TLR4, NLRP3, MBL2, IL6, IL1RN, IL1B, CX3CR1, CCR5, AGT, ACE, and F2. GO and KEGG analyses yielded 302 GO terms (q < 0.05) and 29 signaling pathways (q < 0.05), respectively, mainly including coronavirus disease-COVID-19 and cytokine-cytokine receptor interaction. IL6 and AGT were central in the PPI, with 8 and 5 connections, respectively. In this study, we identified 11 genes associated with both COVID-19 and three comorbidities that may contribute to infection and disease severity. The key genes IL6 and AGT are involved in regulating immune response, cytokine activity, and viral infection. Therefore, RAAS inhibitors, AGT antisense nucleotides, cytokine inhibitors, vitamin D, fenofibrate, and vaccines regulating non-immune and immune factors could be potential strategies to prevent and cure COVID-19. The study provides a basis for further investigation of genes and pathways with predictive value for the risk of infection and prognosis and could help guide drug and vaccine development to improve treatment efficacy and the development of personalised treatments, especially for COVID-19 individuals with common comorbidities.Hypertension, diabetes mellitus, and coronary artery disease are common comorbidities and dangerous factors for infection and serious COVID-19. Polymorphisms in genes associated with comorbidities may help observe susceptibility and disease severity variation. However, specific genetic factors and the extent to which they can explain variation in susceptibility of severity are unclear. Therefore, we evaluated candidate genes associated with COVID-19 and hypertension, diabetes mellitus, and coronary artery disease. In particular, we performed searches against OMIM, NCBI, and other databases, protein-protein interaction network construction, and GO and KEGG pathway enrichment analyses. Results showed that the associated overlapping genes were SARS-CoV-2, with its highly infectious property, has spread quickly worldwide, leading the WHO to officially and publicly declare COVID-19 a global pandemic 2+ via pore proteins, as well as virus particle assembly and release from host cells The envelope of SARS-CoV-2 mainly comprises four constitutive proteins, the spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. This viral S protein can bind to the host ACE2 and split into S1 and S2 subunits by transmembrane serine protease 2 (TMPRSS2). Human ACE2 can interact with the receptor-binding domain (RBD) on the S1 subunit, and the fusion peptide on the S2 subunit enters the infected host cell membrane PNPLA3 variant rs738409 and the TLL-1 variant rs17047200 is related to SARS-COV-2-induced infection TMPRSS2 variants rs12329760 and rs2298659 are associated with the severity of COVID-19, especially in young men and older women. It has also been predicted that rs12329760 could affect the stability of TMPRSS2 protease and have a protective effect on patients TMPRSS2 synonymous variants rs61735792 and rs61735794 were significantly associated with infection, whereas ACE2 and furin were not significantly associated with SARS-COV-2 infection ACE2 variant rs41303171 is significantly more frequent in patients with COVID-19 than in controls PCSK3 variant rs769208985 is associated with COVID-19 infection During the course of the COVID-19 epidemic, differences in rates of infection and disease outcomes among populations have been observed. There are various risk factors for COVID-19, among which human genetic polymorphisms play an important role. Eduardo et al. Most patients with COVID-19 have comorbidities, which may be risk factors for susceptibility and severity Variants with increased transmissibility, including delta (B.1.617.2), lambda (C.37), gamma (P1), beta (B.1.351), and alpha (B.1.1.7), have recently appeared and spread worldwide Bioinformatics approaches can be used to integrate and analyse genetic information and other data types, explore the mechanisms underlying specific pathological conditions, and identify new therapeutic targets. NCBI, OMIM, and other common databases were used to identify genes associated with COVID-19 as well as hypertension, DM, and CAD to predict susceptibility and severity in this study. A protein-protein interaction (PPI) network was generated using Cytoscape, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Nonetheless, the candidate susceptibility genes require further validation in larger studies to identify potential therapeutic targets for new adjuvant drugs and vaccines and develop personalised preventive measures and treatment plans.http://www.omim.org/), KMDB/MutationView (http://mutationview.jp/MutationViewV2Server/), DisGeNET database (https://www.disgenet.org/), and NCBI database MutationView provides human disease-related gene mutations covering the eye, ear, heart, tumor, autoimmune disease, muscle, and blood disease genes. The DisGeNET database collects information for associations between mutation sites and diseases. The NCBI database includes information for COVID-19-related genes.Disease-related genes were identified using the search terms “hypertension”, “diabetes mellitus”, “coronary artery disease”, and “COVID-19.” Four databases were used to screen for genes related to hypertension, DM, CAD, and COVID-19, including OMIM (http://www.bioinformatics.com.cn/). An online platform The related genes between COVID-19 and three comorbidities were cross-analysed using Bioinformatics (https://www.bioconductor.org/) packages “stringi,” “DOSE,” “apeglm,” “BiocManager,” “clusterProfiler,” and “pathview” to carry out GO analysis for common disease genes, KEGG analysis, and visual graphic display. The screening criteria for enrichment were p < 0.01 and q < 0.01. The p-values were estimated using the hypergeometric test and corrected for multiple testing with the Benjamini-Hochberg method. Additionally, q-values were estimated to control for the false discovery rate. The R script is provided in Supplementary File S1. A network graph of intersecting genes was constructed using Cytoscape (version 3.7.0).R (version 4.1.0) was used to load the Bioconductor  were identified  were used. After removing duplicate data, 733, 743, and 692 genes associated with hypertension, DM and CAD were identified, respectively. After superposition and the deletion of duplicate data for 150 genes related to COVID-19 from the SARS-CoV-2 data in NCBI and 108 genes from the gene map of OMIM, 245 genes were obtained. Then, a Venn diagram of overlapping genes was drawn using an online Bioinformatics platform. Eleven common genes , including lipopolysaccharide, bacterial molecules, biological stimulation, acute inflammation, regulation of transcription factors, cytokine activity, JAK-STAT receptor signaling pathway, immunity, and metabolic regulation. The lateral plasma membrane was the only enriched cellular component (CC). The genes were associated with 15 molecular functions (MF), including cytokine binding and activity, chemokine binding and receptor activity, and cell receptor-ligand binding. The top five BP, MF, and CC terms are shown in Figure Yersinia infection, influenza A, lipid and atherosclerosis, Salmonella and Escherichia coli infection, and NLR pathway  of 8 and 5, respectively  I/II in the renin-angiotensin system (RAS). It exerts physiological effects on target organs, including the kidney, blood vessels, and adrenal gland, and regulates the vascular tone, heart functions, and vascular remodelling AGT rs699 and found that asymptomatic patients have a lower frequency of the T/C genotype compared to symptomatic patients with COVID-19. The AGT rs699 SNP is potentially valuable tool for predicting clinical COVID-19 outcomes. The transfusion of AGT antisense nucleotides to inhibit AGT expression in male C57BL/6J mice for 14 days significantly reduced the expression of TMPRSS2 mRNA in the lungs AGT may have a protective effect against viral entry.The core gene ACE polymorphisms and COVID-19 has also been reported. ACE encodes an enzyme involved in regulating blood pressure and electrolyte balance, which catalyses transforming ANG I into ANG II with biologically active and participates in the imbalance of ACE2/ACE in the pathogenic process of SARS-CoV-2. The intron 16 of ACE is inserted/deleted 287bp to cause polymorphisms, which is currently the most studied polymorphism in ACE. There is a clear relationship between the polymorphism and blood ACE level ACE-I/D genotype that may be detected for predicting the ponderance of COVID-19 ACE is a potential susceptibility gene for COVID-19.A relationship between F2 encodes prothrombin. The rs1799963 and rs3136516 F2 polymorphisms are associated with increases in the prothrombin level/activity and the risk of thrombosis F2 polymorphisms in COVID-19 are needed.The intersecting gene MBL2 encodes a vital molecule in the innate immune system, a soluble mannose-binding lectin. An MBL2 deficiency is related to the susceptibility of infectious diseases CCR5-deficient mice have shown that the Th1 immune response is suppressed, increasing susceptibility to viral and bacterial infection  CCR5 gene is related to a higher incidence of HCV CCR5 Δ32 variant produces a truncated protein and observably decreases receptor formulation, suppressing the immune response Genes involved in immune system regulation may be related to variation in COVID-19 outcomes. Pathogens proliferate in the host in chronic illnesses, such as DM, affecting innate immunity in vitro studies and computer simulations supports the interaction between S proteins and immune receptors, including NLRs, CLRs, and TLRs Among KEGG signalling pathways identified in the study, TLR, NLR, and CLR signalling pathways play vital roles in initiating innate immune response, which can activate immune system and destroy immune tolerance state, which can disrupt immune tolerance state. It has been noted that cells expressing little or no ACE2 are still susceptible to the virus, suggesting that the S protein invades the host via receptors other than ACE2 IL1B, IL1R1, and IL1RN, likely cause a cytokine storm and critical COVID-19 The immune system is out of control to excessively release inflammatory mediators, resulting in a cytokine storm, a critical feature of COVID-19 recognized as the main reason causing serious outcomes. High levels of proinflammatory cytokines were observed in patients with COVID-19, such as IL1, IL1β, IL2, IL6, and TNF-α ATG and ACE of the RAS are related to the ACE/ACE2 balance. The renin-angiotensin-aldosterone system (RAAS) blocker ACE-I/ARB has a protective effect against COVID-19, and RAAS inhibitors may be associated with a lower probability of death Non-immune and immune factors are targets for the identification of new auxiliary drugs for COVID-19. The core genes Ligands are used as immunogenic adjuvants to activate TLR and NLR for enhancing the efficacy of vaccines and promoting a strong immune response TLR4, NLRP3, MBL2, IL6, IL1RN, IL1B, CX3CR1, CCR5, AGT, ACE, and F2. Studies of COVID-19 have evaluated the roles of polymorphisms in ACE2, TMPRSS2, IL-6, ACE, MBL2, AGT, and CCR5. However, the roles of polymorphisms in F2, NLRP3, TLR4, CX3CR, IL1RN, and IL1B in COVID-19 have not been established. This study could provide a reference for subsequent studies of susceptibility genes and marker genes of COVID-19 severity, and suggest that there are shared genetic mechanisms underlying COVID-19 and comorbidities, and reveal potential treatments. These results are of particular value for screening high-risk groups and for improving treatment efficacy and the development of personalised treatments, especially for COVID-19 individuals with the three comorbidities.In this study, the genes associated with both three common comorbidities and COVID-19 were screened through various databases. Candidate genes for the prediction of susceptibility and severity of COVID-19 included However, this study had some limitations. Database-based genomic data only provided a preliminarily explanation of the connection between three common comorbidities and COVID-19. The results should be validated in large population studies as well as functional assays. Additionally, this study focused on three common comorbidities. Other potential factors, such as smoking, obesity, and region, were not included in this study, and more mechanisms underlying associations between multiple factors and COVID-19 need to be explored. Basic and clinical research on related genes and drugs is required to provide more strategies for preventing and curing COVID-19.Supplementary file.Click here for additional data file.Supplementary table 1.Click here for additional data file.Supplementary table 2.Click here for additional data file.Supplementary table 3.Click here for additional data file.


The mechanisms and physiological implications of regulated cell death (RCD) have been extensively studied. Among the regulatory mechanisms of RCD, ubiquitination and deubiquitination enable post-translational regulation of signaling by modulating substrate degradation and signal transduction. Deubiquitinases (DUBs) are involved in diverse molecular pathways of RCD. Some DUBs modulate multiple modalities of RCD by regulating various substrates and are powerful regulators of cell fate. However, the therapeutic targeting of DUB is limited, as the physiological consequences of modulating DUBs cannot be predicted. In this review, the mechanisms of DUBs that regulate multiple types of RCD are summarized. This comprehensive summary aims to improve our understanding of the complex DUB/RCD regulatory axis comprising various molecular mechanisms for diverse physiological processes. Additionally, this review will enable the understanding of the advantages of therapeutic targeting of DUBs and developing strategies to overcome the side effects associated with the therapeutic applications of DUB modulators. Regulated cell death progresses through defined molecular cascades that cells can modulate to determine cell fate. Previous studies have examined the molecular characteristics and physiological significance of different types of RCD ,2,3.This review focuses on deubiquitinases (DUBs), which are regulatory factors of RCD, shared among different types of RCD. DUBs play critical roles in intrinsic apoptosis, a widely studied type of RCD. Additionally, this review focuses on the role of DUBs in extrinsic apoptosis, necroptosis, pyroptosis, paraptosis, ferroptosis, and autophagic cell death. Studies on the roles of DUBs in other types of RCD are limited; hence, the correlation between DUBs and other types of RCD has been excluded from this review.Apoptosis, a type of RCD, is characterized by cell shrinkage, membrane blebbing, and DNA fragmentation. Generally, apoptosis is considered a “non-inflammatory cell death”, as the cell debris is engulfed by the immune cells. Extrinsic ligands and cellular stress trigger apoptosis through the activation of caspases. Intrinsic apoptosis is induced by various cellular stresses, such as growth factor depletion, DNA damage, endoplasmic reticulum (ER) stress, increased reactive oxygen species (ROS) generation, replication stress, microtubular alterations, or mitotic defects. These stimuli promote mitochondrial outer membrane permeabilization (MOMP), which is the formation of pores in the mitochondrial outer membrane. Among the BCL-2 family proteins, BAX and BAK mediate MOMP, whereas BCL-XL, MCL1, BCL-2, and BFL-1 inhibited the activities of BAX and BAK. MOMP activation results in the release of mitochondrial components, such as CYCS and SMAC. APAF1 and procaspase-9 assemble to form an apoptosome, which activates the initiator caspase (caspase-9). Activated caspase-9 cleaves caspase-3 and caspase-7, which subsequently activate downstream proteins ,2,31,2,3Anoikis, which is induced by the detachment of cells from the extracellular matrix, is mediated by both intrinsic and extrinsic apoptosis-related factors. Hence, anoikis is critical for the elimination of non-adherent cells, such as tumor cells .Dependence receptors, which monitor the levels of their ligands in the surrounding environment, can induce caspase-dependent apoptosis when their ligands do not reach the threshold concentration. DCC, UNC5B (receptor for netrin 1), PTCH1 (receptor for sonic hedgehog), and NTRK3 (receptor for neurotrophin), which are mediators of dependence receptor signaling, induce apoptosis through the activation of caspases, p53, or E2F1 .Extracellular and intracellular insults activate caspase-independent necroptosis through sequential phosphorylation and activation of RIPK3 and MLKL. Activated MLKL undergoes oligomerization and induces plasma membrane rupture and cell swelling, which exposes damage-associated molecular patterns (DAMPs) or pathogen-associated molecular patterns (PAMPs) in the microenvironment. This results in a proinflammatory response in the surrounding microenvironment, which is distinct from the inflammatory response activated during apoptotic cell death in which cellular materials are trapped in apoptotic bodies . VariousPyroptosis, an inflammatory cell death, is induced by DAMPs, PAMPs, lipopolysaccharide (LPS), TAK1 inhibition, and death receptors. Exposure to DAMP/PAMP recruits the inflammasome, in which caspase-1 is activated. Activated caspase-1 promotes IL-1β and IL-18 maturation and secretion and cleaves gasdermin D (GSDMD). The N-terminal fragment of GSDMD forms pores in the plasma membrane and induces a pyroptosis phenotype. Alternatively, cytosolic LPS binds and activates caspase-4/5 (caspase-11 in mice). The activation of caspase-4/5 promotes the formation of the inflammasome and thus converges with the activation of caspase-1. Death receptor-activated caspase-3 cleaves GSDME. The N-terminal fragment of GSDME induces pyroptosis d. The chThe critical role of deubiquitination in pyroptotic cell death was identified using G5, a DUB inhibitor. Treatment with G5 suppresses the pyroptosis cascade and upregulates the ubiquitination of the NOD-like receptor pyrin domain-containing protein 3 (NLRP3) .Ferroptosis, which was first identified in 2012, is characterized by iron accumulation, lipid peroxidation, and shrunken mitochondria with increased membrane density and decreased the number of cristae. Previous studies have reported that ferroptosis is involved in various diseases, including cancer, ischemic reperfusion, fibrotic diseases, and autoimmune diseases. Ferroptosis is induced by multiple molecular cascades, all of which lead to the accumulation of phospholipid hydroperoxides. System Xc−, which comprises the SLC7A11/SLC3A2 heterodimer, sustains reductive cellular capacity by importing cystine into the cells and exporting glutamate. The transported cystine is reduced to cysteine, which is utilized to synthesize glutathione (GSH). Glutathione peroxidases (GPXs) utilize GSH to downregulate ROS levels e. InhibiThe correlation between ferroptosis and DUBs was examined using a general DUB inhibitor. The broad-spectrum DUB inhibitor PdPT downregulates the protein levels of GPX4 and upregulates GPX4 ubiquitination. PdPT treatment induces both apoptosis and ferroptosis. DUB inhibitor-mediated induction of GPX4 proteasomal degradation has been suggested as a potential anticancer therapy because cancer cell lines and primary cancer cells are sensitive to ferroptosis .Paraptosis or paraptosis-like cell death is characterized by ER dilation, mitochondrial swelling accompanied by ER/mitochondrial stress, and disruption of proteostasis and ion/redox homeostasis. The molecular cascade that directly mediates paraptosis has not yet been identified. However, c-JUN N-terminal kinases (JNK) 1, MEK2, and the inhibitory protein AIP1/Alix are reported to be involved in paraptosis f 15]. T. T15]. TOne study demonstrated a general correlation between DUBs and paraptosis using chemical compounds. Treatment with the hinokitiol copper complex (HK-Cu), a broad proteasomal DUB inhibitor, increases the accumulation of ubiquitinated proteins and induces paraptosis-like cell death. Inhibitors of apoptosis, autophagy, necroptosis, ferroptosis and parthanatos do not suppress HK-Cu-induced cell death. However, elimination of ROS suppresses HK-Cu-induced cell death .+/K+-ATPase, is characterized by membrane rupture and organelle ballooning  to substrate proteins. The ubiquitination at lysine and methionine-1 residues is considered to be canonical ubiquitination. Noncanonical ubiquitination refers to ubiquitination at serine, threonine, and cysteine residues. The following three enzymes catalyze ubiquitination: E1, E2, and E3. E1 catalyzes the ATP-dependent activation of Ub. Activated Ub forms a thioester bond with E2, which transfers Ub to the substrate along with E3 ligase. The substrates are conjugated with the monomers or polymers of Ub. Polyubiquitination is classified based on the linkage between Ub monomers. Both canonical and noncanonical ubiquitination have critical impacts on cellular functions, including protein degradation and signaling cascades through ubiquitination patterns, including mono-ubiquitination, poly-ubiquitination with variations of linkage types such as M1-polyubiquitination and K48-polyubiquitination ,20,21,22DUBs modulate the stability and signaling activity of substrates by cleaving the ubiquitin conjugates on the substrates a. Based In particular, DUBs regulate the molecular cascades of RCD and determine cell survival and death. DUBs are critical mediators of the pathological roles of RCD, such as infection, tissue injury, degenerative diseases, cancer, development, and tissue homeostasis ,26,27. ISeveral DUBs have been revealed to regulate multiple types of RCD through their diverse substrates and molecular pathways. Downstream factors mediating the regulation of RCD by DUBs include factors that directly modulate RCDs, such as BAX, RIPs, and c-FLIP, and regulators of other cellular functions, such as histone, AKT, and p62. These diverse downstream cascades of DUBs result in complex regulatory effects of DUBs on RCD. First, each DUB can modulate different types of RCD. Second, each DUB can either promote or suppress the same type of RCD, depending on the downstream signaling. For example, USP7 promotes intrinsic apoptosis through p53, SUV39H1, and PLK1 and suppresses intrinsic apoptosis through MDM2 and Maf and suppresses the ER stress response. In addition, USP7 promotes extrinsic apoptosis by promoting RIPK1 activity and ferroptosis by suppressing SCL7A11 expression a 28,29,,42,43,44Consequently, of these divergent molecular regulations, DUBs are involved in diverse physiological and pathological processes associated with RCD. For example, UCHL1 modulates several physiological and pathological processes, including malignant diseases, tissue homeostasis, tissue injury, metabolic diseases, and degenerative diseases, by regulating RCD. UCHL1 suppresses diverse types of cancer by enhancing intrinsic apoptosis. The positive UCHL1/apoptosis axis is required for spermatogenesis and is involved in suppressing cardiac hypertrophy. In contrast, the deregulated UCHL1/apoptosis axis aggravates hypoxic brain injury. By suppressing intrinsic apoptosis, UCHL1 ameliorates type 2 diabetes and Alzheimer’s disease. Conversely, UCHL1 promotes high-glucose-induced extrinsic apoptosis and necroptosis, which promote diabetic nephropathy a 55,56,,68,69,70In malignant diseases, DUBs can aggravate or ameliorate cancers, depending on their downstream RCD. For example, UCHL5/USP14 suppresses apoptosis and autophagic cell death to promote cancer. Several types of cancers are sensitized to cell death by depleting or pharmacological inhibition of UCHL5/USP14 b. In conThese examples show the complicated nature of the DUB/RCD/physiology regulatory axis. As described below, 19 DUBs have been found to regulate multiple types of RCD. This is summarized in Although USP5 preferentially cleaves free ubiquitin chains that are not anchored to substrates, it also deubiquitinates diverse proteins. Several cellular physiological and pathological functions, including development, heat-shock-induced stress response, immune response, cancer, and neuropathology, are regulated by the USP5-mediated deubiquitination of various substrates . USP5 suDrosophila. The depletion of USP5 induces developmental defects in the eye through the dysregulation of apoptosis and the JNK pathway [USP5 deubiquitinates and stabilizes c-Maf, a transcription factor related to tumor and immune cell differentiation, and suppresses apoptosis in multiple myeloma cells. The depletion of USP5 promotes apoptosis, which is suppressed upon overexpression of c-Maf . Short h pathway .Helicobacter pylori, exhibits growth-inhibitory effects against HCC by suppressing the expression of USP5, consequently activating the p53-p14ARF pathway and inducing apoptosis [The regulation of USP5 also has been reported to affect apoptosis and physiological functions of USP5. USP5 is reported to protect hepatocellular carcinoma (HCC) against apoptosis by suppressing p14ARF/p53 signaling in HCC tissues and cell lines. Hpn, a protein from poptosis ,76. miR-poptosis . USP5 inpoptosis .USP7 contains a catalytic USP domain between the N-terminal poly-Q/TRAF-like domain and the C-terminal Ub-like domain. Previous studies have examined the role of USP7, a representative DUB of p53, in human pathological processes, including cancer, neuronal disorders, and metabolic disorders . The molUSP7 regulates p53-mediated apoptosis by directly stabilizing p53 and indirectly by regulating the transcriptional activity of p53. USP7 stabilizes p53 directly through deubiquitination. In contrast, USP7 stabilizes MDM2 to suppress p53 stability. The final consequence is dependent on the experimental and physiological conditions ,194,195.The apoptotic functions of USP7 inhibitors have also been reported to be mediated by other cellular targets. P5091 and P22077 induced ER/ROS stress and consequently promoted apoptosis in both p53 (+) and (−) HCT116 cells . P5091 aUSP7 protects non-malignant cells from apoptosis. P5091 and P22077 induce apoptosis in late-stage erythroblasts and inhibit terminal erythroid differentiation, which requires USP7 activity to remove K48-linked polyubiquitin chains on GATA1 . In thymIn addition to intrinsic apoptosis, USP7 is involved in extrinsic apoptosis and ferroptosis. USP7 and TRIM27 deubiquitinate RIPK1 during TNFα signaling and promote extrinsic apoptosis. The loss of USP7 or TRIM27 abolishes TNFα/CHX-induced apoptosis in vitro and in vivo . USP7 prUSP8-knockout (KO) mice have revealed that USP8 is involved in liver failure and immune cell maintenance [USP8, which contains a C-terminal USP domain, is reported to be involved in endosomal trafficking, immune cell regulation, cell death, and Cushing’s disease. Studies on ntenance . USP8 reThe depletion of USP8 promotes intrinsic apoptosis by suppressing AKT activity in cholangiocarcinoma (CCA) . USP8 prUSP10 regulates multiple cellular pathways, including DNA damage response, metabolism, ribosome recycling, stress granules, and hematopoiesis . USP10 hUSP10 exhibits both anti-apoptotic and proapoptotic functions under DNA damage-induced stress conditions. DNA damage promotes ataxia telangiectasia mutated (ATM)-dependent phosphorylation of USP10, which undergoes nuclear translocation. The DUB activity of USP10 protects p53 from MDM2-mediated degradation and enhances radiation-induced apoptosis mediated by p53 . miRNA-1USP10-KO cells are sensitive to arsenite-induced apoptosis [Additionally, USP10 suppresses other cellular stresses linked to intrinsic apoptosis and facilitates cell survival. The interaction between USP10 and p62 promotes aggresome formation and protects cells from apoptosis induced by the accumulation of ubiquitinated proteins . ROS-indpoptosis . The virpoptosis .USP10-KO mice exhibited severe injury and inflammation. In this model, USP10 suppresses apoptosis by inhibiting TAK1 [USP10-KO hematopoietic stem cells exhibit increased apoptotic cell death induced by cytokine deprivation [USP10 is also involved in maintaining non-malignant tissue homeostasis and modulation of tissue injury response by suppressing intrinsic apoptosis. In the ischemia-reperfusion model, ing TAK1 ,90. USP1ing TAK1 . USP10 irivation .RNAi screening revealed that USP10 is required for curcumin-induced paraptosis. The knockdown of USP10 or treatment with spoutin-1 (USP10 inhibitor) downregulates mitochondrial dilation, phosphorylation of ERK and JNK, polyubiquitinated protein accumulation, and CHOP .USP11, which is an X-linked retinal disorder gene, regulates several cellular functions, including histone regulation, NF-κB signaling, DNA repair, and viral infection, and is associated with multiple types of cancers . AdditioUSP11 also regulates DNA damage-induced intrinsic apoptosis. Under genotoxic stress conditions, USP11 stabilizes the p21 protein level, which is upregulated upon DNA damage. The depletion of USP11 inhibits p21 protein expression and increases the sensitivity of cells to apoptosis . USP11 iIn human breast cancer tissue, USP11 expression was reported to be positively correlated with XIAP. WT USP11 (but not the C318A mutant) deubiquitinates and stabilizes X-linked inhibitor of apoptosis (XIAP) in a xenograft mouse model, which results in the suppression of anoikis and apoptosis and enhanced tumor growth .USP11 deubiquitinates and stabilizes c-IAP-2. The siRNA-mediated knockdown of USP11 or treatment with USP11 inhibitor sensitizes cells to SMAC mimetics and promotes extrinsic apoptosis induced by TRAIL and TNFα . The expUSP15, which contains a C-terminal USP domain, is associated with oncogenic signaling, Parkinson’s disease, and antiviral immune response. Additionally, USP15 positively or negatively regulates apoptosis induced by multiple stimuli by targeting various substrates . USP15 mUSP15 promotes p53-mediated apoptosis during high-risk human papillomavirus infection. The interaction between the viral protein E6 and p53 promotes the ubiquitination and degradation of p53. USP15 prevents E6-mediated degradation of p53 and activates apoptosis in the HeLa cell line . The depUSP15 deubiquitinates and stabilizes MDM2, resulting in suppressing p53 activity and apoptosis in cancer cell lines. Additionally, USP15 promotes nuclear factor of activated T-cells, cytoplasmic 2 (NFATc2) activity, which enhances T-cell activity against tumors. This indicates the complex role of USP15 in tumor progression . In multUSP18, a representative deISGylating enzyme, reverses the ISG15 conjugation induced by IFN signaling. In addition to ISG-15, USP18 cleaves the ubiquitin chain conjugated to proteins. USP18 is involved in pathogenic infections, inflammation, neurological disorders, and cancer by regulating IFN signaling and other substrates . In thisUSP18-KO cells are sensitive to irradiation-induced apoptosis, suggesting that USP18 is a potential therapeutic target [+ T cells (Mem) of patients infected with HIV, INF signaling increases the expression level of USP18, which is correlated with increased apoptosis. PTEN expression was upregulated, and pS473 AKT was downregulated, depending on IFN and UPS18. Therefore, USP18 exacerbates HIV infection-related pathology by reducing the maintenance of memory T cells in patients [In IFN-treated acute myeloid leukemia cell lines, depletion of USP18 inhibited cell proliferation and induced apoptosis. c target . Some stc target . Additioc target ,109. Howpatients .Furthermore, USP18 suppresses apoptosis independent of IFN signaling by targeting other molecular pathways, including AKT, epidermal growth factor receptor (EGFR), p53, caspases, BCL-2, and Notch1. In cervical cancer cell lines, USP18 suppresses apoptosis through activation of the AKT pathway. Treatment with LY294002, a PI3K/AKT inhibitor, mitigated USP18 overexpression-induced suppression of cell death . The depUSP20 is involved in tumorigenesis, inflammation, metabolism, and DNA repair by regulating diverse cellular substrates ,201,202.USP20 promotes the TNFα/NF-κB cascade by deubiquitinating and stabilizing p62, which then forms a complex with PKCζ/RIPK1. The depletion of USP20 promotes TNFα/cycloheximide-induced apoptosis . USP20 dUSP22 regulates various substrates, including histones, telomere repeat binding factor 1 (TRF1), sirtuin 1 (SIRT1), and cyclins. The expression of USP22 is correlated with a poor diagnosis of multiple types of cancers and spinocerebellar ataxia 7 . The oncIn gastric cancer, USP22 stabilizes the c-Myc/nicotinamide phosphoribosyltransferase (NAMPT)/SIRT1 signaling cascade, which further activates forkhead box protein O1 (FOXO1) and YAP. The stabilized YAP suppresses apoptosis . USP22 aA recent study revealed that USP22 promotes necroptosis. USP22 cleaves the ubiquitin chain from K518 of RIPK3. The loss of USP22 attenuates TNFα/BV6/zVAD-FMK-induced necroptosis but does not affect TNFα/BV6-induced apoptosis and RIPK1 phosphorylation .USP22 also promotes tissue injury-associated cell death. In a diabetes model, USP22 promoted high glucose-induced apoptosis in podocytes by enhancing ROS production, upregulating the expression of caspase-3 and BAX, and promoting the secretion of inflammatory cytokines .CYLD alleles are lost. A similar phenotype of skin tumor development was observed in CYLD-KO mice. NF-κB activity and cyclin D1 levels were upregulated in Cyld-KO mice. Furthermore, CYLD-deficient cancer cells are resistant to cell death induced by anticancer compounds [Cylindromatosis (CYLD) is a tumor suppressor identified in patients with cylindromas in whom both ompounds ,205,206.ompounds . AlthougCYLD is recruited to the TNFR1 complex, which is dependent on spermatogenesis associated 2 (SPATA2). In the complex, CYLD cleaves K63- and M1-linked polyubiquitin chains. The loss of CYLD stabilizes the TNFR1 complex and NF-κB activity and consequently suppresses TNFα-induced cell death ,209,210.CYLD is also involved in cardiac injury-induced apoptosis through the regulation of autophagy. A cardiomyopathy study using transverse aortic arch constriction (TAC) revealed that autophagic efflux induced by mTOR reactivation after TAC protects cardiac cells against apoptosis. The overexpression of CYLD in cardiomyocytes results in the accumulation of K48-linked polyubiquitin chains in cells, and the suppression of mTOR activity and autolysosomal clearance leads to cardiac defects and apoptosis .A20 (TNFAIP3) comprises an N-terminal OTU domain with DUB activity and seven C-terminal zinc finger (ZnF) domains. ZnF4 and ZnF7 bind to K63- or M1-linked polyubiquitin chains and exhibit E3 ligase activity. A20, which is reported to be an anti-inflammatory regulator, is involved in multiple regulatory mechanisms in cell death and inflammatory diseases . The preVarious studies using different models have reported contradictory findings regarding the function of A20 in TNFR1 complex signaling. A20, a pro-survival gene induced by NF-κB, downregulates NF-κB signaling and inhibits sustained inflammation . In addiPorphyromonas gingivalis and TNFα/CHX in a periodontal inflammation model [In contrast, A20 is reported to suppress pathogen-induced apoptosis, DR4/5-induced apoptosis, pyroptosis, and autophagy-related cell death. The depletion of A20 sensitizes immortalized gingival keratinocytes to inflammation and apoptosis induced by on model . Treatmeon model . In TRAIon model . In DR4/on model .A20 regulates pyroptosis by binding to the inflammasome and deubiquitinating caspase-1 at K133 in the presence of RIPK3. The deletion of A20 promotes pyroptotic cell death and inflammation by upregulating caspase-1 activity . In a diA20 is also involved in the inflammatory pathology of the intestine. Mass spectrometry analysis revealed that A20 interacted with ATG16L1. Although the ubiquitination of ATG16L1 was not observed in this study, depletion of A20 upregulated the levels of ATG16L1 and LC3-II. The double knockout of A20 and ATG16L1 in the intestinal epithelium results in spontaneous inflammatory bowel disease (IBD)-like pathology. Additionally, the organoid undergoes cell death, which is not rescued upon treatment with the anti-TNFα antibody, zVAD, Nec-1, and zVAD/Nec-1 .OTULIN, which contains an OTU domain, exclusively cleaves M1-linked polyubiquitin chains. Structural studies have revealed that only the M1-linked polyubiquitin chain can exhibit optimal orientation in the catalytic triad of OTULIN . OTULIN Molecular studies and studies using mouse models have suggested that OTULIN promotes cell death. OTULIN overexpression suppressed LUBAC activity and downregulated the LUBAC-mediated polyubiquitination of complex 1. This results in decreased NF-κB activity, and TNFα signaling shifts to the proapoptotic pathway. Moreover, OTULIN binds to the ubiquitin chain of complex 1 and directly suppresses NF-κB activity, independent of its DUB activity ,148.Otulin-KO has been shown to promote liver inflammation and damage. Hepatocyte cell death was upregulated in conditional KO mice, which was reversed by ripk1D138N knock-in or Fadd KO. This indicated that apoptosis mediates the pathology of the Otulin-KO liver. Interestingly, the pathological phenotypes in KO mice are not dependent on TNFR but are dependent on mTOR and IFN signaling. Thus, OTULIN may have additional molecular mechanisms to suppress cell death independent of TNFR [Conversely, OTULIN depletion suppressed LUBAC activity. In these studies, OTULIN-deficient cells were prone to apoptotic or necroptotic cell death. The ubiquitination of TNFR1 complex components is downregulated in mouse embryonic fibroblasts expressing the catalytically inactive OTULIN mutant (C129A). OTULIN prevents the inhibitory self-ubiquitination of LUBAC, which increases the susceptibility of cells to TNFα-induced cell death ,151,152. of TNFR ,154.OTUB1 specifically cleaves the K48-linked ubiquitin chain. OTUB1 also inhibits ubiquitin transfer to the substrate by binding to the E2-Ub complex, independent of DUB activity . OTUB1 pOTUB1 has been reported to stabilize p53 and consequently mediate DNA damage-induced apoptosis. Mechanistically, OTUB1 downregulated MDM2-mediated ubiquitination of p53. The D88A mutant of OTUB1 could not stabilize p53. Thus, mutant OTUB1 protects p53 through its E2-binding activity . OTUB1 iOTUB1 knockdown in HCC cell lines upregulated proapoptotic BAX and caspase levels and suppressed cell growth [The anti-apoptotic role of OTUB1 has been reported to be mediated through other substrates. FOXM1, a transcription factor related to DNA damage responses, is associated with chemotherapy resistance in cancer. In the epirubicin-resistant cell line, the upregulated expression of OTUB1 stabilizes FOXM1 through deubiquitination. This results in enhanced resistance to chemotherapy/DNA damage-induced apoptosis . A simill growth . In an il growth .In addition to intrinsic apoptosis, OTUB1 also protects cells from extrinsic cell death. In tumor necrosis factor-like weak inducer of apoptosis (TWEAK)-induced apoptosis, OTUB1 stabilizes c-IAP-1 by cleaving its K48-linked ubiquitin chain, which results in the suppression of apoptosis. siRNA-mediated depletion of OTUB1 facilitates apoptosis and decreases NF-κB activation .OTUB1 suppresses ferroptosis by directly stabilizing SLC7A11 protein, in contrast to BAP1 and USP7, which regulate the transcription of SLC7A1. OTUB1 C91A mutant, but not the D88A mutant, could stabilize SLC7A11. This suggests that OTUB1 stabilizes SLC7A11 through its E2-inhibiting activity and not its DUB activity. This positive regulation of SLC7A11 by OTUB1 is enhanced by CD44, which binds to SLC7A11 via a different domain .BAP1, a tumor suppressor, is involved in the DNA repair machinery, regulation of cell death, and metabolism. BAP1 mutations result in familial BAP1 cancer syndrome. Various mechanistic studies have revealed the role of BAP1 in multiple cancers . HoweverBAP1 is reported to be mutated in malignant mesothelioma (MMe). Cells harboring mutant BAP1 are resistant to gemcitabine, which induces DNA damage and various types of cell death, including apoptosis, necrosis, and necroptosis. The depletion of BAP1 yielded similar results, suggesting that the antitumor function of BAP1 is mediated by the activation of cell death . BAP1 se2+ flux into the mitochondria from the ER, which results in increased mitochondrial apoptosis in cells exposed to DNA-damaging agents [BAP1 also induces cell death in cancer cells independent of transcriptional regulation. In the ER, BAP1 colocalizes with and binds to inositol 1,4,5-trisphosphate receptor type 3 (IP3R3). The BAP1-mediated stabilization of IP3R3 promotes Cag agents . In neurg agents .However, BAP1 also suppresses apoptosis by regulating gene expression, DNA repair, and ER stress, which overlap with its proapoptotic mechanisms. In cutaneous melanoma tissues, BAP1 is not lost or mutated. Furthermore, shRNA-mediated depletion of BAP1 increases apoptosis and downregulates cell growth. Depletion of BAP1 results in reduced levels of survivin. Thus, BAP1 acts as a tumorigenic protein in this malignancy . BAP1 prBcl2 and Mcl2), which is the opposite of the regulation by BAP1. Therefore, cancer cells without RNF2 activity on the promoters of Bcl2 and Mcl2 are not sensitized to apoptosis, which facilitates tumorigenesis [Molecular studies have revealed the compensatory mechanisms involved in cancer cells with the loss of BAP1 expression and lack of accelerated cell death. The activity of RNF2 is required to promote apoptosis in BAP1-depleted cells. RNF2 promotes apoptosis by ubiquitinating H2A to silence pro-survival genes , the serum levels of UCHL1 and proapoptotic BAX are significantly correlated with neuronal apoptotic injury . During UCHL1 in human IAPP (hIAPP) transgenic mice increases the accumulation of lysosomes, IAPP, and cleaved caspase in β cells [UCHL1 is one of the downregulated genes in gentamicin-treated cells. The shRNA-mediated depletion of UCHL1 sensitizes cells to gentamicin-induced cell death and is associated with defects in autophagosomal clearance [Some studies have reported the anti-apoptotic role of UCHL1, especially in tissue injury or degenerative models. UCHL1 relieves the apoptotic burden induced by the accumulation of intracellular toxic oligomers of islet amyloid polypeptide (IAPP) in pancreatic beta (β) cells, resulting in the suppression of type 2 diabetes. The loss of  β cells . During  β cells . In a mo β cells . UCHL1 plearance .UCHL1 was also reported to suppress anchorage-dependent apoptosis (anoikis). The expression of WT, and not that of a catalytically inactive mutant of UCHL1, enhances focal adhesion kinase (FAK)-mediated adhesion signaling, even in the absence of cellular adhesion .UCHL5, USP14, and RNP11 are the three DUBs in the 19S regulatory particle of the proteasome. DUB activity and allosteric regulation of UCHL5 and USP14 promote or suppress proteasomal degradation of substrates. In various cancers, the expression of UCHL5 and USP14 is upregulated. Several pharmacological inhibitors of UCHL5 and USP14 have been developed . The inhIn drug-resistant cancer cells, inhibitors of UCHL5 and USP14 mitigate resistance and sensitize cancer cells to cell death by modulating diverse cellular mechanisms. These inhibitors induce apoptosis in multiple myeloma by upregulating ER stress  and accuMycobacterium tuberculosis-induced macrophage pyroptosis. EST12 secreted by the pathogen cleaves the K48-linked polyubiquitin chains of NLRP3 through UCHL5. Knockdown of UCHL5 completely inhibits EST12-mediated deubiquitination of NLRP3, which suppresses pyroptosis. This indicates that UCHL5 is required for the EST12/RACK/pyroptosis response in macrophages and the clearance of pathogens by the host [Additionally, UCHL5 can induce cell death in a pathogenic infection model. UCHL5 is also involved in the host .To delineate the effect of UCHL5 and USP14, the USP14-specific inhibitor IU1 has been used in diverse pathological models. Depletion or pharmacological inhibition of USP14 revealed the anti-cell death functions of USP14. Treatment with IU1 induces the degradation of COPS6, a negative regulator of p53. Hence, IU1 upregulates p53 and p21 protein levels and consequently promotes apoptotic cell death . In addiInterestingly, UCHL5 and USP14 are associated with the suppression of autophagy, which affects apoptosis and autophagy-dependent cell death. In human podocytes, USP14-mediated deubiquitination and stabilization of SPAG5 contribute to podocyte injury, a clinical predictor of diabetic nephropathy. The USP14/SPAG5-positive-regulatory axis inhibits autophagy and promotes apoptosis by activating AKT/mTOR . The nicBRCC36 is a component of BRCC, which is a complex comprising BRCA1, BRCA2, and BARD1. Previous studies have reported that BRCC36 is involved in DNA repair ,185. BRCIn radiation-induced apoptosis, BRCC36 and BRCC45 enhance the E3 ligase activity of BRCC, promoting the DNA repair activity of BRCC. Thus, BRCC36-mediated suppression of apoptosis is dependent on BRCC. The depletion of BRCC36 impairs BRCA1 phosphorylation and sensitizes cells to ionizing radiation-induced apoptosis ,185.Vdr-KO mice are highly prone to LPS-induced sepsis, and an additional NLRP3-KO rescues the phenotypes [BRCC36 also promotes pyroptosis via DUB activity. Treatment with G5, a general DUB inhibitor, suppresses pyroptosis and promotes the ubiquitination of NLRP3. In this study, BRCC36 was identified to be critical for NLRP3 activation by LPS, HLLOMe, and silica . Anotherenotypes . An NLRPenotypes .STAMBPL1, a member of the AMSH DUB family, is reportedly involved in cancer . StudiesSTAMBPL1 directly stabilizes XIAP through deubiquitination and consequently inhibits lysosomal degradation of XIAP. The depletion of STAMBPL1 downregulates XIAP levels and promotes ROS-induced intrinsic apoptosis . The natAs summarized in The diverse molecular mechanisms underlying the modulation of RCD by DUBs lead to the physiological multifunctionality of the DUB/RCD axis. Each DUB/RCD axis modulates several pathological conditions that harbor specific molecular alterations, such as tumorigenesis, tissue injury, degenerative diseases, metabolic disorders, and pathogenic infections. Thus, the regulation of DUB activity is a potential therapeutic strategy for various pathological conditions associated with RCD.However, the multifunctionality of DUBs and their inhibitors is associated with both advantages and disadvantages for modulating RCD to treat diseases. For example, one DUB may have multiple molecular cascades that converge to similar consequences, such as the suppression of cell death in cancer. Hence, DUB inhibitors induce cancer cell death through multiple mechanisms, which would challenge developing drug resistance in cancer cells. In addition, the inhibitor could be effective against multiple types of cancers with different types of molecular alterations. In other cases, the activities of one DUB may result in either cell death or survival, depending on the cellular context. Hence, inhibitors of DUBs can alleviate or aggravate the disease. Furthermore, different tissues may respond differentially to a single DUB inhibitor, which further complicates the potential application of the DUB/RCD axis as a therapeutic target.Furthermore, studies on the roles of DUBs in RCD and the associated pathophysiology have been biased toward intrinsic apoptosis, as described in the current review. Therefore, the regulatory function of DUBs and their physiological effects on other types of RCD must be elucidated in future studies.


Drought is one of the most serious abiotic stress factors limiting crop yields. Although sunflower is considered a moderate drought-tolerant plant, drought stress still has a negative impact on sunflower yield as cultivation expands into arid regions. The extent of drought stress is varieties and time-dependent, however, the molecular response mechanisms of drought tolerance in sunflower with different varieties are still unclear. Here, we performed comparative physiological and transcriptome analyses on two sunflower inbred lines with different drought tolerance at the seedling stage. The analysis of nine physiological and biochemical indicators showed that the leaf surface area, leaf relative water content, and cell membrane integrity of drought tolerance inbred line were higher than those of drought-sensitive inbred line under drought stress, indicating that DT had stronger drought resistance. Transcriptome analyses identified 24,234 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed the up-regulated genes were mainly enriched in gibberellin metabolism and rRNA processing, while the down-regulated genes were mainly enriched in cell-wall, photosynthesis, and terpene metabolism. Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis showed genes related to GABAergic synapse, ribosome biogenesis were up-regulated, while genes related with amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, photosynthesis were down-regulated. Mapman analysis revealed differences in plant hormone-signaling genes over time and between samples. A total of 1,311 unique putative transcription factors (TFs) were identified from all DEGs by iTAK, among which the high abundance of transcription factor families include bHLH, AP2/ERF, MYB, C2H2, etc. Weighted gene co-expression network analysis (WGCNA) revealed a total of 2,251 genes belonging to two modules, respectively, which were significantly associated with six traits. GO and KEGG enrichment analysis of these genes was performed, followed by visualization with Cytoscape software, and the top 20 Hub genes were screened using the CytoHubba plugin. Helianthus annuus L.) is a globally important oilseed food that is mainly cultivated for the production of edible oil, with the seeds containing 36–52% edible oil and 28–32% protein [Sunflower R package  clustersThe research was conducted in the city of Hohhot , Inner Mongolia Province, China. In early August 2020. The drought-sensitive inbred lines K55(denoted as ‘DS’) and the drought-tolerant K58(denoted as ‘DT) that selected from 226 varieties in our previous study. Seeds were sterilized with 3% sodium hypochlorite for 5 min, followed by washing 3 times with sterile distilled water. Then germinated on two layers of wet filter papers in petri-dishes at room temperature (19°C to 25°C) for 24 h according to the procedures of Lei et al [After the third leaf was fully expanded, all seedlings were stopped irrigation and subjected to drought stress according to Pereyra et al . Based o2O2 consumption at 240 nm [A total of nine physiological and biochemical traits were measured in this study. LSA was calculated using the length-width coefficient method . The relt 240 nm . The leat 240 nm . The fret 240 nm . The Solt 240 nm . The levt 240 nm .Total mRNA was isolated using the RNA prep Pure Plant Kit DP411 according to the instruction manual. RNA concentration and purity were measured using a NanoDrop 2000 spectrophotometer. RNA integrity was assessed using an Agilent 2100 LabChip GX  by 1% agarose gel electrophoresis. A single library requires 2μg of RNA, with a concentration ≥ 40 ng/μL, OD260/280 between 1.7–2.5, OD260/230 between 0. 5–2. 5, and RNA integrity number (RIN) > 6.5. The mRNA was then enriched with Oligo (dT) magnetic beads. The mRNA was added with fragmentation buffer and cut into short fragments. RNA was reverse transcribed into cDNA using six-base random primers. The double-stranded cDNA samples were purified, end-repaired, added with poly(A) tails, and then ligated to the sequencing adapters to create cDNA libraries. After the libraries had passed the quality test, all samples were sequenced from both ends with a Novaseq 6000 (Illumina) system and sequences of paired 150-bp were obtained.Raw reads of sequencing were processed by FastQC (version 0.11.9) for quality control. Meanwhile, Q30, GC-content, and sequence duplication levels were calculated. High-quality clean reads were mapped to the sunflower reference genome(GeneBank NO. GCA_002127325. 2)  using Hi2(Fold Changes)| ≥ 1 was considered to be DEGs.The alignment SAM files were converted to BAM format using Samtools (version 1.11), The processed BAM files were further processed with StringTie software(2.1.4) . Expresshttp://revigo.irb.hr/) was used to remove redundant GO-terms [Gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis were performed to reveal the biological functions of genes and pathways of DEGs by ClusterProfiler(version 4.0.0) R-package . Fasta fGO-terms . The iTAGO-terms .WGCNA analysis  was condhttps://www.sangon.com/newPrimerDesign), and were synthesized by Shenggong Inc. The detail of primers was shown in the -△△Ct [To verify the RNA-seq results, we randomly selected 10 DEGs for Quantitative reverse transcription PCR(RT-qPCR) analysis. Total RNA of 24 samples was isolated from leaves by Trizol reagent  following the protocol. The integrity of RNA was confirmed by agarose gel electrophoresis with 4S Green Plus  staining of 5S, 18S, and 28S RNA. Samples that had an A260/280 ratio of 1.8–2.0 and A260/A230 ratio of 2–2.5 were considered acceptable, Reverse transcription was performed using standard procedures of the BiomarkerScript II 1st Strand cDNA Synthesis Kit (Biomarker). RT-qPCR analysis was performed in FTC-3000TM real-time quantitative thermal cycler  using a Biomarker 2X SYBR Green Fast qPCR Mix . Gene-specific primers were designed using a free online primer design tool  and all data were presented as the mean ± SD (n = 3). The data were analyzed by one-way analysis of variance (ANOVA). Means were compared by the Tukey’s honestly significant difference (Tukey’s HSD) method at the p<0. 05. The bar graphs were drawn by Graphpad Prism (v8.0.2).The LSA of both varieties decreased in the early stage (day 7) of drought stress, and a subsequent increase in the later stage, while the rate and magnitude of the increase were greater in the DT than in DS. Sustained drought stress resulted in a reduction in RWC, and DS decreased more rapidly than DT. The REC, CAT, POD, and Pro were increased with the drought stress time, while a bigger level of increase was observed in DS than in DT . A similA total of 193.33 Gb clean data were obtained after quality control. The Q30 value of each library ranged from 93.57% to 94.97%, and the GC content ranged from 44.82% to 45.85%. The mapping ratio ranged from 85.71% to 92.48%, of which 75.1% to 81.31% were uniquely mapped. Details of transcriptome sequencing and alignment with the reference genome were shown in To assess the correlations of the 24 samples, we then conducted a clustering analysis. The transcriptome data of three biological replicates from each drought stress time-point exhibited a good correlation . Then, tA total of 24,234 DEGs were obtained at three drought stress time points for two varieties, including 11,483 in DS and 18,922 in DT .The number of down-regulated genes was higher than up-regulated genes at the same drought stress time . Up-reguTo reveal the functional differences of DEGs, GO enrichment analysis was carried out using the 24,234 DEGs. The GO terms were subdivided into three categories: biological process (BP), cellular component (CC), and molecular functions (MF)  S4 Tabl.To make the results more concise, we compared the number of genes enriched in the common GO-term across varieties, and only the most significant BP GO-terms were analyzed.For up-regulated DEGs, somatic embryogenesis (GO:0010262) was the only common GO-terms at 7 day. At 14 day, five common GO-terms  were all related to gibberellin, and the number of genes enriched to the same GO-terms in DT was higher than that in DS. However, the opposite was observed at day 21, when the number of genes enriched to the common GO terms was higher for DS than for DT, and a total of 22 common GO-terms were enriched at 21 day under drought stress, most of them were related to rRNA and snRNA, such as rRNA processing (GO:0006364), endonucleolytic cleavage involved in rRNA processing (GO:0000478), and snRNA modification (GO:0040031). For down-regulated DEGs, there were 15,33, and 18 common GO-terms enriched at day 7, 14, and 21, respectively. DEGs at 7 day were mainly enriched in cell wall , microtubule organization , and auxin signal-related  GO-terms. On day 14, the down-regulated genes were mainly enriched in photosynthesis , sugar synthesis/metabolism  related GO-terms. Among the top 10 go-terms enriched at day 21, 4 of them were also detected at day 14 , and the GO-terms enriched in this period were mainly processes related to sugar metabolism  and terpene metabolism  , indicatKEGG enrichment analysis was conducted to identify pathways for these DEGs. . We compOverall, the number of up-regulated genes was less than that of down-regulated genes, so fewer pathways were enriched. In addition, DT enriched more genes in the same metabolic pathway than DS on days 7 and 14, while the reverse was found on days 21.For up-regulated DEGs, GABAergic synapse pathway was enriched at both day 7 and day 14. In addition to this, on day 14, genes were also enriched to the MAPK signaling pathway, Valine, leucine, and isoleucine degradation, while Ribosome biogenesis in eukaryotes was the only common pathway enriched by up-regulated DEGs at day 21.For down-regulated DEGs, there were 12, 26, and 15 common pathways were enriched on days 7, 14, and 21, respectively, some of which were already reported to be drought-related pathways. Major pathways on day 7 were Amino sugar and nucleotide sugar metabolism, Starch and sucrose metabolism, ABC transporters, and Terpenoid backbone biosynthesis, while on day 14, more photosynthesis-related pathways were obtained, such as Photosynthesis proteins, Photosynthesis, and Photosynthesis- antenna proteins. The top pathways on day 21 were Monoterpenoid biosynthesis, Sesquiterpenoid and triterpenoid biosynthesis and alpha-Linolenic acid metabolism.Notably, among the top 10 pathways, 2 pathways , were enriched at 3 time points simultaneously, and 3 pathways  were enriched at both 14 and 21 day. These pathways may be closely related to the drought resistance of sunflowers.TFs play a key role in plant response to abiotic stress. A total of 1,311 presumed TFs were identified in the present study from all 24,234 DEGs , among wThe total number and the proportion of up/down-regulated genes in each TF family among different varieties and drought stress times were demonstrated in A large number of TFs genes were expressed on days 7 and 14 in DT, especially on day 14, when the proportion of TFs ranged from 30.4% (HB-HD-ZIP) to 53.3% (HSF) of the total number. In addition, genes belonging to MYB, HB-HD-ZIP, and bHLH families had higher down-regulation rates in both varieties. The down-regulation rate of the MYB transcription factor was 96.43% and 100% in DS7 and DT21, respectively. The down-regulation rate of HB-HD-ZIP ranged from 60.00% in DT21 to 81.77% in DS7, while the down-regulation rate of the bHLH transcription factor ranged from 60.00% in DS21 to 83.91% in DT14. Meanwhile, genes belonging to the bZIP, WRKY, AP/ERF, NAC, and HSF TFs families had a relatively high up-regulation rates, especially in DT14, when both the total number and the up-regulation rate reached the highest level. A total of 56, 68, 74, 78, and 24 genes belonging to bZIP, WRKY, AP/ERF, NAC, and HSF families were identified in DT14, with up-regulation rates of 69.64%, 88.24%, 52.70%, 78.21%, and 87.50%, respectively.MapMan was used to provide an overview of the DEGs at the metabolic level. The "metabolic overview" panel provides metabolic overview, which is divided into CHO metabolism, lipids metabolism, secondary metabolism, amino acids, while the “drought stress” panel showed in detail the expression profile of DEGs related to hormone signaling, TFs, and redox state under drought stress. In general, the results of Mapman analysis, such as metabolism profile of “cell wall”, “terpen”, “starch and sucrose” and transcript factors were in good consistency with the results of GO, KEGG, and TFs analysis, which proved the reliability of our results.In addition, Mapman revealed that the most significant differences in gene number and expression level were observed at 14-days of drought stress, so our analysis focused on the results at day 14 Figs  and S5. There were 129, 64, 58, 99, 21, 22, and 45 genes identified in DT that belonged to Auxin, Br, ABA, ethylene, SA, JA and gibberellins, while 27, 24, 21, 22, 14, 26, and 17 genes belonged to the above seven phytohormones in DS, respectively. It can be seen that the number of DS is lower than that of DT, except for JA. In addition, we found that the proportion of up/down-regulated genes in JA and SA were significantly different between the two varieties, with 19% of the SA genes up-regulated in DT and all of these genes down-regulated in DS; the proportion of up-regulated JA genes in DT was 45.45%, while in DS it was only 3.85%.−4), while lightslateblue modules  positively associated with the REC, CAT, POD, Pro, and MDA (−8), 0.57(p = 4 × 10−3), 0.81(p = 3× 10−6), 0.82(p = 2 × 10−6) and 0.6(p = 2 × 10−3), respectively. This phenomenon may indicate possible correlations between genes that determine different drought-resistant traits.All 24,234 DEGs were retained for WGCNA unsigned co-expression network analysis. After clustering the samples, an outlier (DS14C) was removed in subsequent analysis . The sof and MDA , with coGenes in the blue 4 module were enriched in 20 GO-terms, after de-redundancy, 15 GO-terms were obtained, of which 11 in BP and 4 in MF. The top three significant GO-terms ranked by p-value for the BP were GO:0016036(cellular response to phosphate starvation), GO:0006664(glycolipid metabolic process), and GO:1903509(liposaccharide metabolic process). Genes in the lightslateblue module were enriched in 65 de-redundancy GO-term, including 30 in BP, 17 in CC, and 18 in MF. The top three significant GO-terms for the BP were GO:0006364 (rRNA processing), GO:0002181 (cytoplasmic translation), and GO:0071826 (ribonucleoprotein complex subunit organization) .Pathway analysis revealed that genes in the blue4 module were enriched in glycerolipid metabolism, vitamin B6 metabolism, and glycerophospholipid metabolism, while in lightslateblue module, genes were enriched in ribosome biogenesis in eukaryotes and translation factors .The top 10 hub genes in each module were identified via the cytoHubba plug-in , Table 2r2) of 0. 8431 and 0. 8173 in DS and DT, respectively, endorsing our RNA-seq data were reliable , hydrogen peroxide (H2O2), and hydroxyl radicals(·OH), is a important class of signaling molecules that maintain relative balance in the plant under normal conditions [+ in the electron transport chain, and a large number of electrons leak to O2, generating excessive ROS [2- to H2O2 through dismutation reaction, and then H2O2 is finally eliminated by POD and CAT. Our results showed that two antioxidant enzymes  and MDA increased with the continuation of drought stress, and the enzyme activities were higher in DS than DT at different time points. indicating that DS suffered more oxidative damage, while SOD decreased at day 21, which may indicate a decrease in O2- production at day 21.Reactive oxygen varieties(ROS), including singlet oxygen  compared to Pro [In the present study, as drought stress sustained, RWC continued to decrease, and DT was higher than DS at different time points, indicating that DT maintained a higher cell turgor. The Pro content continued to increase, and it is slightly higher in DS than in DT at the same time. While in the early stage of drought stress, SS of both varieties decreased significantly, then gradually increased, and DS was higher than DT at day 21, indicating that DS was still affected by intense stress at day 21. Al Hakimi A. et al. suggested that SS content can more accurately identify drought tolerance in durum wheat , sucrose and starch metabolism, Terpene biosynthesis, and Photosynthesis and Carbon fixation.GABA plays an important role in the response to abiotic stresses through ion channel regulation . ExogenoAegilops tauschii [Plants mitigate the effects of drought stress by regulating the expression of carbohydrate-related genes , and suctauschii  and maiztauschii . A previtauschii . In thisCarbon accumulated under drought conditions also promotes the synthesis of secondary metabolites, and terpene accumulation is involved in many functions in growth, development, and resistance to environmental stresses , and TerSimilar to the results of GO analysis, multiple photosynthesis-related pathways were enriched by down-regulated genes at day 14, Carbon fixation in photosynthetic organism pathway enriched by down-regulated DEGs in at least 2 time points simultaneously. These finding give additional evidence of the inhibition of photosynthesis at mid-period under drought stress.TFs as key regulators of transcription important in plant responses to drought stress. A large number of TFs were observed by iTAK in two inbred lines belonging to bHLH, AP2/ERF-ERF, MYB, NAC, and WRKY families.The AP2/ERF TFs family is one of the largest plant-specific TFs families that share a well-conserved DNA-binding domain –82. A loOsMYB4 genes showed improved tolerance to drought stress by stimulating the expression of MYB TFs [The proteins of MYC/MYB families are found in both plants and animals with varied functions ,87. Tran MYB TFs . In thisWRKY proteins have been extensively studied for their important regulatory roles in plant defense and disease resistance . WRKY3  and WRKYHabHLH159 and HabHLH024 genes showed high expression under drought stress [bHLH are widely distributed in all eukaryotes and are one of the largest families of TFs, playing a crucial role in plant growth, development, and stress response ,94. A prt stress . Anothert stress . HoweverA recent study by Li et al.  identifiPhytohormones, including auxin, ABA, ethylene, JA, SA, Br, and gibberellins, play an important role in drought resistance by influencing the physiological processes of plants ,97. ManyABA is one of the main plant hormones directly involved in drought stress response  and has 2+ and NO signaling systems [Ethylene induces stomatal closure through Ca systems  to reduc systems –108. Aux systems . A study systems . Our resJA and its conjugates, such as methyl jasmonate (MeJA) and jasmonoyl-isoleucine (JA-Ile), collectively known as jasmonates (JAs). JAs are associated with the closure of stomata , and alsWGCNA is a progressive analysis method in which variable genes are divided into co-expression modules through an unsigned network based on DEGs . Each moPathway analysis showed genes in blue 4 module enriched in glycerolipid metabolism and Glycerophospholipid metabolism, two in the top ten genes ranked by cytoHubba plug-in were annotated Monogalactosyldiacylglycerol (MGDG) synthase. Glycerolipids, including phospholipids (PLs) and glycolipids (GLs), are the most abundant lipids in plants and are involved in responses and tolerance to abiotic conditions such as drought, heat, and low temperature ,115. ChmThe maintenance of inorganic phosphate homeostasis is essential for plant growth and yield . GO analThe PK family involves many signaling pathways that are triggered during stress and development processes . Among tTriticum aestivum L.) leaves induced by H2S under drought stress according to H Li et al [Although genes in lightslateblue module were far more than in blue 4, but only two KEGG pathways were enriched, and the “Ribosome biogenesis in eukaryotes” pathway was the most significant. CytoHubba analysis showed that the top 10 genes all encoded ribosomal proteins. Up-regulated genes were enriched in the KEGG pathway of ‘ribosome biogenesis in eukaryotes’ in wheatClick here for additional data file.S2 Fig(TIF)Click here for additional data file.S3 Fig(TIF)Click here for additional data file.S4 Fig(TIF)Click here for additional data file.S5 Fig(TIF)Click here for additional data file.S6 Fig(TIF)Click here for additional data file.S7 Fig(TIF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.S6 Table(XLSX)Click here for additional data file.S7 Table(XLSX)Click here for additional data file.S8 Table(XLSX)Click here for additional data file.S9 Table(XLSX)Click here for additional data file.S10 Table(XLSX)Click here for additional data file.


The capacity of T cells to identify and kill cancer cells has become a central pillar of immune-based cancer therapies. However, T cells are characterized by a dysfunctional state in most tumours. A major obstacle for proper T-cell function is the metabolic constraints posed by the tumour microenvironment (TME). In the TME, T cells compete with cancer cells for macronutrients  and micronutrients . While the role of macronutrients in T-cell activation and function is well characterized, the contribution of micronutrients and especially ions in anti-tumour T-cell activities is still under investigation. Notably, ions are important for most of the signalling pathways regulating T-cell anti-tumour function. In this review, we discuss the role of six biologically relevant ions in T-cell function and in anti-tumour immunity, elucidating potential strategies to adopt to improve immunotherapy via modulation of ion metabolism. T lymphocytes undergo a metabolic reprogramming upon TCR-stimulation, which sustains the biosynthetic requirements of clonal expansion and differentiation. Indeed, the engagement of specific metabolic pathways requires the presence of particular metabolites that are not only necessary to promote the synthesis of ATP and macromolecules but also to mediate signalling regulation of T-cell function and fate ,2,3. TheThe role of glucose, amino acids, and lipids in the regulation of T-cell responses against cancer has been studied and reviewed extensively elsewhere ,12,13,14+) is the most abundant ion in mammalian cells, with intracellular K+ levels ([K+]i) reaching ~130 mM, while extracellular levels [K+]e are ~3–5 mM  ([K+]e) is not directly caused by membrane-potential variations or Ca2+ signalling alterations but is rather due to an increase in intracellular [K+]i, which affects the Akt-mTOR pathway , suggesting that K+ might not only be involved in the regulation of anti-tumour immunity but also in the adaptation of cancer-cell metabolism in the TME. Altogether, these studies support the concept that K+ acts as a suppressive element of anti-tumour immunity. However, a more recent report by Vodnala et al. (2019) showed that despite dampening T-cell effector functions, mTOR inactivation derived from high [K+]e is accompanied by a decreased nutrient uptake, which initiates a starvation response. The authors define this state as ‘functional caloric restriction’, characterised by autophagy induction and acetyl-CoA-dependent epigenetic remodelling (+]e reduced the acetylation of effector/exhaustion-associated loci of genes such as Pdcd1 (PD1), Cd244 (2B4), and Havcr2 (Tim-3) while preserving T-cell stemness through the induction of TCF1 expression. Consequently, T cells exposed to high [K+]e during in vitro expansion enhanced T-cell persistence and anti-tumour response upon adoptive cell transfer in a B16 melanoma mouse model .,18.+, whd KCa3.1 , suggestionality ,30,31. Modelling . Specifise model . On the B, Tbet) . Althoug2+) is one of the most abundant metals found in the tissues of mammals, and it is crucial for intracellular processes regulating energy production, development, antioxidant defence and immune response . In. In2+ isoduction . Howeverturation . As a co of TILs ,42,43. Iresponse ,45. Indevaccines  41,46].,46.2+ is2+) is the second most abundant trace metal in the human body after iron. It is an essential component of several proteins , le, le2+) i as IL-2 . Similartivation ,62. Whilin vitro  and in tin vitro . Notablygression .2+ homeostasis in T-cell differentiation and exhaustion within the TME. The evidence gathered so far places Zn2+ metabolism as a potential target to dampen the immunosuppressive mechanism adopted by cancer cells. However, how Zn2+ acts as an immunosuppressive factor and which zinc-dependent proteins are involved in the process has yet to be defined.Finally, in the B16F10 murine melanoma model, it has been observed that TILs upregulate metallothieins and zinc-finger transcription factors, such as GATA-3 and IKZF2  66], in, in66], 2−) is taken up through the diet in either organic forms, seleno-L-methionine (SeMet) and seleno-L-cysteine (SeCys), or as inorganic forms, selenide and selenite, which are all ultimately metabolized within mammalian cells into SeCys. Indeed, SeCys, also known as the 21st amino acid, is an essential element of selenoprotein catalytic sites Sec and described that loss of selenoprotein synthesis in T cells leads to ROS hyperproduction and suppression of T-cell expansion after TCR stimulation i), most of it is complexed to ATP or bonded to other molecules functioning as a cofactor. In T cells, [Mg2+]i levels are finely regulated by the ion channels MAGT1, TRPM7, mediating Mg2+ influx, and SLC41A1, mediating Mg2+ efflux through Na+ exchange (Magnesium (Mgexchange  76]..2+) is t2+ influx, which acts as second messenger in TCR signalling  conditions  . On. On2+ ineration) ,78,80. Ieration) ,82. In Xnfection ,82,83.2+ is important for the stabilisation of DNA structure and operates as a cofactor for enzymes involved in DNA repair, suggesting that Mg2+ deprivation might lead to accumulation of DNA damage and carcinogenesis. Accordingly, low Mg2+ intake is associated with higher risk of pancreatic, lung, and breast cancer [+ T cells in hepatitis B virus (HBV)-infected patients show a decline in [Mg2+]i and MAGT1 expression associated with PD-1 upregulation and loss of NKG2D . On. On2+) ificiency . Further T cells . Notablyogenesis .2+ in an inflammatory context. In autoinflammatory diseases, iron deposition is frequently observed. According to Wang et al., Fe2+ promotes proinflammatory cytokine production in immune cells, including T cells [2+ is released by tumour-associated macrophages (TAMs) and tumour-associated neutrophils (TANs) in the TME. In this scenario, Fe2+ might sustain TAMs and TANs in supporting cancer progression and impairing T and B cell activity by inducing cell death. Fe2+ has been involved in the induction of ferroptosis by mechanisms that are still poorly understood [2+ secretion by TAMs and TANs is not directly proven, it is likely that high Fe2+ levels may contribute to the induction of ferroptosis in T cells and cancer cells. Furthermore, TAMs and TANs can also impair proper APC maturation and antigen presentation [2+ concentration in the tumour microenvironment could be a promising approach to improve current therapies [A recent report revealed a role of Fe T cells . On the derstood . Althougentation ,102. In herapies .Many clinical trials have demonstrated therapeutic efficacy of T-cell based immunotherapy, which exploits the capacity of T cells to recognize and kill a specific target, including cancer cells . While i


Unfortunately, platinum resistance develops in a significant number of patients and is a determinant of clinical outcome. Extensive research has been conducted to understand and overcome platinum resistance, and mechanisms of resistance can be categorized into several broad biological processes, including (1) regulation of drug entry, exit, accumulation, sequestration, and detoxification, (2) enhanced repair and tolerance of platinum-induced DNA damage, (3) alterations in cell survival pathways, (4) alterations in pleiotropic processes and pathways, and (5) changes in the tumor microenvironment. As a resource to the cancer research community, we provide a comprehensive overview accompanied by a manually curated database of the >900 genes/proteins that have been associated with platinum resistance over the last 30 years of literature. The database is annotated with possible pathways through which the curated genes are related to platinum resistance, types of evidence, and hyperlinks to literature sources. The searchable, downloadable database is available online at  The DSeveral excellent reviews have been published covering the topic of platinum resistance –4, althoSLC31A1/CTR1, SLC22A1/OCT1, SLC22A2/OCT2, and SLC22A3/OCT3) can lead to platinum resistance (Supplementary Table RAB5C or TFRC) are also associated with platinum resistance , result in platinum resistance [In addition to blocking entry, enhanced drug efflux can lead to cisplatin resistance. Two copper exporters, P-type ATPases encoded by n export  and incrsistance . Elevatesistance .GCLC and GCLM) and glutathione synthase (encoded by GSS) [GCLC, GSTA1, and GSTP1, are associated with platinum resistance in cell lines; and correlations between platinum resistance and elevated levels of GSTP1 were found in cancer patient samples, which correlated with poor survival  are correlated with reduced survival in patients receiving platinum-based therapy  and metallothioneins, which avidly bind and inactivate platinum drugs. GSH is synthesized in a two-step process requiring glutamate cysteine ligase (encoded by  by GSS) . Once sy by GSS) . IncreasThe main cytotoxic effect of platinum is due to the formation of DNA adducts leading to a DNA damage response (DDR) that ultimately results in apoptosis. Cancer cells have developed multiple mechanisms to thwart this response by blocking the DDR at multiple levels.MLH1, MSH2, and MSH6 are all correlated with increased platinum resistance in cell lines and patients of some cancer types  proteins  . These pPlatinum adducts result in DNA intrastrand and interstrand crosslinks (ICL), which result in activation of the DDR. ICL repair involves parts of nuclear excision repair (NER), homologous repair (HR), translesion synthesis (TLS), and Fanconi anemia (FA) proteins.ERCC1 and ERCC4/XPF is associated with cisplatin resistance in ovarian cancer cells, while knockdown of ERCC1 enhanced cellular sensitivity to cisplatin [ERCC1, ERCC2/XPD, ERCC3/XPB, ERCC4/XPF, ERCC5/XPG, ERCC6, ERCC8, and XPA are prognostic for favorable response to platinum , which require HR or NHEJ for repair. HR-defective (HRD) cancers are often more sensitive to platinum than their HR-proficient counterparts. Two critical components of the HR system are encoded by  cancers  and BRCA outcome . Over tiunctions . In addisitivity , and higc cancer . Furtherr [BRCA1 . Somaticplatinum . Unlike platinum . AlteredPOLH, POLI, POLK, REV1, as well as REV3L/POLZ and MAD2L2/REV7, and increased expression of these genes is correlated with platinum resistance [POLH is associated with cisplatin resistance in lung and bladder cancer  or nucleosome remodeling factor CHD4 restored cisplatin resistance in BRCA2-deficient B lymphocytes and an ovarian cancer cell line via inhibition of recruitment of MRE11A and diminished degradation of replication forks, independent of HR [RADX was found to antagonize the fork-stabilizing activity of BRCA2 and RAD51. Like PAXIP1 and CHD4, loss of RADX restores fork protection and cisplatin resistance to BRCA2-depleted cells without restoring HR [HROB) interacts with RPA1 and MCM8/9 to facilitate HR and replication fork progression. Loss of HROB resulted in cisplatin sensitivity, slower replication fork progression, and increased fork stalling in response to cisplatin [BRCA2 mutated ovarian cancers with reduced PAXIP1 or CHD4 expression are associated with shorter progression-free survival and shorter overall survival [Besides their role in HR, y MRE11A . Knockdont of HR , 28. Mororing HR . On the isplatin . Consistsurvival , 28. Fursurvival . TherefoUNG/UNG1 and POLB is negatively associated with platinum resistance; (2) activity of FEN1, LIG3, and XRCC1 are positively correlated with platinum resistance; and (3) APEX1 and MUTYH are either positively or negatively associated with platinum resistance, depending on cell context (Supplementary Table The relationship between BER and platinum resistance is complicated: (1) activity of CDKN1A/p21Cip, CDKN1B/p27Kip1, and CDKN1C/p57Kip2 [Cip have been associated with increased platinum resistance [CDKN2A/p16INK4a, where decreased levels can result in platinum resistance, while in other cases, result in platinum sensitivity  patients  [In healthy cells, reactive oxygen species (ROS) are formed during the process of aerobic metabolism and are maintained at low levels. In cancer cells, oxidative stress leads to elevated ROS levels. Platinum therapy increases ROS levels, mostly via the mitochondria . SeveralD1/TrxR1 , and oth1 [MNSOD , 45. Nor1 [MNSOD . Cancer 3, GPX4) .G6PD and PGD, the Pentose Phosphate Pathway (PPP) enzymes required for NADPH production, are present in cisplatin-resistant ovarian cancer cell lines, and knockdown of either gene sensitizes cisplatin-resistant cells  and Aldehyde dehydrogenases , were found to be associated with cisplatin resistance in various types of cancer patients including gastrointestinal, ovarian, bladder, NSCLC, and cervical cancer  that tags HIFs for degradation is linked to platinum resistance in renal cancer  are positively correlated with platinum resistance (Supplementary Table Platinum therapy results in endoplasmic reticulum (ER) stress, which triggers the unfolded protein response (UPR) due to the accumulation of misfolded proteins and disturbances in redox regulation . To mainMetabolic reprogramming is an established hallmark of cancer. The Warburg effect was first discovered as a feature of metabolic reprogramming in cancer cells, whereby cancer cells have increased glucose uptake, hyperactivated glycolysis, decreased oxidative phosphorylation (OXPHOS), and the accumulation of lactate, even in the presence of abundant oxygen and functioning mitochondria . AlthougSLC2A1/GLUT1, HK2, ENO1, PGK1, PDK1, PDK4, and PFKFB3, was found to correlate with resistance in some cancer cell lines and clinical tissue samples [There are reports supporting the role of enhanced aerobic glycolysis in promoting platinum resistance . Convers samples   are found to be correlated with platinum resistance in cancer patients of various types  phenotypes, which are linked to cancer progression and treatment resistance. Several studies support the hypothesis that CSCs are responsible for chemoresistance and tumor relapse after conventional chemotherapy removes the bulk population of non-CSCs , 97. MulMYC is common [MYC is associated with platinum resistance in ovarian cancer [MYC promotes platinum resistance mainly through transactivation of a broad range of genes that drive glucose metabolism, glutamine metabolism, one carbon metabolism, fatty acid synthesis, oxidative phosphorylation, nucleotide synthesis, and protein biogenesis, which results in increased cell survival and proliferation [MYC promotes glutamine import by directly inducing the expression of key glutamine transporters SLC7A5, SLC1A5, and GLS [SHMT2), which results in elevated NADPH [NFE2L2/NRF, a master transcription factor regulating ROS-detoxifying enzymes [In human ovarian tumors, amplification of s common , 99, andn cancer . MYC proferation . For exa and GLS  and it i and GLS . The mec and GLS , 103. Myed NADPH , and by  enzymes .NFKB1, NFKB2, RELA, RELB, and REL) [CHUK/IKKα and IKBKB/IKKβ [TRAF1, TRAF2, BIRC2/cIAP1, BIRC3/cIAP2, XIAP, BCL2A1/Blf/A1, BCL2L1/Bcl-XL, and CFLAR/FLIP [NQO1, SOD1, and SOD2 [Another well-known transcription factor complex that promotes cancer cell survival is nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB), a family of transcription factors constituted by dimers of different combinations of 5 proteins sharing structural homology (and REL) . Higher and REL) . InteresBKB/IKKβ . MechaniLAR/FLIP , 109, asand SOD2 . NFκB aland SOD2 , which aERBB2/HER2/NEU, which activates the PI3K/Akt pathway, is associated with platinum resistance in ovarian, NSCLC, and HNSCC cancer patients (Supplementary Table FOS and JUN), and overexpression of these genes are associated with platinum resistance, while downregulation re-sensitizes tumor cells to platinum [Receptor tyrosine kinase (RTK) signaling triggers cell growth and blocks apoptosis, enhancing cancer cell survival and proliferation in the presence of platinum and other anti-cancer drugs , 113. Maplatinum   on cells are primarily mediated by integrins, a family of cell surface receptors that attach cells to the matrix and trigger signal transduction . Alteratsistance ; high exsistance , and higsistance . Some ofTumor-promoting chronic inflammation leads to an innate immune response that promotes cancer development and progression and can contribute to platinum resistance . ActivatTNF/TNFA expression enhances cisplatin resistance in cell lines, and elevated expression is associated with poor patient outcome  [HSP70 and HMOX1/HO-1 [Other platinum resistance mechanisms induced by the innate immune response include upregulation of the AP1 oncogenes (and JUN) , upregulOX1/HO-1 , 132, inOX1/HO-1 , and actOX1/HO-1 .The accompanying gene table  restoration of DDR via a mutation ; b) alteon [EZH2 ; c) acti2 [HIF1A ; d) acti2 [HIF1A ; e) inhi2 [HIF1A ; and f) se HDAC4 . Clonal se HDAC4 . This muMYC promotes platinum resistance through activation of a broad range of genes that promote proliferation, redox balance, and energy generation. However, MYC is also implicated in platinum-induced p53 mediated apoptosis [MYC is associated with platinum resistance in TP53 mutant ovarian cancer [CHEK2, serves as another example. In some ovarian cancer cell lines, the cell cycle checkpoint and DDR functions of CHEK2 causes increased resistance to cisplatin [CHEK2 is associated with favorable response to cisplatin-based therapy [TXN) is associated with lower ROS and decreased cisplatin-resistance in a lung cancer cell line [TXN is associated with an increased resistance to cisplatin in other cell lines [Further confounding our ability to therapeutically target mechanisms of platinum resistance is that specific mechanisms can be context dependent. For example, upregulation of poptosis . While hn cancer , 100, thn cancer . The celisplatin . However therapy , 146. Th therapy  and, the therapy , while d therapy . However therapy , 133. Foell line . In contll lines , 149. ThPlatinum drugs are effective anticancer drugs used for treatment of epithelial neoplasms. Unfortunately, in a large number of cases, tumors are able to subvert the cytotoxic effects of platinum, resulting in platinum resistance and cancer mortality. Here, we have reviewed the evidence supporting the hypothesis that a large number of genes can contribute to platinum resistance either directly or indirectly. We also provide a manually annotated database of these genes that can be incorporated into large-scale omics analyses to facilitate development of therapies aimed at overcoming platinum resistance.Table S1Table S2Table S3pt_resistance_mechanisms.gmt