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Yang Y, Lu X, Liu N, Ma S, Zhang H, Zhang Z, Yang K, Jiang M, Zheng Z, Qiao Y, Hu Q, Huang Y, Zhang Y, Xiong M, Liu L, Jiang X, Reddy P, Dong X, Xu F, Wang Q, Zhao Q, Lei J, Sun S, Jing Y, Li J, Cai Y, Fan Y, Yan K, Jing Y, Haghani A, Xing M, Zhang X, Zhu G, Song W, Horvath S, Rodriguez Esteban C, Song M, Wang S, Zhao G, Li W, Izpisua Belmonte JC, Qu J, Zhang W, Liu GH. Metformin decelerates aging clock in male monkeys. Cell 2024:S0092-8674(24)00914-0. [PMID: 39270656 DOI: 10.1016/j.cell.2024.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/10/2024] [Accepted: 08/12/2024] [Indexed: 09/15/2024]
Abstract
In a rigorous 40-month study, we evaluated the geroprotective effects of metformin on adult male cynomolgus monkeys, addressing a gap in primate aging research. The study encompassed a comprehensive suite of physiological, imaging, histological, and molecular evaluations, substantiating metformin's influence on delaying age-related phenotypes at the organismal level. Specifically, we leveraged pan-tissue transcriptomics, DNA methylomics, plasma proteomics, and metabolomics to develop innovative monkey aging clocks and applied these to gauge metformin's effects on aging. The results highlighted a significant slowing of aging indicators, notably a roughly 6-year regression in brain aging. Metformin exerts a substantial neuroprotective effect, preserving brain structure and enhancing cognitive ability. The geroprotective effects on primate neurons were partially mediated by the activation of Nrf2, a transcription factor with anti-oxidative capabilities. Our research pioneers the systemic reduction of multi-dimensional biological age in primates through metformin, paving the way for advancing pharmaceutical strategies against human aging.
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Affiliation(s)
- Yuanhan Yang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyong Lu
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Ma
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Zhiyi Zhang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kuan Yang
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Jiang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zikai Zheng
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yicheng Qiao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinchao Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou 510060, China
| | - Ying Huang
- Chongqing Fifth People's Hospital, Chongqing 400060, China
| | - Yiyuan Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Muzhao Xiong
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixiao Liu
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Jiang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pradeep Reddy
- Altos Labs San Diego Institute of Science, San Diego, CA, USA
| | - Xueda Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanshu Xu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoran Wang
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Zhao
- National Clinical Research Center for Geriatric Disorders, Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Jinghui Lei
- National Clinical Research Center for Geriatric Disorders, Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Shuhui Sun
- Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Ying Jing
- National Clinical Research Center for Geriatric Disorders, Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Jingyi Li
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Biomarker Consortium (ABC), Beijing 100101, China
| | - Yusheng Cai
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yanling Fan
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Kaowen Yan
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yaobin Jing
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; International Center for Aging and Cancer, Hainan Medical University, Haikou 571199, China
| | - Amin Haghani
- Altos Labs San Diego Institute of Science, San Diego, CA, USA
| | - Mengen Xing
- Oujiang Laboratory, Center for Geriatric Medicine and Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research for Mental Disorders, The First-Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guodong Zhu
- Institute of Gerontology, Guangzhou Geriatric Hospital, Guangzhou Medical University, Guangzhou, China
| | - Weihong Song
- Oujiang Laboratory, Center for Geriatric Medicine and Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research for Mental Disorders, The First-Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Steve Horvath
- Altos Labs San Diego Institute of Science, San Diego, CA, USA
| | | | - Moshi Song
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wang
- National Clinical Research Center for Geriatric Disorders, Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Biomarker Consortium (ABC), Beijing 100101, China
| | - Guoguang Zhao
- Department of Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing 100053, China; National Medical Center for Neurological Diseases, Beijing 100053, China; Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Jing Qu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China; Aging Biomarker Consortium (ABC), Beijing 100101, China.
| | - Weiqi Zhang
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Aging Biomarker Consortium (ABC), Beijing 100101, China.
| | - Guang-Hui Liu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; National Clinical Research Center for Geriatric Disorders, Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing 100053, China; University of Chinese Academy of Sciences, Beijing 100049, China; Aging Biomarker Consortium (ABC), Beijing 100101, China.
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2
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Di Giorgio E, Dalla E, Tolotto V, D’Este F, Paluvai H, Ranzino L, Brancolini C. HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair. Nucleic Acids Res 2024; 52:8218-8240. [PMID: 38874468 PMCID: PMC11317144 DOI: 10.1093/nar/gkae501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Access to DNA is the first level of control in regulating gene transcription, a control that is also critical for maintaining DNA integrity. Cellular senescence is characterized by profound transcriptional rearrangements and accumulation of DNA lesions. Here, we discovered an epigenetic complex between HDAC4 and HDAC1/HDAC2 that is involved in the erase of H2BK120 acetylation. The HDAC4/HDAC1/HDAC2 complex modulates the efficiency of DNA repair by homologous recombination, through dynamic deacetylation of H2BK120. Deficiency of HDAC4 leads to accumulation of H2BK120ac, impaired recruitment of BRCA1 and CtIP to the site of lesions, accumulation of damaged DNA and senescence. In senescent cells this complex is disassembled because of increased proteasomal degradation of HDAC4. Forced expression of HDAC4 during RAS-induced senescence reduces the genomic spread of γH2AX. It also affects H2BK120ac levels, which are increased in DNA-damaged regions that accumulate during RAS-induced senescence. In summary, degradation of HDAC4 during senescence causes the accumulation of damaged DNA and contributes to the activation of the transcriptional program controlled by super-enhancers that maintains senescence.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Emiliano Dalla
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Vanessa Tolotto
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Francesca D’Este
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Harikrishnareddy Paluvai
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Liliana Ranzino
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
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3
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Ren Z, Zhang S, Shi L, Zhou A, Lin X, Zhang J, Zhu X, Huang L, Li K. Integrated ATAC-seq and RNA-seq Analysis of In Vitro Cultured Skeletal Muscle Satellite Cells to Understand Changes in Cell Proliferation. Cells 2024; 13:1031. [PMID: 38920660 PMCID: PMC11201436 DOI: 10.3390/cells13121031] [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: 05/25/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Skeletal muscle satellite cells, the resident stem cells in pig skeletal muscle, undergo proliferation and differentiation to enable muscle tissue repair. The proliferative and differentiative abilities of these cells gradually decrease during in vitro cultivation as the cell passage number increases. Despite extensive research, the precise molecular mechanisms that regulate this process are not fully understood. To bridge this knowledge gap, we conducted transcriptomic analysis of skeletal muscle satellite cells during in vitro cultivation to quantify passage number-dependent changes in the expression of genes associated with proliferation. Additionally, we explored the relationships between gene transcriptional activity and chromatin accessibility using transposase-accessible chromatin sequencing. This revealed the closure of numerous open chromatin regions, which were primarily located in intergenic regions, as the cell passage number increased. Integrated analysis of the transcriptomic and epigenomic data demonstrated a weak correlation between gene transcriptional activity and chromatin openness in expressed genic regions; although some genes (e.g., GNB4 and FGD5) showed consistent relationships between gene expression and chromatin openness, a substantial number of differentially expressed genes had no clear association with chromatin openness in expressed genic regions. The p53-p21-RB signaling pathway may play a critical regulatory role in cell proliferation processes. The combined transcriptomic and epigenomic approach taken here provided key insights into changes in gene expression and chromatin openness during in vitro cultivation of skeletal muscle satellite cells. These findings enhance our understanding of the intricate mechanisms underlying the decline in cellular proliferation capacity in cultured cells.
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Affiliation(s)
- Zeyu Ren
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Siyi Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Liangyu Shi
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
| | - Ao Zhou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
| | - Xin Lin
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China;
| | - Jing Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan Polytechnic University, Wuhan 430023, China; (Z.R.); (S.Z.); (L.S.); (A.Z.)
| | - Xiusheng Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Lei Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
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4
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Guo S, Tang Q, Gao X, Hu L, Hu K, Zhang H, Zhang Q, Lai Y, Liu Y, Wang Z, Chang S, Zhang Y, Hu H, An D, Peng Y, Cai H, Shi J. EZH2 inhibition induces senescence via ERK1/2 signaling pathway in multiple myeloma. Acta Biochim Biophys Sin (Shanghai) 2024; 56:1055-1064. [PMID: 38804044 PMCID: PMC11322866 DOI: 10.3724/abbs.2024077] [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: 11/29/2023] [Accepted: 02/04/2024] [Indexed: 05/29/2024] Open
Abstract
Epigenetic modifications play an important role in cellular senescence, and enhancer of zeste homolog 2 (EZH2) is a key methyltransferase involved in epigenetic remodeling in multiple myeloma (MM) cells. We have previously demonstrated that GSK126, a specific EZH2 inhibitor, exhibits anti-MM therapeutic efficacy and safety in vivo and in vitro; however, its specific mechanism remains unclear. This study shows that GSK126 induces cellular senescence in MM, which is characterized by the accumulation of senescence-associated heterochromatin foci (SAHF) and p21, and increased senescence-associated β galactosidase activity. Furthermore, EZH2 is inhibited in ribonucleotide reductase regulatory subunit M2 (RRM2)-overexpressing OCI-MY5 and RPMI-8226 cells. RRM2 overexpression inhibits the methyltransferase function of EZH2 and promotes its degradation through the ubiquitin-proteasome pathway, thereby inducing cellular senescence. In this senescence model, Lamin B1, a key component of the nuclear envelope and a marker of senescence, does not decrease but instead undergoes aberrant accumulation. Meanwhile, phosphorylation of extracellular signal-regulated protein kinase (ERK1/2) is significantly increased. The inhibition of ERK1/2 phosphorylation in turn partially restores Lamin B1 level and alleviates senescence. These findings suggest that EZH2 inhibition increases Lamin B1 level and induces senescence by promoting ERK1/2 phosphorylation. These data indicate that EZH2 plays an important role in MM cellular senescence and provide insights into the relationships among Lamin B1, p-ERK1/2, and cellular senescence.
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Affiliation(s)
- Shushan Guo
- Shanghai Clinical CollegeAnhui Medical UniversityShanghai200072China
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
- The Fifth Clinical Medical College of Anhui Medical UniversityHefei230022China
| | - Qiongwei Tang
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Xuejie Gao
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Liangning Hu
- Department of HematologySir Run Run Shaw HospitalZhejiang UniversityHangzhou310016China
| | - Ke Hu
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Hui Zhang
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Qikai Zhang
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Yue Lai
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Yujie Liu
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Zhuning Wang
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Shuaikang Chang
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Yifei Zhang
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Huifang Hu
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Dong An
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Yu Peng
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Haiyan Cai
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Jumei Shi
- Shanghai Clinical CollegeAnhui Medical UniversityShanghai200072China
- Department of HematologyShanghai East HospitalTongji University School of MedicineShanghai200120China
- The Fifth Clinical Medical College of Anhui Medical UniversityHefei230022China
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5
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Chen J, Zhang H, Yi X, Dou Q, Yang X, He Y, Chen J, Chen K. Cellular senescence of renal tubular epithelial cells in acute kidney injury. Cell Death Discov 2024; 10:62. [PMID: 38316761 PMCID: PMC10844256 DOI: 10.1038/s41420-024-01831-9] [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: 11/19/2023] [Revised: 01/14/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024] Open
Abstract
Cellular senescence represents an irreversible state of cell-cycle arrest during which cells secrete senescence-associated secretory phenotypes, including inflammatory factors and chemokines. Additionally, these cells exhibit an apoptotic resistance phenotype. Cellular senescence serves a pivotal role not only in embryonic development, tissue regeneration, and tumor suppression but also in the pathogenesis of age-related degenerative diseases, malignancies, metabolic diseases, and kidney diseases. The senescence of renal tubular epithelial cells (RTEC) constitutes a critical cellular event in the progression of acute kidney injury (AKI). RTEC senescence inhibits renal regeneration and repair processes and, concurrently, promotes the transition of AKI to chronic kidney disease via the senescence-associated secretory phenotype. The mechanisms underlying cellular senescence are multifaceted and include telomere shortening or damage, DNA damage, mitochondrial autophagy deficiency, cellular metabolic disorders, endoplasmic reticulum stress, and epigenetic regulation. Strategies aimed at inhibiting RTEC senescence, targeting the clearance of senescent RTEC, or promoting the apoptosis of senescent RTEC hold promise for enhancing the renal prognosis of AKI. This review primarily focuses on the characteristics and mechanisms of RTEC senescence, and the impact of intervening RTEC senescence on the prognosis of AKI, aiming to provide a foundation for understanding the pathogenesis and providing potentially effective approaches for AKI treatment.
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Affiliation(s)
- Juan Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Huhai Zhang
- Department of Nephrology, Southwest Hospital, Army Medical University, 400042, Chongqing, China
| | - Xiangling Yi
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Qian Dou
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Xin Yang
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Yani He
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Jia Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China.
| | - Kehong Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China.
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, China.
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6
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Wen Y, Chen H, Wang Y, Sun Y, Dou F, Du X, Liu T, Chen C. Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging. Hereditas 2024; 161:3. [PMID: 38173016 PMCID: PMC10763334 DOI: 10.1186/s41065-023-00306-8] [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: 11/02/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Vascular aging is an important pathophysiological basis for the senescence of various organs and systems in the human body, and it is a common pathogenetic trigger for many chronic diseases in the elderly. METHODS The extracellular vesicles (EVs) from young and aged umbilical vein endothelial cells were isolated and identified by qPCR the differential expression levels of 47 mRNAs of genes closely related to aging in the two groups. RESULTS There were significant differences in the expression levels of 18 genes (we noted upregulation in PLA2G12A, TP53BP1, CD144, PDE11A, FPGT, SERPINB4, POLD1, and PPFIBP2 and downregulation in ATP2C2, ROBO2, RRM2, GUCY1B1, NAT1-14, VEGFR2, WTAPP1, CD146, DMC1, and GRIK2). Subsequent qPCR identification of the above-mentioned genes in PBMCs and plasma-EVs from the various age groups revealed that the trend in expression levels in peripheral blood plasma-EVs of the different age groups was approximately the same as that in PBMCs. Of these mRNAs, the expression of four genes-PLA2G12A, TP53BP1, OPRL1, and KIAA0895-was commensurate with increasing age. In contradistinction, the expression trend of four genes (CREG1, PBX1, CD34, and SLIT2) was inversely proportional to the increase in age. Finally, by taking their intersection, we determined that the expression of TP53BP1 was upregulated with increasing human age and that CD34 and PBX1 were downregulated with increasing age. CONCLUSION Our study indicates that human peripheral blood plasma-EV-derived TP53BP1, CD34, and PBX1 potentially comprise a noninvasive biomarker for assessing and predicting vascular aging.
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Affiliation(s)
- Yichao Wen
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China
| | - Haiyang Chen
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China
| | - Yu Wang
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Yiqing Sun
- Eberly College of Science, Penn State University, University Park, PA, USA
| | - Fangfang Dou
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China
| | - Xiling Du
- School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Te Liu
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China.
| | - Chuan Chen
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China.
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Kalinin A, Zubkova E, Menshikov M. Integrated Stress Response (ISR) Pathway: Unraveling Its Role in Cellular Senescence. Int J Mol Sci 2023; 24:17423. [PMID: 38139251 PMCID: PMC10743681 DOI: 10.3390/ijms242417423] [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: 11/02/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Cellular senescence is a complex process characterized by irreversible cell cycle arrest. Senescent cells accumulate with age, promoting disease development, yet the absence of specific markers hampers the development of selective anti-senescence drugs. The integrated stress response (ISR), an evolutionarily highly conserved signaling network activated in response to stress, globally downregulates protein translation while initiating the translation of specific protein sets including transcription factors. We propose that ISR signaling plays a central role in controlling senescence, given that senescence is considered a form of cellular stress. Exploring the intricate relationship between the ISR pathway and cellular senescence, we emphasize its potential as a regulatory mechanism in senescence and cellular metabolism. The ISR emerges as a master regulator of cellular metabolism during stress, activating autophagy and the mitochondrial unfolded protein response, crucial for maintaining mitochondrial quality and efficiency. Our review comprehensively examines ISR molecular mechanisms, focusing on ATF4-interacting partners, ISR modulators, and their impact on senescence-related conditions. By shedding light on the intricate relationship between ISR and cellular senescence, we aim to inspire future research directions and advance the development of targeted anti-senescence therapies based on ISR modulation.
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Affiliation(s)
- Alexander Kalinin
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia; (A.K.); (E.Z.)
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ekaterina Zubkova
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia; (A.K.); (E.Z.)
| | - Mikhail Menshikov
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia; (A.K.); (E.Z.)
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8
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Cheng B, Li L, Wu Y, Luo T, Tang C, Wang Q, Zhou Q, Wu J, Lai Y, Zhu D, Du T, Huang H. The key cellular senescence related molecule RRM2 regulates prostate cancer progression and resistance to docetaxel treatment. Cell Biosci 2023; 13:211. [PMID: 37968699 PMCID: PMC10648385 DOI: 10.1186/s13578-023-01157-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/28/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Prostate cancer is a leading cause of cancer-related deaths among men worldwide. Docetaxel chemotherapy has proven effective in improving overall survival in patients with castration-resistant prostate cancer (CRPC), but drug resistance remains a considerable clinical challenge. METHODS We explored the role of Ribonucleotide reductase subunit M2 (RRM2), a gene associated with senescence, in the sensitivity of prostate cancer to docetaxel. We evaluated the RRM2 expression, docetaxel resistance, and ANXA1 expression in prostate cancer cell lines and tumour xenografts models. In addition, We assessed the impact of RRM2 knockdown, ANXA1 over-expression, and PI3K/AKT pathway inhibition on the sensitivity of prostate cancer cells to docetaxel. Furthermore, we assessed the sensitivity of prostate cancer cells to the combination treatment of COH29 and docetaxel. RESULTS Our results demonstrated a positive association between RRM2 expression and docetaxel resistance in prostate cancer cell lines and tumor xenograft models. Knockdown of RRM2 increased the sensitivity of prostate cancer cells to docetaxel, suggesting its role in mediating resistance. Furthermore, we observed that RRM2 stabilizes the expression of ANXA1, which in turn activates the PI3K/AKT pathway and contributes to docetaxel resistance. Importantly, we found that the combination treatment of COH29 and docetaxel resulted in a synergistic effect, further augmenting the sensitivity of prostate cancer cells to docetaxel. CONCLUSION Our findings suggest that RRM2 regulates docetaxel resistance in prostate cancer by stabilizing ANXA1-mediated activation of the PI3K/AKT pathway. Targeting RRM2 or ANXA1 may offer a promising therapeutic strategy to overcome docetaxel resistance in prostate cancer.
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Affiliation(s)
- Bisheng Cheng
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Lingfeng Li
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yongxin Wu
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Tianlong Luo
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Chen Tang
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Qiong Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 511430, China
| | - Qianghua Zhou
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Jilin Wu
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yiming Lai
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Dingjun Zhu
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
| | - Tao Du
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
| | - Hai Huang
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
- Guangdong Provincial Clinical Research Center for Urological Diseases, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
- Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, Guangdong, China.
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9
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Hou Y, Song Q, Wang Y, Liu J, Cui Y, Zhang X, Zhang J, Fu J, Cao M, Zhang C, Liu C, Wang X, Duan H, Wang P. Downregulation of Krüppel-like factor 14 accelerated cellular senescence and aging. Aging Cell 2023; 22:e13950. [PMID: 37551728 PMCID: PMC10577553 DOI: 10.1111/acel.13950] [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: 04/11/2023] [Revised: 07/02/2023] [Accepted: 07/17/2023] [Indexed: 08/09/2023] Open
Abstract
Aging has been considered as a risk factor in many diseases, thus, comprehensively understanding the cellular and molecular mechanisms of delayed aging is important. Here we investigated whether Krüppel-like factor 14 (KLF14) is a suppressor of cellular senescence and aging. In our research, KLF14 levels significantly decreased not only in the lymphocytes of healthy people but also in the cells and tissues of mice with aging. We performed in vitro and in vivo experiments on cells and mice to reveal the function of KLF14 in aging. KLF14 deficiency facilitates cellular senescence and aging-related pathologies in C57BL/6J mice, whereas KLF14 overexpression attenuates cellular senescence. Mechanistically, KLF14 delays aging by binding to the POLD1 promoter to positively regulate POLD1 expression. Remarkably, cellular senescence mediated by KLF14 downregulation could be alleviated by POLD1 expression. In addition, perhexiline, an agonist of KLF14, could delay cellular senescence and aging-related pathologies in senescence-accelerated P8 mice by inducing POLD1 expression, as perhexiline could enhance the effect of KLF14's transcription activation to POLD1 by elevating the binding level of KLF14 to the POLD1 promoter. Our data indicate that KLF14 might be a critical element in aging by upregulating POLD1 expression, indicating that the activation of KLF14 may delay aging and aging-associated diseases.
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Affiliation(s)
- Yuli Hou
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Qiao Song
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Yaqi Wang
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Jing Liu
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Yuting Cui
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Xiaomin Zhang
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Jingjing Zhang
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Jingxuan Fu
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Min Cao
- Department of Clinical LaboratoryBeijing Huairou HospitalBeijingChina
| | - Chi Zhang
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Congcong Liu
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Xiaoling Wang
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
| | - Huanli Duan
- Departments of Pathology, Xuanwu HospitalCapital Medical UniversityBeijingChina
| | - Peichang Wang
- Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric DiseasesCapital Medical UniversityBeijingChina
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10
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Huang X, Duijf PHG, Sriram S, Perera G, Vasani S, Kenny L, Leo P, Punyadeera C. Circulating tumour DNA alterations: emerging biomarker in head and neck squamous cell carcinoma. J Biomed Sci 2023; 30:65. [PMID: 37559138 PMCID: PMC10413618 DOI: 10.1186/s12929-023-00953-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023] Open
Abstract
Head and Neck cancers (HNC) are a heterogeneous group of upper aero-digestive tract cancer and account for 931,922 new cases and 467,125 deaths worldwide. About 90% of these cancers are of squamous cell origin (HNSCC). HNSCC is associated with excessive tobacco and alcohol consumption and infection with oncogenic viruses. Genotyping tumour tissue to guide clinical decision-making is becoming common practice in modern oncology, but in the management of patients with HNSCC, cytopathology or histopathology of tumour tissue remains the mainstream for diagnosis and treatment planning. Due to tumour heterogeneity and the lack of access to tumour due to its anatomical location, alternative methods to evaluate tumour activities are urgently needed. Liquid biopsy approaches can overcome issues such as tumour heterogeneity, which is associated with the analysis of small tissue biopsy. In addition, liquid biopsy offers repeat biopsy sampling, even for patients with tumours with access limitations. Liquid biopsy refers to biomarkers found in body fluids, traditionally blood, that can be sampled to provide clinically valuable information on both the patient and their underlying malignancy. To date, the majority of liquid biopsy research has focused on blood-based biomarkers, such as circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), and circulating microRNA. In this review, we will focus on ctDNA as a biomarker in HNSCC because of its robustness, its presence in many body fluids, adaptability to existing clinical laboratory-based technology platforms, and ease of collection and transportation. We will discuss mechanisms of ctDNA release into circulation, technological advances in the analysis of ctDNA, ctDNA as a biomarker in HNSCC management, and some of the challenges associated with translating ctDNA into clinical and future perspectives. ctDNA provides a minimally invasive method for HNSCC prognosis and disease surveillance and will pave the way in the future for personalized medicine, thereby significantly improving outcomes and reducing healthcare costs.
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Affiliation(s)
- Xiaomin Huang
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, QLD, Brisbane, Australia
| | - Pascal H G Duijf
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- University Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Sharath Sriram
- Functional Materials and Microsystems Research Group and the Micro Nano Research Facility, RMIT University, Melbourne, Australia
| | - Ganganath Perera
- Functional Materials and Microsystems Research Group and the Micro Nano Research Facility, RMIT University, Melbourne, Australia
| | - Sarju Vasani
- Department of Otolaryngology, Royal Brisbane Women's Hospital, Brisbane, QLD, Australia
- The School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Lizbeth Kenny
- The School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Paul Leo
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Translational Genomics Centre, Brisbane, QLD, Australia
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, QLD, Brisbane, Australia.
- Menzies Health Institute Queensland (MIHQ), Griffith University, Gold coast, QLD, Australia.
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11
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Chen C, Wang J, Pan D, Wang X, Xu Y, Yan J, Wang L, Yang X, Yang M, Liu G. Applications of multi-omics analysis in human diseases. MedComm (Beijing) 2023; 4:e315. [PMID: 37533767 PMCID: PMC10390758 DOI: 10.1002/mco2.315] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 08/04/2023] Open
Abstract
Multi-omics usually refers to the crossover application of multiple high-throughput screening technologies represented by genomics, transcriptomics, single-cell transcriptomics, proteomics and metabolomics, spatial transcriptomics, and so on, which play a great role in promoting the study of human diseases. Most of the current reviews focus on describing the development of multi-omics technologies, data integration, and application to a particular disease; however, few of them provide a comprehensive and systematic introduction of multi-omics. This review outlines the existing technical categories of multi-omics, cautions for experimental design, focuses on the integrated analysis methods of multi-omics, especially the approach of machine learning and deep learning in multi-omics data integration and the corresponding tools, and the application of multi-omics in medical researches (e.g., cancer, neurodegenerative diseases, aging, and drug target discovery) as well as the corresponding open-source analysis tools and databases, and finally, discusses the challenges and future directions of multi-omics integration and application in precision medicine. With the development of high-throughput technologies and data integration algorithms, as important directions of multi-omics for future disease research, single-cell multi-omics and spatial multi-omics also provided a detailed introduction. This review will provide important guidance for researchers, especially who are just entering into multi-omics medical research.
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Affiliation(s)
- Chongyang Chen
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
- Co‐innovation Center of NeurodegenerationNantong UniversityNantongChina
| | - Jing Wang
- Shenzhen Key Laboratory of Modern ToxicologyShenzhen Medical Key Discipline of Health Toxicology (2020–2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Donghui Pan
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Xinyu Wang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Yuping Xu
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Junjie Yan
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Lizhen Wang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Xifei Yang
- Shenzhen Key Laboratory of Modern ToxicologyShenzhen Medical Key Discipline of Health Toxicology (2020–2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Min Yang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Gong‐Ping Liu
- Co‐innovation Center of NeurodegenerationNantong UniversityNantongChina
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Ministry of Education of China and Hubei Province for Neurological DisordersTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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12
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Laub V, Devraj K, Elias L, Schulte D. Bioinformatics for wet-lab scientists: practical application in sequencing analysis. BMC Genomics 2023; 24:382. [PMID: 37420172 PMCID: PMC10326960 DOI: 10.1186/s12864-023-09454-7] [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: 03/23/2023] [Accepted: 06/15/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Genomics data is available to the scientific community after publication of research projects and can be investigated for a multitude of research questions. However, in many cases deposited data is only assessed and used for the initial publication, resulting in valuable resources not being exploited to their full depth. MAIN: A likely reason for this is that many wetlab-based researchers are not formally trained to apply bioinformatic tools and may therefore assume that they lack the necessary experience to do so themselves. In this article, we present a series of freely available, predominantly web-based platforms and bioinformatic tools that can be combined in analysis pipelines to interrogate different types of next-generation sequencing data. Additionally to the presented exemplary route, we also list a number of alternative tools that can be combined in a mix-and-match fashion. We place special emphasis on tools that can be followed and used correctly without extensive prior knowledge in programming. Such analysis pipelines can be applied to existing data downloaded from the public domain or be compared to the results of own experiments. CONCLUSION Integrating transcription factor binding to chromatin (ChIP-seq) with transcriptional output (RNA-seq) and chromatin accessibility (ATAC-seq) can not only assist to form a deeper understanding of the molecular interactions underlying transcriptional regulation but will also help establishing new hypotheses and pre-testing them in silico.
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Affiliation(s)
- Vera Laub
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany.
| | - Kavi Devraj
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Lena Elias
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
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13
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Liu Y, Zhang Q, Ni W, Ji G, Xu H. A strategy for the treatment of gastrointestinal cancer: Targeting tumor senescent cells. Front Mol Biosci 2023; 10:1139840. [PMID: 36950520 PMCID: PMC10025555 DOI: 10.3389/fmolb.2023.1139840] [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: 01/07/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Gastrointestinal (GI) cancer includes a variety of cancers with high incidence that seriously threaten the lives of people worldwide. Although treatment strategies continue to improve, patient benefits are still very limited, and the ongoing search for new treatment strategies remains a priority. Cell senescence is closely related to the occurrence and development of tumors. For GI cancer, cell senescence may not only promote cancer but also bring new opportunities for treatment. Combined with relevant studies, we review the dual role of cell senescence in GI cancer, including the mechanism of inducing cell senescence, biomarkers of senescent cells, and potential of targeted senescence therapy for GI cancer.
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Affiliation(s)
- Yujing Liu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qiang Zhang
- Department of Digestive Endoscopy, Jiangsu Province Hospital of Traditional Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Wenjing Ni
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, China
- *Correspondence: Guang Ji, ; Hanchen Xu,
| | - Hanchen Xu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Frontiers Science Center of Disease and Syndrome Biology of Inflammatory Cancer Transformation, Shanghai, China
- *Correspondence: Guang Ji, ; Hanchen Xu,
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