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Zhu W, Liu C, Xi K, Li A, Shen LA, Li Y, Jia M, He Y, Chen G, Liu C, Chen Y, Chen K, Sun F, Zhang D, Duan C, Wang H, Wang D, Zhao Y, Meng X, Zhu D. Discovery of Novel 1-Phenylpiperidine Urea-Containing Derivatives Inhibiting β-Catenin/BCL9 Interaction and Exerting Antitumor Efficacy through the Activation of Antigen Presentation of cDC1 Cells. J Med Chem 2024. [PMID: 38912577 DOI: 10.1021/acs.jmedchem.3c02079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Aberrant activation of the Wnt/β-catenin signaling is associated with tumor development, and blocking β-catenin/BCL9 is a novel strategy for oncogenic Wnt/β-catenin signaling. Herein, we presented two novel β-catenin variations and exposed conformational dynamics in several β-catenin crystal structures at the BCL9 binding site. Furthermore, we identified a class of novel urea-containing compounds targeting β-catenin/BCL9 interaction. Notably, the binding modalities of inhibitors were greatly affected by the conformational dynamics of β-catenin. Among them, 28 had a strong affinity for β-catenin (Kd = 82 nM), the most potent inhibitor reported. In addition, 13 and 35 not only activate T cells but also promote the antigen presentation of cDC1, showing robust antitumor efficacy in the CT26 model. Collectively, our study demonstrated a series of potent small-molecule inhibitors targeting β-catenin/BCL9, which can enhance antigen presentation and activate cDC1 cells, delivering a potential strategy for boosting innate and adaptive immunity to overcome immunotherapy resistance.
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Affiliation(s)
- Wenhua Zhu
- Anhui University of Chinese Medicine, Hefei 230012, China
- Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong 226133, China
| | - Cuiting Liu
- Anhui University of Chinese Medicine, Hefei 230012, China
- Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong 226133, China
| | - Kang Xi
- Anhui University of Chinese Medicine, Hefei 230012, China
- Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong 226133, China
| | - Anqi Li
- School of Basic Medical Sciences, Fudan University, Shanghai 201210, China
| | - Li-An Shen
- School of Basic Medical Sciences, Fudan University, Shanghai 201210, China
| | - Yana Li
- Anhui University of Chinese Medicine, Hefei 230012, China
- Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong 226133, China
| | - Miaomiao Jia
- Anhui University of Chinese Medicine, Hefei 230012, China
- Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong 226133, China
| | - Yangbo He
- Anhui University of Chinese Medicine, Hefei 230012, China
- Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong 226133, China
| | - Gang Chen
- Anhui University of Chinese Medicine, Hefei 230012, China
- Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong 226133, China
| | - Chenglong Liu
- School of Basic Medical Sciences, Fudan University, Shanghai 201210, China
| | - Yangqiang Chen
- Anhui University of Chinese Medicine, Hefei 230012, China
- Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong 226133, China
| | - Kai Chen
- Shanghai Jiao Tong University, Shanghai 201210, China
| | - Fan Sun
- Shanghai Jiao Tong University, Shanghai 201210, China
| | - Daizhou Zhang
- Shandong Academy of Pharmaceutical Science, Jinan 250101, China
| | - Chonggang Duan
- Shandong Academy of Pharmaceutical Science, Jinan 250101, China
| | - Heng Wang
- School of Basic Medical Sciences, Fudan University, Shanghai 201210, China
| | | | - Yujun Zhao
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd., Shanghai 201203, China
| | - Xiangjing Meng
- Shandong Academy of Pharmaceutical Science, Jinan 250101, China
| | - Di Zhu
- School of Basic Medical Sciences, Fudan University, Shanghai 201210, China
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Dakal TC, George N, Xu C, Suravajhala P, Kumar A. Predictive and Prognostic Relevance of Tumor-Infiltrating Immune Cells: Tailoring Personalized Treatments against Different Cancer Types. Cancers (Basel) 2024; 16:1626. [PMID: 38730579 PMCID: PMC11082991 DOI: 10.3390/cancers16091626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
TIICs are critical components of the TME and are used to estimate prognostic and treatment responses in many malignancies. TIICs in the tumor microenvironment are assessed and quantified by categorizing immune cells into three subtypes: CD66b+ tumor-associated neutrophils (TANs), FoxP3+ regulatory T cells (Tregs), and CD163+ tumor-associated macrophages (TAMs). In addition, many cancers have tumor-infiltrating M1 and M2 macrophages, neutrophils (Neu), CD4+ T cells (T-helper), CD8+ T cells (T-cytotoxic), eosinophils, and mast cells. A variety of clinical treatments have linked tumor immune cell infiltration (ICI) to immunotherapy receptivity and prognosis. To improve the therapeutic effectiveness of immune-modulating drugs in a wider cancer patient population, immune cells and their interactions in the TME must be better understood. This study examines the clinicopathological effects of TIICs in overcoming tumor-mediated immunosuppression to boost antitumor immune responses and improve cancer prognosis. We successfully analyzed the predictive and prognostic usefulness of TIICs alongside TMB and ICI scores to identify cancer's varied immune landscapes. Traditionally, immune cell infiltration was quantified using flow cytometry, immunohistochemistry, gene set enrichment analysis (GSEA), CIBERSORT, ESTIMATE, and other platforms that use integrated immune gene sets from previously published studies. We have also thoroughly examined traditional limitations and newly created unsupervised clustering and deconvolution techniques (SpatialVizScore and ProTICS). These methods predict patient outcomes and treatment responses better. These models may also identify individuals who may benefit more from adjuvant or neoadjuvant treatment. Overall, we think that the significant contribution of TIICs in cancer will greatly benefit postoperative follow-up, therapy, interventions, and informed choices on customized cancer medicines.
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Affiliation(s)
- Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur 313001, Rajasthan, India
| | - Nancy George
- Department of Biotechnology, Chandigarh University, Mohali 140413, Punjab, India;
| | - Caiming Xu
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of the City of Hope, Monrovia, CA 91010, USA;
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O. 690525, Kerala, India;
| | - Abhishek Kumar
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
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Xu X, Xu Z, Yang B, Yi K, He F, Sun A, Li J, Luo Y, Wang J. Assessing the Effects of Dietary Cadmium Exposure on the Gastrointestinal Tract of Beef Cattle via Microbiota and Transcriptome Profile. Animals (Basel) 2023; 13:3104. [PMID: 37835710 PMCID: PMC10571678 DOI: 10.3390/ani13193104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Cadmium (Cd) is an environmental pollutant, widely existing in soil, and can be absorbed and accumulated by plants. Hunan Province exhibits the worst cadmium contamination of farmland in China. Ruminants possess an abundant microbial population in the rumen, which enables them to tolerate various poisonous plants. To investigate whether the rumen microbiota could respond to Cd and mitigate the toxicity of Cd-accumulated maize to ruminants, 6-month-old cattle were fed with 85.82% (fresh basis) normal whole-plant maize silage diet (CON, n = 10) or Cd-accumulated whole-plant maize silage diet (CAM, n = 10) for 107 days. When compared to the CON cattle, CAM cattle showed significantly higher gain-to-feed ratio and an increased total bacterial population in the rumen, but a decreased total bacterial population in the colon. CAM cattle had higher relative abundance of Prevotella and Lachnospiraceae ND3007 group in the rumen, and Lachnospiraceae NK4A136 group and Clostridia vadinBB60 group in the colon. Notably, microbial correlations were enhanced in all segments of CAM cattle, especially Peptostreptococcaceae in the jejunum. Transcriptome analysis revealed down-regulation of several immune-related genes in the rumen of CAM cattle, and differentially expressed genes in the rumen were mostly involved in immune regulation. These findings indicated that feeding Cd-accumulated maize diet with a Cd concentration of 6.74 mg/kg dry matter (DM) could stimulate SCFA-related bacteria in the rumen, induce hormesis to promote weight gain, and improve energy utilization of cattle.
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Affiliation(s)
- Xinxin Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (X.X.); (Z.X.); (B.Y.)
| | - Zebang Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (X.X.); (Z.X.); (B.Y.)
| | - Bin Yang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (X.X.); (Z.X.); (B.Y.)
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China; (K.Y.); (F.H.); (A.S.); (J.L.)
| | - Fang He
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China; (K.Y.); (F.H.); (A.S.); (J.L.)
| | - Ao Sun
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China; (K.Y.); (F.H.); (A.S.); (J.L.)
| | - Jianbo Li
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China; (K.Y.); (F.H.); (A.S.); (J.L.)
| | - Yang Luo
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (X.X.); (Z.X.); (B.Y.)
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China; (K.Y.); (F.H.); (A.S.); (J.L.)
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (X.X.); (Z.X.); (B.Y.)
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Sasamoto N, Stewart PA, Wang T, Thompson ZJ, Yoder SJ, Hecht JL, Cleveland JL, Conejo‐Garcia J, Fridley BL, Terry KL, Tworoger SS. Associations between prediagnostic aspirin use and ovarian tumor gene expression. Cancer Med 2023; 12:18405-18417. [PMID: 37525619 PMCID: PMC10523980 DOI: 10.1002/cam4.6386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/25/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Aspirin use has been associated with reduced ovarian cancer risk, yet the underlying biological mechanisms are not fully understood. To gain mechanistic insights, we assessed the association between prediagnosis low and regular-dose aspirin use and gene expression profiles in ovarian tumors. METHODS RNA sequencing was performed on high-grade serous, poorly differentiated, and high-grade endometrioid ovarian cancer tumors from the Nurses' Health Study (NHS), NHSII, and New England Case-Control Study (n = 92 cases for low, 153 cases for regular-dose aspirin). Linear regression identified differentially expressed genes associated with aspirin use, adjusted for birth decade and cohort. False discovery rates (FDR) were used to account for multiple testing and gene set enrichment analysis was used to identify biological pathways. RESULTS No individual genes were significantly differentially expressed in ovarian tumors in low or regular-dose aspirin users accounting for multiple comparisons. However, current versus never use of low-dose aspirin was associated with upregulation of immune pathways (e.g., allograft rejection, FDR = 5.8 × 10-10 ; interferon-gamma response, FDR = 2.0 × 10-4 ) and downregulation of estrogen response pathways (e.g., estrogen response late, FDR = 4.9 × 10-8 ). Ovarian tumors from current regular aspirin users versus never users were also associated with upregulation in interferon pathways (FDR <1.5 × 10-4 ) and downregulation of multiple extracellular matrix (ECM) architecture pathways (e.g., ECM organization, 4.7 × 10-8 ). CONCLUSION Our results suggest low and regular-dose aspirin may impair ovarian tumorigenesis in part via enhancing adaptive immune response and decreasing metastatic potential supporting the likely differential effects on ovarian carcinogenesis and progression by dose of aspirin.
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Affiliation(s)
- Naoko Sasamoto
- Department of Obstetrics and GynecologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Paul A. Stewart
- Department of Biostatistics and BioinformaticsH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Tianyi Wang
- Department of Cancer EpidemiologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Zachary J. Thompson
- Department of Biostatistics and BioinformaticsH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Sean J. Yoder
- Molecular Genomics Core FacilityH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Jonathan L. Hecht
- Department of PathologyBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - John L. Cleveland
- Department of Tumor BiologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Jose Conejo‐Garcia
- Department of ImmunologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Brooke L. Fridley
- Department of Biostatistics and BioinformaticsH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Kathryn L. Terry
- Department of Obstetrics and GynecologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
- Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
| | - Shelley S. Tworoger
- Department of Cancer EpidemiologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
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Fan S, Liu Y, Lin Z, Zhang Y, Zhang N, Zhao Y, Zhou J, Mao A, Wang L, Feng Y, He X, Wang L, Pan Q. ZNF655 promotes the progression of hepatocellular carcinoma through PSMB8. Cell Biol Int 2023; 47:1535-1546. [PMID: 37272200 DOI: 10.1002/cbin.12050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 04/18/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a type of liver cancer that is associated with high mortality rates. This study aims to investigate the role of ZNF655, a member of the zinc finger protein family, in the development of HCC. Immunohistochemical staining analysis was conducted to evaluate the expression of ZNF655 in HCC patient samples. Lentivirus-mediated ZNF655 knockdown was established in HCC cell lines (BEL-7402 and HCCLM3). The effects of ZNF655 on different aspects of HCC cell behavior such as proliferation, apoptosis, cycle, migration and tumor formation were examined. Downstream targets of ZNF655 in HCC were identified and verified through loss/gain-of-function experiments. Clinically, ZNF655 expression was elevated in HCC and increased with the severity of the disease. Functionally, inhibition of ZNF655 expression reduced the progression of HCC cells by decreasing proliferation, causing apoptosis, arresting cell cycle retention in G2, suppressing migration, and attenuating tumor formation in mice. Mechanistically, the proteasome subunit beta type-8 (PSMB8) was found to be co-expressed with ZNF655 in HCC, and PSMB8 knockdown weakened the promotion of ZNF655 overexpression on HCC. In summary, these findings suggest that ZNF655 promotes the progression of HCC through PSMB8, and inhibition of its expression may be a promising therapeutic target for HCC.
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Affiliation(s)
- Shasha Fan
- Department of Oncology, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, Hunan Normal University, Changsha, Hunan, China
| | - Yu Liu
- Department of Pathology, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Zhenhai Lin
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yongfa Zhang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Zhang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiming Zhao
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaming Zhou
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Anrong Mao
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Longrong Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yun Feng
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xigan He
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qi Pan
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Yang L, Liu X, Huang X, Zhang L, Yan H, Hou X, Wang L, Wang L. Metabolite and Proteomic Profiling of Serum Reveals the Differences in Molecular Immunity between Min and Large White Pig Breeds. Int J Mol Sci 2023; 24:ijms24065924. [PMID: 36982998 PMCID: PMC10056118 DOI: 10.3390/ijms24065924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/30/2023] Open
Abstract
Pig diseases seriously threaten the health of pigs and the benefits of pig production. Previous research has indicated that Chinese native pigs, such as the Min (M) pig, has a better disease resistance ability than Large White (LW) pigs. However, the molecular mechanism of this resistance is still unclear. In our study, we used serum untargeted metabolomics and proteomics, interrogated to characterize differences in the molecular immunities between six resistant and six susceptible pigs raised in the same environment. A total of 62 metabolites were identified as being significantly exhibited in M and LW pigs. Ensemble feature selection (EFS) machine learning methods were used to predict biomarkers of metabolites and proteins, and the top 30 were selected and retained. Weighted gene co-expression network analysis (WGCNA) confirmed that four key metabolites, PC (18:1 (11 Z)/20:0), PC (14:0/P-18: 0), PC (18:3 (6 Z, 9 Z, 12 Z)/16:0), and PC (16:1 (9 Z)/22:2 (13 Z, 16 Z)), were significantly associated with phenotypes, such as cytokines, and different pig breeds. Correlation network analysis showed that 15 proteins were significantly correlated with the expression of both cytokines and unsaturated fatty acid metabolites. Quantitative trait locus (QTL) co-location analysis results showed that 13 of 15 proteins co-localized with immune or polyunsaturated fatty acid (PUFA)-related QTL. Moreover, seven of them co-localized with both immune and PUFA QTLs, including proteasome 20S subunit beta 8 (PSMB8), mannose binding lectin 1 (MBL1), and interleukin-1 receptor accessory protein (IL1RAP). These proteins may play important roles in regulating the production or metabolism of unsaturated fatty acids and immune factors. Most of the proteins could be validated with parallel reaction monitoring, which suggests that these proteins may play an essential role in producing or regulating unsaturated fatty acids and immune factors to cope with the adaptive immunity of different pig breeds. Our study provides a basis for further clarifying the disease resistance mechanism of pigs.
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Affiliation(s)
- Liyu Yang
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Liu
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyu Huang
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Sciences, Shanxi Agricultural University, Taigu 030800, China
| | - Longchao Zhang
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hua Yan
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinhua Hou
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixian Wang
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ligang Wang
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Elhawary NA, Ekram SN, Abumansour IS, Azher ZA, AlJahdali IA, Alyamani NM, Naffadi HM, Sindi IA, Baazeem A, Nassir AM, Mufti AH. Sequence Variants in PSMB8/PSMB9 Immunoproteasome Genes and Risk of Urothelial Bladder Carcinoma. Cureus 2023; 15:e36293. [PMID: 36937130 PMCID: PMC10022703 DOI: 10.7759/cureus.36293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND The PSMB8 and PSMB9 immunoproteasome genes are essential in cell processes, such as decisions on cell survival or death, the cell cycle, and cellular differentiation. Because recent evidence has demonstrated an immunological role for proteasomes in various malignancies, including urothelial bladder carcinoma (UBC), we evaluated single nucleotide polymorphisms (SNPs) in PSMB9 and PSMB8. We determined any associations between these SNPs and susceptibility to UBC in the Saudi community. METHODS Samples of genomic DNA were taken from buccal cells of 111 patients with UBC and 78 healthy controls. TaqMan Real-Time PCR was used to determine genotype distributions and allele frequencies for the PSMB9 rs17587 G>A and PSMB8 rs2071543 G>T SNPs. We used SNPStats (https://www.snpstats.net) to choose each SNP's best interactive inheritance model. RESULTS The PSMB9 rs17587 SNP was associated with the risk of UBC (odds ratio [OR] = 5.21, P < 0.0001). In contrast, the PSMB8 rs2071543 SNP showed no association with UBC risk (OR = 1.13, P = 0.7871). In terms of genotypic distribution, the rs17587 G>A SNP was more frequent in UBC cases than controls in both the dominant (OR = 7.5; 95% confidence interval, 3.7-15.1; P = 0.0051) and recessive (OR = 17.11, 95% confidence interval 5.1-57.4; P = 0.0026) models. Genotypic distribution of the PSMB8 rs2071543 G>T SNP was not significantly different between cases and controls in any interactive inheritance models (P > 0.05). CONCLUSION These results suggest a potential role for PSMB9 as a biomarker for increased UBC risk. Discovering more genetic variants within immunoproteasome genes related to antigen presentation could help further our understanding of this risk.
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Affiliation(s)
| | - Samar N Ekram
- Medical Genetics, Umm Al-Qura University, Mecca, SAU
| | | | - Zohor A Azher
- Medical Genetics, Umm Al-Qura University, Mecca, SAU
| | | | | | | | | | | | | | - Ahmad H Mufti
- Medical Genetics, Umm Al-Qura University, Mecca, SAU
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Chen G, Chen P, Zhou J, Luo G. Pan-Cancer Analysis of Histone Methyltransferase KMT2D with Potential Implications for Prognosis and Immunotherapy in Human Cancer. Comb Chem High Throughput Screen 2023; 26:83-92. [PMID: 35189794 DOI: 10.2174/1386207325666220221092318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/13/2021] [Accepted: 12/21/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pan-cancer analysis is an efficient tool to obtain a panoramic view of cancer- related genes and identify their oncogenic processes, facilitating the development of new therapeutic targets. Lysine methyltransferase 2D (KMT2D), acting as a major enhancer coactivator for mammalian cells, is one of the most frequently mutated genes across various cancer types and is considered an oncogene and a rationale for epigenetic therapeutic targets. OBJECTIVE This study was designed to explore the potential role of KMT2D in human cancer through a pan-cancer analysis. METHODS The expression of KMT2D was assessed in normal tissues and cell lines, and pancancers from The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), and Genotype-Tissue Expression (GTE) datasets were used to explore its correlation with prognosis, immune cell infiltration, tumor mutation burden, microsatellite instability, and mismatch repair. RESULTS KMT2D expression was heterogeneous across different cancer types. Increased KMT2D indicated a worse prognosis in adrenocortical carcinoma (ACC), brain lower-grade glioma (LGG), and mesothelioma (MESO), while patients with high KMT2D expression showed better outcomes in renal clear cell carcinoma (KIRC). Moreover, KMT2D expression was positively correlated with immune cell infiltration and negative tumor mutation burden in multiple cancers. In addition, a significant correlation between KMT2D and immune checkpoint-related genes or mismatch repair genes was identified. CONCLUSIONS These findings support the hypothesis that KMT2D is not only a potential biomarker for prognosis and immunotherapy response prediction but also an essential immune regulator in human cancer.
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Affiliation(s)
- Guoning Chen
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Peijie Chen
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Jianwen Zhou
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Guangcheng Luo
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
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9
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Xie T, Fan G, Huang L, Lou N, Han X, Xing P, Shi Y. Analysis on methylation and expression of PSMB8 and its correlation with immunity and immunotherapy in lung adenocarcinoma. Epigenomics 2022; 14:1427-1448. [PMID: 36683462 DOI: 10.2217/epi-2022-0282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Aim: To find biomarkers for immunity and immunotherapy in lung adenocarcinoma (LUAD) through multiomics analysis. Materials & methods: The multiomics data of patients with LUAD were downloaded from the TCGA and GEO databases. CIBERSORT, quanTIseq, ESTIMATEScore, k-means clustering, gene set enrichment analysis, gene set variation analysis, immunophenoscore and logistic regression were used in this study. Results: PSMB8 HypoMet-HighExp group patients have more active immune-related pathways, more antitumor immune cells, less protumor immune cells, higher immunophenoscore and longer progression-free survival of immune checkpoint inhibitor therapy than HyperMet-LowExp group. In multivariate analysis, PSMB8 showed an independent value. Conclusion: The combination of DNA methylation and mRNA expression of PSMB8 could independently distinguish types of tumor immune microenvironment and predict programmed cell death protein 1/programmed cell death-ligand 1 inhibitors' effects in patients with LUAD.
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Affiliation(s)
- Tongji Xie
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Guangyu Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Liling Huang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Ning Lou
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe & Rare Diseases, NMPA Key Laboratory for Clinical Research & Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Puyuan Xing
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
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10
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Sereda EE, Kolegova ES, Kakurina GV, Korshunov DA, Sidenko EA, Doroshenko AV, Slonimskaya EM, Kondakova IV. Five-year survival in luminal breast cancer patients: relation with intratumoral activity of proteasomes. TRANSLATIONAL BREAST CANCER RESEARCH : A JOURNAL FOCUSING ON TRANSLATIONAL RESEARCH IN BREAST CANCER 2022; 3:23. [PMID: 38751528 PMCID: PMC11093047 DOI: 10.21037/tbcr-22-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 05/18/2024]
Abstract
Background The purpose of the study was to analyze the relationship between the caspase-like (CL) and chymotrypsin-like (ChTL) activities of proteasomes and the 5-year overall and metastasis-free survival rates in patients with luminal breast cancer. Methods The study included 117 patients with primary operable invasive breast cancer (T1-2N0-1M0). Tissue samples from breast cancer patients were obtained as a result of the radical mastectomy or breast conserving surgery, which was a first line of therapy. The ChTL and CL proteasomes activities in the tumor tissue and in the surrounding adjacent breast tissues were assessed using the fluorometric method. The coefficients of ChTL (cChTL) and CL (cCL) proteasomes activities were also determined. The coefficients were calculated as the ratio of the corresponding proteasomes activity in the tumor tissue to the surrounding adjacent breast tissues. Within 5 years of follow-up, hematogenous metastases occurred in 14% of patients with luminal A breast cancer, in 31% of patients with luminal B human epidermal growth factor receptor-2 (HER-2) negative and in 23% of patients with luminal B HER-2 positive breast cancers. The study protocol was approved by the Local Ethics Committee of the Cancer Research Institute of Tomsk National Research Medical Center. Written informed consent was obtained from all patients. Results An increase in the ChTL and CL proteasomes activities was shown in all studied molecular subtypes of breast cancer compared to adjacent tissues. It was found that the cChTL of >35.9 U/mg protein and the cCL of >2.21 in breast cancer patients were associated with the development of distant metastases. In patients with luminal A breast cancer, the 5-year metastasis-free survival rates were associated only with the value of cCL of proteasomes (log-rank test: P=0.008). In patients with luminal B HER-2 negative breast cancer, the 5-year metastasis-free survival rates were associated with the levels of ChTL and cCL proteasomes activities (log-rank test: P=0.02 and P=0.04, respectively). Conclusions The data obtained on the correlation of 5-year metastasis-free survival rates with the level of proteasomes activities indicate the possibility of their use as additional prognostic criteria for breast cancer.
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Affiliation(s)
- Elena E. Sereda
- Laboratory of Tumor Biochemistry, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine and Biology, Siberian State Medical University, Tomsk, Russia
| | - Elena. S. Kolegova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Gelena V. Kakurina
- Laboratory of Tumor Biochemistry, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine and Biology, Siberian State Medical University, Tomsk, Russia
| | - Dmitriy A. Korshunov
- Laboratory of Tumor Biochemistry, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Evgenia A. Sidenko
- Laboratory of Tumor Biochemistry, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Artem V. Doroshenko
- General Oncology Department, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Elena M. Slonimskaya
- General Oncology Department, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Irina V. Kondakova
- Laboratory of Tumor Biochemistry, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
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11
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Baek M, Chai JC, Choi HI, Yoo E, Binas B, Lee YS, Jung KH, Chai YG. Comprehensive transcriptome profiling of BET inhibitor-treated HepG2 cells. PLoS One 2022; 17:e0266966. [PMID: 35486664 PMCID: PMC9053788 DOI: 10.1371/journal.pone.0266966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver cancer and poor prognosis. Emerging evidence suggests that epigenetic alterations play a crucial role in HCC, suggesting epigenetic inhibition as a promising therapeutic approach. Indeed, the bromodomain and extra-terminal (BET) inhibitors inhibit the proliferation and invasion of various cancers but still lack a strong mechanistic rationale. Here, we identified the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) in human HCC cell line HepG2 treated with the BET inhibitors, JQ1, OTX015, or ABBV-075. We analyzed the correlation between DEmRNAs and DElncRNAs in common for the three inhibitors based on their expression profiles and performed functional annotation pathway enrichment analysis. Most of these shared DEmRNAs and DElncRNAs, including some novel transcripts, were downregulated, indicating decreased proliferation/adhesion and increased apoptosis/inflammation. Our study suggests that BET proteins play a crucial role in regulating cancer progression-related genes and provide a valuable resource for novel putative biomarkers and therapeutic targets in HCC.
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Affiliation(s)
- Mina Baek
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
- Institute of Natural Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Jin Choul Chai
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hae In Choi
- Department of Bionanotechnology, Hanyang University, Seoul, Republic of Korea
| | - Eunyoung Yoo
- Department of Bionanotechnology, Hanyang University, Seoul, Republic of Korea
| | - Bert Binas
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Young Seek Lee
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- * E-mail: (YGC); (KHJ); (YSL)
| | - Kyoung Hwa Jung
- Department of Biopharmaceutical System, Gwangmyeong Convergence Technology Campus of Korea Polytechnic II, Incheon, Republic of Korea
- * E-mail: (YGC); (KHJ); (YSL)
| | - Young Gyu Chai
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
- Department of Bionanotechnology, Hanyang University, Seoul, Republic of Korea
- * E-mail: (YGC); (KHJ); (YSL)
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12
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Tian T, Fu J, Li D, Liu Y, Sun H, Wang X, Zhang X, Zhang D, Zheng T, Zhao Y, Pang D. Methylation of Immune-Related Genes in Peripheral Blood Leukocytes and Breast Cancer. Front Oncol 2022; 12:817565. [PMID: 35223499 PMCID: PMC8867609 DOI: 10.3389/fonc.2022.817565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Abnormal DNA methylation contributes to breast cancer (BC). Immune-related genes play crucial roles in BC development and progression. This study aims to investigate the effect of methylation of immune-related genes in peripheral blood leukocytes (PBLs) on BC risk. GSE51032 and GSE104942 datasets were used to identify significantly differentially methylated CpG sites (DMCs) of immune-related genes. A case-control study was conducted using MethylTarget sequencing to validate the relationship between the methylation levels of the screened genes and BC risk. We also evaluated the association between methylation haplotypes of screened genes and BC risk. Moreover, we sorted the blood leukocytes into T cells, B cells, and monocytes to detect the difference of DNA methylation in different cell subtypes. A total of five DMCs were screened from GEO datasets, including cg01760846 (PSMC1), cg07141527 (SPPL3), cg15658543 (CARD11), cg21568368 (PSMB8), and cg24045276 (NCF2). In the case-control study, there were significant associations between methylation of the CpG sites in the five genes and BC risk. Methylation haplotype burdens of PSMC1, CARD11, and PSMB8 were associated with reduced BC risk. Moreover, there were heterogeneities in the methylation levels of the genes in different cell subtypes. In conclusion, methylation of PSMC1, SPPL3, CARD11, PSMB8, and NCF2 in PBLs were associated with BC risk. The five-gene methylation could be the potential biomarkers for predicting BC risk.
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Affiliation(s)
- Tian Tian
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - JinMing Fu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - DaPeng Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - YuPeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - HongRu Sun
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Xuan Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - XianYu Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ding Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Ting Zheng
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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Guo Q, Zhu Q, Zhang T, Qu Q, Cheang I, Liao S, Chen M, Zhu X, Shi M, Li X. Integrated bioinformatic analysis reveals immune molecular markers and potential drugs for diabetic cardiomyopathy. Front Endocrinol (Lausanne) 2022; 13:933635. [PMID: 36046789 PMCID: PMC9421304 DOI: 10.3389/fendo.2022.933635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/27/2022] [Indexed: 11/15/2022] Open
Abstract
Diabetic cardiomyopathy (DCM) is a pathophysiological condition induced by diabetes mellitus that often causes heart failure (HF). However, their mechanistic relationships remain unclear. This study aimed to identify immune gene signatures and molecular mechanisms of DCM. Microarray data from the Gene Expression Omnibus (GEO) database from patients with DCM were subjected to weighted gene co-expression network analysis (WGCNA) identify co-expression modules. Core expression modules were intersected with the immune gene database. We analyzed and mapped protein-protein interaction (PPI) networks using the STRING database and MCODE and filtering out 17 hub genes using cytoHubba software. Finally, potential transcriptional regulatory factors and therapeutic drugs were identified and molecular docking between gene targets and small molecules was performed. We identified five potential immune biomarkers: proteosome subunit beta type-8 (PSMB8), nuclear factor kappa B1 (NFKB1), albumin (ALB), endothelin 1 (EDN1), and estrogen receptor 1 (ESR1). Their expression levels in animal models were consistent with the changes observed in the datasets. EDN1 showed significant differences in expression in both the dataset and the validation model by real-time quantitative PCR (qPCR) and Western blotting(WB). Subsequently, we confirmed that the potential transcription factors upstream of EDN1 were PRDM5 and KLF4, as its expression was positively correlated with the expression of the two transcription factors. To repurpose known therapeutic drugs, a connectivity map (CMap) database was retrieved, and nine candidate compounds were identified. Finally, molecular docking simulations of the proteins encoded by the five genes with small-molecule drugs were performed. Our data suggest that EDN1 may play a key role in the development of DCM and is a potential DCM biomarker.
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