. The phylogeny of the 12 ClMDH genes was divided into five branches. From phylogenetic tree analysis, ClMDH were only contained in Group 2, suggesting that these genes might play distinct roles in Chinese fir compared with MDH from other plants. Conserved motifs, protein–protein interaction networks and three-dimensional structures of ClMDH genes were highly conserved, suggesting their functionally was conserved.In this study, 12 cis-element analysis of ClMDH genes was conducted, and we found all 12 ClMDH genes were involved in light, hormone and stress responsiveness. The expression profile of FPKM-based ClMDH genes showed different expression in root and leaf tissues of Chinese fir. qRT-PCR expression analysis showed that ClMDH genes were highly upregulated under low-phosphorus stress compared with the control. These findings provide a basis for further revealing the mechanism of MDH genes in the stress response signaling pathway in Chinese fir.In addition, collinearity analysis and TFs regulatory network analysis were also carried out. Segmental duplication and tandem duplication occurred during Chinese fir domestication. A


Sepsis, a syndrome caused by a dysregulated host response to infection and characterized by life-threatening organ dysfunction, particularly septic shock and sepsis-associated organ dysfunction (SAOD), is a medical emergency associated with high morbidity, high mortality, and long-term sequelae. Tissue-resident macrophages (TRMs) are a subpopulation of macrophages derived primarily from yolk sac progenitors and fetal liver during embryogenesis, located primarily in non-lymphoid tissues in adulthood, capable of local self-renewal independent of hematopoiesis, and developmentally and functionally restricted to the non-lymphoid organs in which they reside. TRMs are the first line of defense against life-threatening conditions such as sepsis, tumor growth, traumatic-associated organ injury, and surgical-associated injury. In the context of sepsis, TRMs can be considered as angels or demons involved in organ injury. Our proposal is that sepsis, septic shock, and SAOD can be attenuated by modulating TRMs in different organs. This review summarizes the pathophysiological mechanisms of TRMs in different organs or tissues involved in the development and progression of sepsis. •TRMs are the first line of defense against life-threatening conditions, including sepsis.•The function of the TRMs has two sides - the angelic and the demonic - in sepsis.•For protection against sepsis and SAOD, TRMs should be the focus of research. In a stTissue-resident macrophages (TRMs) are a subpopulation of macrophages in tissues characterized by organ heterogeneity, homogeneity of origin , and local self-renewal independent of hematopoiesis during adulthood  [[9], 1. TRMs arin vivo cell tracking that some vital TRMs play a protective role in SAOD by clearing damaged mitochondria, expressing pro-inflammatory cytokines  receptor antagonists, inhibiting pro-inflammatory cytokine secretion , forming immune cell scaffolds, maintaining cellular homeostasis, promoting tissue repair, and other mechanisms, and even showing potential therapeutic value [Sepsis can be divided into two stages, early and late, based on immunologic characteristics . Simultaic value . Howeveric value . Thus, wThis review provides a comprehensive overview of different types of TRMs and common organ dysfunction caused by sepsis. We briefly summarize the origin of different TRMs, their phenotypes, and their functions in different organs. In particular, we focus on the pathophysiological mechanisms of TRMs involved in the progression of sepsis and SAOD. We will discuss how sepsis disrupts the crosstalk between TRMs and tissue cells in different organs to maintain organ homeostasis and how TRMs protect the human body against SAOD, as well as their potential therapeutic value. Our search strategy was essential as follows: “TS= (resident macrophage*) AND TS= (sepsis × OR septic*)".1.11.1.1Sepsis-associated encephalopathy (SAE) is a common diffuse central nervous system (CNS) dysfunction that often occurs in the setting of sepsis, septic shock, or SIRS . In the 1.1.2Microglia, a population of CNS-resident macrophages, are long-lived yolk sac-derived cells within the CNS parenchyma that remain in a stable state throughout adulthood and self-renew without the contribution of bone marrow cells . Microgl1.1.3In the context of infection, microglia undergo significant morphological transitions in response to pathogen-associated molecular patterns (PAMPs), such as LPS, and initiate primary inflammatory responses ,48. In t1.21.2.1Septic cardiomyopathy (SCM), a life-threatening complication, is usually considered a cardiohomeostasis disorder caused by sepsis and septic shock as long as physicians can rule out other types of chronic and acute cardiovascular diseases ,53. Acco1.2.2C–C chemokine receptor type 2 (CCR2), T-cell immunoglobulin, mucin domain containing 4 (TIMD4), major histocompatibility complex-II (MHC-II), and lymphatic vessel endothelial hyaluronan receptor 1 (LYVE1), the subsets of CRMs, derived from the yolk sac, are CCR2－MHC-IIlowTIMD4＋LYVE1－ and CCR2－MHC-IIhighTIMD4+LYVE1+ [C-X3-C motif chemokine receptor (CX3CR) 1＋CCR2－Ly6C－MHC-II－CRMs directly promote the proliferation of cardiomyocytes through the jagged-1-Notch1 axis, thus ameliorating cardiac injury. CX3CR 1＋CCR2－Ly6C－MHC-II－CRMs can be converted into CX3CR1＋CCR2－Ly6C－MHC-II＋CRMs by changes in the cellular redox state, which is the main population in the adult mouse heart [highCRMs [The cardiac-resident macrophages (CRMs), derived from yolk sac progenitors, are continuously self-renewing with a turnover period of nearly 5 weeks, which contributes to the maintenance of cardiac homeostasis, such as immune surveillance, angiogenesis, antifibrosis, electrical conduction, adaptive myocardial remodeling, clearance and degradation of apoptotic cardiomyocytes . In the 4+LYVE1+ . In the se heart . It showhighCRMs .1.2.3There is a growing body of direct evidence supporting the theory that CRMs could maintain cardiac homeostasis and protect patients from SCM by inhibiting excessive inflammatory responses, removing dysfunctional mitochondria shed by cardiomyocytes, preventing metabolic disorders, and maintaining cardiac electrical activities ,60,61.high CD163＋ resistin-like alpha (RETNLA)＋, MHC-IIlow, and MHC-IIhigh CRMs [Like the dysfunction of other organs, SCM is caused by a dysregulation of the host response to the infection, involving many pathways of the infectious inflammatory response, especially the excessive local cardiac and systemic inflammatory response in the early stage of sepsis, driven by PAMPs and damage-associated molecular patterns (DAMPs) ,52. Simiigh CRMs ,60.high CD163＋RETNLA＋CRMs subpopulation has an active ability to scavenge cardiomyocyte-ejected mitochondria, which is critical for supporting cardiac function and promoting cardiac homeostasis under septic stress, according to a recent study that combined scRNA-seq with fate-mapping techniques to analyze dynamic changes in CRMs in a CLP-induced septic heart model [The heart is a highly energy-consuming organ ,68. Mostrt model .1.31.3.1etc [Sepsis-associated vascular injury (SAVI) is a life-threatening pathophysiological feature of septic shock and acute organ injury, including vascular hyporesponsiveness, vascular relaxation, hypotension, leakage, microcirculatory abnormalities, disseminated intravascular coagulation, and even circulatory failure ,27. Vascetc . Thus, tetc ,40,78. Tetc . In the etc ,40,63,781.3.2Perivascular Macrophages (PVMs), the highly organically heterogeneous and organ-specific subpopulation of macrophages, are located within the vessel wall, on the surface of the vessel lumen, or close to the vessel ,80. In a1.3.3i.e. expressing characteristics of both monocytes and macrophages [In addition to phagocytosis and antibody presentation, PVMs play a role in maintaining vascular homeostasis by directly interacting with VECs and VSMCs to regulate permeability, maintain vascular integrity, and promote vascular development ,81,83,84rophages . In sepsrophages ,47,50,85rophages ,86.1.41.4.1According to the Berlin Criteria, acute lung injury (ALI) or acute respiratory distress syndrome (ARDS), caused by non-pulmonary sepsis, severe pneumonia, aspiration of gastric contents, trauma, severe pancreatitis, burns, aspiration injury, near-drowning, multiple transfusions, shock, and other unusual conditions, is characterized as acute hypoxic respiratory failure with bilateral chest radiographic infiltrates and cannot be fully explained by heart failure or fluid overload . There i1.4.2AMs, the lung resident macrophages, originate and develop from the fetal liver during embryonic hematopoiesis mainly through granulocyte-macrophage colony-stimulating factor, peroxisome proliferator-activated receptor-γ, and transforming growth factor-β-mediated signaling pathways and self-renewal, which facilitates the maintenance of the abundance of AM and serves as the first line of defense of the airways . During 1.4.3The severity of organ injury in sepsis is determined by changes in macrophage phenotype, specifically the pro-inflammatory phenotype (M1 subtype) and the anti-inflammatory phenotype (M2-like subtype) . In the Escherichia coli-induced) septic mouse models, researchers performed the double hit of intratracheal challenge with Pseudomonas aeruginosa and found that non-pulmonary septic mice, characterized by defective lung bacterial clearance and increased mortality rate, are highly susceptible to double-hit, while pulmonary septic mice are the opposite. The root cause of this experiment result is that non-pulmonary and pulmonary sepsis modulated the amount of AMs and some important immune functions differently via Toll-like receptor (TLR) 2-dependent crosstalk between Regulatory T cells and AMs [Clinical observations show that primary sites of infection are the most important determinants of sepsis severity, particularly in the lung, abdomen, and bloodstream ,89,100.  and AMs .ALI or ARDS is associated with impaired AM efferocytosis: the reduction of AM efferocytosis in sepsis-induced ARDS patients correlates with increased alveolar inflammation, which may contribute to serious clinical outcomes, including mortality . Activat1.51.5.1Myb is a critical transcription factor for the self-renewal of hematopoietic stem cells (HSCs). LPMs have been shown to be independent of the development of the HSCs and the transcription factor Myb [PRMs, which typically include large peritoneal macrophages (LPMs) and small peritoneal macrophages (SPMs), are long-term resident macrophages that develop well only in the peritoneal cavity ,12,23. Lctor Myb . Under pctor Myb ,23,36. Pctor Myb ,105. How1.5.2−/− mice is improved, accompanied by increased peritoneal infiltration of leukocytes (neutrophils and macrophages) and local proinflammatory cytokines/chemokine production , and reduced plasma and peritoneal bacterial loads. These effects are attributed to the enhanced ERK/MAPK signaling pathway and complement receptor 1/2 (CR1/2) expression of PRMs following Spred2 gene knockout [+, F4/80hi, MHC-IIlow) are rapidly increased in the peritoneum from 18 to 66 h after CLP. Surprisingly, SPMs  are not increased until 14 days after CLP. Changes in monocyte numbers by CCR2 deficiency or adoptive transfer of monocytes did not significantly affect animal survival. Depletion of LPMs significantly increases the mortality of the CLP model [Both animal experiments and clinical studies show that the ERK/MAPK signaling pathway plays a critical role in the pathogenesis of sepsis and septic shock ,21,22. Sknockout ,106. In LP model ,106. TheLP model ,106,107.LP model .Myb−LPMs reduced the severity of sepsis and SAOD such as liver and lung, improved the survival rate of septic rats by 30 %, and reduced the bacterial load by enhancing bacterial phagocytosis [+Gr-1+myeloid cells exacerbated death in the S. aureus infection model. Meanwhile, by using the LPS-induced sepsis model, they further confirmed that the number of Sca-1 was only increased in macrophages. Sca-1+ macrophages developed from PRMs. LPS-induced Sca-1+PRMs formation was partially interrupted by an anti–IFN–γ antibody, indicating that IFN-γ was necessary for this process. Compared with the sca-1−macrophages, the LPS-stimulated products such as IL-6, TNF-α, and CCL2 were lower in Sca-1+PRMs. Depletion of Sca-1+PRMs significantly increased survival rate and reduced acute organ injury [In the experiments, ocytosis . Stem ceocytosis . Sca-1+Gn injury .1.5.3E. coli infection, the LPMs not only led to rapid pyrolysis, bacterial clearance, and release of inflammatory mediators, but also polymerized multilayer cellular aggregates with thrombin-dependent fibrin. Therefore, LPM polymerization provided a physical scaffold that effectively controlled the abdominal infection [−Tim4−SPMs, F4/80+Tim4+LPMs realized the important functions for the homeostasis of coagulation function [+Tim4+PRMs were present in the physical scaffold after 4 h of e. Coli infection, ranging from small to large (＞8 μm), in dense aggregation [Abdominal bacterial infection, one of the deadliest causes of sepsis, is polymicrobial and is becoming a common clinical challenge with few treatments ,111,112.nfection . Comparefunction . The perregation . In summ1.61.6.1high monocytes that enter the gastrointestinal via the CCR2-CCL2 axis, regulated by Nr4a1. The remaining GRMs are mainly derived from CX3CR1highLy6Clowmonocytes [Gut-resident macrophages (GRMs), characterized by the expression of chemokine receptor CX3CR1, belong to a group of heterogeneous immune cells that reside in the gastrointestinal tract for a long time . Most GRonocytes ,116. Ly6onocytes . GRMs ca1.6.2high monocytes into GRMs, inhibited the expression of pro-inflammatory cytokines (TNF-α and IL-1β), promoted the expression of CD31 and vascular endothelial cadherin in the gastrointestinal, and inhibited the translocation of intestinal bacteria into lymph nodes and lungs [Acute gastrointestinal dysfunction (AGD) induced by sepsis, which promotes the translocation of intestinal bacteria and toxins, contributed to SIRS, the pathological process of sepsis, and SAOD ,35. Appr1.71.7.1The liver is a critical organ for immune homeostasis and metabolism, and it is the major injured organ in the early stage of sepsis, especially within 24 h, caused by pro-inflammatory cytokines, sepsis-induced microthrombosis, complement activation, bacterial pathogens, and others, which is commonly known as sepsis-associated liver dysfunction (SALD) and even liver failure (SALF) ,118,119.1.7.2The liver is the largest reservoir of macrophages, including KCs, monocyte-derived macrophages, and capsular macrophages, highlighting that the liver is the immunological hub. KCs, the unique liver-resident macrophages, are the major population of liver macrophages (∼90 %), which are derived from yolk sac-derived erythromyeloid progenitors during embryogenesis and undergo self-renewal throughout adulthood . There i1.7.3KCs serve as the gatekeepers for bacteria phagocytosis and endotoxin removal  via STING, interferon regulatory transcription factor 3, TLR4/MyD88/NF-κB, JNK/USP13, and other signaling pathways; at the same time, KCs may be a double-edged sword in that they produce a large number of pro-inflammatory cytokines such as IFN-β, TNF-α, IL-6, and IL-1β), ROS, and lipid superoxide, and recruit other inflammatory cells into the liver, which further initiate local inflammatory cascades, cell death, and oxidative stress that induces irreversible hepatocytes damage and liver injury . TherefoStreptococcus pneumoniae, Klebsiella pneumoniae, and Escherichia coli, which belong to the highly virulent categories of capsular serotypes [Streptococcus pneumoniae and Escherichia coli) in a systematic infection that helped to circumvent the mammalian host's most potent antibacterial machinery against the early stage of sepsis via capsular serotype-specific receptors and complement receptors [Capsules, the outermost antiphagocytic structures of many bacteria and fungi, are critical to evading the recognition and binding by phagocytes and adaptive immunity, which promote intracellular survival, virulence, and translocation of many pathogens . Encapsuerotypes ,127. Theeceptors .C-type lectin domain family 4 member F (CLEC4F), a C-type lectin receptor specifically expressed by KCs (CD68+KCs), has a high binding affinity for glycoproteins being exposed to β-galactose or β-N-acetylgalactosamine [Platelets are abundant but short-lived blood cells that have many physiological functions, including hemostasis, vascular integrity, and immunity. Excessive platelet activation caused by sepsis leads to thrombosis and coagulopathy . Most pltosamine ,132. A stosamine . This re1.81.8.1e.g., adrenal heterogeneity in the arterial phase of contrast-enhanced computed tomography (CT), hollow adrenal gland sign on dual-phase contrast-enhanced CT, and adrenal iodine concentration derived from dual-layer spectral detector CT, physicians can predict the outcome of patients during the acute phase of septic shock [The adrenal gland, composed of a medulla and a cortex, is a key component of the body's stress response system, which can be affected by microbial infections . In humaic shock ,136,138.ic shock ,135,137.1.8.2Like other tissue-resident macrophages, adrenal gland-resident macrophages (AGRMs) are derived from the yolk sac during embryonic development, localize in all the regions of the adrenal gland, and play an important role in immune-adrenal interactions ,63,140. 1.8.3＋AGRMs rather than adrenocortical cells [trans-well co-culture model of THP1 (human monocyte) derived macrophages and ATC7 zona fasciculata adrenocortical cells, the LPS treatment results in the increased level of IL-6 mRNA in ATC7 cells, while the expression levels of key adrenal steroidogenic enzymes, including StAR and DAX-1, are significantly decreased. The treatment with the glucocorticoid dexamethasone prevents the effects of LPS stimulation on the mRNA levels of IL-6, StAR, and DAX-1 in ATC7 cells co-cultured with THP-1 cells [i.e. systemic C. albicans infection [Sepsis-induced mitochondrial oxidative stress and dysfunction in adrenal glands result in RAI . Nitric al cells . Accordial cells ,137,142.nfection .1.91.9.1Sepsis-associated acute kidney injury (SA-AKI), preferably defined as the presence of AKI within 7 days of the sepsis onset , is the most common organ injury 25～75 %) in patients with sepsis and is strongly associated with adverse outcomes, including chronic kidney disease, cardiovascular events, and increased risk of death 5～75 % in,76. The 1.9.2Kidney-resident macrophages (KRMs), which are derived from erythromyeloid precursors during embryogenesis and have the capacity for self-renewal in adult tissues with little or no peripheral blood input, maintain renal homeostasis, monitor the immune microenvironment of the kidney, promote angiogenesis, and control the pathology of AKI and cystic kidney disease . KRMs ar1.9.3Candida infections, a common fungal cause of sepsis, are often associated with renal disease, potentially leading to AKI [＋＋KRMs do not directly eradicate Candida, they prevent AKI caused by Candida infections by promoting the secretion of IFN-γ and the neutrophil ROS response and inhibiting Candida growth [C-reactive protein (CRP), an acute fluid phase protein, is closely associated with inflammation and infection, particularly sepsis, and can activate macrophages [−KRMs are damaged and can exacerbate SA-AKI in mice; also, intraperitoneal injection of synthetic CRP peptide 1 h after CLP can effectively prevent or control SA-AKI by increasing the number of Ly6C−KRMs, enhancing and maintaining Ly6C−KRMs ROS production, and changing Ly6C−KRMs toward M2-like subtype [hi KRMs are involved in immunoregulation following injury, the selective depletion of F4/80hi KRMs would exacerbate SA-AKI [hi KRMs express the IL-1 receptor antagonist and restrict the generation of IL-6 in endothelial cells to ameliorate SA-AKI, representing a macrophage-endothelial cell immunoregulatory axis in SA-AKI [KRMs comprise discrete subpopulations that cannot be conventionally divided. These subpopulations exert varying degrees of influence on anti-inflammatory, pro-angiogenic, and tissue homeostatic in the presence of LPS . Acute sg to AKI ,151. Altrophages . In the  subtype . F4/80 a subtype ,147. Sine SA-AKI ,150. F4/n SA-AKI .1.101.10.1PP-cells in various sizes, where the primary function is to regulate blood glucose, gastrointestinal motility, pancreatic secretion, and gallbladder contraction [～15 %, and 40～70 % of these patients develop a secondary pancreatic infection, sepsis, and even sepsis-associated acute organ injury, with a mortality rate of 80 % [The pancreas is a long and narrow gland that consists of two main parts: the exocrine gland and the endocrine gland . The exotraction ,152. Acutraction . Patient of 80 % .1.10.2Pancreatic-resident macrophages (PARMs) are in a heterogeneous family of cells with different origins and phenotypes, characterized by a long half-life and self-maintenance in the adult pancreas . PARMs i1.10.3e.g. the F4/80low CD11c＋subset is found in the islets, whereas the F4/80hi CD11c－subset is found in the peripheral islet area [hi PARMs is induced by the administration of LPS and caerulein-induced AP, and this effect is also associated with NLRP3 inflammasome-induced inflammation in response to pancreatic injury [The phenotype of PARMs depends on their location, let area . In NF-κc injury . Islet-rc injury . Obesityc injury ,155,157.c injury . Therefo1.111.11.1The spleen is a complex organ with highly organized compartmentalization and an intricate microcirculatory system. It is a gatekeeper of systemic immunity, initiating and maintaining immune responses to blood-borne pathogens to prevent potentially life-threatening sepsis ,159. Spl1.11.2As a result of adaptation to tissue-specific environments, splenic-resident macrophages (SRMs), including red and white pulp macrophages, marginal zone macrophages (MZMs), and marginal zone metallophilic macrophages (MMMs), identified by immunohistochemistry based on localization, morphology, and membrane antigen expression, are extremely heterogeneous .1.11.3＋SRMs are a subset population of SRMs located in the splenic marginal zone and at the front line of host defense against bloodborne pathogens [pneumococcus into an ex vivo porcine splenic perfusion model, researchers observed complete clearance of bacteria in the blood and an increase in bacterial counts in the spleen. In a time course study, they further confirmed that each focus of infection originated from the replication of single pneumococcal cells within peri-follicular CD169＋SRMs [ex vivo model that was used to study bacterial replication susceptibility, a non-human primate model such as baboon and papio cynocephalus can be used to study splenic involvement during pneumonia, and the mouse model can be used to study experimental intravenous or intranasal pneumococcal infection. For instance, in the mouse model, researchers have observed an initial reduction of bacteria in the blood and life-threatening sepsis hours later, representing a population bottleneck driven by efficient clearance of pneumococci by CD169＋SRMs, but occasionally accompanied by intracellular replication of bacteria engulfed by CD169＋SRMs, where the proliferation of these sequestered bacteria provides a reservoir for dissemination of pneumococci into the bloodstream [high shortening their lifespan in favor of immature Ly6Glow neutrophils that have a defective oxidative burst [＋SRMs; the platelet aggregates could interact with infused platelets and contribute to platelet infusion refractoriness. Also, they found that macrophages played an important role in mediating sepsis-associated thrombocytopenia [The splenic marginal zone, including MZMs and MMMs, is a critical microanatomical region for pathogen defense that transmits information about pathogens from the innate to the adaptive immune system ,162,164.athogens ,162,165.169＋SRMs . Similarodstream ,165,167.odstream ,93,127. ve burst ,114,131.ve burst ,163. In ytopenia ,163,168.1.121.12.1TNF-α mRNA levels, plasma thiobarbituric acid reactive substances, and protein carbonates are increased in visceral AT, while total plasma antioxidant capacity is decreased [The function of the adipose tissue (AT) is complex, and the disruption of the physiological processes of this tissue can lead to pathophysiological conditions, including infectious diseases and non-infectious chronic diseases, especially in obese populations ,169. Morecreased ,154.1.12.2AT-resident macrophages (ATRMs) have long been thought to differentiate from local adipose tissue stromal vascular cells and mesenchymal stem cells or from peripheral monocytes that enter the AT by diapedesis, which are thought to be self-renewing and independent of bone marrow progenitors, a well-characterized regulator of AT inflammation ,170. Als1.12.3＋/CD68＋ATRMs from AT and subsequently cultured them under LPS-mimicking sepsis conditions. They found that CD45＋/CD68＋ATRMs were abundant in the cultures and they were the major producers of TNF-α. In contrast, the TNF-α/IL-10 ratio was lowest in CD45＋/CD68＋ATRMs, and it was elevated in both AMs and PRMs, associated with differential activation of the NF-κB signaling pathway. At the same time, obesity makes CD45＋/CD68＋ATRMs switch to a more pro-inflammatory program [Sepsis is associated with an increased number of total ATRMs and their M2-like subtype in visceral adipose tissue ,154. In  program . Thus, o program . Further program . This su＋ATRMs and related MyD88-and TRIF-mediated downstream pathways in progenitor cells and AT, which lead to the polarization of CD11c＋ATRMs [etc [Mif gene deletion shifted ATRMs toward the M2-like subtype, while Mif-2 knockout shifted ATRMs toward the M1-like subtype, and Mif deficiency increased the viability of fibroblasts [TLRs play a critical role in the immune-inflammatory response associated with sepsis ,101,125.1c＋ATRMs . The expRMs [etc ,169,170.RMs [etc ,108,127.2etc.) and demonic - due to their phenotype, functional molecules secreted, developmental stage, level of activation, immune microenvironment of the organ in which they are located, and the different stages of the sepsis course. TRMs should be the focus of research for protection against sepsis and SAOD. We should use techniques such as scRNA-seq, in vivo cell tracking, and mass spectrometry flow cytometry analysis to deeply characterize TRMs in different organs during sepsis, explore their commonalities such as characteristic markers, and further use protocols such as nanoparticles, in vitro cellular interference followed by transfusion, and characteristic inhibitors or agonists to explore TRMs for their potential therapeutic value.Sepsis is a rapidly progressive disease and is highly susceptible to the complications of septic shock and SAOD. Although current guidelines for managing sepsis and associated complications are continually being updated and reduce sepsis mortality, septic shock, SAOD, sepsis recurrence, and the presence of comorbidities are independently associated with increased sepsis mortality, particularly in the presence of acute injury to vital organs such as the cardiovascular, brain, kidney, liver, and lung. In addition to systemic life-threatening pathophysiological mechanisms, local mechanisms of organ injury are involved in the development and progression of SAOD. A growing body of evidence confirms that TRMs are involved in sepsis and SAOD. Although the function of TRMs has two sides – angelic , and the National Natural Science Foundation of Tianjin, China (Grant numbers 18JCQNJC10500).This work was supported by the There is no additional data available for this study.Yulei Gao: Conceptualization, Funding acquisition, Supervision, Writing – original draft, Writing – review & editing. Xin Tian: Writing – original draft, Writing – review & editing. Xiang Zhang: Writing – original draft. Grace Divine Milebe Nkoua: Writing – review & editing. Fang Chen: Writing – original draft. Yancun Liu: Writing – review & editing. Yanfen Chai: Conceptualization, Funding acquisition, Supervision, Writing – review & editing.The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.