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Nguyen MU, Iqbal J, Potgieter S, Huang W, Pfeffer J, Woo S, Zhao C, Lawlor M, Yang R, Rizly R, Halstead A, Dent S, Sáenz JB, Zheng H, Yuan ZF, Sidoli S, Ellison CE, P. Verzi M. KAT2A and KAT2B prevent double-stranded RNA accumulation and interferon signaling to maintain intestinal stem cell renewal. SCIENCE ADVANCES 2024; 10:eadl1584. [PMID: 39110797 PMCID: PMC11305398 DOI: 10.1126/sciadv.adl1584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 07/02/2024] [Indexed: 08/10/2024]
Abstract
Histone acetyltransferases KAT2A and KAT2B are paralogs highly expressed in the intestinal epithelium, but their functions are not well understood. In this study, double knockout of murine Kat2 genes in the intestinal epithelium was lethal, resulting in robust activation of interferon signaling and interferon-associated phenotypes including the loss of intestinal stem cells. Use of pharmacological agents and sterile organoid cultures indicated a cell-intrinsic double-stranded RNA trigger for interferon signaling. Acetyl-proteomics and sequencing of immunoprecipitated double-stranded RNA were used to interrogate the mechanism behind this response, which identified mitochondria-encoded double-stranded RNA as the source of intrinsic interferon signaling. Kat2a and Kat2b therefore play an essential role in regulating mitochondrial functions and maintaining intestinal health.
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Affiliation(s)
- Mai-Uyen Nguyen
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Jahangir Iqbal
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Sarah Potgieter
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Winston Huang
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Julie Pfeffer
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Sean Woo
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Matthew Lawlor
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Richard Yang
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Rahma Rizly
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Angela Halstead
- Division of Gastroenterology, Departments of Medicine and Molecular Cell Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Sharon Dent
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - José B. Sáenz
- Division of Gastroenterology, Departments of Medicine and Molecular Cell Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Zuo-Fei Yuan
- St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Simone Sidoli
- Albert Einstein College of Medicine, The Bronx, NY, USA
| | - Christopher E. Ellison
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, Division of Environmental & Population Health Biosciences, EOHSI, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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Liu S, Zhang P, Wu Y, Zhou H, Wu H, Jin Y, Wu D, Wu G. SLC25A19 is a novel prognostic biomarker related to immune invasion and ferroptosis in HCC. Int Immunopharmacol 2024; 136:112367. [PMID: 38823177 DOI: 10.1016/j.intimp.2024.112367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
SLC25A19 is a mitochondrial thiamine pyrophosphate (TPP) carrier that mediates TPP entry into the mitochondria. SLC25A19 has been recognized to play a crucial role in many metabolic diseases, but its role in cancer has not been clearly reported. Based on clinical data from The Cancer Genome Atlas (TCGA), the following parameters were analyzed among HCC patients: SLC25A19 expression, enrichment analyses, immune infiltration, ferroptosis and prognosis analyses. In vitro, the SLC25A19 high expression was validated by qRT-PCR and Immunohistochemistry. Subsequently, a series of cell function experiments, including CCK8, EdU, clone formation, trans-well and scratch assays, were conducted to illustrate the effect of SLC25A19 on the growth and metastasis of cancer cells. Meanwhile, indicators related to ferroptosis were also detected. SCL25A19 is highly expressed in HCC and predicts a poor prognosis. Elevated SLC25A19 expression in HCC patients was markedly associated with T stage, pathological status (PS), tumor status (TS), histologic grade (HG), and AFP. Our results indicate that SLC25A19 has a generally good prognosis predictive and diagnostic ability. The results of gene enrichment analyses showed that SLC25A19 is significantly correlated with immune infiltration, fatty acid metabolism, and ferroptosis marker genes. In vitro experiments have confirmed that silencing SLC25A19 can significantly inhibit the proliferation and migration ability of cancer cells and induce ferroptosis in HCC. In conclusion, these findings indicate that SLC25A19 is novel prognostic biomarker related to immune invasion and ferroptosis in HCC, and it is an excellent candidate for therapeutic target against HCC.
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Affiliation(s)
- Shiqi Liu
- Hepatobiliary Surgery Department, First Hospital of China Medical, University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning, Province, PR China; Key Laboratory of General Surgery of Liaoning Province, the First Affiliated Hospital of China Medical University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning Province, PR China
| | - Pengjie Zhang
- Hepatobiliary Surgery Department, First Hospital of China Medical, University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning, Province, PR China; Key Laboratory of General Surgery of Liaoning Province, the First Affiliated Hospital of China Medical University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning Province, PR China
| | - Yubo Wu
- Hepatobiliary Surgery Department, First Hospital of China Medical, University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning, Province, PR China; Key Laboratory of General Surgery of Liaoning Province, the First Affiliated Hospital of China Medical University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning Province, PR China
| | - Haonan Zhou
- Hepatobiliary Surgery Department, First Hospital of China Medical, University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning, Province, PR China; Key Laboratory of General Surgery of Liaoning Province, the First Affiliated Hospital of China Medical University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning Province, PR China
| | - Haomin Wu
- Hepatobiliary Surgery Department, First Hospital of China Medical, University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning, Province, PR China; Key Laboratory of General Surgery of Liaoning Province, the First Affiliated Hospital of China Medical University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning Province, PR China
| | - Yifan Jin
- Hepatobiliary Surgery Department, First Hospital of China Medical, University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning, Province, PR China; Key Laboratory of General Surgery of Liaoning Province, the First Affiliated Hospital of China Medical University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning Province, PR China
| | - Di Wu
- Hepatobiliary Surgery Department, First Hospital of China Medical, University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning, Province, PR China; Key Laboratory of General Surgery of Liaoning Province, the First Affiliated Hospital of China Medical University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning Province, PR China
| | - Gang Wu
- Hepatobiliary Surgery Department, First Hospital of China Medical, University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning, Province, PR China; Key Laboratory of General Surgery of Liaoning Province, the First Affiliated Hospital of China Medical University, No.155, Nanjingbei Street, 110001 Shenyang, Liaoning Province, PR China.
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Zhang Y, Wang Y, Zhang W, Feng S, Xing Y, Wang T, Huang N, Li K, Zhang A. Comprehensive transcriptomic analysis identifies SLC25A4 as a key predictor of prognosis in osteosarcoma. Front Genet 2024; 15:1410145. [PMID: 38957810 PMCID: PMC11217516 DOI: 10.3389/fgene.2024.1410145] [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: 03/31/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024] Open
Abstract
Background Osteosarcoma (OS) is highly malignant and prone to local infiltration and distant metastasis. Due to the poor outcomes of OS patients, the study aimed to identify differentially expressed genes (DEGs) in OS and explore their role in the carcinogenesis and progression of OS. Methods RNA sequencing was performed to identify DEGs in OS. The functions of the DEGs in OS were investigated using bioinformatics analysis, and DEG expression was verified using RT-qPCR and Western blotting. The role of SLC25A4 was evaluated using gene set enrichment analysis (GSEA) and then investigated using functional assays in OS cells. Results In all, 8353 DEGs were screened. GO and KEGG enrichment analyses indicated these DEGs showed strong enrichment in the calcium signaling pathway and pathways in cancer. Moreover, the Kaplan-Meier survival analysis showed ten hub genes were related to the outcomes of OS patients. Both SLC25A4 transcript and protein expression were significantly reduced in OS, and GSEA suggested that SLC25A4 was associated with cell cycle, apoptosis and inflammation. SLC25A4-overexpressing OS cells exhibited suppressed proliferation, migration, invasion and enhanced apoptosis. Conclusion SLC25A4 was found to be significantly downregulated in OS patients, which was associated with poor prognosis. Modulation of SLC25A4 expression levels may be beneficial in OS treatment.
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Affiliation(s)
- Ying Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yinghui Wang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Wenyan Zhang
- School of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Shaojie Feng
- Research Center of Translational Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yuanxin Xing
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Tianjiao Wang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Nana Huang
- Department of Neurology, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ka Li
- Department of Orthopedics, Qilu Hospital of Shandong University, Jinan, China
| | - Aijun Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
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Tian J, Jia K, Wang T, Guo L, Xuan Z, Michaelis EK, Swerdlow RH, Du H. Hippocampal transcriptome-wide association study and pathway analysis of mitochondrial solute carriers in Alzheimer's disease. Transl Psychiatry 2024; 14:250. [PMID: 38858380 PMCID: PMC11164935 DOI: 10.1038/s41398-024-02958-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024] Open
Abstract
The etiopathogenesis of late-onset Alzheimer's disease (AD) is increasingly recognized as the result of the combination of the aging process, toxic proteins, brain dysmetabolism, and genetic risks. Although the role of mitochondrial dysfunction in the pathogenesis of AD has been well-appreciated, the interaction between mitochondrial function and genetic variability in promoting dementia is still poorly understood. In this study, by tissue-specific transcriptome-wide association study (TWAS) and further meta-analysis, we examined the genetic association between mitochondrial solute carrier family (SLC25) genes and AD in three independent cohorts and identified three AD-susceptibility genes, including SLC25A10, SLC25A17, and SLC25A22. Integrative analysis using neuroimaging data and hippocampal TWAS-predicted gene expression of the three susceptibility genes showed an inverse correlation of SLC25A22 with hippocampal atrophy rate in AD patients, which outweighed the impacts of sex, age, and apolipoprotein E4 (ApoE4). Furthermore, SLC25A22 downregulation demonstrated an association with AD onset, as compared with the other two transcriptome-wide significant genes. Pathway and network analysis related hippocampal SLC25A22 downregulation to defects in neuronal function and development, echoing the enrichment of SLC25A22 expression in human glutamatergic neurons. The most parsimonious interpretation of the results is that we have identified AD-susceptibility genes in the SLC25 family through the prediction of hippocampal gene expression. Moreover, our findings mechanistically yield insight into the mitochondrial cascade hypothesis of AD and pave the way for the future development of diagnostic tools for the early prevention of AD from a perspective of precision medicine by targeting the mitochondria-related genes.
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Affiliation(s)
- Jing Tian
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS, USA
| | - Kun Jia
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS, USA
| | - Tienju Wang
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS, USA
| | - Lan Guo
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Elias K Michaelis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Russell H Swerdlow
- Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Heng Du
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS, USA.
- Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, USA.
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Gao LP, Li TD, Yang SZ, Ma HM, Wang X, Zhang DK. NAT10-mediated ac 4C modification promotes stemness and chemoresistance of colon cancer by stabilizing NANOGP8. Heliyon 2024; 10:e30330. [PMID: 38726177 PMCID: PMC11079091 DOI: 10.1016/j.heliyon.2024.e30330] [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: 12/07/2023] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Background Colon cancer (CC) stem cells can self-renew as well as expand, thereby promoting tumor progression and conferring resistance to chemotherapeutic agents. The acetyltransferase NAT10 mediates N4-acetylcytidine (ac4C) modification, which in turn drives tumorigenesis, metastasis, stemness properties maintenance, and cell fate decisions. Nonetheless, the specific involvement of ac4C modification mediated by NAT10 in regulating stemness and chemosensitivity in CC remains undetermined. Methods The levels of NAT10 in normal colon and chemoresistant CC tissues were determined utilizing quantitative real-time polymerase chain reaction alongside immunohistochemistry. Assessing cancer cell stemness and chemosensitivity was conducted by various methods including spheroid and colony formation, western blotting, and flow cytometry. RNA-Seq was used to identify target genes, and RNA immunoprecipitation analysis was used to explore the potential mechanisms. Results We observed NAT10 overexpression and increased ac4C modification levels in chemoresistant CC tissues. The in vivo and in vitro analysis findings suggested that NAT10 promoted CC cell stemness while suppressing their chemosensitivity. Conversely, Remodelin, a NAT10-specific inhibitor, enhanced CC cell chemosensitivity. Mechanistically, NAT10 increased the level of NANOGP8 ac4C modification and promoted NANOGP8 mRNA stability. Conclusions NAT10 promotes the maintenance of stemness and chemoresistance in CC cells by augmenting the mRNA stability of NANOGP8. The inhibition of NAT10 via Remodelin improves chemotherapeutic efficacy and impedes CC progression.
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Affiliation(s)
- Li-ping Gao
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
| | - Ting-dong Li
- Department of Musculoskeletal Tumor, Gansu Provincial Cancer Hospital, Gansu Provincial Academic Institute for Medical Research, Lanzhou, PR China
| | - Su-zhen Yang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
| | - Hui-min Ma
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
| | - Xiang Wang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
| | - De-kui Zhang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
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Chen J, Xia Y, Ben Y, Lu X, Dou K, Ding Y, Han X, Yang F, Wang J, Li D. Embryonic exposure to aluminum chloride blocks the onset of spermatogenesis through disturbing the dynamics of testicular tight junctions via upregulating Slc25a5 in offspring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170128. [PMID: 38242464 DOI: 10.1016/j.scitotenv.2024.170128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Studies have revealed neurotoxicity, hepatotoxicity, and developmental and reproductive toxicity in mice exposed to aluminum. However, relatively few studies have been conducted to clarify the mechanism underlying the impact of embryonic exposure to aluminum on the development of the male reproductive system in offspring. Pregnant mice were administered aluminum chloride (AlCl3) by gavage from day 12.5 of gestation until birth. Our findings demonstrated that embryonic exposure to AlCl3 disrupted testicular development and spermatogenesis by impairing testicular architecture, reducing sperm count, and upregulating the expression of tight junction (TJ) protein between Sertoli cells (SCs). Further in vitro studies revealed that treatment with AlCl3 stabilized TJ proteins Occludin and ZO-1 expression by inhibiting ERK signaling pathway activation, thereby upregulating Slc25a5 expression which induced ATP production leading to disruption of cytoskeletal protein homeostasis. Therefore, the study provided a new mechanistic insight into how AlCl3 exposure interfered with testicular development and spermatogenesis while suggesting that Slc25a5 might be a target affected by AlCl3 influencing cell metabolism.
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Affiliation(s)
- Junhan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, Division of Anatomy and Histo-embryology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Yunhui Xia
- State Key Laboratory of Analytical Chemistry for Life Science, Division of Anatomy and Histo-embryology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Yu Ben
- State Key Laboratory of Analytical Chemistry for Life Science, Division of Anatomy and Histo-embryology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Xinyan Lu
- State Key Laboratory of Analytical Chemistry for Life Science, Division of Anatomy and Histo-embryology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Kou Dou
- State Key Laboratory of Analytical Chemistry for Life Science, Division of Anatomy and Histo-embryology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Yibing Ding
- Translational Medicine Core Facilities, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Xiaodong Han
- State Key Laboratory of Analytical Chemistry for Life Science, Division of Anatomy and Histo-embryology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Fenglian Yang
- Industrial College of biomedicine and health industry, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Junli Wang
- Industrial College of biomedicine and health industry, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China; Reproductive Medicine, Guangxi Medical and Health Key Discipline Construction Project, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, China.
| | - Dongmei Li
- State Key Laboratory of Analytical Chemistry for Life Science, Division of Anatomy and Histo-embryology, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China.
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Wang T, Guo K, Yang S, Zhang D, Cui H, Yin J, Yuan S, Wang Y, Qi Y, Wu W. Identification and validation of SLCO4C1 as a biological marker in hepatocellular carcinoma based on anoikis classification features. Aging (Albany NY) 2024; 16:1440-1462. [PMID: 38226966 PMCID: PMC10866452 DOI: 10.18632/aging.205438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/04/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) exhibits a high degree of invasiveness and is closely associated with rapid disease progression. Multiple lines of evidence indicate a strong correlation between anoikis resistance and tumor progression, invasion, and metastasis. Nevertheless, the classification of anoikis in HCC and the investigation of novel biological target mechanisms in this context continue to pose challenges, requiring further exploration. METHODS Combined with HCC samples from TCGA, GEO and ICGC databases, cluster analysis was conducted on anoikis genes, revealing novel patterns among different subtypes. Significant gene analysis of different gene subtypes was performed using WCGNA. The anoikis prognostic risk model was established by Lasso-Cox. Go, KEGG, and GSEA were applied to investigate pathway enrichment primarily observed in risk groups. We compared the disparities in immune infiltration, TMB, tumor microenvironment (TME), and drug sensitivity between the two risk groups. RT-qPCR and Western blotting were performed to validate the expression levels of SLCO4C1 in HCC. The biological functions of SLCO4C1 in HCC cells were assessed through various experiments, including CCK8 assay, colony formation assay, invasion migration assay, wound healing assay, and flow cytometry analysis. RESULTS HCC was divided into 2 anoikis subtypes, and the subtypeB had a better prognosis. An anoikis prognostic model based on 12 (COPZ2, ACTG2, IFI27, SPP1, EPO, SLCO4C1, RAB26, STC2, RAC3, NQO1, MYCN, HSPA1B) risk genes is important for survival and prognosis. Significant differences were observed in immune cell infiltration, TME, and drug sensitivity analysis between the risk groups. SLCO4C1 was downregulated in HCC. SLCO4C1 downregulation promoted the proliferation, invasion, migration, and apoptosis of HCC cells. The tumor-suppressive role of SLCO4C1 in HCC has been confirmed. CONCLUSIONS Our study presents a novel anoikis classification method for HCC that reveals the association between anoikis features and HCC. The anoikis feature is a critical biomarker bridging tumor cell death and tumor immunity. In this study, we provided the first evidence of SLCO4C1 functioning as a tumor suppressor in HCC.
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Affiliation(s)
- Tianbing Wang
- Department of General Surgery, Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
| | - Kai Guo
- Department of General Surgery, Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
| | - Shoushan Yang
- Anhui No. 2 Provincial People’s Hospital Clinical College of Anhui Medical University, Hefei 230000, China
- Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei 230000, China
- Department of General Surgery, Luan Fourth People’s Hospital, Luan 237000, China
| | - Di Zhang
- Clinical Genomic Center, Hefei KingMed for Clinical Laboratory, Hefei 230000, China
| | - Haodong Cui
- Anhui No. 2 Provincial People’s Hospital Clinical College of Anhui Medical University, Hefei 230000, China
- Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei 230000, China
| | - Jimin Yin
- Anhui No. 2 Provincial People’s Hospital Clinical College of Anhui Medical University, Hefei 230000, China
- Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei 230000, China
| | - Shuhui Yuan
- Anhui Huaheng Biotechnology Co., Ltd., Hefei 230000, China
| | - Yong Wang
- Department of General Surgery, Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
| | - Yong Qi
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230000, China
| | - Wenyong Wu
- Anhui No. 2 Provincial People’s Hospital Clinical College of Anhui Medical University, Hefei 230000, China
- Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei 230000, China
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Du W, Xia G, Chen L, Geng L, Xu R, Han Q, Ying X, Yu H. Clinical value of SLC12A9 for diagnosis and prognosis in colorectal cancer. Aging (Albany NY) 2023; 15:15419-15433. [PMID: 38157260 PMCID: PMC10781446 DOI: 10.18632/aging.205360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE The goal of the study is to assess the clinical value and the potential mechanism of SLC12A9 combing transcriptome and single cell sequencing data. METHODS In this study, the expression level and the receiver operating characteristic curve analysis of SLC12A9 in CRC and normal tissue were analyzed in multiple data cohort. The standardized mean difference (SMD) calculation and the summary receiver operating characteristic (SROC) analysis were performed further to detect its diagnostic ability and expression level. KM survival analysis was performed to assess the prognosis value of SLC12A9. The expression level of SLC12A9 in different clinical characteristics was analyzed to explore the clinical value. Single cell data was studied to reveal the potential mechanism of SLC12A9. The correlation analysis of immunoinfiltration was performed to detect the potential immune cell related to SLC12A9. The nomogram was drawn to assess the probable mortality rate of CRC patient. RESULTS We found that SLC12A9 was significantly up-regulated with the moderate diagnostic value in CRC. Patients with overexpressed SLC12A9 had a worse prognosis. SLC12A9 was related to Age, Pathologic N stage, Pathologic M stage, Lymphatic invasion and Pathologic stage (p < 0.05). The 1, 3 and 5-year survival rates of patient named TCGA-G4-6309 are 0.959, 0.897 and 0.827. PCR also showed that SLC12A9 was overexpressed in CRC comparing with normal tissue. CONCLUSION In conclusion, our study comprehensively analyzed the clinical value of SLC12A9 and its potential mechanism, as well as immune cell infiltration, which may accelerate the diagnosis and improve the prognosis of CRC.
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Affiliation(s)
- Wang Du
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui 236000, China
| | - Guozhi Xia
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui 236000, China
| | - Liang Chen
- Department of Hepatobiliary and Pancreatic Surgery, Conversion therapy center for Hepatobiliary and Pancreatic Tumors, First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314041, China
| | - Lingjun Geng
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui 236000, China
| | - Rubin Xu
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui 236000, China
| | - Qingqing Han
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui 236000, China
| | - Xiaomei Ying
- Suzhou Hospital of Anhui Medical University, Suzhou, Anhui 234000, China
| | - Hongzhu Yu
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui 236000, China
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Chen N, Luo J, Zhou T, Shou Y, Du C, Song G, Xu L, Zhao K, Jin Y, Li C, Yu D. Lysine β-hydroxybutyrylation promotes lipid accumulation in alcoholic liver disease. Biochem Pharmacol 2023:115936. [PMID: 38012969 DOI: 10.1016/j.bcp.2023.115936] [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: 09/14/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Continuous (chronic or sub-chronic) alcohol consumption induces a metabolic byproduct known as ketone bodies, and the accumulation of ketones leads to a life-threatening syndrome called alcoholic ketoacidosis. However, the mechanism underlining the physiological effects of ketone accumulation in alcoholic liver disease (ALD) is still in its infancy. Here, we discovered that mitochondrial acetyl-CoA accumulation was diverted into the ketogenesis pathway in ethanol-fed mice and ethanol-exposed hepatocytes. Unexpectedly, global protein lysine β-hydroxybutyrylation (Kbhb) was induced in response to increased ketogenesis-derived β-hydroxybutyrate (BHB) levels both in hepatocytes and in livers of mice. Focusing on the solute carrier family (SLCs), we found that SLC25A5 presented obvious Kbhb at lysine residues 147 and 166. Kbhb modifications at these two lysine residues stabilized SLC25A5 expression by blocking ubiquitin-proteasome pathway. Subsequent mutation analysis revealed that Kbhb of SLC25A5 at K147 and K166 had site-specific regulatory roles by increasing peroxisome proliferator activated receptor gamma (PPARγ) expression, which further promoting lipogenesis. Additionally, 3-hydroxy-3-methylglutaryl-coenzyme A synthase 2 (HMGCS2), a rate-limiting enzyme for BHB production, was profoundly induced by ethanol exposure, and knockout of Hmgcs2 with CRISPR/Cas9 attenuated SLC25A5 Kbhb. Together, our study demonstrated a widespread Kbhb landscape under ethanol exposure and clarified a physiological effect of Kbhb modification on liver lipid accumulation.
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Affiliation(s)
- Ningning Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Jiao Luo
- School of Public Health, Qingdao University, Qingdao, China
| | - Tao Zhou
- School of Public Health, Qingdao University, Qingdao, China
| | - Yingqing Shou
- School of Public Health, Qingdao University, Qingdao, China
| | - Chenlong Du
- School of Public Health, Qingdao University, Qingdao, China
| | - Ge Song
- School of Public Health, Qingdao University, Qingdao, China
| | - Lin Xu
- School of Public Health, Qingdao University, Qingdao, China
| | - Kunming Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuan Jin
- School of Public Health, Qingdao University, Qingdao, China
| | - Chuanhai Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China.
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10
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Puurand M, Tepp K, Kaambre T. Diving into cancer OXPHOS - The application of metabolic control analysis to cell and tissue research. Biosystems 2023; 233:105032. [PMID: 37739307 DOI: 10.1016/j.biosystems.2023.105032] [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: 05/09/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023]
Abstract
Knowing how the oxidative phosphorylation (OXPHOS) system in cancer cells operates differently from that of normal cells would help find compounds that specifically paralyze the energy metabolism of cancer cells. The first experiments in the study of mitochondrial respiration using the metabolic control analysis (MCA) method were done with isolated liver mitochondria in the early 80s of the last century. Subsequent studies have shown that the regulation of mitochondrial respiration by ADP in isolated mitochondria differs significantly from a model of mitochondria in situ, where the contacts with components in the cytoplasm are largely preserved. The method of selective permeabilization of the outer membrane of the cells allows the application of MCA to evaluate the contribution of different components of the OXPHOS system to its functioning while mitochondria are in a natural state. In this review, we summarize the use of MCA to study OXPHOS in cancer using permeabilized cells and tissues. In addition, we give examples of how this data fits into cancer research with a completely different approach and methodology.
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Affiliation(s)
- Marju Puurand
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia.
| | - Kersti Tepp
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Tuuli Kaambre
- Laboratory of Chemical Biology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
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11
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Nguyen MU, Potgieter S, Huang W, Pfeffer J, Woo S, Zhao C, Lawlor M, Yang R, Halstead A, Dent S, Sáenz JB, Zheng H, Yuan ZF, Sidoli S, Ellison CE, Verzi M. KAT2 paralogs prevent dsRNA accumulation and interferon signaling to maintain intestinal stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556156. [PMID: 37732252 PMCID: PMC10508741 DOI: 10.1101/2023.09.04.556156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Histone acetyltransferases KAT2A and KAT2B are paralogs highly expressed in the intestinal epithelium, but their functions are not well understood. In this study, double knockout of murine Kat2 genes in the intestinal epithelium was lethal, resulting in robust activation of interferon signaling and interferon-associated phenotypes including the loss of intestinal stem cells. Use of pharmacological agents and sterile organoid cultures indicated a cell-intrinsic double-stranded RNA trigger for interferon signaling. Acetyl-proteomics and dsRIP-seq were employed to interrogate the mechanism behind this response, which identified mitochondria-encoded double-stranded RNA as the source of intrinsic interferon signaling. Kat2a and Kat2b therefore play an essential role in regulating mitochondrial functions as well as maintaining intestinal health.
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Affiliation(s)
- Mai-Uyen Nguyen
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Sarah Potgieter
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Winston Huang
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Julie Pfeffer
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Sean Woo
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Matthew Lawlor
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Richard Yang
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Angela Halstead
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis, St. Louis, MO
| | - Sharon Dent
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - José B. Sáenz
- Division of Gastroenterology, Departments of Medicine and Molecular Cell Biology, Washington University in St. Louis, St. Louis, MO
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Zuo-Fei Yuan
- St. Jude Children’s Research Hospital, Memphis, TN
| | | | | | - Michael Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, Division of Environmental & Population Health Biosciences, EOHSI, Rutgers, The State University of New Jersey, Piscataway, NJ
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12
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Ross KE, Zhang G, Akcora C, Lin Y, Fang B, Koomen J, Haura EB, Grimes M. Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer. PLoS Comput Biol 2023; 19:e1010690. [PMID: 36996232 PMCID: PMC10089347 DOI: 10.1371/journal.pcbi.1010690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 04/11/2023] [Accepted: 03/11/2023] [Indexed: 04/01/2023] Open
Abstract
We analyzed large-scale post-translational modification (PTM) data to outline cell signaling pathways affected by tyrosine kinase inhibitors (TKIs) in ten lung cancer cell lines. Tyrosine phosphorylated, lysine ubiquitinated, and lysine acetylated proteins were concomitantly identified using sequential enrichment of post translational modification (SEPTM) proteomics. Machine learning was used to identify PTM clusters that represent functional modules that respond to TKIs. To model lung cancer signaling at the protein level, PTM clusters were used to create a co-cluster correlation network (CCCN) and select protein-protein interactions (PPIs) from a large network of curated PPIs to create a cluster-filtered network (CFN). Next, we constructed a Pathway Crosstalk Network (PCN) by connecting pathways from NCATS BioPlanet whose member proteins have PTMs that co-cluster. Interrogating the CCCN, CFN, and PCN individually and in combination yields insights into the response of lung cancer cells to TKIs. We highlight examples where cell signaling pathways involving EGFR and ALK exhibit crosstalk with BioPlanet pathways: Transmembrane transport of small molecules; and Glycolysis and gluconeogenesis. These data identify known and previously unappreciated connections between receptor tyrosine kinase (RTK) signal transduction and oncogenic metabolic reprogramming in lung cancer. Comparison to a CFN generated from a previous multi-PTM analysis of lung cancer cell lines reveals a common core of PPIs involving heat shock/chaperone proteins, metabolic enzymes, cytoskeletal components, and RNA-binding proteins. Elucidation of points of crosstalk among signaling pathways employing different PTMs reveals new potential drug targets and candidates for synergistic attack through combination drug therapy.
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Affiliation(s)
- Karen E Ross
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Guolin Zhang
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Cuneyt Akcora
- Department of Computer Science and Statistics, University of Manitoba, Winnipeg, Manitoba Canada
| | - Yu Lin
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Bin Fang
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - John Koomen
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Mark Grimes
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
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13
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Song C, Zhu L, Gu J, Wang T, Shi L, Li C, Chen L, Xie S, Lu Y. A necroptosis-related lncRNA signature was identified to predict the prognosis and immune microenvironment of IDH-wild-type GBM. Front Oncol 2022; 12:1024208. [PMID: 36601479 PMCID: PMC9806237 DOI: 10.3389/fonc.2022.1024208] [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: 08/21/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Necroptosis-related genes are essential for the advancement of IDH-wild-type GBM. However, the putative effects of necroptosis-related lncRNAs (nrlncRNAs) in IDH-wild-type GBM remain unknown. Methods By using the TCGA and GTEx databases, a nrlncRNA prognostic signature was created using LASSO Cox regression. The median risk score was used to categorize the patients into low and high-risk groups. To confirm the validity, univariate, multivariate Cox regression and ROC curves were used. Furthermore, by enrichment analysis, immune correlation analysis, and drug sensitivity analysis, the targeted lncRNAs were selected for further verification. As the highest upregulated expression in tumor than peritumor specimens, RP11-131L12.4 was selected for phenotype and functional experiments in primary GBM cells. Results Six lncRNAs were proved to be closely related to necroptosis in IDH-1-wild-type GBM, which were used to create a new signature. For 1-, 2-, and 3-year OS, the AUCs were 0.709, 0.645 and 0.694, respectively. Patients in the low-risk group had a better prognosis, stronger immune function activity, and more immune cell infiltration. In contrast, enrichment analysis revealed that the malignant phenotype was more prevalent in the high-risk group. In vitro experiments indicated that RP11-131L12.4 increased the tumor proliferation, migration and invasion, but decreased the necroptosis. Moreover, this nrlncRNA was also proved to be negatively associated with patient prognosis. Conclusion The signature of nrlncRNAs may aid in the formulation of tailored and precise treatment for individuals with IDH-wild-type GBM. RP11-131L12.4 may play indispensable role in necroptosis suppression.
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Affiliation(s)
- Chong Song
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China,Department of Neurosurgery, The Central Hospital of Dalian University of Technology, Dalian, China
| | - Liwen Zhu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Junwei Gu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tong Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Linyong Shi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chiyang Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Chen
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sidi Xie
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China,Nanfang Neurology Research Institution, Nanfang Hospital, Southern Medical University, Guangzhou, China,Nanfang Glioma Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,*Correspondence: Sidi Xie, ; Yuntao Lu,
| | - Yuntao Lu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China,Nanfang Neurology Research Institution, Nanfang Hospital, Southern Medical University, Guangzhou, China,Nanfang Glioma Center, Nanfang Hospital, Southern Medical University, Guangzhou, China,*Correspondence: Sidi Xie, ; Yuntao Lu,
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14
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Lyu Q, Yang Q, Hao J, Yue Y, Wang X, Tian J, An L. A small proportion of X-linked genes contribute to X chromosome upregulation in early embryos via BRD4-mediated transcriptional activation. Curr Biol 2022; 32:4397-4410.e5. [PMID: 36108637 DOI: 10.1016/j.cub.2022.08.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
Abstract
Females have two X chromosomes and males have only one in most mammals. X chromosome inactivation (XCI) occurs in females to equalize X-dosage between sexes. Besides, mammals also balance the dosage between X chromosomes and autosomes via X chromosome upregulation (XCU) to fine-tune X-linked expression and thus maintain genomic homeostasis. Despite some studies highlighting the importance of XCU in somatic cells, little is known about how XCU is achieved and its developmental role during early embryogenesis. Herein, using mouse preimplantation embryos as the model, we reported that XCU initially occurs upon major zygotic genome activation and co-regulates X-linked expression in cooperation with imprinted XCI during preimplantation development. An in-depth analysis further indicated, unexpectedly, only a small proportion of, but not X chromosome-wide, X-linked genes contribute greatly to XCU. Furthermore, we identified that bromodomain containing 4 (BRD4) plays a key role in the transcription activation of XCU during preimplantation development. BRD4 deficiency or inhibition caused an impaired XCU, thus leading to reduced developmental potential and mitochondrial dysfunctions of blastocysts. Our finding was also supported by the tight association of BRD4 dysregulation and XCU disruption in the pathology of cholangiocarcinoma. Thus, our results not only advanced the current knowledge of X-dosage compensation and provided a mechanism for understanding XCU initiation but also presented an important clue for understanding the developmental and pathological role of XCU.
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Affiliation(s)
- Qingji Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Qianying Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jia Hao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Yuan Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Xiaodong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jianhui Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Lei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China.
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15
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Peng X, Xu Z, Guo Y, Zhu Y. Necroptosis-Related Genes Associated With Immune Activity and Prognosis of Colorectal Cancer. Front Genet 2022; 13:909245. [PMID: 35783272 PMCID: PMC9243386 DOI: 10.3389/fgene.2022.909245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022] Open
Abstract
This study aims at screening out the key necroptosis-related genes in colorectal cancer and elucidating the role of necroptosis-related genes in the immune activity and prognosis of colorectal cancer (CRC). The CRC patients’ data were downloaded from The Cancer Genome Atlas (TCGA). The non-negative matrix factorization method was applied to identify new molecular subgroups. Survival analysis and single sample Gene Set Enrichment Analysis were performed to determinate the differences in the overall survival time and immune status of the subgroups. Prognostic model was constructed on the basis of univariate Cox regression and LASSO analysis. Functional analyses were used to explore the potential mechanisms. Based on prognostic related necroptosis genes, we identify two molecular subgroups with significantly different survival. The better prognosis was associated with more active immune infiltration and upregulated expression of immune checkpoints. We screened nine necroptosis related genes as key prognostic genes and established a risk model, which showed a good potential for survival prediction in colorectal cancer. Nomogram assessment showed that the model had high reliability for predicting the prognosis of colorectal cancer patients. The high-risk and low-risk group also has different sensitivity to immunotherapy and commonly used drugs for colorectal cancer. Overall, necroptosis related genes were involved in the immune microenvironment of colorectal cancer patient, could be utilized to predict the prognosis of colorectal cancer and develop more individualized treatment.
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Affiliation(s)
- Xinyi Peng
- The First Clinical College of Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Zhili Xu
- The First Clinical College of Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Yong Guo
- The First Clinical College of Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, China
- *Correspondence: Yong Guo, ; Ying Zhu,
| | - Ying Zhu
- The First Clinical College of Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, China
- *Correspondence: Yong Guo, ; Ying Zhu,
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16
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Liu S, Zhang RF, You Y, You W, Ruan GC, Liu YP, Zhang SY, Li Y, Feng YL, Yan XM, Zhou WX, Li JN, Li J, Qian JM. The genomic landscape of Cronkhite-Canada syndrome: Possible clues for pathogenesis. J Dig Dis 2022; 23:288-294. [PMID: 35678525 DOI: 10.1111/1751-2980.13101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Cronkhite-Canada syndrome (CCS) is a rare hamartomatous polyposis syndrome with a proposed association with chronic autoimmune inflammation. To date, genetic background of patients with CCS remains less investigated. In this study we aimed to explore the genomic landscape of CCS. METHODS Whole exome sequencing was performed on peripheral blood samples extracted from 18 patients with CCS. Potential function-impacting germline variants were filtered by R software. Through systematic data analysis, a number of genetic variants were identified. Enrichment analysis was performed using the R package ClusterProfiler. RESULTS Overall, 3960 low-frequency (<0.05 or not reported in the Exome Aggregation Consortium East Asian, 1000 Genomes, or ESP6500 database) potentially function-impacting germline variants were identified, with 18 genes (FDFT1, LOC400863, MUC3A, MUC4, ZNF806, GXYLT1, MUC6, PABPC3, PSPH, ZFPM1, CIC, LOC283710, ARSD, GOLGA6L2, LOC388282, SLC25A5, TMEM247, WDR89) involved over half the patients. Functional enrichment of these genes revealed several biological processes in relation to innate immune responses and glycosylation. Only one likely pathogenic germline variant of an hamartomatous polyposis syndrome-associated gene, PTCH1, was detected in one patient. CONCLUSIONS CCS has genomic alteration patterns completely distinct from those of traditional hamartomatous polyposis syndrome. The germline mutation landscape indicates potential roles of innate immune responses and glycosylation in the pathogenesis of CCS.
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Affiliation(s)
- Shuang Liu
- Department of Allergy, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Run Feng Zhang
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Yan You
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Wen You
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Ge Chong Ruan
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Ya Ping Liu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Sheng Yu Zhang
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Yue Li
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Yun Lu Feng
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Xue Min Yan
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Wei Xun Zhou
- Department of Pathology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Jing Nan Li
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Ji Li
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Jia Ming Qian
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
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