1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Hu H, Liu F, Gao P, Huang Y, Jia D, Reilly J, Chen X, Han Y, Sun K, Luo J, Li P, Zhang Z, Wang Q, Lu Q, Luo D, Shu X, Tang Z, Liu M, Ren X. Cross-species single-cell landscapes identify the pathogenic gene characteristics of inherited retinal diseases. Front Genet 2024; 15:1409016. [PMID: 39055259 PMCID: PMC11269129 DOI: 10.3389/fgene.2024.1409016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/30/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Inherited retinal diseases (IRDs) affect ∼4.5 million people worldwide. Elusive pathogenic variants in over 280 genes are associated with one or more clinical forms of IRDs. It is necessary to understand the complex interaction among retinal cell types and pathogenic genes by constructing a regulatory network. In this study, we attempt to establish a panoramic expression view of the cooperative work in retinal cells to understand the clinical manifestations and pathogenic bases underlying IRDs. Methods Single-cell RNA sequencing (scRNA-seq) data on the retinas from 35 retina samples of 3 species (human, mouse, and zebrafish) including 259,087 cells were adopted to perform a comparative analysis across species. Bioinformatic tools were used to conduct weighted gene co-expression network analysis (WGCNA), single-cell regulatory network analysis, cell-cell communication analysis, and trajectory inference analysis. Results The cross-species comparison revealed shared or species-specific gene expression patterns at single-cell resolution, such as the stathmin family genes, which were highly expressed specifically in zebrafish Müller glias (MGs). Thirteen gene modules were identified, of which nine were associated with retinal cell types, and Gene Ontology (GO) enrichment of module genes was consistent with cell-specific highly expressed genes. Many IRD genes were identified as hub genes and cell-specific regulons. Most IRDs, especially the retinitis pigmentosa (RP) genes, were enriched in rod-specific regulons. Integrated expression and transcription regulatory network genes, such as congenital stationary night blindness (CSNB) genes GRK1, PDE6B, and TRPM1, showed cell-specific expression and transcription characteristics in either rods or bipolar cells (BCs). IRD genes showed evolutionary conservation (GNAT2, PDE6G, and SAG) and divergence (GNAT2, MT-ND4, and PDE6A) along the trajectory of photoreceptors (PRs) among species. In particular, the Leber congenital amaurosis (LCA) gene OTX2 showed high expression at the beginning of the trajectory of both PRs and BCs. Conclusion We identified molecular pathways and cell types closely connected with IRDs, bridging the gap between gene expression, genetics, and pathogenesis. The IRD genes enriched in cell-specific modules and regulons suggest that these diseases share common etiological bases. Overall, mining of interspecies transcriptome data reveals conserved transcriptomic features of retinas across species and promising applications in both normal retina anatomy and retina pathology.
Collapse
Affiliation(s)
- Hualei Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jamas Reilly
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jiong Luo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pei Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zuxiao Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Daji Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinhua Shu
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
3
|
Kaushik A, Chang I, Han X, He Z, Komlosi ZI, Ji X, Cao S, Akdis CA, Boyd S, Pulendran B, Maecker HT, Davis MM, Chinthrajah RS, DeKruyff RH, Nadeau KC. Single cell multi-omic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients. Front Immunol 2024; 15:1374828. [PMID: 39026668 PMCID: PMC11255397 DOI: 10.3389/fimmu.2024.1374828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction Innate lymphoid cells (ILCs) are enriched at mucosal surfaces where they respond rapidly to environmental stimuli and contribute to both tissue inflammation and healing. Methods To gain insight into the role of ILCs in the pathology and recovery from COVID-19 infection, we employed a multi-omics approach consisting of Abseq and targeted mRNA sequencing to respectively probe the surface marker expression, transcriptional profile and heterogeneity of ILCs in peripheral blood of patients with COVID-19 compared with healthy controls. Results We found that the frequency of ILC1 and ILC2 cells was significantly increased in COVID-19 patients. Moreover, all ILC subsets displayed a significantly higher frequency of CD69-expressing cells, indicating a heightened state of activation. ILC2s from COVID-19 patients had the highest number of significantly differentially expressed (DE) genes. The most notable genes DE in COVID-19 vs healthy participants included a) genes associated with responses to virus infections and b) genes that support ILC self-proliferation, activation and homeostasis. In addition, differential gene regulatory network analysis revealed ILC-specific regulons and their interactions driving the differential gene expression in each ILC. Discussion Overall, this study provides mechanistic insights into the characteristics of ILC subsets activated during COVID-19 infection.
Collapse
Affiliation(s)
- Abhinav Kaushik
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Iris Chang
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Xiaorui Han
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Ziyuan He
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Zsolt I. Komlosi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
- Swiss Institute of Allergy and Asthma (SIAF), University of Zurich, Davos, Switzerland
| | - Xuhuai Ji
- Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Shu Cao
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Cezmi A. Akdis
- Swiss Institute of Allergy and Asthma (SIAF), University of Zurich, Davos, Switzerland
- Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
| | - Scott Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Bali Pulendran
- Department of Pathology, Stanford University, Stanford, CA, United States
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Holden T. Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, United States
| | - Mark M. Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - R. Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Rosemarie H. DeKruyff
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| |
Collapse
|
4
|
Grothusen GP, Chang R, Cao Z, Zhou N, Mittal M, Datta A, Wulfridge P, Beer T, Wang B, Zheng N, Tang HY, Sarma K, Greenberg RA, Shi J, Busino L. DCAF15 control of cohesin dynamics sustains acute myeloid leukemia. Nat Commun 2024; 15:5604. [PMID: 38961054 PMCID: PMC11222469 DOI: 10.1038/s41467-024-49882-x] [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: 08/03/2023] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
The CRL4-DCAF15 E3 ubiquitin ligase complex is targeted by the aryl-sulfonamide molecular glues, leading to neo-substrate recruitment, ubiquitination, and proteasomal degradation. However, the physiological function of DCAF15 remains unknown. Using a domain-focused genetic screening approach, we reveal DCAF15 as an acute myeloid leukemia (AML)-biased dependency. Loss of DCAF15 results in suppression of AML through compromised replication fork integrity and consequent accumulation of DNA damage. Accordingly, DCAF15 loss sensitizes AML to replication stress-inducing therapeutics. Mechanistically, we discover that DCAF15 directly interacts with the SMC1A protein of the cohesin complex and destabilizes the cohesin regulatory factors PDS5A and CDCA5. Loss of PDS5A and CDCA5 removal precludes cohesin acetylation on chromatin, resulting in uncontrolled chromatin loop extrusion, defective DNA replication, and apoptosis. Collectively, our findings uncover an endogenous, cell autonomous function of DCAF15 in sustaining AML proliferation through post-translational control of cohesin dynamics.
Collapse
Affiliation(s)
- Grant P Grothusen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renxu Chang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhendong Cao
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nan Zhou
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monika Mittal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arindam Datta
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phillip Wulfridge
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Thomas Beer
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Baiyun Wang
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Kavitha Sarma
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luca Busino
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
5
|
Prathipati P, Pathania AS, Chaturvedi NK, Gupta SC, Byrareddy SN, Coulter DW, Challagundla KB. SAP30, an oncogenic driver of progression, poor survival, and drug resistance in neuroblastoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:101543. [PMID: 38817681 PMCID: PMC11137595 DOI: 10.1016/j.omtn.2022.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/18/2022] [Indexed: 06/01/2024]
Abstract
Neuroblastoma is the most devastating extracranial solid malignancy in children. Despite an intense treatment regimen, the prognosis for high-risk neuroblastoma patients remains poor, with less than 40% survival. So far, MYCN amplification status is considered the most prognostic factor but corresponds to only ∼25% of neuroblastoma patients. Therefore, it is essential to identify a better prognosis and therapy response marker in neuroblastoma patients. We applied robust bioinformatic data mining tools, such as weighted gene co-expression network analysis, cisTarget, and single-cell regulatory network inference and clustering on two neuroblastoma patient datasets. We found Sin3A-associated protein 30 (SAP30), a driver transcription factor positively associated with high-risk, progression, stage 4, and poor survival in neuroblastoma patient cohorts. Tumors of high-risk neuroblastoma patients and relapse-specific patient-derived xenografts showed higher SAP30 levels. The advanced pharmacogenomic analysis and CRISPR-Cas9 screens indicated that SAP30 essentiality is associated with cisplatin resistance and further showed higher levels in cisplatin-resistant patient-derived xenograft tumor cell lines. Silencing of SAP30 induced cell death in vitro and led to a reduced tumor burden and size in vivo. Altogether, these results indicate that SAP30 is a better prognostic and cisplatin-resistance marker and thus a potential drug target in high-risk neuroblastoma.
Collapse
Affiliation(s)
- Philip Prathipati
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
| | - Anup S. Pathania
- Department of Biochemistry and Molecular Biology & Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nagendra K. Chaturvedi
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Subash C. Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Siddappa N. Byrareddy
- Department of Biochemistry and Molecular Biology & Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Don W. Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishore B. Challagundla
- Department of Biochemistry and Molecular Biology & Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- The Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
6
|
De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nat Biotechnol 2024; 42:916-926. [PMID: 37537502 PMCID: PMC11180611 DOI: 10.1038/s41587-023-01881-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/22/2023] [Indexed: 08/05/2023]
Abstract
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.
Collapse
Grants
- R01 DA047237 NIDA NIH HHS
- R00 AG059918 NIA NIH HHS
- U19 AI057266 NIAID NIH HHS
- G0B5619N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
- RF1 MH128842 NIMH NIH HHS
- UM1 HG009436 NHGRI NIH HHS
- 1S80920N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
- UM1 HG012076 NHGRI NIH HHS
- RM1 HG007735 NHGRI NIH HHS
- G094121N Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
- R35 GM124704 NIGMS NIH HHS
- UM1 HG009442 NHGRI NIH HHS
- Wellcome Trust
- H.H. received support for the project PID2020-115439GB-I00- funded by MCIN/AEI/ 10.13039/501100011033. This publication is also supported as part of a project (BCLLATLAS and ESPACE) that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement No 810287 and 874710).
- M.R.C. is supported by the National Institutes on Aging K99/R00AG059918.
- K.B.M. is supported by Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194).
- S.A.T. is supported by Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194).
- This work was supported by funding from the Rita Allen Foundation (W.J.G.), the Human Frontiers Science (RGY006S) (W.J.G.). W.J.G. is a Chan Zuckerberg Biohub investigator and acknowledges grants 2017-174468 and 2018-182817 from the Chan Zuckerberg Initiative, and the National Institutes of Health grants RM1-HG007735, UM1-HG009442, UM1-HG009436, R01- HG00990901, and U19- AI057266 (to W.J.G.). W.J.G. acknowledges funding from Emerson Collective.
- This work was supported by an ERC Consolidator Grant to S.A. (no. 724226_cis- CONTROL), KU Leuven (grant no. C14/22/125 to S.A.), Foundation Against Cancer (grant no, F/2020/1396 to S.A.), F.W.O. (grants G0I2722N, G0B5619N and G094121N to S.A.), Aligning Science Across Parkinson’s (ASAP, grant no. ASAP-000430 to S.A.)
Collapse
Affiliation(s)
- Florian V De Rop
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chris Flerin
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Albert Rafels
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Valerie Christiaens
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | | | - Wendy Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Fabiana Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | | | | | | | - Ryan Mulqueen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Akram Taherinasab
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
| | - Patrick Maschmeyer
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Jörn Pezoldt
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Camille Lucie Germaine Lambert
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Marta Iglesias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sebastián R Najle
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Zain Y Dossani
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Luciano G Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Zach Burkett
- Digital Biology Group, Bio-Rad, Pleasanton, CA, USA
| | | | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Satish Pillai
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Arnau Sebé-Pedrós
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics/Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Theodore P Braun
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute of Integrative Cancer Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Stein Aerts
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
7
|
Xiao Y, Jin W, Qian K, Ju L, Wang G, Wu K, Cao R, Chang L, Xu Z, Luo J, Shan L, Yu F, Chen X, Liu D, Cao H, Wang Y, Cao X, Zhou W, Cui D, Tian Y, Ji C, Luo Y, Hong X, Chen F, Peng M, Zhang Y, Wang X. Integrative Single Cell Atlas Revealed Intratumoral Heterogeneity Generation from an Adaptive Epigenetic Cell State in Human Bladder Urothelial Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308438. [PMID: 38582099 PMCID: PMC11200000 DOI: 10.1002/advs.202308438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/22/2024] [Indexed: 04/08/2024]
Abstract
Intratumor heterogeneity (ITH) of bladder cancer (BLCA) contributes to therapy resistance and immune evasion affecting clinical prognosis. The molecular and cellular mechanisms contributing to BLCA ITH generation remain elusive. It is found that a TM4SF1-positive cancer subpopulation (TPCS) can generate ITH in BLCA, evidenced by integrative single cell atlas analysis. Extensive profiling of the epigenome and transcriptome of all stages of BLCA revealed their evolutionary trajectories. Distinct ancestor cells gave rise to low-grade noninvasive and high-grade invasive BLCA. Epigenome reprograming led to transcriptional heterogeneity in BLCA. During early oncogenesis, epithelial-to-mesenchymal transition generated TPCS. TPCS has stem-cell-like properties and exhibited transcriptional plasticity, priming the development of transcriptionally heterogeneous descendent cell lineages. Moreover, TPCS prevalence in tumor is associated with advanced stage cancer and poor prognosis. The results of this study suggested that bladder cancer interacts with its environment by acquiring a stem cell-like epigenomic landscape, which might generate ITH without additional genetic diversification.
Collapse
Affiliation(s)
- Yu Xiao
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Wan Jin
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
- Euler TechnologyBeijing102206China
| | - Kaiyu Qian
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Lingao Ju
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Gang Wang
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Kai Wu
- Euler TechnologyBeijing102206China
| | - Rui Cao
- Department of UrologyBeijing Friendship HospitalCapital Medical UniversityBeijing100050China
| | | | - Zilin Xu
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Jun Luo
- Department of PathologyZhongnan Hospital of Wuhan UniversityWuhan430071China
| | | | - Fang Yu
- Department of PathologyZhongnan Hospital of Wuhan UniversityWuhan430071China
| | | | | | - Hong Cao
- Department of PathologyZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Yejinpeng Wang
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Xinyue Cao
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
- Clinical Trial CenterZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Wei Zhou
- Hubei Key Laboratory of Medical Technology on TransplantationInstitute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan UniversityWuhan430071China
| | - Diansheng Cui
- Department of UrologyHubei Cancer HospitalWuhan430079China
| | - Ye Tian
- Department of UrologyBeijing Friendship HospitalCapital Medical UniversityBeijing100050China
| | - Chundong Ji
- Department of UrologyThe Affiliated Hospital of Panzhihua UniversityPanzhihua617099China
| | - Yongwen Luo
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Xin Hong
- Department of UrologyPeking University International HospitalBeijing102206China
| | - Fangjin Chen
- Center for Quantitative BiologySchool of Life SciencesPeking UniversityBeijing100091China
| | - Minsheng Peng
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunming650201China
- Kunming College of Life ScienceUniversity of Academy of SciencesKunming650201China
| | - Yi Zhang
- Euler TechnologyBeijing102206China
| | - Xinghuan Wang
- Department of Urology, Hubei Key Laboratory of Urological Diseases, Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
- Medical Research InstituteWuhan UniversityWuhan430071China
| |
Collapse
|
8
|
Gong X, He W, Jin W, Ma H, Wang G, Li J, Xiao Y, Zhao Y, Chen Q, Guo H, Yang J, Qi Y, Dong W, Fu M, Li X, Liu J, Liu X, Yin A, Zhang Y, Wei Y. Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia. Genome Biol 2024; 25:117. [PMID: 38715110 PMCID: PMC11075363 DOI: 10.1186/s13059-024-03265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. RESULTS By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia is attributed to immature trophoblast and maldeveloped endothelial cells. Delayed epigenetic reprogramming during early extraembryonic tissue development leads to generation of excessive immature trophoblast cells. We find reduction of de novo DNA methylation in these trophoblast cells results in selective overexpression of maternally imprinted genes, including the endoretrovirus-derived gene PEG10 (paternally expressed gene 10). PEG10 forms virus-like particles, which are transferred from the trophoblast to the closely proximate endothelial cells. In normal pregnancy, only a low amount of PEG10 is transferred to maternal cells; however, in preeclampsia, excessive PEG10 disrupts maternal vascular development by inhibiting TGF-beta signaling. CONCLUSIONS Our study reveals the intricate epigenetic mechanisms that regulate trans-generational genetic conflict and ultimately ensure proper maternal-fetal interface formation.
Collapse
Affiliation(s)
- Xiaoli Gong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wei He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wan Jin
- Euler Technology, Beijing, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Ma
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiaxin Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | | | | | - Jiexia Yang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Dong
- Maternity Ward, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Meng Fu
- Department of Obstetrics and Gynecology, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiaojuan Li
- Euler Technology, Beijing, China
- Present Address: International Max Planck Research School for Genome Science, and University of Göttingen, Göttingen Center for Molecular Biosciences, Göttingen, Germany
| | | | - Xinghui Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China.
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China.
| | - Yi Zhang
- Euler Technology, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
| |
Collapse
|
9
|
Zhang G, Fu Y, Yang L, Ye F, Zhang P, Zhang S, Ma L, Li J, Wu H, Han X, Wang J, Guo G. Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq. Dev Cell 2024; 59:793-811.e8. [PMID: 38330939 DOI: 10.1016/j.devcel.2024.01.015] [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: 06/01/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
Despite recent advances in single-cell genomics, the lack of maps for single-cell candidate cis-regulatory elements (cCREs) in non-mammal species has limited our exploration of conserved regulatory programs across vertebrates and invertebrates. Here, we developed a combinatorial-hybridization-based method for single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) named CH-ATAC-seq, enabling the construction of single-cell accessible chromatin landscapes for zebrafish, Drosophila, and earthworms (Eisenia andrei). By integrating scATAC censuses of humans, monkeys, and mice, we systematically identified 152 distinct main cell types and around 0.8 million cell-type-specific cCREs. Our analysis provided insights into the conservation of neural, muscle, and immune lineages across species, while epithelial cells exhibited a higher organ-origin heterogeneity. Additionally, a large-scale gene regulatory network (GRN) was constructed in four vertebrates by integrating scRNA-seq censuses. Overall, our study provides a valuable resource for comparative epigenomics, identifying the evolutionary conservation and divergence of gene regulation across different species.
Collapse
Affiliation(s)
- Guodong Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Shuang Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Hanyu Wu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China.
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China.
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou, China.
| |
Collapse
|
10
|
Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S, Alsinet C, Caratù G, Moutinho C, Ruiz S, Lorden P, Lunazzi G, Colomer D, Frigola G, Blevins W, Romero-Rivero L, Jiménez-Martínez V, Vidal A, Mateos-Jaimez J, Maiques-Diaz A, Ovejero S, Moreaux J, Palomino S, Gomez-Cabrero D, Agirre X, Weniger MA, King HW, Garner LC, Marini F, Cervera-Paz FJ, Baptista PM, Vilaseca I, Rosales C, Ruiz-Gaspà S, Talks B, Sidhpura K, Pascual-Reguant A, Hauser AE, Haniffa M, Prosper F, Küppers R, Gut IG, Campo E, Martin-Subero JI, Heyn H. An atlas of cells in the human tonsil. Immunity 2024; 57:379-399.e18. [PMID: 38301653 PMCID: PMC10869140 DOI: 10.1016/j.immuni.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.
Collapse
Affiliation(s)
| | | | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marco Matteo Bühler
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Sonal Rashmi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Clara Alsinet
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Catia Moutinho
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Sara Ruiz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Patricia Lorden
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Giulia Lunazzi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Will Blevins
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Lucia Romero-Rivero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Anna Vidal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Judith Mateos-Jaimez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Maiques-Diaz
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France; Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Sara Palomino
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Hamish W King
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Peter M Baptista
- Department of Otorhinolaryngology, University of Navarra, Pamplona, Spain
| | - Isabel Vilaseca
- Otorhinolaryngology Head-Neck Surgery Department, Hospital Clínic, IDIBAPS Universitat de Barcelona, Barcelona, Spain
| | - Cecilia Rosales
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Benjamin Talks
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Otolaryngology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Keval Sidhpura
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anna Pascual-Reguant
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Felipe Prosper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Departamento de Hematología, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Ivo Glynne Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
11
|
Liu W, Huang K, Yang XZ, Wang P. Transcriptomic and network analysis identifies shared and unique pathways and immune changes across fibrotic interstitial lung diseases. Aging (Albany NY) 2024; 16:3200-3230. [PMID: 38349858 PMCID: PMC10929820 DOI: 10.18632/aging.205530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/01/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Interstitial lung disease (ILD) encompasses a diverse group of disorders characterized by chronic inflammation and fibrosis of the pulmonary interstitium. Three ILDs, namely idiopathic pulmonary fibrosis (IPF), fibrotic hypersensitivity pneumonitis (fHP), and connective tissue disease-associated ILD (CTD-ILD), exhibit similar progressive fibrosis phenotypes, yet possess distinct etiologies, encouraging us to explore their different underlying mechanisms. METHODS Transcriptome data of fibrotic lung tissues from patients with IPF, fHP, and CTD-ILD were subjected to functional annotation, network, and pathway analyses. Additionally, we employed the xCell deconvolution algorithm to predict immune cell infiltration in patients with fibrotic ILDs and healthy controls. RESULTS We identified a shared progressive fibrosis-related module in these diseases which was related to extracellular matrix (ECM) degradation and production and potentially regulated by the p53 family transcription factors. In IPF, neuron-related processes emerged as a critical specific mechanism in functional enrichment. In fHP, we observed that B cell signaling and immunoglobulin A (IgA) production may act as predominant processes, which was further verified by B cell infiltration and the central role of CD19 gene. In CTD-ILD, active chemokine processes were enriched, and active dendritic cells (aDCs) were predicted to infiltrate the lung tissues. CONCLUSIONS This study revealed shared and specific molecular and cellular pathways among IPF, fHP, and CTD-ILD, providing a basis for understanding their pathogenesis and identifying potential therapeutic targets.
Collapse
Affiliation(s)
- Wenhao Liu
- Eight-Year Program of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Kangping Huang
- Eight-Year Program of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xin-Zhuang Yang
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine and Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Ping Wang
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
12
|
Wang M, Liu Y, Sun R, Liu F, Li J, Yan L, Zhang J, Xie X, Li D, Wang Y, Li S, Zhu X, Li R, Lu F, Xiao Z, Wang H. Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy. Nat Genet 2024; 56:294-305. [PMID: 38267607 PMCID: PMC10864176 DOI: 10.1038/s41588-023-01647-w] [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: 07/26/2022] [Accepted: 12/11/2023] [Indexed: 01/26/2024]
Abstract
The human placenta has a vital role in ensuring a successful pregnancy. Despite the growing body of knowledge about its cellular compositions and functions, there has been limited research on the heterogeneity of the billions of nuclei within the syncytiotrophoblast (STB), a multinucleated entity primarily responsible for placental function. Here we conducted integrated single-nucleus RNA sequencing and single-nucleus ATAC sequencing analyses of human placentas from early and late pregnancy. Our findings demonstrate the dynamic heterogeneity and developmental trajectories of STB nuclei and their correspondence with human trophoblast stem cell (hTSC)-derived STB. Furthermore, we identified transcription factors associated with diverse STB nuclear lineages through their gene regulatory networks and experimentally confirmed their function in hTSC and trophoblast organoid-derived STBs. Together, our data provide insights into the heterogeneity of human STB and represent a valuable resource for interpreting associated pregnancy complications.
Collapse
Affiliation(s)
- Meijiao Wang
- The Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yawei Liu
- The Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
- Medical Center of Soochow University, Suzhou, China
- Suzhou Dushu Lake Hospital, Suzhou, China
| | - Run Sun
- The Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fenting Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, China
| | - Jiaqian Li
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Long Yan
- The Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jixiang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinwei Xie
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Dongxu Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiming Wang
- The Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shiwen Li
- The Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xili Zhu
- The Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Peking University Third Hospital, Beijing, China.
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Zhenyu Xiao
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- School of Life Science, Beijing Institute of Technology, Beijing, China.
| | - Hongmei Wang
- The Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
13
|
Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Santos CP, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O, Albertin CB. Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology. Integr Comp Biol 2023; 63:1226-1239. [PMID: 37370232 PMCID: PMC10755191 DOI: 10.1093/icb/icad087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.
Collapse
Affiliation(s)
- Tom Baden
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - John Briseño
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Gabrielle Coffing
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Sophie Cohen-Bodénès
- Laboratoire des Systèmes Perceptifs, Département d'Etudes Cognitives, Ecole Normale Supérieure, PSL University, CNRS, 75005 Paris, France
| | - Amy Courtney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Dominick Dickerson
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Gül Dölen
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Camino Gestal
- Laboratory of Marine Molecular Pathobiology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo 36208, Spain
| | | | - Elizabeth Heath-Heckman
- Departments of Integrative Biology and Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaz Hua
- Department of Ecology and Evolution, University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Ryosuke Kimbara
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Kanagawa 238-0225, Japan
| | - Mirela Król
- Adam Mickiewicz University in Poznań, Poznań 61-712, Poland
| | - Zdeněk Lajbner
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | - Nicolás Lichilín
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, P.O. Box 129188 Abu Dhabi, United Arab Emirates
| | - Matthew J McCoy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michele K Nishiguchi
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Spencer V Nyholm
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Eve Otjacques
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
- Division of Biosphere Sciences and Engineering, Carnegie Institution for Science, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Pedro Antonio Pérez-Ferrer
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 N. Lake Blvd., Merced, CA 95343, USA
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
| | - Judit R Pungor
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Thea F Rogers
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Joshua J C Rosenthal
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
| | - Lisa Rouressol
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Noelle Rubas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii Manoa, Honolulu, HI 96822, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Catarina Pereira Santos
- MARE—Marine and Environmental Sciences Centre & ARNET—Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
| | - Darrin T Schultz
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Jeremea O Songco-Casey
- Biology Department: Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - Ian Erik Stewart
- Neural Circuits and Behaviour Lab, Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany
| | - Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Surangkana Tuanapaya
- Laboratory of genetics and applied breeding of molluscs, Fisheries College, Ocean University of China, Qingdao 266100, China
| | - Nidhi Vijayan
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT 06269, USA
| | | | - Lucia Zifcakova
- Physics and Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495, Japan
| | | | - Willem Weertman
- Friday Harbor Laboratory, University of Washington, Seattle, WA 98250, USA
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Caroline B Albertin
- Marine Biological Laboratory, The Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA 02543-1015, USA
| |
Collapse
|
14
|
Kosakamoto H, Obata F, Kuraishi J, Aikawa H, Okada R, Johnstone JN, Onuma T, Piper MDW, Miura M. Early-adult methionine restriction reduces methionine sulfoxide and extends lifespan in Drosophila. Nat Commun 2023; 14:7832. [PMID: 38052797 DOI: 10.1038/s41467-023-43550-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
Methionine restriction (MetR) extends lifespan in various organisms, but its mechanistic understanding remains incomplete. Whether MetR during a specific period of adulthood increases lifespan is not known. In Drosophila, MetR is reported to extend lifespan only when amino acid levels are low. Here, by using an exome-matched holidic medium, we show that decreasing Met levels to 10% extends Drosophila lifespan with or without decreasing total amino acid levels. MetR during the first four weeks of adult life only robustly extends lifespan. MetR in young flies induces the expression of many longevity-related genes, including Methionine sulfoxide reductase A (MsrA), which reduces oxidatively-damaged Met. MsrA induction is foxo-dependent and persists for two weeks after cessation of the MetR diet. Loss of MsrA attenuates lifespan extension by early-adulthood MetR. Our study highlights the age-dependency of the organismal response to specific nutrients and suggests that nutrient restriction during a particular period of life is sufficient for healthspan extension.
Collapse
Affiliation(s)
- Hina Kosakamoto
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan
| | - Fumiaki Obata
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan.
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
| | - Junpei Kuraishi
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hide Aikawa
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Rina Okada
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan
| | - Joshua N Johnstone
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Taro Onuma
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan
| | - Matthew D W Piper
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
15
|
Bollepogu Raja KK, Yeung K, Shim YK, Li Y, Chen R, Mardon G. A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines. Nat Commun 2023; 14:7205. [PMID: 37938573 PMCID: PMC10632452 DOI: 10.1038/s41467-023-43037-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
The Drosophila eye is a powerful model system to study the dynamics of cell differentiation, cell state transitions, cell maturation, and pattern formation. However, a high-resolution single cell genomics resource that accurately profiles all major cell types of the larval eye disc and their spatiotemporal relationships is lacking. Here, we report transcriptomic and chromatin accessibility data for all known cell types in the developing eye. Photoreceptors appear as strands of cells that represent their dynamic developmental timelines. As photoreceptor subtypes mature, they appear to assume a common transcriptomic profile that is dominated by genes involved in axon function. We identify cell type maturation genes, enhancers, and potential regulators, as well as genes with distinct R3 or R4 photoreceptor specific expression. Finally, we observe that the chromatin accessibility between cones and photoreceptors is distinct. These single cell genomics atlases will greatly enhance the power of the Drosophila eye as a model system.
Collapse
Affiliation(s)
- Komal Kumar Bollepogu Raja
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Kelvin Yeung
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yoon-Kyung Shim
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| |
Collapse
|
16
|
Rader AE, Bayarmagnai B, Frolov MV. Combined inactivation of RB and Hippo converts differentiating Drosophila photoreceptors into eye progenitor cells through derepression of homothorax. Dev Cell 2023; 58:2261-2274.e6. [PMID: 37848027 PMCID: PMC10842633 DOI: 10.1016/j.devcel.2023.09.003] [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: 12/27/2022] [Revised: 08/06/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
The retinoblastoma (RB) and Hippo pathways interact to regulate cell proliferation and differentiation. However, the mechanism of interaction is not fully understood. Drosophila photoreceptors with inactivated RB and Hippo pathways specify normally but fail to maintain their neuronal identity and dedifferentiate. We performed single-cell RNA sequencing to elucidate the cause of dedifferentiation and to determine the fate of these cells. We find that dedifferentiated cells adopt a progenitor-like fate due to inappropriate activation of the retinal differentiation suppressor homothorax (hth) by Yki/Sd. This results in the activation of a distinct Yki/Hth transcriptional program, driving photoreceptor dedifferentiation. We show that Rbf physically interacts with Yki and, together with the GAGA factor, inhibits the hth expression. Thus, RB and Hippo pathways cooperate to maintain photoreceptor differentiation by preventing inappropriate expression of hth in differentiating photoreceptors. Our work highlights the importance of both RB and Hippo pathway activities for maintaining the state of terminal differentiation.
Collapse
Affiliation(s)
- Alexandra E Rader
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Battuya Bayarmagnai
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Maxim V Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
| |
Collapse
|
17
|
Zane F, Bouzid H, Sosa Marmol S, Brazane M, Besse S, Molina JL, Cansell C, Aprahamian F, Durand S, Ayache J, Antoniewski C, Todd N, Carré C, Rera M. Smurfness-based two-phase model of ageing helps deconvolve the ageing transcriptional signature. Aging Cell 2023; 22:e13946. [PMID: 37822253 PMCID: PMC10652310 DOI: 10.1111/acel.13946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 10/13/2023] Open
Abstract
Ageing is characterised at the molecular level by six transcriptional 'hallmarks of ageing', that are commonly described as progressively affected as time passes. By contrast, the 'Smurf' assay separates high-and-constant-mortality risk individuals from healthy, zero-mortality risk individuals, based on increased intestinal permeability. Performing whole body total RNA sequencing, we found that Smurfness distinguishes transcriptional changes associated with chronological age from those associated with biological age. We show that transcriptional heterogeneity increases with chronological age in non-Smurf individuals preceding the other five hallmarks of ageing that are specifically associated with the Smurf state. Using this approach, we also devise targeted pro-longevity genetic interventions delaying entry in the Smurf state. We anticipate that increased attention to the evolutionary conserved Smurf phenotype will bring about significant advances in our understanding of the mechanisms of ageing.
Collapse
Affiliation(s)
- Flaminia Zane
- Université Paris Cité, INSERM UMR U1284ParisFrance
- Institut de Biologie Paris Seine, Sorbonne UniversitéParisFrance
| | - Hayet Bouzid
- Université Paris Cité, INSERM UMR U1284ParisFrance
- Institut de Biologie Paris Seine, Sorbonne UniversitéParisFrance
| | | | - Mira Brazane
- Institut de Biologie Paris Seine, Sorbonne UniversitéParisFrance
| | | | | | - Céline Cansell
- Université Paris‐Saclay, AgroParisTech, INRAE, UMR PNCAPalaiseauFrance
| | - Fanny Aprahamian
- Metabolomics and Cell Biology Platforms, UMS AMMICaInstitut Gustave RoussyVillejuifFrance
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le CancerUniversité de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de FranceParisFrance
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, UMS AMMICaInstitut Gustave RoussyVillejuifFrance
- Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le CancerUniversité de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de FranceParisFrance
| | - Jessica Ayache
- Institut Jacques Monod, CNRS UMR 7592, Université Paris CitéParisFrance
| | | | - Nicolas Todd
- Eco‐Anthropologie (EA), Muséum National d'Histoire Naturelle, CNRSUniversité de Paris, Musée de l'HommeParisFrance
| | - Clément Carré
- Institut de Biologie Paris Seine, Sorbonne UniversitéParisFrance
| | - Michael Rera
- Université Paris Cité, INSERM UMR U1284ParisFrance
| |
Collapse
|
18
|
Tillé L, Cropp D, Charmoy M, Reichenbach P, Andreatta M, Wyss T, Bodley G, Crespo I, Nassiri S, Lourenco J, Leblond MM, Lopez-Rodriguez C, Speiser DE, Coukos G, Irving M, Carmona SJ, Held W, Verdeil G. Activation of the transcription factor NFAT5 in the tumor microenvironment enforces CD8 + T cell exhaustion. Nat Immunol 2023; 24:1645-1653. [PMID: 37709986 DOI: 10.1038/s41590-023-01614-x] [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: 09/09/2021] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
Persistent exposure to antigen during chronic infection or cancer renders T cells dysfunctional. The molecular mechanisms regulating this state of exhaustion are thought to be common in infection and cancer, despite obvious differences in their microenvironments. Here we found that NFAT5, an NFAT family transcription factor that lacks an AP-1 docking site, was highly expressed in exhausted CD8+ T cells in the context of chronic infections and tumors but was selectively required in tumor-induced CD8+ T cell exhaustion. Overexpression of NFAT5 in CD8+ T cells reduced tumor control, while deletion of NFAT5 improved tumor control by promoting the accumulation of tumor-specific CD8+ T cells that had reduced expression of the exhaustion-associated proteins TOX and PD-1 and produced more cytokines, such as IFNɣ and TNF, than cells with wild-type levels of NFAT5, specifically in the precursor exhausted PD-1+TCF1+TIM-3-CD8+ T cell population. NFAT5 did not promote T cell exhaustion during chronic infection with clone 13 of lymphocytic choriomeningitis virus. Expression of NFAT5 was induced by TCR triggering, but its transcriptional activity was specific to the tumor microenvironment and required hyperosmolarity. Thus, NFAT5 promoted the exhaustion of CD8+ T cells in a tumor-selective fashion.
Collapse
Affiliation(s)
- Laure Tillé
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Daniela Cropp
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Mélanie Charmoy
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | - Patrick Reichenbach
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Massimo Andreatta
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tania Wyss
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gabrielle Bodley
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | - Isaac Crespo
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sina Nassiri
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joao Lourenco
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marine M Leblond
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Cristina Lopez-Rodriguez
- Immunology Unit, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniel E Speiser
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Santiago J Carmona
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Werner Held
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | - Grégory Verdeil
- Department of Oncology, UNIL CHUV, University of Lausanne, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
19
|
Chen H, Ma R, Zhou B, Yang X, Duan F, Wang G. Integrated immunological analysis of single-cell and bulky tissue transcriptomes reveals the role of interactions between M0 macrophages and naïve CD4 + T cells in the immunosuppressive microenvironment of cervical cancer. Comput Biol Med 2023; 163:107151. [PMID: 37348264 DOI: 10.1016/j.compbiomed.2023.107151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/27/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
In recent decades, the incidence and mortality of cervical cancer have declined in developed countries due to the implementation of screening and vaccination programs. However, cervical cancer remains one of the major culprits of cancer-related deaths in young women. Current studies have found that immune cell-related intercellular communication in the tumor microenvironment has a large impact on the construction of the immunosuppressive microenvironment. In this study, we performed a comprehensive immune analysis on bulk RNA-seq and scRNA-seq data obtained from cervical cancer and revealed that two highly plastic cell populations, M0 macrophages and naïve CD4+ T cells, were significantly correlated with prognosis and clinical phenotypes. Notably, signaling between M0 macrophages and naïve CD4+ T cells as well as intracellular transcription factor activity were significantly altered in the tumor state. Furthermore, we identified overlapping genes between the transcription factor target genes of M0 macrophages or naïve CD4+ T cells and the differentially expressed genes in each type of cell, and these overlapping genes were subsequently subjected to an analysis using the LASSO regression model. Finally, we generated a score index that was significantly associated with the clinical prognosis of cervical cancer. In conclusion, interventions to improve the communication between M0 macrophages and naïve CD4+ T cells may help to improve the immunosuppressive microenvironment of cervical cancer and prevent immune evasion. The relevant molecular mechanisms need to be further validated by experimental and cohort studies.
Collapse
Affiliation(s)
- Huaqiu Chen
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China; Department of Laboratory, Xichang People's Hospital, Sichuan, 615000, China
| | - Rong Ma
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China; Department of Laboratory, The First People's Hospital of Qujing, Yunnan Province, 655000, China
| | - Bingjie Zhou
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China; Maternity and Obstetrics Department of Fangshan District Maternity and Child Health Hospital of Beijing, Fangshan District of Beijing, 102488, China
| | - Xitong Yang
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China
| | - Fuhui Duan
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China
| | - Guangming Wang
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China.
| |
Collapse
|
20
|
Das BK, Kannan A, Velasco GJ, Kunika MD, Lambrecht N, Nguyen Q, Zhao H, Wu J, Gao L. Single-cell dissection of Merkel cell carcinoma heterogeneity unveils transcriptomic plasticity and therapeutic vulnerabilities. Cell Rep Med 2023; 4:101101. [PMID: 37421947 PMCID: PMC10394170 DOI: 10.1016/j.xcrm.2023.101101] [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: 12/07/2022] [Revised: 03/23/2023] [Accepted: 06/13/2023] [Indexed: 07/10/2023]
Abstract
Merkel cell carcinoma (MCC), a rare but aggressive skin cancer, remains a challenge in the era of precision medicine. Immune checkpoint inhibitors (ICIs), the only approved therapy for advanced MCC, are impeded by high primary and acquired resistance. Hence, we dissect transcriptomic heterogeneity at single-cell resolution in a panel of patient tumors, revealing phenotypic plasticity in a subset of treatment-naive MCC. The tumor cells in a "mesenchymal-like" state are endowed with an inflamed phenotype that portends a better ICI response. This observation is also validated in the largest whole transcriptomic dataset available from MCC patient tumors. In contrast, ICI-resistant tumors predominantly express neuroepithelial markers in a well-differentiated state with "immune-cold" landscape. Importantly, a subtle shift to "mesenchymal-like" state reverts copanlisib resistance in primary MCC cells, highlighting potential strategies in patient stratification for therapeutics to harness tumor cell plasticity, augment treatment efficacy, and avert resistance.
Collapse
Affiliation(s)
- Bhaba K Das
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA
| | - Aarthi Kannan
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA; Department of Dermatology, University of California-Irvine, Irvine, CA 92697, USA
| | - Graham J Velasco
- Pathology Department, Tibor Rubin VA Medical Center, VA Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Mikaela D Kunika
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA
| | - Nils Lambrecht
- Pathology Department, Tibor Rubin VA Medical Center, VA Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Quy Nguyen
- Genomics Research and Technology Hub, Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Haibo Zhao
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA
| | - Jie Wu
- Genomics Research and Technology Hub, Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Ling Gao
- Southern California Institute for Research and Education, Long Beach, CA 90822, USA; Department of Dermatology, University of California-Irvine, Irvine, CA 92697, USA; Dermatology Section, Tibor Rubin VA Medical Center, VA Long Beach Healthcare System, Long Beach, CA 90822, USA.
| |
Collapse
|
21
|
Nakano S, Kashio S, Nishimura K, Takeishi A, Kosakamoto H, Obata F, Kuranaga E, Chihara T, Yamauchi Y, Isobe T, Miura M. Damage sensing mediated by serine proteases Hayan and Persephone for Toll pathway activation in apoptosis-deficient flies. PLoS Genet 2023; 19:e1010761. [PMID: 37319131 DOI: 10.1371/journal.pgen.1010761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The mechanisms by which the innate immune system senses damage have been extensively explored in multicellular organisms. In Drosophila, various types of tissue damage, including epidermal injury, tumor formation, cell competition, and apoptosis deficiency, induce sterile activation of the Toll pathway, a process that requires the use of extracellular serine protease (SP) cascades. Upon infection, the SP Spätzle (Spz)-processing enzyme (SPE) cleaves and activates the Toll ligand Spz downstream of two paralogous SPs, Hayan and Persephone (Psh). However, upon tissue damage, it is not fully understood which SPs establish Spz activation cascades nor what damage-associated molecules can activate SPs. In this study, using newly generated uncleavable spz mutant flies, we revealed that Spz cleavage is required for the sterile activation of the Toll pathway, which is induced by apoptosis-deficient damage of wing epidermal cells in adult Drosophila. Proteomic analysis of hemolymph, followed by experiments with Drosophila Schneider 2 (S2) cells, revealed that among hemolymph SPs, both SPE and Melanization Protease 1 (MP1) have high capacities to cleave Spz. Additionally, in S2 cells, MP1 acts downstream of Hayan and Psh in a similar manner to SPE. Using genetic analysis, we found that the upstream SPs Hayan and Psh contributes to the sterile activation of the Toll pathway. While SPE/MP1 double mutants show more impairment of Toll activation upon infection than SPE single mutants, Toll activation is not eliminated in these apoptosis-deficient flies. This suggests that Hayan and Psh sense necrotic damage, inducing Spz cleavage by SPs other than SPE and MP1. Furthermore, hydrogen peroxide, a representative damage-associated molecule, activates the Psh-Spz cascade in S2 cells overexpressing Psh. Considering that reactive oxygen species (ROS) were detected in apoptosis-deficient wings, our findings highlight the importance of ROS as signaling molecules that induce the activation of SPs such as Psh in response to damage.
Collapse
Affiliation(s)
- Shotaro Nakano
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Soshiro Kashio
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kei Nishimura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Asuka Takeishi
- Neural Circuit of Multisensory Integration RIKEN Hakubi Research Team, RIKEN Center for Brain Science, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Hina Kosakamoto
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Fumiaki Obata
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Erina Kuranaga
- Laboratory of Histogenetic Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Takahiro Chihara
- Program of Biomedical Science and Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
22
|
Salih MM, Robinson EK, Malekos E, Perez E, Capili A, Kim K, Zhang WZ, Cloonan SM, Carpenter S. LincRNA-Cox2 Regulates Smoke-induced Inflammation in Murine Macrophages. Am J Respir Cell Mol Biol 2023; 68:511-522. [PMID: 36657060 DOI: 10.1165/rcmb.2022-0413oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/19/2023] [Indexed: 01/20/2023] Open
Abstract
Cigarette smoke (CS) exposure is a risk factor for many chronic diseases, including chronic obstructive pulmonary disease, but the mechanism by which smoke exposure can alter homeostasis and bring about chronic inflammation is poorly understood. Here, we showcase a novel role for smoke in regulating long noncoding RNAs, showing that it activates lincRNA-Cox2, which we previously characterized as functional in inflammatory regulation. Exposing lincRNA-Cox2 murine models to smoke in vivo confirmed lincRNA-Cox2 as a regulator of inflammatory gene expression in response to smoke both systemically and within the lung. We also report that lincRNA-Cox2 negatively regulates genes in smoked bone marrow-derived macrophages exposed to LPS stimulation. In addition to the effects on long noncoding RNAs, we also report dysregulated transcription and splicing of inflammatory protein-coding genes in the bone marrow niche after CS exposure in vivo. Collectively, this work provides insights into how innate immune signaling from gene expression to splicing is altered after in vivo exposure to CS and highlights an important new role for lincRNA-Cox2 in regulating immune genes after smoke exposure.
Collapse
Affiliation(s)
- Mays Mohammed Salih
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| | - Elektra Kantzari Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| | - Eric Malekos
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| | - Elizabeth Perez
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Allyson Capili
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Kihwan Kim
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - William Z Zhang
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Suzanne M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College, Dublin, Ireland
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| |
Collapse
|
23
|
Corria-Osorio J, Carmona SJ, Stefanidis E, Andreatta M, Ortiz-Miranda Y, Muller T, Rota IA, Crespo I, Seijo B, Castro W, Jimenez-Luna C, Scarpellino L, Ronet C, Spill A, Lanitis E, Romero P, Luther SA, Irving M, Coukos G. Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8 + T cells. Nat Immunol 2023; 24:869-883. [PMID: 37081150 PMCID: PMC10154250 DOI: 10.1038/s41590-023-01477-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/01/2023] [Indexed: 04/22/2023]
Abstract
To date, no immunotherapy approaches have managed to fully overcome T-cell exhaustion, which remains a mandatory fate for chronically activated effector cells and a major therapeutic challenge. Understanding how to reprogram CD8+ tumor-infiltrating lymphocytes away from exhausted effector states remains an elusive goal. Our work provides evidence that orthogonal gene engineering of T cells to secrete an interleukin (IL)-2 variant binding the IL-2Rβγ receptor and the alarmin IL-33 reprogrammed adoptively transferred T cells to acquire a novel, synthetic effector state, which deviated from canonical exhaustion and displayed superior effector functions. These cells successfully overcame homeostatic barriers in the host and led-in the absence of lymphodepletion or exogenous cytokine support-to high levels of engraftment and tumor regression. Our work unlocks a new opportunity of rationally engineering synthetic CD8+ T-cell states endowed with the ability to avoid exhaustion and control advanced solid tumors.
Collapse
Affiliation(s)
- Jesus Corria-Osorio
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland.
- AGORA Cancer Research Center, Lausanne, Switzerland.
| | - Santiago J Carmona
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Evangelos Stefanidis
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
| | - Massimo Andreatta
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Yaquelin Ortiz-Miranda
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Tania Muller
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Ioanna A Rota
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Isaac Crespo
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Bili Seijo
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Wilson Castro
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Cristina Jimenez-Luna
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
| | | | - Catherine Ronet
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Aodrenn Spill
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Evripidis Lanitis
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
| | - Pedro Romero
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Sanjiv A Luther
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne; and Department of Oncology, Lausanne University Hospital, Epalinges, Switzerland.
- AGORA Cancer Research Center, Lausanne, Switzerland.
| |
Collapse
|
24
|
Rader AE, Bayarmagnai B, Frolov MV. Combined inactivation of RB and Hippo pathways converts differentiating photoreceptors into eye progenitor cells through derepression of homothorax. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.23.537991. [PMID: 37163078 PMCID: PMC10168227 DOI: 10.1101/2023.04.23.537991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The RB and Hippo pathways interact to regulate cell proliferation and differentiation. However, their mechanism of interaction is not fully understood. Drosophila photoreceptors with inactivated RB and Hippo pathways specify normally but fail to maintain neuronal identity and dedifferentiate. We performed single-cell RNA-sequencing to elucidate the cause of dedifferentiation and the fate of these cells. We find that dedifferentiated cells adopt a progenitor-like fate due to inappropriate activation of the retinal differentiation suppressor homothorax (hth) by Yki/Sd. This results in activation of the Yki/Hth transcriptional program, driving photoreceptor dedifferentiation. We show that Rbf physically interacts with Yki which, together with the GAGA factor, inhibits hth expression. Thus, RB and Hippo pathways cooperate to maintain photoreceptor differentiation by preventing inappropriate expression of hth in differentiating photoreceptors. Our work accentuates the importance of both RB and Hippo pathway activity for maintaining the state of terminal differentiation.
Collapse
Affiliation(s)
- Alexandra E Rader
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago IL 60607
| | - Battuya Bayarmagnai
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago IL 60607
| | - Maxim V Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago IL 60607
| |
Collapse
|
25
|
Simigdala N, Chalari A, Sklirou AD, Chavdoula E, Papafotiou G, Melissa P, Kafalidou A, Paschalidis N, Pateras IS, Athanasiadis E, Konstantopoulos D, Trougakos IP, Klinakis A. Loss of Kmt2c in vivo leads to EMT, mitochondrial dysfunction and improved response to lapatinib in breast cancer. Cell Mol Life Sci 2023; 80:100. [PMID: 36933062 PMCID: PMC10024673 DOI: 10.1007/s00018-023-04734-7] [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: 05/04/2022] [Revised: 01/22/2023] [Accepted: 02/22/2023] [Indexed: 03/19/2023]
Abstract
Deep sequencing of human tumours has uncovered a previously unappreciated role for epigenetic regulators in tumorigenesis. H3K4 methyltransferase KMT2C/MLL3 is mutated in several solid malignancies, including more than 10% of breast tumours. To study the tumour suppressor role of KMT2C in breast cancer, we generated mouse models of Erbb2/Neu, Myc or PIK3CA-driven tumorigenesis, in which the Kmt2c locus is knocked out specifically in the luminal lineage of mouse mammary glands using the Cre recombinase. Kmt2c knock out mice develop tumours earlier, irrespective of the oncogene, assigning a bona fide tumour suppressor role for KMT2C in mammary tumorigenesis. Loss of Kmt2c induces extensive epigenetic and transcriptional changes, which lead to increased ERK1/2 activity, extracellular matrix re-organization, epithelial-to-mesenchymal transition and mitochondrial dysfunction, the latter associated with increased reactive oxygen species production. Loss of Kmt2c renders the Erbb2/Neu-driven tumours more responsive to lapatinib. Publicly available clinical datasets revealed an association of low Kmt2c gene expression and better long-term outcome. Collectively, our findings solidify the role of KMT2C as a tumour suppressor in breast cancer and identify dependencies that could be therapeutically amenable.
Collapse
Affiliation(s)
- Nikiana Simigdala
- Present Address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Anna Chalari
- Present Address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Aimilia D. Sklirou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Chavdoula
- Present Address: Biomedical Research Foundation Academy of Athens, Athens, Greece
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH USA
| | - George Papafotiou
- Present Address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Pelagia Melissa
- Present Address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Aimilia Kafalidou
- Present Address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Nikolaos Paschalidis
- Present Address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Ioannis S. Pateras
- 2nd Department of Pathology, Medical School, “Attikon” University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Ioannis P. Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Apostolos Klinakis
- Present Address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| |
Collapse
|
26
|
Gu L, Wang Z, Gu H, Wang H, Liu L, Zhang WB. Atf4 regulates angiogenic differences between alveolar bone and long bone macrophages by regulating M1 polarization, based on single-cell RNA sequencing, RNA-seq and ATAC-seq analysis. J Transl Med 2023; 21:193. [PMID: 36918894 PMCID: PMC10012539 DOI: 10.1186/s12967-023-04046-1] [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: 12/04/2022] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
In the repair of maxillofacial bone defects, autogenous craniofacial bone can often provide superior clinical results over long bone grafts. Most current studies have focused on the osteogenic differences between alveolar bone marrow (ABM) and long bone marrow (LBM), however, studies about the angiogenic differences between the two are currently lacking. We downloaded single-cell RNA sequencing (scRNA-seq) of mouse ABM and LBM respectively from the public database, and the data were processed by using Seurat package. CellphoneDB2 results showed that macrophages had the strongest interaction with mesenchymal stem cells (MSCs) and endothelial cells (ECs). ELISA results confirmed that ABM macrophages secreted a higher level of vascular endothelial growth factor A (Vegfa) compared to LBM macrophages, which further promoted angiogenesis of ECs and MSCs. Using SCENIC package, six key transcription factors (TFs) were identified to regulate the difference between ABM and LBM macrophages, and activating transcription factor 4 (Atf4) was confirmed to be more expressed in ABM macrophages by polymerase chain reaction (PCR) and western blot (WB), with predicted target genes including Vegfa. Besides, the result of scRNA-seq implied ABM macrophages more in M1 status than LBM macrophages, which was confirmed by the following experiments. From the results of another assay for transposase accessible chromatin sequencing (ATAC-seq) and RNA-seq about M1 macrophages, Atf4 was also confirmed to regulate the M1 polarization. So, we suspected that Atf4 regulated the different expression of Vegfa between ABM and LBM macrophages by activating M1 polarization. After knocking down Atf4, the expression of M1 polarization markers and Vegfa were downregulated and vasculogenic differences were eliminated, which were subsequently reversed by the addition of LPS/IFN-γ. Our study might provide a new idea to improve the success rate of autologous bone grafting and treatment of oral diseases.
Collapse
Affiliation(s)
- Lanxin Gu
- Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210029, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, 210029, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210029, China
| | - Zhongyuan Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Hong Gu
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, 210029, China
| | - Hua Wang
- Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210029, China.
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, 210029, China.
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210029, China.
| | - Luwei Liu
- Department of Orthodontics, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, 210029, China.
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, 210029, China.
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, 210029, China.
| | - Wei-Bing Zhang
- Department of Stomatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China.
- Department of Stomatology, Medical Center of Soochow University, Suzhou, China.
- Department of Stomatology, Suzhou Dushu Lake Hospital, Suzhou, China.
| |
Collapse
|
27
|
Liu W, Han F, Wan M, Yang XZ. Integrated bioinformatics analysis identifies shared immune changes between ischemic stroke and COVID 19. Front Immunol 2023; 14:1102281. [PMID: 36969251 PMCID: PMC10030956 DOI: 10.3389/fimmu.2023.1102281] [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: 11/18/2022] [Accepted: 02/23/2023] [Indexed: 03/10/2023] Open
Abstract
Although COVID-19 is primarily a respiratory disease, its neurological complications, such as ischemic stroke (IS), have aroused growing concerns and reports. However, the molecular mechanisms that underlie IS and COVID-19 are not well understood. Therefore, we implemented transcriptomic analysis from eight GEO datasets consist of 1191 samples to detect common pathways and molecular biomarkers in IS and COVID-19 that help understand the linkage between them. Differentially expressed genes (DEGs) were detected for IS and COVID-19 separately for finding shared mechanisms and we found that immune-related pathways were outlined with statistical significance. JAK2, which was identified as a hub gene, was supposed to be a potential therapeutic gene targets during the immunological process of COVID-19 and IS. Besides, we found a decrease in the proportion of CD8+ T and T helper 2 cells in the peripheral circulation of both COVID and IS patients, and NCR3 expression was significantly correlated with this change. In conclusion, we demonstrated that transcriptomic analyses reported in this study could make a deeper understanding of the common mechanism and might be promising for effective therapeutic for IS and COVID-19.
Collapse
Affiliation(s)
- Wenhao Liu
- Eight-year program of Clinical Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Han
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengyao Wan
- Eight-year program of Clinical Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin-Zhuang Yang
- Medical Research Center, State Key laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Xin-Zhuang Yang,
| |
Collapse
|
28
|
Lin SC, Yu G, Lee YC, Song JH, Song X, Zhang J, Panaretakis T, Logothetis CJ, Komatsu Y, Yu-Lee LY, Wang G, Lin SH. Endothelial-to-osteoblast transition in normal mouse bone development. iScience 2023; 26:105994. [PMID: 36798441 PMCID: PMC9926118 DOI: 10.1016/j.isci.2023.105994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/23/2022] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Metastatic prostate cancer (PCa) in bone induces bone-forming lesions. We have previously shown that PCa-induced bone originates from endothelial cells (ECs) that have undergone EC-to-osteoblast (OSB) transition. Here, we investigated whether EC-to-OSB transition also occurs during normal bone formation. We developed an EC and OSB dual-color reporter mouse (DRM) model that marks EC-OSB hybrid cells with red and green fluorescent proteins. We observed EC-to-OSB transition (RFP and GFP co-expression) in both endochondral and intramembranous bone formation during embryonic development and in adults. Co-expression was confirmed in cells isolated from DRM. Bone marrow- and lung-derived ECs underwent transition to OSBs and mineralization in osteogenic medium. RNA-sequencing revealed GATA family transcription factors were upregulated in EC-OSB hybrid cells and knockdown of GATA3 inhibited BMP4-induced mineralization. Our findings support that EC-to-OSB transition occurs during normal bone development and suggest a new paradigm regarding the endothelial origin of OSBs.
Collapse
Affiliation(s)
- Song-Chang Lin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guoyu Yu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu-Chen Lee
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian H. Song
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Theocharis Panaretakis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher J. Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yoshihiro Komatsu
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Li-Yuan Yu-Lee
- Departments of Medicine and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Guocan Wang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sue-Hwa Lin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
29
|
Yun J, Hansen S, Morris O, Madden DT, Libeu CP, Kumar AJ, Wehrfritz C, Nile AH, Zhang Y, Zhou L, Liang Y, Modrusan Z, Chen MB, Overall CC, Garfield D, Campisi J, Schilling B, Hannoush RN, Jasper H. Senescent cells perturb intestinal stem cell differentiation through Ptk7 induced noncanonical Wnt and YAP signaling. Nat Commun 2023; 14:156. [PMID: 36631445 PMCID: PMC9834240 DOI: 10.1038/s41467-022-35487-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/06/2022] [Indexed: 01/13/2023] Open
Abstract
Cellular senescence and the senescence-associated secretory phenotype (SASP) are implicated in aging and age-related disease, and SASP-related inflammation is thought to contribute to tissue dysfunction in aging and diseased animals. However, whether and how SASP factors influence the regenerative capacity of tissues remains unclear. Here, using intestinal organoids as a model of tissue regeneration, we show that SASP factors released by senescent fibroblasts deregulate stem cell activity and differentiation and ultimately impair crypt formation. We identify the secreted N-terminal domain of Ptk7 as a key component of the SASP that activates non-canonical Wnt / Ca2+ signaling through FZD7 in intestinal stem cells (ISCs). Changes in cytosolic [Ca2+] elicited by Ptk7 promote nuclear translocation of YAP and induce expression of YAP/TEAD target genes, impairing symmetry breaking and stem cell differentiation. Our study discovers secreted Ptk7 as a factor released by senescent cells and provides insight into the mechanism by which cellular senescence contributes to tissue dysfunction in aging and disease.
Collapse
Affiliation(s)
- Jina Yun
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Simon Hansen
- NBE Therapeutics, Hochbergstrasse 60C, 4057, Basel, Switzerland
| | - Otto Morris
- Exscientia Ltd., The Schrödinger Building Oxford Science Park, Oxford, OX4 4GE, UK
| | - David T Madden
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Clare Peters Libeu
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Arjun J Kumar
- Fred Hutch/University of Washington, 1100 Fairview Ave. N., Seattle, WA, 98109, USA
| | - Cameron Wehrfritz
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Aaron H Nile
- Calico Labs LLC., 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Yingnan Zhang
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Lijuan Zhou
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yuxin Liang
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Zora Modrusan
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Michelle B Chen
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - David Garfield
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Rami N Hannoush
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Heinrich Jasper
- Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA.
| |
Collapse
|
30
|
Tsai CH, Chuang YM, Li X, Yu YR, Tzeng SF, Teoh ST, Lindblad KE, Di Matteo M, Cheng WC, Hsueh PC, Kao KC, Imrichova H, Duan L, Gallart-Ayala H, Hsiao PW, Mazzone M, Ivanesevic J, Liu X, de Visser KE, Lujambio A, Lunt SY, Kaech SM, Ho PC. Immunoediting instructs tumor metabolic reprogramming to support immune evasion. Cell Metab 2023; 35:118-133.e7. [PMID: 36599297 PMCID: PMC10375941 DOI: 10.1016/j.cmet.2022.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/06/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023]
Abstract
Immunoediting sculpts immunogenicity and thwarts host anti-tumor responses in tumor cells during tumorigenesis; however, it remains unknown whether metabolic programming of tumor cells can be guided by immunosurveillance. Here, we report that T cell-mediated immunosurveillance in early-stage tumorigenesis instructs c-Myc upregulation and metabolic reprogramming in tumor cells. This previously unexplored tumor-immune interaction is controlled by non-canonical interferon gamma (IFNγ)-STAT3 signaling and supports tumor immune evasion. Our findings uncover that immunoediting instructs deregulated bioenergetic programs in tumor cells to empower them to disarm the T cell-mediated immunosurveillance by imposing metabolic tug-of-war between tumor and infiltrating T cells and forming the suppressive tumor microenvironment.
Collapse
Affiliation(s)
- Chin-Hsien Tsai
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei City, Taiwan
| | - Yu-Ming Chuang
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Xiaoyun Li
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Yi-Ru Yu
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sheue-Fen Tzeng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei City, Taiwan
| | - Shao Thing Teoh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Katherine E Lindblad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario Di Matteo
- Laboratory of Tumor Inflammation and angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Tumor Inflammation and angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Wan-Chen Cheng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Pei-Chun Hsueh
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Kung-Chi Kao
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Wien, Austria
| | - Likun Duan
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Pei-Wen Hsiao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei City, Taiwan
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Tumor Inflammation and angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Julijana Ivanesevic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Wien, Austria
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Karin E de Visser
- Division of Tumor Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sophia Y Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
31
|
Huang L, Shi Y, Hu J, Ding J, Guo Z, Yu B. Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease. Urolithiasis 2022; 51:13. [PMID: 36484839 DOI: 10.1007/s00240-022-01384-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022]
Abstract
Nephrolithiasis is one of the most common and frequent urologic diseases worldwide. The molecular mechanism of kidney stone formation is complex and remains to be illustrated. Transcript factors (TFs) that influenced the expression pattern of multiple genes, as well as microRNAs, important posttranscriptional modulators, play vital roles in this disease progression. Datasets of nephrolithiasis mice and kidney stone patients were acquired from Gene Expression Omnibus repository. TFs were predicted from differentially expressed genes by RcisTarget. The target genes of differential-expressed microRNAs were predicted by miRWalk. MicroRNA-mRNA network and PPI network were constructed. Functional enrichment analysis was performed via Metascape and Cytoscape identified hub genes. The assay of quantitative real-time PCR (q-PCR) and immunochemistry and the datasets of oxalate diet-induced nephrolithiasis mice kidneys and kidney stone patients' samples were utilized to validate the bioinformatic results. We identified three potential key TFs (Egr1, Rxra, Max), which can be modulated by miR-181a-5p, miR-7b-3p and miR-22-3p, respectively. The TFs and their regulated hub genes influenced the progression of nephrolithiasis via altering the expression of genes enriched in the functions of fibrosis, cell proliferation and molecular transportation and metabolism. The expression changes of transcription factors were consistent in q-PCR and immunochemistry results. For regulated hub genes, they showed consistent expression changes in oxalate diet-induced nephrolithiasis mice model and human kidneys with stones. The identified and verified three TFs, which may be modulated by microRNAs in nephrolithiasis disease progression, mainly influence biological processes responding to fibrosis, proliferation and molecular transportation and metabolism. The transcript influence showed consistency in multiple nephrolithiasis mice models and kidney stone patients.
Collapse
Affiliation(s)
- Linxi Huang
- Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People's Republic of China
- Department of Cell Biology, Naval Medical University (Second Military Medical University), 800 Xiangyin Road, Shanghai, 200433, People's Republic of China
| | - Yuxuan Shi
- Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Junjie Hu
- Department of Cell Biology, Naval Medical University (Second Military Medical University), 800 Xiangyin Road, Shanghai, 200433, People's Republic of China
| | - Jiarong Ding
- Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Zhiyong Guo
- Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People's Republic of China.
| | - Bing Yu
- Department of Cell Biology, Naval Medical University (Second Military Medical University), 800 Xiangyin Road, Shanghai, 200433, People's Republic of China.
| |
Collapse
|
32
|
Papazoglou A, Huang M, Bulik M, Lafyatis A, Tabib T, Morse C, Sembrat J, Rojas M, Valenzi E, Lafyatis R. Epigenetic Regulation of Profibrotic Macrophages in Systemic Sclerosis-Associated Interstitial Lung Disease. Arthritis Rheumatol 2022; 74:2003-2014. [PMID: 35849803 PMCID: PMC9771864 DOI: 10.1002/art.42286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/26/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Systemic sclerosis-associated interstitial lung disease (SSc-ILD) is the leading cause of death in patients with SSc with unclear pathogenesis and limited treatment options. Evidence strongly supports an important role for profibrotic secreted phosphoprotein 1 (SPP1)-expressing macrophages in SSc-ILD. This study was undertaken to define the transcriptome and chromatin structural changes of SPP1 SSc-ILD macrophages in order to better understand their role in promoting fibrosis and to identify transcription factors associated with open chromatin driving their altered phenotype. METHODS We performed single-cell RNA sequencing (scRNA-Seq) on 11 explanted SSc-ILD and healthy control lung samples, as well as single-cell assay for transposase-accessible chromatin sequencing on 5 lung samples to define altered chromatin accessibility of SPP1 macrophages. We predicted transcription factors regulating SPP1 macrophages using single-cell regulatory network inference and clustering (SCENIC) and determined transcription factor binding sites associated with global alterations in SPP1 chromatin accessibility using Signac/Seurat. RESULTS We identified distinct macrophage subpopulations using scRNA-Seq analysis in healthy and SSc-ILD lungs and assessed gene expression changes during the change of healthy control macrophages into SPP1 macrophages. Analysis of open chromatin validated SCENIC predictions, indicating that microphthalmia-associated transcription factor, transcription factor EB, activating transcription factor 6, sterol regulatory element binding transcription factor 1, basic helix-loop-helix family member E40, Kruppel-like factor 6, ETS variant transcription factor 5, and/or members of the activator protein 1 family of transcription factors regulate SPP1 macrophage differentiation. CONCLUSION Our findings shed light on the underlying changes in chromatin structure and transcription factor regulation of profibrotic SPP1 macrophages in SSc-ILD. Similar alterations in SPP1 macrophages may underpin fibrosis in other organs involved in SSc and point to novel targets for the treatment of SSc-ILD, specifically targeting profibrotic macrophages.
Collapse
Affiliation(s)
- Anna Papazoglou
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mengqi Huang
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melissa Bulik
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Annika Lafyatis
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christina Morse
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University, Columbus, OH, USA
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
33
|
Kowalczyk W, Romanelli L, Atkins M, Hillen H, Bravo González-Blas C, Jacobs J, Xie J, Soheily S, Verboven E, Moya IM, Verhulst S, de Waegeneer M, Sansores-Garcia L, van Huffel L, Johnson RL, van Grunsven LA, Aerts S, Halder G. Hippo signaling instructs ectopic but not normal organ growth. Science 2022; 378:eabg3679. [DOI: 10.1126/science.abg3679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Hippo signaling pathway is widely considered a master regulator of organ growth because of the prominent overgrowth phenotypes caused by experimental manipulation of its activity. Contrary to this model, we show here that removing Hippo transcriptional output did not impair the ability of the mouse liver and
Drosophila
eyes to grow to their normal size. Moreover, the transcriptional activity of the Hippo pathway effectors Yap/Taz/Yki did not correlate with cell proliferation, and hyperactivation of these effectors induced gene expression programs that did not recapitulate normal development. Concordantly, a functional screen in
Drosophila
identified several Hippo pathway target genes that were required for ectopic overgrowth but not normal growth. Thus, Hippo signaling does not instruct normal growth, and the Hippo-induced overgrowth phenotypes are caused by the activation of abnormal genetic programs.
Collapse
Affiliation(s)
- W. Kowalczyk
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| | - L. Romanelli
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| | - M. Atkins
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - H. Hillen
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| | - C. Bravo González-Blas
- VIB Center for Brain and Disease Research and KU Leuven Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - J. Jacobs
- VIB Center for Brain and Disease Research and KU Leuven Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - J. Xie
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| | - S. Soheily
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| | - E. Verboven
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| | - I. M. Moya
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - S. Verhulst
- Department for Cell Biology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussel-Jette, Belgium
| | - M. de Waegeneer
- VIB Center for Brain and Disease Research and KU Leuven Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - L. Sansores-Garcia
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| | - L. van Huffel
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| | - R. L. Johnson
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L. A. van Grunsven
- Department for Cell Biology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussel-Jette, Belgium
| | - S. Aerts
- VIB Center for Brain and Disease Research and KU Leuven Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - G. Halder
- VIB Center for Cancer Biology and KU Leuven Department of Oncology, KU Leuven, Leuven, Belgium
| |
Collapse
|
34
|
Drum Z, Lanno S, Gregory SM, Shimshak S, Barr W, Gatesman A, Schadt M, Sanford J, Arkin A, Assignon B, Colorado S, Dalgarno C, Devanny T, Ghandour T, Griffin R, Hogan M, Horowitz E, McGhie E, Multer J, O'Halloran H, Ofori-Darko K, Pokushalov D, Richards N, Sagarin K, Taylor N, Thielking A, Towle P, Coolon J. Genomics analysis of Drosophila sechellia response to Morinda citrifolia fruit diet. G3 (BETHESDA, MD.) 2022; 12:jkac153. [PMID: 35736356 PMCID: PMC9526069 DOI: 10.1093/g3journal/jkac153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 05/24/2022] [Indexed: 11/20/2022]
Abstract
Drosophila sechellia is an island endemic host specialist that has evolved to consume the toxic fruit of Morinda citrifolia, also known as noni fruit. Recent studies by our group and others have examined genome-wide gene expression responses of fruit flies to individual highly abundant compounds found in noni responsible for the fruit's unique chemistry and toxicity. In order to relate these reductionist experiments to the gene expression responses to feeding on noni fruit itself, we fed rotten noni fruit to adult female D. sechellia and performed RNA-sequencing. Combining the reductionist and more wholistic approaches, we have identified candidate genes that may contribute to each individual compound and those that play a more general role in response to the fruit as a whole. Using the compound specific and general responses, we used transcription factor prediction analyses to identify the regulatory networks and specific regulators involved in the responses to each compound and the fruit itself. The identified genes and regulators represent the possible genetic mechanisms and biochemical pathways that contribute to toxin resistance and noni specialization in D. sechellia.
Collapse
Affiliation(s)
- Zachary Drum
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Stephen Lanno
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Sara M Gregory
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Serena Shimshak
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Will Barr
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Austin Gatesman
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Mark Schadt
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Jack Sanford
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Aaron Arkin
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Brynn Assignon
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Sofia Colorado
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Carol Dalgarno
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Trevor Devanny
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Tara Ghandour
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Rose Griffin
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Mia Hogan
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Erica Horowitz
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Emily McGhie
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Jake Multer
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Hannah O'Halloran
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Kofi Ofori-Darko
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Dmitry Pokushalov
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Nick Richards
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Kathleen Sagarin
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Nicholas Taylor
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Acadia Thielking
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Phie Towle
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| | - Joseph Coolon
- Department of Biology, Wesleyan University, Middletown, CT 06457, USA
| |
Collapse
|
35
|
Armaka M, Konstantopoulos D, Tzaferis C, Lavigne MD, Sakkou M, Liakos A, Sfikakis PP, Dimopoulos MA, Fousteri M, Kollias G. Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis. Genome Med 2022; 14:78. [PMID: 35879783 PMCID: PMC9316748 DOI: 10.1186/s13073-022-01081-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/30/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Synovial fibroblasts (SFs) are specialized cells of the synovium that provide nutrients and lubricants for the proper function of diarthrodial joints. Recent evidence appreciates the contribution of SF heterogeneity in arthritic pathologies. However, the normal SF profiles and the molecular networks that govern the transition from homeostatic to arthritic SF heterogeneity remain poorly defined. METHODS We applied a combined analysis of single-cell (sc) transcriptomes and epigenomes (scRNA-seq and scATAC-seq) to SFs derived from naïve and hTNFtg mice (mice that overexpress human TNF, a murine model for rheumatoid arthritis), by employing the Seurat and ArchR packages. To identify the cellular differentiation lineages, we conducted velocity and trajectory analysis by combining state-of-the-art algorithms including scVelo, Slingshot, and PAGA. We integrated the transcriptomic and epigenomic data to infer gene regulatory networks using ArchR and custom-implemented algorithms. We performed a canonical correlation analysis-based integration of murine data with publicly available datasets from SFs of rheumatoid arthritis patients and sought to identify conserved gene regulatory networks by utilizing the SCENIC algorithm in the human arthritic scRNA-seq atlas. RESULTS By comparing SFs from healthy and hTNFtg mice, we revealed seven homeostatic and two disease-specific subsets of SFs. In healthy synovium, SFs function towards chondro- and osteogenesis, tissue repair, and immune surveillance. The development of arthritis leads to shrinkage of homeostatic SFs and favors the emergence of SF profiles marked by Dkk3 and Lrrc15 expression, functioning towards enhanced inflammatory responses and matrix catabolic processes. Lineage inference analysis indicated that specific Thy1+ SFs at the root of trajectories lead to the intermediate Thy1+/Dkk3+/Lrrc15+ SF states and culminate in a destructive and inflammatory Thy1- SF identity. We further uncovered epigenetically primed gene programs driving the expansion of these arthritic SFs, regulated by NFkB and new candidates, such as Runx1. Cross-species analysis of human/mouse arthritic SF data determined conserved regulatory and transcriptional networks. CONCLUSIONS We revealed a dynamic SF landscape from health to arthritis providing a functional genomic blueprint to understand the joint pathophysiology and highlight the fibroblast-oriented therapeutic targets for combating chronic inflammatory and destructive arthritic disease.
Collapse
Affiliation(s)
- Marietta Armaka
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
| | - Dimitris Konstantopoulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Christos Tzaferis
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
- Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Matthieu D Lavigne
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
- Institute of Molecular Biology & Biotechnology, FORTH, Heraklion, Crete, Greece
| | - Maria Sakkou
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
- Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasios Liakos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Petros P Sfikakis
- Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
- First Department of Propaedeutic Internal Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Meletios A Dimopoulos
- Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Maria Fousteri
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
| | - George Kollias
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
- Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece.
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece.
| |
Collapse
|
36
|
Kosakamoto H, Okamoto N, Aikawa H, Sugiura Y, Suematsu M, Niwa R, Miura M, Obata F. Sensing of the non-essential amino acid tyrosine governs the response to protein restriction in Drosophila. Nat Metab 2022; 4:944-959. [PMID: 35879463 DOI: 10.1038/s42255-022-00608-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/15/2022] [Indexed: 11/08/2022]
Abstract
The intake of dietary protein regulates growth, metabolism, fecundity and lifespan across various species, which makes amino acid (AA)-sensing vital for adaptation to the nutritional environment. The general control nonderepressible 2 (GCN2)-activating transcription factor 4 (ATF4) pathway and the mechanistic target of rapamycin complex 1 (mTORC1) pathway are involved in AA-sensing. However, it is not fully understood which AAs regulate these two pathways in living animals and how they coordinate responses to protein restriction. Here we show in Drosophila that the non-essential AA tyrosine (Tyr) is a nutritional cue in the fat body necessary and sufficient for promoting adaptive responses to a low-protein diet, which entails reduction of protein synthesis and mTORC1 activity and increased food intake. This adaptation is regulated by dietary Tyr through GCN2-independent induction of ATF4 target genes in the fat body. This study identifies the Tyr-ATF4 axis as a regulator of the physiological response to a low-protein diet and sheds light on the essential function of a non-essential nutrient.
Collapse
Affiliation(s)
- Hina Kosakamoto
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- RIKEN Center for Biosystems and Dynamics Research, Kobe, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Naoki Okamoto
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Hide Aikawa
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Ryusuke Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Fumiaki Obata
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- RIKEN Center for Biosystems and Dynamics Research, Kobe, Japan.
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan.
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| |
Collapse
|
37
|
Ma S, Wang S, Ye Y, Ren J, Chen R, Li W, Li J, Zhao L, Zhao Q, Sun G, Jing Y, Zuo Y, Xiong M, Yang Y, Wang Q, Lei J, Sun S, Long X, Song M, Yu S, Chan P, Wang J, Zhou Q, Belmonte JCI, Qu J, Zhang W, Liu GH. Heterochronic parabiosis induces stem cell revitalization and systemic rejuvenation across aged tissues. Cell Stem Cell 2022; 29:990-1005.e10. [PMID: 35613617 DOI: 10.1016/j.stem.2022.04.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 03/18/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022]
Abstract
The young circulatory milieu capable of delaying aging in individual tissues is of interest as rejuvenation strategies, but how it achieves cellular- and systemic-level effects has remained unclear. Here, we constructed a single-cell transcriptomic atlas across aged tissues/organs and their rejuvenation in heterochronic parabiosis (HP), a classical model to study systemic aging. In general, HP rejuvenated adult stem cells and their niches across tissues. In particular, we identified hematopoietic stem and progenitor cells (HSPCs) as one of the most responsive cell types to young blood exposure, from which a continuum of cell state changes across the hematopoietic and immune system emanated, through the restoration of a youthful transcriptional regulatory program and cytokine-mediated cell-cell communications in HSPCs. Moreover, the reintroduction of the identified rejuvenating factors alleviated age-associated lymphopoiesis decline. Overall, we provide comprehensive frameworks to explore aging and rejuvenating trajectories at single-cell resolution and revealed cellular and molecular programs that instruct systemic revitalization by blood-borne factors.
Collapse
Affiliation(s)
- Shuai Ma
- State Key Laboratory of Membrane 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; The Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Yanxia Ye
- 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
| | - Jie Ren
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Ruiqing Chen
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Li
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Liyun Zhao
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Qian Zhao
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Guoqiang Sun
- 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
| | - Ying Jing
- 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
| | - Yuesheng Zuo
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muzhao Xiong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanhan Yang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghui Lei
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Shuhui Sun
- State Key Laboratory of Membrane 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
| | - Xiao Long
- Division of Plastic Surgery, Peking Union Medical College Hospital, Beijing 100032, China
| | - Moshi Song
- State Key Laboratory of Membrane 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
| | - Shuyang Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Piu Chan
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Jianwei Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Zhou
- 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; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | | | - Jing Qu
- 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; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| |
Collapse
|
38
|
ASC proneural factors are necessary for chromatin remodeling during neuroectodermal to neuroblast fate transition to ensure the timely initiation of the neural stem cell program. BMC Biol 2022; 20:107. [PMID: 35549704 PMCID: PMC9102361 DOI: 10.1186/s12915-022-01300-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 04/20/2022] [Indexed: 11/11/2022] Open
Abstract
Background In both Drosophila and mammals, the achaete-scute (ASC/ASCL) proneural bHLH transcription factors are expressed in the developing central and peripheral nervous systems, where they function during specification and maintenance of the neural stem cells in opposition to Notch signaling. In addition to their role in nervous system development, ASC transcription factors are oncogenic and exhibit chromatin reprogramming activity; however, the impact of ASC on chromatin dynamics during neural stem cell generation remains elusive. Here, we investigate the chromatin changes accompanying neural commitment using an integrative genetics and genomics methodology. Results We found that ASC factors bind equally strongly to two distinct classes of cis-regulatory elements: open regions remodeled earlier during maternal to zygotic transition by Zelda and less accessible, Zelda-independent regions. Both classes of cis-elements exhibit enhanced chromatin accessibility during neural specification and correlate with transcriptional regulation of genes involved in a variety of biological processes necessary for neuroblast function/homeostasis. We identified an ASC-Notch regulated TF network that includes likely prime regulators of neuroblast function. Using a cohort of ASC target genes, we report that ASC null neuroblasts are defectively specified, remaining initially stalled, unable to divide, and lacking expression of many proneural targets. When mutant neuroblasts eventually start proliferating, they produce compromised progeny. Reporter lines driven by proneural-bound enhancers display ASC dependency, suggesting that the partial neuroblast identity seen in the absence of ASC genes is likely driven by other, proneural-independent, cis-elements. Neuroblast impairment and the late differentiation defects of ASC mutants are corrected by ectodermal induction of individual ASC genes but not by individual members of the TF network downstream of ASC. However, in wild-type embryos, the induction of individual members of this network induces CNS hyperplasia, suggesting that they synergize with the activating function of ASC to consolidate the chromatin dynamics that promote neural specification. Conclusions We demonstrate that ASC proneural transcription factors are indispensable for the timely initiation of the neural stem cell program at the chromatin level by regulating a large number of enhancers in the vicinity of neural genes. This early chromatin remodeling is crucial for both neuroblast homeostasis as well as future progeny fidelity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01300-8.
Collapse
|
39
|
Wang H, Morrison CA, Ghosh N, Tea JS, Call GB, Treisman JE. The Blimp-1 transcription factor acts in non-neuronal cells to regulate terminal differentiation of the Drosophila eye. Development 2022; 149:dev200217. [PMID: 35297965 PMCID: PMC8995086 DOI: 10.1242/dev.200217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/07/2022] [Indexed: 09/10/2023]
Abstract
The formation of a functional organ such as the eye requires specification of the correct cell types and their terminal differentiation into cells with the appropriate morphologies and functions. Here, we show that the zinc-finger transcription factor Blimp-1 acts in secondary and tertiary pigment cells in the Drosophila retina to promote the formation of a bi-convex corneal lens with normal refractive power, and in cone cells to enable complete extension of the photoreceptor rhabdomeres. Blimp-1 expression depends on the hormone ecdysone, and loss of ecdysone signaling causes similar differentiation defects. Timely termination of Blimp-1 expression is also important, as its overexpression in the eye has deleterious effects. Our transcriptomic analysis revealed that Blimp-1 regulates the expression of many structural and secreted proteins in the retina. Blimp-1 may function in part by repressing another transcription factor; Slow border cells is highly upregulated in the absence of Blimp-1, and its overexpression reproduces many of the effects of removing Blimp-1. This work provides insight into the transcriptional networks and cellular interactions that produce the structures necessary for visual function.
Collapse
Affiliation(s)
- Hongsu Wang
- Skirball Institutefor Biomolecular Medicine and Department of Cell Biology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Carolyn A. Morrison
- Skirball Institutefor Biomolecular Medicine and Department of Cell Biology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Neha Ghosh
- Skirball Institutefor Biomolecular Medicine and Department of Cell Biology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Joy S. Tea
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095, USA
| | - Gerald B. Call
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095, USA
| | - Jessica E. Treisman
- Skirball Institutefor Biomolecular Medicine and Department of Cell Biology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, USA
| |
Collapse
|
40
|
Characterization of Accessible Chromatin Regions in Cattle Rumen Epithelial Tissue during Weaning. Genes (Basel) 2022; 13:genes13030535. [PMID: 35328088 PMCID: PMC8949786 DOI: 10.3390/genes13030535] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/17/2022] Open
Abstract
Weaning in ruminants is characterized by the transition from a milk-based diet to a solid diet, which drives a critical gastrointestinal tract transformation. Understanding the regulatory control of this transformation during weaning can help to identify strategies to improve rumen health. This study aimed to identify regions of accessible chromatin in rumen epithelial tissue in pre- and post-weaning calves and investigate differentially accessible regions (DARs) to uncover regulatory elements in cattle rumen development using the ATAC-seq approach. A total of 126,071 peaks were identified, covering 1.15% of the cattle genome. From these accessible regions, 2766 DARs were discovered. Gene ontology enrichment resulted in GO terms related to the cell adhesion, anchoring junction, growth, cell migration, motility, and morphogenesis. In addition, putative regulatory canonical pathways were identified (TGFβ, integrin-linked kinase, integrin signaling, and regulation of the epithelial–mesenchymal transition). Canonical pathways integrated with co-expression results showed that TGFβ and ILK signaling pathways play essential roles in rumen development through the regulation of cellular adhesions. In this study, DARs during weaning were identified, revealing enhancers, transcription factors, and candidate target genes that represent potential biomarkers for the bovine rumen development, which will serve as a molecular tool for rumen development studies.
Collapse
|
41
|
Fishman H, Madiwale S, Geron I, Bari V, Van Loocke W, Kirschenbaum Y, Ganmore I, Kugler E, Rein-Gil A, Friedlander G, Schiby G, Birger Y, Strehl S, Soulier J, Knoechel B, Ferrando A, Noy-Lotan S, Nagler A, Mulloy JC, Van Vlierberghe P, Izraeli S. ETV6-NCOA2 fusion induces T/myeloid mixed-phenotype leukemia through transformation of nonthymic hematopoietic progenitor cells. Blood 2022; 139:399-412. [PMID: 34624096 PMCID: PMC9906988 DOI: 10.1182/blood.2020010405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 09/26/2021] [Indexed: 01/05/2023] Open
Abstract
Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. The pathogenesis is largely unknown, and the treatment is challenging. We previously reported the specific association of the recurrent t(8;12)(q13;p13) chromosomal translocation that creates the ETV6-NCOA2 fusion with T/myeloid leukemias. Here we report that ETV6-NCOA2 initiates T/myeloid leukemia in preclinical models; ectopic expression of ETV6-NCOA2 in mouse bone marrow hematopoietic progenitors induced T/myeloid lymphoma accompanied by spontaneous Notch1-activating mutations. Similarly, cotransduction of human cord blood CD34+ progenitors with ETV6-NCOA2 and a nontransforming NOTCH1 mutant induced T/myeloid leukemia in immunodeficient mice; the immunophenotype and gene expression pattern were similar to those of patient-derived ETV6-NCOA2 leukemias. Mechanistically, we show that ETV6-NCOA2 forms a transcriptional complex with ETV6 and the histone acetyltransferase p300, leading to derepression of ETV6 target genes. The expression of ETV6-NCOA2 in human and mouse nonthymic hematopoietic progenitor cells induces transcriptional dysregulation, which activates a lymphoid program while failing to repress the expression of myeloid genes such as CSF1 and MEF2C. The ETV6-NCOA2 induced arrest at an early immature T-cell developmental stage. The additional acquisition of activating NOTCH1 mutations transforms the early immature ETV6-NCOA2 cells into T/myeloid leukemias. Here, we describe the first preclinical model to depict the initiation of T/myeloid leukemia by a specific somatic genetic aberration.
Collapse
Affiliation(s)
- Hila Fishman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Shreyas Madiwale
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Ifat Geron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Vase Bari
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | - Wouter Van Loocke
- Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - Yael Kirschenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Itamar Ganmore
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Eitan Kugler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Avigail Rein-Gil
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ginette Schiby
- Institute for Pathology Laboratory, Hematology Institute, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Yehudit Birger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Sabine Strehl
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Jean Soulier
- Genomes and Cell Biology of Disease, Hôpital Saint-Louis, Paris, France
| | - Birgit Knoechel
- Dana-Farber Cancer Institute, Boston Children's Hospital, Boston, MA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Sharon Noy-Lotan
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Arnon Nagler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Hematology Division Bone Marrow Transplants and Cord-Blood Bank, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - James C. Mulloy
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | | | - Shai Izraeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
- Department of System Biology, City of Hope, Duarte, CA
| |
Collapse
|
42
|
Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung T, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, Mathelier A. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res 2022; 50:D165-D173. [PMID: 34850907 PMCID: PMC8728201 DOI: 10.1093/nar/gkab1113] [Citation(s) in RCA: 920] [Impact Index Per Article: 460.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022] Open
Abstract
JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.
Collapse
Affiliation(s)
- Jaime A Castro-Mondragon
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Rafael Riudavets-Puig
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Ieva Rauluseviciute
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Jeremy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Paul Boddie
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305, USA
| | - Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Tiffany Y Leung
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Alejandro Aguirre
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | | | - Daniel Schmelter
- UCSC Genome Browser, University of California Santa Cruz, Santa Cruz, CA95060, USA
| | - Damir Baranasic
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | | | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK2200 Copenhagen N, Denmark
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| |
Collapse
|
43
|
Schönberger K, Obier N, Romero-Mulero MC, Cauchy P, Mess J, Pavlovich PV, Zhang YW, Mitterer M, Rettkowski J, Lalioti ME, Jäcklein K, Curtis JD, Féret B, Sommerkamp P, Morganti C, Ito K, Ghyselinck NB, Trompouki E, Buescher JM, Pearce EL, Cabezas-Wallscheid N. Multilayer omics analysis reveals a non-classical retinoic acid signaling axis that regulates hematopoietic stem cell identity. Cell Stem Cell 2022; 29:131-148.e10. [PMID: 34706256 PMCID: PMC9093043 DOI: 10.1016/j.stem.2021.10.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 08/05/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
Hematopoietic stem cells (HSCs) rely on complex regulatory networks to preserve stemness. Due to the scarcity of HSCs, technical challenges have limited our insights into the interplay between metabolites, transcription, and the epigenome. In this study, we generated low-input metabolomics, transcriptomics, chromatin accessibility, and chromatin immunoprecipitation data, revealing distinct metabolic hubs that are enriched in HSCs and their downstream multipotent progenitors. Mechanistically, we uncover a non-classical retinoic acid (RA) signaling axis that regulates HSC function. We show that HSCs rely on Cyp26b1, an enzyme conventionally considered to limit RA effects in the cell. In contrast to the traditional view, we demonstrate that Cyp26b1 is indispensable for production of the active metabolite 4-oxo-RA. Further, RA receptor beta (Rarb) is required for complete transmission of 4-oxo-RA-mediated signaling to maintain stem cells. Our findings emphasize that a single metabolite controls stem cell fate by instructing epigenetic and transcriptional attributes.
Collapse
Affiliation(s)
- Katharina Schönberger
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Julian Mess
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg, Germany
| | - Polina V Pavlovich
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Yu Wei Zhang
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Michael Mitterer
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Jasmin Rettkowski
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany
| | - Maria-Eleni Lalioti
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Karin Jäcklein
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Jonathan D Curtis
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Betty Féret
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 Centre National de la Recherche Scientifique (CNRS) et Université de Strasbourg (UNISTRA), U1258 Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
| | - Pia Sommerkamp
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Morganti
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Departments of Cell Biology and Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Departments of Cell Biology and Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Norbert B Ghyselinck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 Centre National de la Recherche Scientifique (CNRS) et Université de Strasbourg (UNISTRA), U1258 Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
| | - Eirini Trompouki
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Nina Cabezas-Wallscheid
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg, Germany.
| |
Collapse
|
44
|
Janssens J, Aibar S, Taskiran II, Ismail JN, Gomez AE, Aughey G, Spanier KI, De Rop FV, González-Blas CB, Dionne M, Grimes K, Quan XJ, Papasokrati D, Hulselmans G, Makhzami S, De Waegeneer M, Christiaens V, Southall T, Aerts S. Decoding gene regulation in the fly brain. Nature 2022; 601:630-636. [PMID: 34987221 DOI: 10.1038/s41586-021-04262-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 11/17/2021] [Indexed: 12/13/2022]
Abstract
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome analysis1-6, three-dimensional morphological classification7 and electron microscopy mapping of the connectome8,9 have revealed an immense diversity of neuronal and glial cell types that underlie an array of functional and behavioural traits in the fly. The identities of these cell types are controlled by gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. Here, to characterize GRNs at the cell-type level in the fly brain, we profiled the chromatin accessibility of 240,919 single cells spanning 9 developmental timepoints and integrated these data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which 70,000 are linked to developmental trajectories involving neurogenesis, reprogramming and maturation. For 40 cell types, uniquely accessible regions were associated with their expressed transcription factors and downstream target genes through a combination of motif discovery, network inference and deep learning, creating enhancer GRNs. The enhancer architectures revealed by DeepFlyBrain lead to a better understanding of neuronal regulatory diversity and can be used to design genetic driver lines for cell types at specific timepoints, facilitating their characterization and manipulation.
Collapse
Affiliation(s)
- Jasper Janssens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joy N Ismail
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Gabriel Aughey
- Department of Life Sciences, Imperial College London, London, UK
| | - Katina I Spanier
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Florian V De Rop
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marc Dionne
- Department of Life Sciences, Imperial College London, London, UK
| | - Krista Grimes
- Department of Life Sciences, Imperial College London, London, UK
| | - Xiao Jiang Quan
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Dafni Papasokrati
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Samira Makhzami
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maxime De Waegeneer
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tony Southall
- Department of Life Sciences, Imperial College London, London, UK
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium. .,Department of Human Genetics, KU Leuven, Leuven, Belgium.
| |
Collapse
|
45
|
Marchiano F, Haering M, Habermann BH. OUP accepted manuscript. Nucleic Acids Res 2022; 50:W490-W499. [PMID: 35524562 PMCID: PMC9252804 DOI: 10.1093/nar/gkac306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/09/2022] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are subcellular organelles present in almost all eukaryotic cells, which play a central role in cellular metabolism. Different tissues, health and age conditions are characterized by a difference in mitochondrial structure and composition. The visual data mining platform mitoXplorer 1.0 was developed to explore the expression dynamics of genes associated with mitochondrial functions that could help explain these differences. It, however, lacked functions aimed at integrating mitochondria in the cellular context and thus identifying regulators that help mitochondria adapt to cellular needs. To fill this gap, we upgraded the mitoXplorer platform to version 2.0 (mitoXplorer 2.0). In this upgrade, we implemented two novel integrative functions, network analysis and transcription factor enrichment, to specifically help identify signalling or transcriptional regulators of mitochondrial processes. In addition, we implemented several other novel functions to allow the platform to go beyond simple data visualization, such as an enrichment function for mitochondrial processes, a function to explore time-series data, the possibility to compare datasets across species and an IDconverter to help facilitate data upload. We demonstrate the usefulness of these functions in three specific use cases. mitoXplorer 2.0 is freely available without login at http://mitoxplorer2.ibdm.univ-mrs.fr.
Collapse
Affiliation(s)
- Fabio Marchiano
- Aix-Marseille University, CNRS, IBDM UMR 7288, 13009 Marseille, France
| | - Margaux Haering
- Aix-Marseille University, CNRS, IBDM UMR 7288, 13009 Marseille, France
| | | |
Collapse
|
46
|
Duraiswamy J, Turrini R, Minasyan A, Barras D, Crespo I, Grimm AJ, Casado J, Genolet R, Benedetti F, Wicky A, Ioannidou K, Castro W, Neal C, Moriot A, Renaud-Tissot S, Anstett V, Fahr N, Tanyi JL, Eiva MA, Jacobson CA, Montone KT, Westergaard MCW, Svane IM, Kandalaft LE, Delorenzi M, Sorger PK, Färkkilä A, Michielin O, Zoete V, Carmona SJ, Foukas PG, Powell DJ, Rusakiewicz S, Doucey MA, Dangaj Laniti D, Coukos G. Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Cancer Cell 2021; 39:1623-1642.e20. [PMID: 34739845 PMCID: PMC8861565 DOI: 10.1016/j.ccell.2021.10.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/06/2021] [Accepted: 10/15/2021] [Indexed: 12/15/2022]
Abstract
The mechanisms regulating exhaustion of tumor-infiltrating lymphocytes (TIL) and responsiveness to PD-1 blockade remain partly unknown. In human ovarian cancer, we show that tumor-specific CD8+ TIL accumulate in tumor islets, where they engage antigen and upregulate PD-1, which restrains their functions. Intraepithelial PD-1+CD8+ TIL can be, however, polyfunctional. PD-1+ TIL indeed exhibit a continuum of exhaustion states, with variable levels of CD28 costimulation, which is provided by antigen-presenting cells (APC) in intraepithelial tumor myeloid niches. CD28 costimulation is associated with improved effector fitness of exhausted CD8+ TIL and is required for their activation upon PD-1 blockade, which also requires tumor myeloid APC. Exhausted TIL lacking proper CD28 costimulation in situ fail to respond to PD-1 blockade, and their response may be rescued by local CTLA-4 blockade and tumor APC stimulation via CD40L.
Collapse
Affiliation(s)
- Jaikumar Duraiswamy
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Riccardo Turrini
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Aspram Minasyan
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Isaac Crespo
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Alizée J Grimm
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Julia Casado
- Research Program of Systems Oncology, University of Helsinki, 00014 Helsinki, Finland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Alexandre Wicky
- Center for Precision Oncology, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Kalliopi Ioannidou
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Wilson Castro
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Christopher Neal
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Amandine Moriot
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Stéphanie Renaud-Tissot
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Victor Anstett
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Noémie Fahr
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Janos L Tanyi
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monika A Eiva
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Connor A Jacobson
- Harvard Ludwig Center, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Department of Oncology, UNIL, 1011 Lausanne, Switzerland
| | - Peter K Sorger
- Harvard Ludwig Center, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anniina Färkkilä
- Research Program of Systems Oncology, University of Helsinki, 00014 Helsinki, Finland; Department of Obstetrics and Gynecology, Helsinki University Hospital, 00014 Helsinki, Finland
| | - Olivier Michielin
- Center for Precision Oncology, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Santiago J Carmona
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Periklis G Foukas
- 2nd Department of Pathology, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Daniel J Powell
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sylvie Rusakiewicz
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Marie-Agnès Doucey
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland.
| |
Collapse
|
47
|
Pieters T, T’Sas S, Vanhee S, Almeida A, Driege Y, Roels J, Van Loocke W, Daneels W, Baens M, Marchand A, Van Trimpont M, Matthijssens F, Morscio J, Lemeire K, Lintermans B, Reunes L, Chaltin P, Offner F, Van Dorpe J, Hochepied T, Berx G, Beyaert R, Staal J, Van Vlierberghe P, Goossens S. Cyclin D2 overexpression drives B1a-derived MCL-like lymphoma in mice. J Exp Med 2021; 218:e20202280. [PMID: 34406363 PMCID: PMC8377631 DOI: 10.1084/jem.20202280] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/24/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive B cell lymphoma with poor long-term overall survival. Currently, MCL research and development of potential cures is hampered by the lack of good in vivo models. MCL is characterized by recurrent translocations of CCND1 or CCND2, resulting in overexpression of the cell cycle regulators cyclin D1 or D2, respectively. Here, we show, for the first time, that hematopoiesis-specific activation of cyclin D2 is sufficient to drive murine MCL-like lymphoma development. Furthermore, we demonstrate that cyclin D2 overexpression can synergize with loss of p53 to form aggressive and transplantable MCL-like lymphomas. Strikingly, cyclin D2-driven lymphomas display transcriptional, immunophenotypic, and functional similarities with B1a B cells. These MCL-like lymphomas have B1a-specific B cell receptors (BCRs), show elevated BCR and NF-κB pathway activation, and display increased MALT1 protease activity. Finally, we provide preclinical evidence that inhibition of MALT1 protease activity, which is essential for the development of early life-derived B1a cells, can be an effective therapeutic strategy to treat MCL.
Collapse
MESH Headings
- Allografts
- Animals
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cyclin D2/genetics
- Cyclin D2/metabolism
- Gene Expression Regulation, Neoplastic
- Lymphoma, Mantle-Cell/drug therapy
- Lymphoma, Mantle-Cell/genetics
- Lymphoma, Mantle-Cell/pathology
- Mice, Inbred C57BL
- Mice, Transgenic
- Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/antagonists & inhibitors
- Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/metabolism
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/pathology
- Neoplastic Cells, Circulating
- Tumor Suppressor Protein p53/genetics
- Xenograft Model Antitumor Assays
- Mice
Collapse
Affiliation(s)
- Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Sara T’Sas
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Stijn Vanhee
- Center for Inflammation Research, Flemish Institute for Biotechnology, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - André Almeida
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Yasmine Driege
- Center for Inflammation Research, Flemish Institute for Biotechnology, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Willem Daneels
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Mathijs Baens
- Center for Innovation and Stimulation of Drug Discovery Leuven, Leuven, Belgium
| | - Arnaud Marchand
- Center for Innovation and Stimulation of Drug Discovery Leuven, Leuven, Belgium
| | - Maaike Van Trimpont
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Filip Matthijssens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Julie Morscio
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Kelly Lemeire
- Center for Inflammation Research, Flemish Institute for Biotechnology, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Béatrice Lintermans
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Lindy Reunes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Patrick Chaltin
- Center for Innovation and Stimulation of Drug Discovery Leuven, Leuven, Belgium
- Center for Drug Design and Discovery, Catholic University of Leuven, Leuven, Belgium
| | - Fritz Offner
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Tino Hochepied
- Center for Inflammation Research, Flemish Institute for Biotechnology, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Geert Berx
- Cancer Research Institute Ghent, Ghent, Belgium
- Center for Inflammation Research, Flemish Institute for Biotechnology, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, Flemish Institute for Biotechnology, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jens Staal
- Center for Inflammation Research, Flemish Institute for Biotechnology, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| |
Collapse
|
48
|
Buchberger E, Bilen A, Ayaz S, Salamanca D, Matas de las Heras C, Niksic A, Almudi I, Torres-Oliva M, Casares F, Posnien N. Variation in Pleiotropic Hub Gene Expression Is Associated with Interspecific Differences in Head Shape and Eye Size in Drosophila. Mol Biol Evol 2021; 38:1924-1942. [PMID: 33386848 PMCID: PMC8097299 DOI: 10.1093/molbev/msaa335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Revealing the mechanisms underlying the breathtaking morphological diversity observed in nature is a major challenge in Biology. It has been established that recurrent mutations in hotspot genes cause the repeated evolution of morphological traits, such as body pigmentation or the gain and loss of structures. To date, however, it remains elusive whether hotspot genes contribute to natural variation in the size and shape of organs. As natural variation in head morphology is pervasive in Drosophila, we studied the molecular and developmental basis of differences in compound eye size and head shape in two closely related Drosophila species. We show differences in the progression of retinal differentiation between species and we applied comparative transcriptomics and chromatin accessibility data to identify the GATA transcription factor Pannier (Pnr) as central factor associated with these differences. Although the genetic manipulation of Pnr affected multiple aspects of dorsal head development, the effect of natural variation is restricted to a subset of the phenotypic space. We present data suggesting that this developmental constraint is caused by the coevolution of expression of pnr and its cofactor u-shaped (ush). We propose that natural variation in expression or function of highly connected developmental regulators with pleiotropic functions is a major driver for morphological evolution and we discuss implications on gene regulatory network evolution. In comparison to previous findings, our data strongly suggest that evolutionary hotspots are not the only contributors to the repeated evolution of eye size and head shape in Drosophila.
Collapse
Affiliation(s)
- Elisa Buchberger
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Anıl Bilen
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Sanem Ayaz
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - David Salamanca
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Present address: Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - Armin Niksic
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Isabel Almudi
- CABD (CSIC/UPO/JA), DMC2 Unit, Pablo de Olavide University Campus, Seville, Spain
| | - Montserrat Torres-Oliva
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Present address: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Fernando Casares
- CABD (CSIC/UPO/JA), DMC2 Unit, Pablo de Olavide University Campus, Seville, Spain
| | - Nico Posnien
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Corresponding author: E-mail:
| |
Collapse
|
49
|
Van Thillo Q, De Bie J, Seneviratne JA, Demeyer S, Omari S, Balachandran A, Zhai V, Tam WL, Sweron B, Geerdens E, Gielen O, Provost S, Segers H, Boeckx N, Marshall GM, Cheung BB, Isobe K, Kato I, Takita J, Amos TG, Deveson IW, McCalmont H, Lock RB, Oxley EP, Garwood MM, Dickins RA, Uyttebroeck A, Carter DR, Cools J, de Bock CE. Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia. Nat Commun 2021; 12:4164. [PMID: 34230493 PMCID: PMC8260768 DOI: 10.1038/s41467-021-24442-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Spi-1 Proto-Oncogene (SPI1) fusion genes are recurrently found in T-cell acute lymphoblastic leukemia (T-ALL) cases but are insufficient to drive leukemogenesis. Here we show that SPI1 fusions in combination with activating NRAS mutations drive an immature T-ALL in vivo using a conditional bone marrow transplant mouse model. Addition of the oncogenic fusion to the NRAS mutation also results in a higher leukemic stem cell frequency. Mechanistically, genetic deletion of the β-catenin binding domain within Transcription factor 7 (TCF7)-SPI1 or use of a TCF/β-catenin interaction antagonist abolishes the oncogenic activity of the fusion. Targeting the TCF7-SPI1 fusion in vivo with a doxycycline-inducible knockdown results in increased differentiation. Moreover, both pharmacological and genetic inhibition lead to down-regulation of SPI1 targets. Together, our results reveal an example where TCF7-SPI1 leukemia is vulnerable to pharmacological targeting of the TCF/β-catenin interaction.
Collapse
Affiliation(s)
- Quentin Van Thillo
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Jolien De Bie
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, UZ Leuven, Leuven, Belgium
| | - Janith A Seneviratne
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sofie Demeyer
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofia Omari
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Anushree Balachandran
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Vicki Zhai
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Wai L Tam
- Technology Innovation Lab, VIB, Gent, Belgium
| | - Bram Sweron
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ellen Geerdens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sarah Provost
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
| | - Glenn M Marshall
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Belamy B Cheung
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kiyotaka Isobe
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Timothy G Amos
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Hannah McCalmont
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ethan P Oxley
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Maximilian M Garwood
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Anne Uyttebroeck
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Daniel R Carter
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia
| | - Jan Cools
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
| | - Charles E de Bock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia.
| |
Collapse
|
50
|
Debackere K, Marcelis L, Demeyer S, Vanden Bempt M, Mentens N, Gielen O, Jacobs K, Broux M, Verhoef G, Michaux L, Graux C, Wlodarska I, Gaulard P, de Leval L, Tousseyn T, Cools J, Dierickx D. Fusion transcripts FYN-TRAF3IP2 and KHDRBS1-LCK hijack T cell receptor signaling in peripheral T-cell lymphoma, not otherwise specified. Nat Commun 2021; 12:3705. [PMID: 34140493 PMCID: PMC8211700 DOI: 10.1038/s41467-021-24037-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of non-Hodgkin lymphomas with poor prognosis. Up to 30% of PTCL lack distinctive features and are classified as PTCL, not otherwise specified (PTCL-NOS). To further improve our understanding of the genetic landscape and biology of PTCL-NOS, we perform RNA-sequencing of 18 cases and validate results in an independent cohort of 37 PTCL cases. We identify FYN-TRAF3IP2, KHDRBS1-LCK and SIN3A-FOXO1 as new in-frame fusion transcripts, with FYN-TRAF3IP2 as a recurrent fusion detected in 8 of 55 cases. Using ex vivo and in vivo experiments, we demonstrate that FYN-TRAF3IP2 and KHDRBS1-LCK activate signaling pathways downstream of the T cell receptor (TCR) complex and confer therapeutic vulnerability to clinically available drugs.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Cell Line, Tumor
- Cell Membrane/metabolism
- Cohort Studies
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Forkhead Box Protein O1/genetics
- Forkhead Box Protein O1/metabolism
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Intracellular Signaling Peptides and Proteins/metabolism
- Kaplan-Meier Estimate
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/genetics
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism
- Lymphoma, T-Cell, Peripheral/genetics
- Lymphoma, T-Cell, Peripheral/metabolism
- Lymphoma, T-Cell, Peripheral/pathology
- Mice
- Mice, Inbred C57BL
- NF-kappa B/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Proto-Oncogene Proteins c-fyn/genetics
- Proto-Oncogene Proteins c-fyn/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Seq
- Receptors, Antigen, T-Cell/metabolism
- Signal Transduction/genetics
- Sin3 Histone Deacetylase and Corepressor Complex/genetics
- Sin3 Histone Deacetylase and Corepressor Complex/metabolism
- bcl-X Protein/antagonists & inhibitors
- bcl-X Protein/metabolism
Collapse
Affiliation(s)
- Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Marlies Vanden Bempt
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Nicole Mentens
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Olga Gielen
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Kris Jacobs
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Michael Broux
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Gregor Verhoef
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Lucienne Michaux
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Carlos Graux
- Mont-Godinne University Hospital, Yvoir, Belgium
| | - Iwona Wlodarska
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Gaulard
- Département de Pathologie, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
- INSERM U955 and Université Paris-Est, Créteil, France
| | - Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Thomas Tousseyn
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
| | - Daan Dierickx
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium.
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium.
| |
Collapse
|