1
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Kurlekar S, Lima JDCC, Li R, Lombardi O, Masson N, Barros AB, Pontecorvi V, Mole DR, Pugh CW, Adam J, Ratcliffe PJ. Oncogenic Cell Tagging and Single-Cell Transcriptomics Reveal Cell Type-Specific and Time-Resolved Responses to Vhl Inactivation in the Kidney. Cancer Res 2024; 84:1799-1816. [PMID: 38502859 PMCID: PMC11148546 DOI: 10.1158/0008-5472.can-23-3248] [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: 10/17/2023] [Revised: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 03/21/2024]
Abstract
Defining the initial events in oncogenesis and the cellular responses they entrain, even in advance of morphologic abnormality, is a fundamental challenge in understanding cancer initiation. As a paradigm to address this, we longitudinally studied the changes induced by loss of the tumor suppressor gene von Hippel Lindau (VHL), which ultimately drives clear cell renal cell carcinoma. Vhl inactivation was directly coupled to expression of a tdTomato reporter within a single allele, allowing accurate visualization of affected cells in their native context and retrieval from the kidney for single-cell RNA sequencing. This strategy uncovered cell type-specific responses to Vhl inactivation, defined a proximal tubular cell class with oncogenic potential, and revealed longer term adaptive changes in the renal epithelium and the interstitium. Oncogenic cell tagging also revealed markedly heterogeneous cellular effects including time-limited proliferation and elimination of specific cell types. Overall, this study reports an experimental strategy for understanding oncogenic processes in which cells bearing genetic alterations can be generated in their native context, marked, and analyzed over time. The observed effects of loss of Vhl in kidney cells provide insights into VHL tumor suppressor action and development of renal cell carcinoma. SIGNIFICANCE Single-cell analysis of heterogeneous and dynamic responses to Vhl inactivation in the kidney suggests that early events shape the cell type specificity of oncogenesis, providing a focus for mechanistic understanding and therapeutic targeting.
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Affiliation(s)
- Samvid Kurlekar
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Joanna D C C Lima
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ran Li
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Olivia Lombardi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Norma Masson
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ayslan B Barros
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Virginia Pontecorvi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David R Mole
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Christopher W Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Julie Adam
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter J Ratcliffe
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
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2
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Fang J, Singh S, Wells B, Wu Q, Jin H, Janke LJ, Wan S, Steele JA, Connelly JP, Murphy AJ, Wang R, Davidoff AM, Ashcroft M, Pruett-Miller SM, Yang J. The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven cancer. RESEARCH SQUARE 2024:rs.3.rs-4390765. [PMID: 38853928 PMCID: PMC11160912 DOI: 10.21203/rs.3.rs-4390765/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
3D cellular-specific epigenetic and transcriptomic reprogramming is critical to organogenesis and tumorigenesis. Here we dissect the distinct cell fitness in 2D (normoxia vs. chronic hypoxia) vs 3D (normoxia) culture conditions. We identify over 600 shared essential genes and additional context-specific fitness genes and pathways. Knockout of the VHL-HIF1 pathway results in incompatible fitness defects under normoxia vs. 1% oxygen or 3D culture conditions. Moreover, deletion of each of the mitochondrial respiratory electron transport chain complex has distinct fitness outcomes. Notably, multicellular organogenesis signaling pathways including TGFβ-SMAD specifically constrict the uncontrolled cell proliferation in 3D while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3 and Mettl14) has opposite outcomes in 2D vs. 3D. We further identify a 3D-dependent synthetic lethality with partial loss of Prmt5 due to a reduction of Mtap expression resulting from 3D-specific epigenetic reprogramming. Our study highlights unique epigenetic, metabolic and organogenesis signaling dependencies under different cellular settings.
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Affiliation(s)
- Jie Fang
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shivendra Singh
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brennan Wells
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Qiong Wu
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Laura J. Janke
- Department of Pathology and Division of Comparative Pathology, St. Jude Children’s Research Hospital, TN 38105, USA
| | - Shibiao Wan
- Bioinformatics and Systems Biology Core and Department of Genetics, Cell Biology and Anatomy University of Nebraska Medical Center, Omaha, NE 68198-5805, USA
| | - Jacob A. Steele
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jon P. Connelly
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Andrew J. Murphy
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ruoning Wang
- Center for Childhood Cancer Research, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH 43025, USA
| | - Andrew M. Davidoff
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, TN 38105
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave, Suite 500, Memphis, TN 38163, USA
| | - Margaret Ashcroft
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, TN 38105
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave, Suite 500, Memphis, TN 38163, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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3
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Marallano VJ, Ughetta ME, Tejero R, Nanda S, Ramalingam R, Stalbow L, Sattiraju A, Huang Y, Ramakrishnan A, Shen L, Wojcinski A, Kesari S, Zou H, Tsankov AM, Friedel RH. Hypoxia drives shared and distinct transcriptomic changes in two invasive glioma stem cell lines. Sci Rep 2024; 14:7246. [PMID: 38538643 PMCID: PMC10973515 DOI: 10.1038/s41598-024-56102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/01/2024] [Indexed: 07/12/2024] Open
Abstract
Glioblastoma (GBM) is the most common primary malignant cancer of the central nervous system. Insufficient oxygenation (hypoxia) has been linked to GBM invasion and aggression, leading to poor patient outcomes. Hypoxia induces gene expression for cellular adaptations. However, GBM is characterized by high intertumoral (molecular subtypes) and intratumoral heterogeneity (cell states), and it is not well understood to what extent hypoxia triggers patient-specific gene responses and cellular diversity in GBM. Here, we surveyed eight patient-derived GBM stem cell lines for invasion phenotypes in 3D culture, which identified two GBM lines showing increased invasiveness in response to hypoxia. RNA-seq analysis of the two patient GBM lines revealed a set of shared hypoxia response genes concerning glucose metabolism, angiogenesis, and autophagy, but also a large set of patient-specific hypoxia-induced genes featuring cell migration and anti-inflammation, highlighting intertumoral diversity of hypoxia responses in GBM. We further applied the Shared GBM Hypoxia gene signature to single cell RNA-seq datasets of glioma patients, which showed that hypoxic cells displayed a shift towards mesenchymal-like (MES) and astrocyte-like (AC) states. Interestingly, in response to hypoxia, tumor cells in IDH-mutant gliomas displayed a strong shift to the AC state, whereas tumor cells in IDH-wildtype gliomas mainly shifted to the MES state. This distinct hypoxia response of IDH-mutant gliomas may contribute to its more favorable prognosis. Our transcriptomic studies provide a basis for future approaches to better understand the diversity of hypoxic niches in gliomas.
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Affiliation(s)
- Valerie J Marallano
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mary E Ughetta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rut Tejero
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sidhanta Nanda
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rohana Ramalingam
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lauren Stalbow
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anirudh Sattiraju
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yong Huang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandre Wojcinski
- Pacific Neuroscience Institute and Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Santosh Kesari
- Pacific Neuroscience Institute and Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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4
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Wang L, Fan J, Yang T, Shen J, Wang L, Ge W. Investigating the therapeutic effects and mechanisms of Roxadustat on peritoneal fibrosis Based on the TGF-β/Smad pathway. Biochem Biophys Res Commun 2024; 693:149387. [PMID: 38145606 DOI: 10.1016/j.bbrc.2023.149387] [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: 10/16/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Peritoneal fibrosis (PF) is particularly common in individuals undergoing peritoneal dialysis (PD). Fibrosis of the parenchymal tissue typically progresses slowly. Therefore, preventing and reducing the advancement of fibrosis is crucial for effective patient treatment. Roxadustat is a hypoxia-inducible factor prolyl hydroxylase inhibitor (HIF-PHI), primarily used to treat and improve renal anemia. Recent studies have found that HIF-1α possesses antioxidant activity and exerts a certain protective effect in ischemic heart disease and spinal cord injury, while it can also delay the progression of pulmonary and renal fibrosis. This study establishes the mice model through intraperitoneal injection of 4.25 % peritoneal dialysate fluid (PDF) and explores the therapeutic effects of Roxadustat by inducing TGF-β1-mediated epithelial-mesenchymal transition (EMT) in Met-5A cells. The aim is to investigate the protective role and mechanisms of Roxadustat against PD-related PF. We observed thicker peritoneal tissue and reduced permeability in animals with PD-related PF samples. This was accompanied by heightened inflammation, which Roxadustat alleviated by lowering the levels of inflammatory cytokines (IL-6, TNF-α). Furthermore, Roxadustat inhibited EMT in PF mice and TGF-β1-induced Met-5A cells, as evidenced by decreased expression of fibrotic markers, such as fibronectin, collagen I, and α-SMA, alongside an elevation in the expression of the epithelial marker, E-cadherin. Roxadustat also significantly decreased the expression of TGF-β1 and the phosphorylation of p-Smad2 and p-Smad3. In conclusion, Roxadustat ameliorates peritoneal fibrosis through the TGF-β/Smad pathway.
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Affiliation(s)
- Lingyun Wang
- Department of Pharmacy, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, China
| | - Jiangqing Fan
- Department of Pharmacy, China Pharmaceutical University Nanjing Drum Tower Hospital, China
| | - Ting Yang
- Department of Pharmacy, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, China
| | - Jizhong Shen
- Department of Pharmacy, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, China.
| | - Lulu Wang
- Department of Pharmacy, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, China; Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, The "Double-First Class" Application Characteristic Discipline of Hunan Province (Pharmaceutical Science), Changsha Medical University, Changsha, 410219, China.
| | - Weihong Ge
- Department of Pharmacy, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, China.
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5
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Semenza GL. Mechanisms of Breast Cancer Stem Cell Specification and Self-Renewal Mediated by Hypoxia-Inducible Factor 1. Stem Cells Transl Med 2023; 12:783-790. [PMID: 37768037 PMCID: PMC10726407 DOI: 10.1093/stcltm/szad061] [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: 03/22/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023] Open
Abstract
Many advanced human cancers contain regions of intratumoral hypoxia, with O2 gradients extending to anoxia. Hypoxia-inducible factors (HIFs) are activated in hypoxic cancer cells and drive metabolic reprogramming, vascularization, invasion, and metastasis. Hypoxia induces breast cancer stem cell (BCSC) specification by inducing the expression and/or activity of the pluripotency factors KLF4, NANOG, OCT4, and SOX2. Recent studies have identified HIF-1-dependent expression of PLXNB3, NARF, and TERT in hypoxic breast cancer cells. PLXNB3 binds to and activates the MET receptor tyrosine kinase, leading to activation of the SRC non-receptor tyrosine kinase and subsequently focal adhesion kinase, which promotes cancer cell migration and invasion. PLXNB3-MET-SRC signaling also activates STAT3, a transcription factor that mediates increased NANOG gene expression. Hypoxia-induced NARF binds to OCT4 and serves as a coactivator by stabilizing OCT4 binding to the KLF4, NANOG, and SOX2 genes and by stabilizing the interaction of OCT4 with KDM6A, a histone demethylase that erases repressive trimethylation of histone H3 at lysine 27, thereby increasing KLF4, NANOG, and SOX2 gene expression. In addition to increasing pluripotency factor expression by these mechanisms, HIF-1 directly activates expression of the TERT gene encoding telomerase, the enzyme required for maintenance of telomeres, which is required for the unlimited self-renewal of BCSCs. HIF-1 binds to the TERT gene and recruits NANOG, which serves as a coactivator by promoting the subsequent recruitment of USP9X, a deubiquitinase that inhibits HIF-1α degradation, and p300, a histone acetyltransferase that mediates acetylation of H3K27, which is required for transcriptional activation.
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Affiliation(s)
- Gregg L Semenza
- Armstrong Oxygen Biology Research Center, Institute for Cell Engineering, and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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6
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Zhu Q, Zhao X, Zhang Y, Li Y, Liu S, Han J, Sun Z, Wang C, Deng D, Wang S, Tang Y, Huang Y, Jiang S, Tian C, Chen X, Yuan Y, Li Z, Yang T, Lai T, Liu Y, Yang W, Zou X, Zhang M, Cui H, Liu C, Jin X, Hu Y, Chen A, Xu X, Li G, Hou Y, Liu L, Liu S, Fang L, Chen W, Wu L. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. Nat Commun 2023; 14:8170. [PMID: 38071219 PMCID: PMC10710513 DOI: 10.1038/s41467-023-43991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Human cancer cell lines have long served as tools for cancer research and drug discovery, but the presence and the source of intra-cell-line heterogeneity remain elusive. Here, we perform single-cell RNA-sequencing and ATAC-sequencing on 42 and 39 human cell lines, respectively, to illustrate both transcriptomic and epigenetic heterogeneity within individual cell lines. Our data reveal that transcriptomic heterogeneity is frequently observed in cancer cell lines of different tissue origins, often driven by multiple common transcriptional programs. Copy number variation, as well as epigenetic variation and extrachromosomal DNA distribution all contribute to the detected intra-cell-line heterogeneity. Using hypoxia treatment as an example, we demonstrate that transcriptomic heterogeneity could be reshaped by environmental stress. Overall, our study performs single-cell multi-omics of commonly used human cancer cell lines and offers mechanistic insights into the intra-cell-line heterogeneity and its dynamics, which would serve as an important resource for future cancer cell line-based studies.
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Affiliation(s)
- Qionghua Zhu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Xin Zhao
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanhang Zhang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanping Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Shang Liu
- BGI Research, 518083, Shenzhen, China
| | - Jingxuan Han
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Zhiyuan Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Chunqing Wang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Daqi Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Yisen Tang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Siyuan Jiang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chi Tian
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xi Chen
- BGI Research, 518083, Shenzhen, China
| | - Yue Yuan
- BGI Research, 518083, Shenzhen, China
| | - Zeyu Li
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tao Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Tingting Lai
- China National GeneBank, 518120, Shenzhen, China
| | - Yiqun Liu
- China National GeneBank, 518120, Shenzhen, China
| | - Wenzhen Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Xuanxuan Zou
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | | | - Huanhuan Cui
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Xin Jin
- BGI Research, 518083, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Ao Chen
- BGI Research, 518083, Shenzhen, China
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China
| | - Xun Xu
- BGI Research, 518083, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yong Hou
- BGI Research, 518083, Shenzhen, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China
| | - Longqi Liu
- BGI Research, 518083, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Shiping Liu
- BGI Research, 518083, Shenzhen, China.
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Liang Wu
- BGI Research, 518083, Shenzhen, China.
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China.
- BGI Research, 401329, Chongqing, China.
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7
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Naas S, Schiffer M, Schödel J. Hypoxia and renal fibrosis. Am J Physiol Cell Physiol 2023; 325:C999-C1016. [PMID: 37661918 DOI: 10.1152/ajpcell.00201.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Renal fibrosis is the final stage of most progressive kidney diseases. Chronic kidney disease (CKD) is associated with high comorbidity and mortality. Thus, preventing fibrosis and thereby preserving kidney function increases the quality of life and prolongs the survival of patients with CKD. Many processes such as inflammation or metabolic stress modulate the progression of kidney fibrosis. Hypoxia has also been implicated in the pathogenesis of renal fibrosis, and oxygen sensing in the kidney is of outstanding importance for the body. The dysregulation of oxygen sensing in the diseased kidney is best exemplified by the loss of stimulation of erythropoietin production from interstitial cells in the fibrotic kidney despite anemia. Furthermore, hypoxia is present in acute or chronic kidney diseases and may affect all cell types present in the kidney including tubular and glomerular cells as well as resident immune cells. Pro- and antifibrotic effects of the transcription factors hypoxia-inducible factors 1 and 2 have been described in a plethora of animal models of acute and chronic kidney diseases, but recent advances in sequencing technologies now allow for novel and deeper insights into the role of hypoxia and its cell type-specific effects on the progression of renal fibrosis, especially in humans. Here, we review existing literature on how hypoxia impacts the development and progression of renal fibrosis.
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Affiliation(s)
- Stephanie Naas
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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8
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Shao B, Ye Z, Sun B, Xiao Z. Molecular Evolutionary Landscape of the Immune Microenvironment of Head and Neck Cancer. Biomolecules 2023; 13:1120. [PMID: 37509156 PMCID: PMC10377423 DOI: 10.3390/biom13071120] [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: 05/04/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer is a highly heterogeneous malignant tumor. Numerous studies have shown that the immune microenvironment of head and neck cancer has a significant impact on its occurrence and development, as well as its prognosis. However, there have been fewer studies related to the accurate immunophenotyping of head and neck cancer. In this study, we used gene expression profile information and clinical information from the TCGA-HNSC cohort (502 samples) and the GSE655858 cohort (270 samples) to identify and independently validate three immune subtypes (Cluster1-Cluster3) with different immune-related molecular profiles and clinical outcomes. Cluster2, which is mainly dominated by B-lymphocyte infiltration, was found to have the best prognosis. In addition, a support vector machine (SVM)-based classifier was constructed, which could accurately classify HNSC based on 19 genes. Furthermore, the results of the prognostic analysis showed activation of antibody-secreting B-lymphocyte function, which showed a good prognostic effect in all three immune subtypes of HNSC. Finally, the immune evolutionary landscape of HNSC was constructed in an attempt to explain the evolutionary pattern of the immune subtypes of HNSC. In summary, we provide a conceptual framework for understanding the tumor immune microenvironment in HNSC and demonstrate the importance of immune infiltration of B lymphocytes in HNSC. Further research is needed to assess the importance of these immunophenotypes in combination drug therapy and to provide a basis for screening appropriate patients for immunotherapy.
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Affiliation(s)
- Baoyi Shao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zheng Ye
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Bo Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhongdang Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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