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Feitosa MF, Lin SJ, Acharya S, Thyagarajan B, Wojczynski MK, Kuipers AL, Kulminski A, Christensen K, Zmuda JM, Brent MR, Province MA. Discovery of genomic and transcriptomic pleiotropy between kidney function and soluble receptor for advanced glycation end products using correlated meta-analyses: The Long Life Family Study. Aging Cell 2024:e14261. [PMID: 38932496 DOI: 10.1111/acel.14261] [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: 01/19/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Patients with chronic kidney disease (CKD) have increased oxidative stress and chronic inflammation, which may escalate the production of advanced glycation end-products (AGEs). High soluble receptor for AGE (sRAGE) and low estimated glomerular filtration rate (eGFR) levels are associated with CKD and aging. We evaluated whether eGFR calculated from creatinine and cystatin C share pleiotropic genetic factors with sRAGE. We employed whole-genome sequencing and correlated meta-analyses on combined genome-wide association study (GWAS) p-values in 4182 individuals (age range: 24-110) from the Long Life Family Study (LLFS). We also conducted transcriptome-wide association studies (TWAS) on whole blood in a subset of 1209 individuals. We identified 59 pleiotropic GWAS loci (p < 5 × 10-8) and 17 TWAS genes (Bonferroni-p < 2.73 × 10-6) for eGFR traits and sRAGE. TWAS genes, LSP1 and MIR23AHG, were associated with eGFR and sRAGE located within GWAS loci, lncRNA-KCNQ1OT1 and CACNA1A/CCDC130, respectively. GWAS variants were eQTLs in the kidney glomeruli and tubules, and GWAS genes predicted kidney carcinoma. TWAS genes harbored eQTLs in the kidney, predicted kidney carcinoma, and connected enhancer-promoter variants with kidney function-related phenotypes at p < 5 × 10-8. Additionally, higher allele frequencies of protective variants for eGFR traits were detected in LLFS than in ALFA-Europeans and TOPMed, suggesting better kidney function in healthy-aging LLFS than in general populations. Integrating genomic annotation and transcriptional gene activity revealed the enrichment of genetic elements in kidney function and aging-related processes. The identified pleiotropic loci and gene expressions for eGFR and sRAGE suggest their underlying shared genetic effects and highlight their roles in kidney- and aging-related signaling pathways.
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Affiliation(s)
- Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University in St Louis School of Medicine, St. Louis, Missouri, USA
| | - Shiow J Lin
- Division of Statistical Genomics, Department of Genetics, Washington University in St Louis School of Medicine, St. Louis, Missouri, USA
| | - Sandeep Acharya
- Department of Computer Science and Engineering, Washington University, St. Louis, Missouri, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University in St Louis School of Medicine, St. Louis, Missouri, USA
| | - Allison L Kuipers
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alexander Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, Southern Denmark University, Odense, Denmark
| | - Joseph M Zmuda
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael R Brent
- Department of Computer Science and Engineering, Washington University, St. Louis, Missouri, USA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University in St Louis School of Medicine, St. Louis, Missouri, USA
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Li T, Lei Z, Wei L, Yang K, Shen J, Hu L. Tumor Necrosis Factor Receptor-Associated Factor 6 and Human Cancer: A Systematic Review of Mechanistic Insights, Functional Roles, and Therapeutic Potential. J Cancer 2024; 15:560-576. [PMID: 38169510 PMCID: PMC10758021 DOI: 10.7150/jca.90059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Cancer imposes a substantial burden and its incidence is persistently increasing in recent years. Cancer treatment has been difficult due to its inherently complex nature. The tumor microenvironment (TME) includes a complex interplay of cellular and noncellular constituents surrounding neoplastic cells, intricately contributing to the tumor initiation and progression. This critical aspect of tumors involves a complex interplay among cancer, stromal, and inflammatory cells, forming an inflammatory TME that promotes tumorigenesis across all stages. Tumor necrosis factor receptor-associated factor 6 (TRAF6) is implicated in modulating various critical processes linked to tumor pathogenesis, including but not limited to the regulation of tumor cell proliferation, invasion, migration, and survival. Furthermore, TRAF6 prominently contributes to various immune and inflammatory pathways. The TRAF6-mediated activation of nuclear factor (NF)-κB in immune cells governs the production of proinflammatory cytokines. These cytokines sustain inflammation and stimulate tumor growth by activating NF-κB in tumor cells. In this review, we discuss various types of tumors, including gastrointestinal cancers, urogenital cancers, breast cancer, lung cancer, head and neck squamous cell carcinoma, uterine fibroids, and glioma. Employing a rigorous and systematic approach, we comprehensively evaluate the functional repertoire and potential roles of TRAF6 in various cancer types, thus highlighting TRAF6 as a compelling and emerging therapeutic target worthy of further investigation and development.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 199 Renai Road, Suzhou 215123, China
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Zhe Lei
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou 215006 Jiangsu, China
| | - Lin Wei
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Kai Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Jinhong Shen
- Shanghai Key Laboratory of Sleep Disordered Breathing, Department of Otolaryngology-Head and Neck Surgery, Otolaryngology Institute of Shanghai Jiaotong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200233, China
| | - Lin Hu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 199 Renai Road, Suzhou 215123, China
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Feitosa MF, Lin SJ, Acharya S, Thyagarajan B, Wojczynski MK, Kuipers AL, Kulminski A, Christensen K, Zmuda JM, Brent MR, Province MA. Discovery of genomic and transcriptomic pleiotropy between kidney function and soluble receptor for advanced glycation end-products using correlated meta-analyses: The Long Life Family Study (LLFS). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.27.23300583. [PMID: 38234834 PMCID: PMC10793516 DOI: 10.1101/2023.12.27.23300583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Patients with chronic kidney disease (CKD) have increased oxidative stress and chronic inflammation, which may escalate the production of advanced glycation end-products (AGE). High soluble receptor for AGE (sRAGE) and low estimated glomerular filtration rate (eGFR) levels are associated with CKD and aging. We evaluated whether eGFR calculated from creatinine and cystatin C share pleiotropic genetic factors with sRAGE. We employed whole-genome sequencing and correlated meta-analyses on combined genomewide association study (GWAS) p -values in 4,182 individuals (age range: 24-110) from the Long Life Family Study (LLFS). We also conducted transcriptome-wide association studies (TWAS) on whole blood in a subset of 1,209 individuals. We identified 59 pleiotropic GWAS loci ( p <5×10 -8 ) and 17 TWAS genes (Bonferroni- p <2.73×10 -6 ) for eGFR traits and sRAGE. TWAS genes, LSP1 and MIR23AHG , were associated with eGFR and sRAGE located within GWAS loci, lncRNA- KCNQ1OT1 and CACNA1A/CCDC130 , respectively. GWAS variants were eQTLs in the kidney glomeruli and tubules, and GWAS genes predicted kidney carcinoma. TWAS genes harbored eQTLs in the kidney, predicted kidney carcinoma, and connected enhancer-promoter variants with kidney function-related phenotypes at p <5×10 -8 . Additionally, higher allele frequencies of protective variants for eGFR traits were detected in LLFS than in ALFA-Europeans and TOPMed, suggesting better kidney function in healthy-aging LLFS than in general populations. Integrating genomic annotation and transcriptional gene activity revealed the enrichment of genetic elements in kidney function and kidney diseases. The identified pleiotropic loci and gene expressions for eGFR and sRAGE suggest their underlying shared genetic effects and highlight their roles in kidney- and aging-related signaling pathways.
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Ding R, Wei H, Jiang X, Wei L, Deng M, Yuan H. Prognosis and pain dissection of novel signatures in kidney renal clear cell carcinoma based on fatty acid metabolism-related genes. Front Oncol 2022; 12:1094657. [PMID: 36568252 PMCID: PMC9780486 DOI: 10.3389/fonc.2022.1094657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC) is a malignant tumor that is characterized by the accumulation of intracellular lipid droplets. The prognostic value of fatty acid metabolism-related genes (FMGs) in RCC remains unclear. Alongside this insight, we collected data from three RCC cohorts, namely, The Cancer Genome Atlas (TCGA), E-MTAB-1980, and GSE22541 cohorts, and identified a total of 309 FMGs that could be associated with RCC prognosis. First, we determined the copy number variation and expression levels of these FMGs, and identified 52 overall survival (OS)-related FMGs of the TCGA-KIRC and the E-MTAB-1980 cohort data. Next, 10 of these genes-FASN, ACOT9, MID1IP1, CYP2C9, ABCD1, CPT2, CRAT, TP53INP2, FAAH2, and PTPRG-were identified as pivotal OS-related FMGs based on least absolute shrinkage and selection operator and Cox regression analyses. The expression of some of these genes was confirmed in patients with RCC by immunohistochemical analyses. Kaplan-Meier analysis showed that the identified FMGs were effective in predicting the prognosis of RCC. Moreover, an optimal nomogram was constructed based on FMG-based risk scores and clinical factors, and its robustness was verified by time-dependent receiver operating characteristic analysis, calibration curve analysis, and decision curve analysis. We have also described the biological processes and the tumor immune microenvironment based on FMG-based risk score classification. Given the close association between fatty acid metabolism and cancer-related pain, our 10-FMG signature may also serve as a potential therapeutic target with dual effects on ccRCC prognosis and cancer pain and, therefore, warrants further investigation.
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Affiliation(s)
- Ruifeng Ding
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Huawei Wei
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xin Jiang
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Liangtian Wei
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, China
| | - Mengqiu Deng
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Hongbin Yuan
- Department of Anesthesiology, Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai, China,*Correspondence: Hongbin Yuan,
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