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Zhou Z, Zhang R, Zhou A, Lv J, Chen S, Zou H, Zhang G, Lin T, Wang Z, Zhang Y, Weng S, Han X, Liu Z. Proteomics appending a complementary dimension to precision oncotherapy. Comput Struct Biotechnol J 2024; 23:1725-1739. [PMID: 38689716 PMCID: PMC11058087 DOI: 10.1016/j.csbj.2024.04.044] [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: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Recent advances in high-throughput proteomic profiling technologies have facilitated the precise quantification of numerous proteins across multiple specimens concurrently. Researchers have the opportunity to comprehensively analyze the molecular signatures in plentiful medical specimens or disease pattern cell lines. Along with advances in data analysis and integration, proteomics data could be efficiently consolidated and employed to recognize precise elementary molecular mechanisms and decode individual biomarkers, guiding the precision treatment of tumors. Herein, we review a broad array of proteomics technologies and the progress and methods for the integration of proteomics data and further discuss how to better merge proteomics in precision medicine and clinical settings.
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Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Ruiqi Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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2
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Yan P, Jimenez ER, Li Z, Bui T, Seehawer M, Nishida J, Foidart P, Stevens LE, Xie Y, Gomez MM, Park SY, Long HW, Polyak K. Midkine as a driver of age-related changes and increase in mammary tumorigenesis. Cancer Cell 2024:S1535-6108(24)00350-7. [PMID: 39366375 DOI: 10.1016/j.ccell.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 07/30/2024] [Accepted: 09/11/2024] [Indexed: 10/06/2024]
Abstract
Aging is a pivotal risk factor for cancer, yet the underlying mechanisms remain poorly defined. Here, we explore age-related changes in the rat mammary gland by single-cell multiomics. Our findings include increased epithelial proliferation, loss of luminal identity, and decreased naive B and T cells with age. We discover a luminal progenitor population unique to old rats with profiles reflecting precancerous changes and identify midkine (Mdk) as a gene upregulated with age and a regulator of age-related luminal progenitors. Midkine treatment of young rats mimics age-related changes via activating PI3K-AKT-SREBF1 pathway and promotes nitroso-N-methylurea-induced mammary tumorigenesis. Midkine levels increase with age in human blood and mammary epithelium, and higher MDK in normal breast tissue is associated with higher breast cancer risk in younger women. Our findings reveal a link between aging and susceptibility to tumor initiation and identify midkine as a mediator of age-dependent increase in breast tumorigenesis.
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Affiliation(s)
- Pengze Yan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ernesto Rojas Jimenez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Triet Bui
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jun Nishida
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pierre Foidart
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Munoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - So Yeon Park
- Department of Pathology, Seoul National University, Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Seoul National University, Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea; Harvard Stem Cell Institute, Cambridge, MA 02142, USA.
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3
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Leote AC, Lopes F, Beyer A. Loss of coordination between basic cellular processes in human aging. NATURE AGING 2024:10.1038/s43587-024-00696-y. [PMID: 39227753 DOI: 10.1038/s43587-024-00696-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/30/2024] [Indexed: 09/05/2024]
Abstract
Age-related loss of gene expression coordination has been reported for distinct cell types and may lead to impaired cellular function. Here we propose a method for quantifying age-related changes in transcriptional regulatory relationships between genes, based on a model learned from external data. We used this method to uncover age-related trends in gene-gene relationships across eight human tissues, which demonstrates that reduced co-expression may also result from coordinated transcriptional responses. Our analyses reveal similar numbers of strengthening and weakening gene-gene relationships with age, impacting both tissue-specific (for example, coagulation in blood) and ubiquitous biological functions. Regulatory relationships becoming weaker with age were established mostly between genes operating in distinct cellular processes. As opposed to that, regulatory relationships becoming stronger with age were established both within and between different cellular functions. Our work reveals that, although most transcriptional regulatory gene-gene relationships are maintained during aging, those with declining regulatory coupling result mostly from a loss of coordination between distinct cellular processes.
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Affiliation(s)
- Ana Carolina Leote
- Cologne Excellence Cluster on Cellular Stress Responses in Age-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Francisco Lopes
- Cologne Excellence Cluster on Cellular Stress Responses in Age-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster on Cellular Stress Responses in Age-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
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4
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Unger Avila P, Padvitski T, Leote AC, Chen H, Saez-Rodriguez J, Kann M, Beyer A. Gene regulatory networks in disease and ageing. Nat Rev Nephrol 2024; 20:616-633. [PMID: 38867109 DOI: 10.1038/s41581-024-00849-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/14/2024]
Abstract
The precise control of gene expression is required for the maintenance of cellular homeostasis and proper cellular function, and the declining control of gene expression with age is considered a major contributor to age-associated changes in cellular physiology and disease. The coordination of gene expression can be represented through models of the molecular interactions that govern gene expression levels, so-called gene regulatory networks. Gene regulatory networks can represent interactions that occur through signal transduction, those that involve regulatory transcription factors, or statistical models of gene-gene relationships based on the premise that certain sets of genes tend to be coexpressed across a range of conditions and cell types. Advances in experimental and computational technologies have enabled the inference of these networks on an unprecedented scale and at unprecedented precision. Here, we delineate different types of gene regulatory networks and their cell-biological interpretation. We describe methods for inferring such networks from large-scale, multi-omics datasets and present applications that have aided our understanding of cellular ageing and disease mechanisms.
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Affiliation(s)
- Paula Unger Avila
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Tsimafei Padvitski
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Ana Carolina Leote
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - He Chen
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Martin Kann
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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5
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Johnson CS, Williams M, Sham K, Belluschi S, Ma W, Wang X, Lau WWY, Kaufmann KB, Krivdova G, Calderbank EF, Mende N, McLeod J, Mantica G, Li J, Grey-Wilson C, Drakopoulos M, Basheer S, Sinha S, Diamanti E, Basford C, Wilson NK, Howe SJ, Dick JE, Göttgens B, Green AR, Francis N, Laurenti E. Adaptation to ex vivo culture reduces human hematopoietic stem cell activity independently of the cell cycle. Blood 2024; 144:729-741. [PMID: 38805639 PMCID: PMC7616366 DOI: 10.1182/blood.2023021426] [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: 06/07/2023] [Revised: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
ABSTRACT Loss of long-term hematopoietic stem cell (LT-HSC) function ex vivo hampers the success of clinical protocols that rely on culture. However, the kinetics and mechanisms through which this occurs remain incompletely characterized. In this study, through time-resolved single-cell RNA sequencing, matched in vivo functional analysis, and the use of a reversible in vitro system of early G1 arrest, we defined the sequence of transcriptional and functional events that occur during the first ex vivo division of human LT-HSCs. We demonstrated that the sharpest loss in LT-HSC repopulation capacity happens early on, between 6 and 24 hours of culture, before LT-HSCs commit to cell cycle progression. During this time window, LT-HSCs adapt to the culture environment, limit the global variability in gene expression, and transiently upregulate gene networks involved in signaling and stress responses. From 24 hours, LT-HSC progression past early G1 contributes to the establishment of differentiation programs in culture. However, contrary to the current assumptions, we demonstrated that the loss of HSC function ex vivo is independent of cell cycle progression. Finally, we showed that targeting LT-HSC adaptation to culture by inhibiting the early activation of JAK/STAT signaling improves HSC long-term repopulating function ex vivo. Collectively, our study demonstrated that controlling early LT-HSC adaptation to ex vivo culture, for example, via JAK inhibition, is critically important to improve HSC gene therapy and expansion protocols.
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Affiliation(s)
- Carys S Johnson
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cell Process Development, Cell and Gene Therapy, GlaxoSmithKline, Stevenage, United Kingdom
| | - Matthew Williams
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Kendig Sham
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Serena Belluschi
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Wenjuan Ma
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Xiaonan Wang
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Winnie W Y Lau
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Gabriela Krivdova
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Emily F Calderbank
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Nicole Mende
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Jessica McLeod
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Giovanna Mantica
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Juan Li
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte Grey-Wilson
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Michael Drakopoulos
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Shaaezmeen Basheer
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Shubhankar Sinha
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Evangelia Diamanti
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Christina Basford
- Cell Process Development, Cell and Gene Therapy, GlaxoSmithKline, Stevenage, United Kingdom
| | - Nicola K Wilson
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Steven J Howe
- Cell Process Development, Cell and Gene Therapy, GlaxoSmithKline, Stevenage, United Kingdom
| | - John E Dick
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Berthold Göttgens
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Anthony R Green
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Natalie Francis
- Cell Process Development, Cell and Gene Therapy, GlaxoSmithKline, Stevenage, United Kingdom
- Department of Gene Therapy and Regenerative Medicine, King's College London, London, United Kingdom
| | - Elisa Laurenti
- Wellcome and Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
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6
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Connolly E, Pan T, Aluru M, Chockalingam S, Dhere V, Gibson G. Loss of immune cell identity with age inferred from large atlases of single cell transcriptomes. Aging Cell 2024:e14306. [PMID: 39143696 DOI: 10.1111/acel.14306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/21/2024] [Accepted: 07/27/2024] [Indexed: 08/16/2024] Open
Abstract
By analyzing two large atlases of almost 4 million cells, we show that immune-senescence involves a gradual loss of cellular identity, reflecting increased cellular heterogeneity, for effector, and cytotoxic immune cells. The effects are largely similar in both males and females and were robustly reproduced in two atlases, one assembled from 35 diverse studies including 678 adults, the other the OneK1K study of 982 adults. Since the mean transcriptional differences among cell-types remain constant across age deciles, there is little evidence for the alternative mechanism of convergence of cell-type identity. Key pathways promoting activation and stemness are down-regulated in aged T cells, while CD8 TEM and CD4 CTLs exhibited elevated inflammatory, and cytotoxicity in older individuals. Elevated inflammatory signaling pathways, such as MAPK and TNF-alpha signaling via NF-kB, also occur across all aged immune cells, particularly amongst effector immune cells. This finding of lost transcriptional identity with age carries several implications, spanning from a fundamental biological understanding of aging mechanisms to clinical perspectives on the efficacy of immunomodulation in elderly people.
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Affiliation(s)
- Erin Connolly
- Center for Integrative Genomics, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tony Pan
- Institute for Data Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia, USA
| | - Maneesha Aluru
- Institute for Data Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sriram Chockalingam
- Institute for Data Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Vishal Dhere
- Winship Cancer Institute, Department of Radiation Oncology, Emory University Hospital Midtown, Atlanta, Georgia, USA
| | - Greg Gibson
- Center for Integrative Genomics, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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7
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Yin K, Büttner M, Deligiannis IK, Strzelecki M, Zhang L, Talavera-López C, Theis F, Odom DT, Martinez-Jimenez CP. Polyploidisation pleiotropically buffers ageing in hepatocytes. J Hepatol 2024; 81:289-302. [PMID: 38583492 DOI: 10.1016/j.jhep.2024.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND & AIMS Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing. METHODS We performed single-nucleus RNA sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent strains that were haploinsufficient for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope. RESULTS We observed that ageing in wild-type mice results in nuclei polyploidy and a marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in the CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A-haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbations. CONCLUSIONS Our results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome. IMPACT AND IMPLICATIONS The functional role of hepatocyte polyploidisation during ageing is poorly understood. Using single-nucleus RNA sequencing and BaseScope approaches, we have studied ploidy dynamics during ageing in murine livers with non-deleterious genetic perturbations. We have identified that hepatocytes present different cellular states and the ability to buffer ageing-associated dysfunctions. Tetraploid nuclei exhibit robust transcriptional networks and are better adapted to genomically overcome perturbations. Novel therapeutic interventions aimed at attenuating age-related changes in tissue function could be exploited by manipulation of ploidy dynamics during chronic liver conditions.
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Affiliation(s)
- Kelvin Yin
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Maren Büttner
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany
| | | | | | - Liwei Zhang
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Carlos Talavera-López
- Division of Infectious Diseases and Tropical Medicine, Ludwig-Maximilian-Universität Klinikum, Germany
| | - Fabian Theis
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany; Technical University of Munich, Department of Mathematics, 85748 Garching. Munich, Germany; German Cancer Research Centre, Heidelberg, Germany.
| | - Duncan T Odom
- German Cancer Research Center, Division of Regulatory Genomics and Cancer Evolution (B270), Heidelberg, Germany; Cancer Research UK Cambridge Institute, University of Cambridge, CB20RE, United Kingdom.
| | - Celia P Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany; Institute of Biotechnology and Biomedicine (BIOTECMED), Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, Spain.
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8
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Lin WH, Opoc FG, Liao CW, Roy K, Steinmetz L, Leu JY. Histone deacetylase Hos2 regulates protein expression noise by potentially modulating the protein translation machinery. Nucleic Acids Res 2024; 52:7556-7571. [PMID: 38783136 PMCID: PMC11260488 DOI: 10.1093/nar/gkae432] [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: 02/02/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Non-genetic variations derived from expression noise at transcript or protein levels can result in cell-to-cell heterogeneity within an isogenic population. Although cells have developed strategies to reduce noise in some cellular functions, this heterogeneity can also facilitate varying levels of regulation and provide evolutionary benefits in specific environments. Despite several general characteristics of cellular noise having been revealed, the detailed molecular pathways underlying noise regulation remain elusive. Here, we established a dual-fluorescent reporter system in Saccharomyces cerevisiae and performed experimental evolution to search for mutations that increase expression noise. By analyzing evolved cells using bulk segregant analysis coupled with whole-genome sequencing, we identified the histone deacetylase Hos2 as a negative noise regulator. A hos2 mutant down-regulated multiple ribosomal protein genes and exhibited partially compromised protein translation, indicating that Hos2 may regulate protein expression noise by modulating the translation machinery. Treating cells with translation inhibitors or introducing mutations into several Hos2-regulated ribosomal protein genes-RPS9A, RPS28B and RPL42A-enhanced protein expression noise. Our study provides an effective strategy for identifying noise regulators and also sheds light on how cells regulate non-genetic variation through protein translation.
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Affiliation(s)
- Wei-Han Lin
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Florica J G Opoc
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Wei Liao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Kevin R Roy
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg 69117, Germany
| | - Jun-Yi Leu
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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9
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Tan Q, Wellmerling JH, Song S, Dresler SR, Meridew JA, Choi KM, Li Y, Prakash Y, Tschumperlin DJ. Targeting CEBPA to restore cellular identity and tissue homeostasis in pulmonary fibrosis. JCI Insight 2024; 9:e175290. [PMID: 39012710 PMCID: PMC11343593 DOI: 10.1172/jci.insight.175290] [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: 09/13/2023] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
Fibrosis in the lung is thought to be driven by epithelial cell dysfunction and aberrant cell-cell interactions. Unveiling the molecular mechanisms of cellular plasticity and cell-cell interactions is imperative to elucidating lung regenerative capacity and aberrant repair in pulmonary fibrosis. By mining publicly available RNA-Seq data sets, we identified loss of CCAAT enhancer-binding protein alpha (CEBPA) as a candidate contributor to idiopathic pulmonary fibrosis (IPF). We used conditional KO mice, scRNA-Seq, lung organoids, small-molecule inhibition, and potentially novel gene manipulation methods to investigate the role of CEBPA in lung fibrosis and repair. Long-term (6 months or more) of Cebpa loss in AT2 cells caused spontaneous fibrosis and increased susceptibility to bleomycin-induced fibrosis. Cebpa knockout (KO) in these mice significantly decreased AT2 cell numbers in the lung and reduced expression of surfactant homeostasis genes, while increasing inflammatory cell recruitment as well as upregulating S100a8/a9 in AT2 cells. In vivo treatment with an S100A8/A9 inhibitor alleviated experimental lung fibrosis. Restoring CEBPA expression in lung organoids ex vivo and during experimental lung fibrosis in vivo rescued CEBPA deficiency-mediated phenotypes. Our study establishes a direct mechanistic link between CEBPA repression, impaired AT2 cell identity, disrupted tissue homeostasis, and lung fibrosis.
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Affiliation(s)
- Qi Tan
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Jack H. Wellmerling
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Shengren Song
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Sara R. Dresler
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Jeffrey A. Meridew
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Kyoung M. Choi
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Yong Li
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Y.S. Prakash
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel J. Tschumperlin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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10
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Wang H, Xiao F, Gao Z, Guo L, Yang L, Li G, Kong Q. Methylation entropy landscape of Chinese long-lived individuals reveals lower epigenetic noise related to human healthy aging. Aging Cell 2024; 23:e14163. [PMID: 38566438 PMCID: PMC11258444 DOI: 10.1111/acel.14163] [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: 12/15/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
The transition from ordered to noisy is a significant epigenetic signature of aging and age-related disease. As a paradigm of healthy human aging and longevity, long-lived individuals (LLI, >90 years old) may possess characteristic strategies in coping with the disordered epigenetic regulation. In this study, we constructed high-resolution blood epigenetic noise landscapes for this cohort by a methylation entropy (ME) method using whole genome bisulfite sequencing (WGBS). Although a universal increase in global ME occurred with chronological age in general control samples, this trend was suppressed in LLIs. Importantly, we identified 38,923 genomic regions with LLI-specific lower ME (LLI-specific lower entropy regions, for short, LLI-specific LERs). These regions were overrepresented in promoters, which likely function in transcriptional noise suppression. Genes associated with LLI-specific LERs have a considerable impact on SNP-based heritability of some aging-related disorders (e.g., asthma and stroke). Furthermore, neutrophil was identified as the primary cell type sustaining LLI-specific LERs. Our results highlight the stability of epigenetic order in promoters of genes involved with aging and age-related disorders within LLI epigenomes. This unique epigenetic feature reveals a previously unknown role of epigenetic order maintenance in specific genomic regions of LLIs, which helps open a new avenue on the epigenetic regulation mechanism in human healthy aging and longevity.
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Affiliation(s)
- Hao‐Tian Wang
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging StudyKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Fu‐Hui Xiao
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging StudyKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Zong‐Liang Gao
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging StudyKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Li‐Yun Guo
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging StudyKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Li‐Qin Yang
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging StudyKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Gong‐Hua Li
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging StudyKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Qing‐Peng Kong
- Key Laboratory of Genetic Evolution & Animal Models (Chinese Academy of Sciences), Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging StudyKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- CAS Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
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11
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Huang D, Jiao X, Huang S, Liu J, Si H, Qi D, Pei X, Lu D, Wang Y, Li Z. Analysis of the heterogeneity and complexity of murine extraorbital lacrimal gland via single-cell RNA sequencing. Ocul Surf 2024; 34:60-95. [PMID: 38945476 DOI: 10.1016/j.jtos.2024.06.005] [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: 08/26/2022] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
PURPOSE The lacrimal gland is essential for maintaining ocular surface health and avoiding external damage by secreting an aqueous layer of the tear film. However, a healthy lacrimal gland's inventory of cell types and heterogeneity remains understudied. METHODS Here, 10X Genome-based single-cell RNA sequencing was used to generate an unbiased classification of cellular diversity in the extraorbital lacrimal gland (ELG) of C57BL/6J mice. From 43,850 high-quality cells, we produced an atlas of cell heterogeneity and defined cell types using classic marker genes. The possible functions of these cells were analyzed through bioinformatics analysis. Additionally, the CellChat was employed for a preliminary analysis of the cell-cell communication network in the ELG. RESULTS Over 37 subclasses of cells were identified, including seven types of glandular epithelial cells, three types of fibroblasts, ten types of myeloid-derived immune cells, at least eleven types of lymphoid-derived immune cells, and five types of vascular-associated cell subsets. The cell-cell communication network analysis revealed that fibroblasts and immune cells play a pivotal role in the dense intercellular communication network within the mouse ELG. CONCLUSIONS This study provides a comprehensive transcriptome atlas and related database of the mouse ELG.
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Affiliation(s)
- Duliurui Huang
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xinwei Jiao
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Shenzhen Huang
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Jiangman Liu
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hongli Si
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Di Qi
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Xiaoting Pei
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Dingli Lu
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Yimian Wang
- Division of Medicine, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Zhijie Li
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China; Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China.
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12
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Chen M, Dahl A. A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data. Nat Commun 2024; 15:5229. [PMID: 38898015 PMCID: PMC11186839 DOI: 10.1038/s41467-024-49242-9] [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: 02/26/2023] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has been widely used to characterize cell types based on their average gene expression profiles. However, most studies do not consider cell type-specific variation across donors. Modelling this cell type-specific inter-individual variation could help elucidate cell type-specific biology and inform genes and cell types underlying complex traits. We therefore develop a new model to detect and quantify cell type-specific variation across individuals called CTMM (Cell Type-specific linear Mixed Model). We use extensive simulations to show that CTMM is powerful and unbiased in realistic settings. We also derive calibrated tests for cell type-specific interindividual variation, which is challenging given the modest sample sizes in scRNA-seq. We apply CTMM to scRNA-seq data from human induced pluripotent stem cells to characterize the transcriptomic variation across donors as cells differentiate into endoderm. We find that almost 100% of transcriptome-wide variability between donors is differentiation stage-specific. CTMM also identifies individual genes with statistically significant stage-specific variability across samples, including 85 genes that do not have significant stage-specific mean expression. Finally, we extend CTMM to partition interindividual covariance between stages, which recapitulates the overall differentiation trajectory. Overall, CTMM is a powerful tool to illuminate cell type-specific biology in scRNA-seq.
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Affiliation(s)
- Minhui Chen
- Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA.
| | - Andy Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA.
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13
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Keenan CR, Coughlan HD, Iannarella N, Tapia Del Fierro A, Keniry A, Johanson TM, Chan WF, Garnham AL, Whitehead LW, Blewitt ME, Smyth GK, Allan RS. Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription. Genome Res 2024; 34:556-571. [PMID: 38719473 PMCID: PMC11146594 DOI: 10.1101/gr.279119.124] [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: 02/16/2024] [Accepted: 04/03/2024] [Indexed: 06/05/2024]
Abstract
H3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes in differentiation and development. Here, we investigate the molecular consequences of heterochromatin loss in cells deficient in both SUV39H1 and SUV39H2 (Suv39DKO), the major mammalian histone methyltransferase enzymes that catalyze heterochromatic H3K9me3 deposition. We reveal a paradoxical repression of protein-coding genes in Suv39DKO cells, with these differentially expressed genes principally in euchromatic (Tn5-accessible, H3K4me3- and H3K27ac-marked) rather than heterochromatic (H3K9me3-marked) or polycomb (H3K27me3-marked) regions. Examination of the three-dimensional (3D) nucleome reveals that transcriptomic dysregulation occurs in euchromatic regions close to the nuclear periphery in 3D space. Moreover, this transcriptomic dysregulation is highly correlated with altered 3D genome organization in Suv39DKO cells. Together, our results suggest that the nuclear lamina-tethering of Suv39-dependent H3K9me3 domains provides an essential scaffold to support euchromatic genome organization and the maintenance of gene transcription for healthy cellular function.
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Affiliation(s)
- Christine R Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia;
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Andres Tapia Del Fierro
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Wing Fuk Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Lachlan W Whitehead
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia;
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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14
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O'Callaghan A, Eling N, Marioni JC, Vallejos CA. BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data. F1000Res 2024; 11:59. [PMID: 38779464 PMCID: PMC11109695 DOI: 10.12688/f1000research.74416.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-to-cell gene expression variability is an inherent feature of complex biological systems, such as immunity and development. Single-cell RNA sequencing is a powerful tool to quantify this heterogeneity, but it is prone to strong technical noise. In this article, we describe a step-by-step computational workflow that uses the BASiCS Bioconductor package to robustly quantify expression variability within and between known groups of cells (such as experimental conditions or cell types). BASiCS uses an integrated framework for data normalisation, technical noise quantification and downstream analyses, propagating statistical uncertainty across these steps. Within a single seemingly homogeneous cell population, BASiCS can identify highly variable genes that exhibit strong heterogeneity as well as lowly variable genes with stable expression. BASiCS also uses a probabilistic decision rule to identify changes in expression variability between cell populations, whilst avoiding confounding effects related to differences in technical noise or in overall abundance. Using a publicly available dataset, we guide users through a complete pipeline that includes preliminary steps for quality control, as well as data exploration using the scater and scran Bioconductor packages. The workflow is accompanied by a Docker image that ensures the reproducibility of our results.
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Affiliation(s)
- Alan O'Callaghan
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Nils Eling
- Institute for Molecular Health Sciences, ETH Zürich, Zürich, 8093, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zürich, CH-8057, Switzerland
| | - John C. Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UK
| | - Catalina A. Vallejos
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Alan Turing Institute, The Alan Turing Institute, London, NW1 2DB, UK
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15
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Ni X, Su H, Li GH, Li R, Lan R, Lv Y, Pang G, Zhang W, Yang Z, Hu C. Specific differences and novel key regulatory genes of sex in influencing exceptional longevity phenotypes. Diabetes Metab Syndr 2024; 18:103039. [PMID: 38762968 DOI: 10.1016/j.dsx.2024.103039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
BACKGROUND AND AIMS Although the life expectancy of women systematically and robustly exceeds that of men, specific differences and molecular mechanisms of sex in influencing longevity phenotypes remain largely unknown. Therefore, we performed transcriptome sequencing of peripheral blood samples to explore regulatory mechanisms of healthy longevity by incorporating sex data. METHODS We selected 34 exceptional longevity (age: 98.26 ± 2.45 years) and 16 controls (age: 52.81 ± 9.78) without advanced outcomes from 1363 longevity and 692 controls recruited from Nanning of Guangxi for RNA sequencing 1. The transcriptome sequencing 1 data of 50 samples were compared by longevity and sex to screen differentially expressed genes (DEGs). Then, 121 aging samples (40-110 years old) without advanced outcomes from 355 longevity and 294 controls recruited from Dongxing of Guangxi were selected for RNA sequencing 2. The genes associated with aging from the transcriptome sequencing 2 of 121 aging samples were filtered out. Finally, the gender-related longevity candidate genes and their possible metabolic pathways were verified by cell model of aging and a real-time polymerase chain reaction (RT-PCR). RESULTS Metabolism differs between male and female and plays a key role in longevity. Moreover, the principal findings of this study revealed a novel key gene, UGT2B11, that plays an important role in regulating lipid metabolism through the peroxisome proliferator activated receptor gamma (PPARG) signalling pathway and ultimately improving lifespan, particularly in females. CONCLUSION The findings suggest specific differences in metabolism affecting exceptional longevity phenotypes between the sexes and offer novel therapeutic targets to extend lifespan by regulating lipid homeostasis.
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Affiliation(s)
- Xiaolin Ni
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Peking Union Medical College, Beijing, 100005, PR China; The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, 100730, PR China.
| | - Huabin Su
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, PR China
| | - Rongqiao Li
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Rushu Lan
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Yuan Lv
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Guofang Pang
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Wei Zhang
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Ze Yang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, 100730, PR China.
| | - Caiyou Hu
- Jiangbin Hospital, Guangxi Zhuang Autonomous Region, 530021, PR China.
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16
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Dobner S, Tóth F, de Rooij LPMH. A high-resolution view of the heterogeneous aging endothelium. Angiogenesis 2024; 27:129-145. [PMID: 38324119 PMCID: PMC11021252 DOI: 10.1007/s10456-023-09904-6] [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: 08/21/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024]
Abstract
Vascular endothelial cell (EC) aging has a strong impact on tissue perfusion and overall cardiovascular health. While studies confined to the investigation of aging-associated vascular readouts in one or a few tissues have already drastically expanded our understanding of EC aging, single-cell omics and other high-resolution profiling technologies have started to illuminate the intricate molecular changes underlying endothelial aging across diverse tissues and vascular beds at scale. In this review, we provide an overview of recent insights into the heterogeneous adaptations of the aging vascular endothelium. We address critical questions regarding tissue-specific and universal responses of the endothelium to the aging process, EC turnover dynamics throughout lifespan, and the differential susceptibility of ECs to acquiring aging-associated traits. In doing so, we underscore the transformative potential of single-cell approaches in advancing our comprehension of endothelial aging, essential to foster the development of future innovative therapeutic strategies for aging-associated vascular conditions.
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Affiliation(s)
- Sarah Dobner
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fanni Tóth
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Laura P M H de Rooij
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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17
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Jia H, Chang Y, Chen Y, Chen X, Zhang H, Hua X, Xu M, Sheng Y, Zhang N, Cui H, Han L, Zhang J, Fu X, Song J. A single-cell atlas of lung homeostasis reveals dynamic changes during development and aging. Commun Biol 2024; 7:427. [PMID: 38589700 PMCID: PMC11001898 DOI: 10.1038/s42003-024-06111-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: 08/08/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Aging is a global challenge, marked in the lungs by function decline and structural disorders, which affects the health of the elderly population. To explore anti-aging strategies, we develop a dynamic atlas covering 45 cell types in human lungs, spanning from embryonic development to aging. We aim to apply the discoveries of lung's development to address aging-related issues. We observe that both epithelial and immune cells undergo a process of acquisition and loss of essential function as they transition from development to aging. During aging, we identify cellular phenotypic alternations that result in reduced pulmonary compliance and compromised immune homeostasis. Furthermore, we find a distinctive expression pattern of the ferritin light chain (FTL) gene, which increases during development but decreases in various types of lung cells during the aging process.
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Affiliation(s)
- Hao Jia
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Chang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yulin Chen
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Traditional Chinese and Western Medicine, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xiao Chen
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hang Zhang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiumeng Hua
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengda Xu
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yixuan Sheng
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ningning Zhang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Cui
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Han
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of General Surgery, Yanan Hospital, Kunming Medical University, Kunming, China
| | - Jian Zhang
- Thoracic Surgery Department, the third affiliated hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China.
| | - Xiaodong Fu
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, National Centre for Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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18
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Braunger JM, Cammarata LV, Sornapudi TR, Uhler C, Shivashankar GV. Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging. Aging Cell 2024; 23:e14056. [PMID: 38062919 PMCID: PMC10928569 DOI: 10.1111/acel.14056] [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: 08/15/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Human life expectancy is constantly increasing and aging has become a major risk factor for many diseases, although the underlying gene regulatory mechanisms are still unclear. Using transcriptomic and chromosomal conformation capture (Hi-C) data from human skin fibroblasts from individuals across different age groups, we identified a tight coupling between the changes in co-regulation and co-localization of genes. We obtained transcription factors, cofactors, and chromatin regulators that could drive the cellular aging process by developing a time-course prize-collecting Steiner tree algorithm. In particular, by combining RNA-Seq data from different age groups and protein-protein interaction data we determined the key transcription regulators and gene regulatory changes at different life stage transitions. We then mapped these transcription regulators to the 3D reorganization of chromatin in young and old skin fibroblasts. Collectively, we identified key transcription regulators whose target genes are spatially rearranged and correlate with changes in their expression, thereby providing potential targets for reverting cellular aging.
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Affiliation(s)
- Jana M. Braunger
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Louis V. Cammarata
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Department of StatisticsHarvard UniversityCambridgeMassachusettsUSA
| | | | - Caroline Uhler
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Laboratory for Information and Decision SystemsMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - G. V. Shivashankar
- Division of Biology and ChemistryPaul Scherrer InstituteVilligenSwitzerland
- Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
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19
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Winkler I, Tolkachov A, Lammers F, Lacour P, Daugelaite K, Schneider N, Koch ML, Panten J, Grünschläger F, Poth T, Ávila BMD, Schneider A, Haas S, Odom DT, Gonçalves Â. The cycling and aging mouse female reproductive tract at single-cell resolution. Cell 2024; 187:981-998.e25. [PMID: 38325365 DOI: 10.1016/j.cell.2024.01.021] [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: 07/25/2022] [Revised: 04/21/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
The female reproductive tract (FRT) undergoes extensive remodeling during reproductive cycling. This recurrent remodeling and how it shapes organ-specific aging remains poorly explored. Using single-cell and spatial transcriptomics, we systematically characterized morphological and gene expression changes occurring in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrous cycle, during decidualization, and into aging. These analyses reveal that fibroblasts play central-and highly organ-specific-roles in FRT remodeling by orchestrating extracellular matrix (ECM) reorganization and inflammation. Our results suggest a model wherein recurrent FRT remodeling over reproductive lifespan drives the gradual, age-related development of fibrosis and chronic inflammation. This hypothesis was directly tested using chemical ablation of cycling, which reduced fibrotic accumulation during aging. Our atlas provides extensive detail into how estrus, pregnancy, and aging shape the organs of the female reproductive tract and reveals the unexpected cost of the recurrent remodeling required for reproduction.
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Affiliation(s)
- Ivana Winkler
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany
| | - Alexander Tolkachov
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Fritjof Lammers
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Perrine Lacour
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Klaudija Daugelaite
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Nina Schneider
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany
| | - Marie-Luise Koch
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Jasper Panten
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany; German Cancer Research Center (DKFZ), Division of Computational Genomics and Systems Genetics, 69120 Heidelberg, Germany
| | - Florian Grünschläger
- Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany; German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Division of Stem Cells and Cancer, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Tanja Poth
- CMCP - Center for Model System and Comparative Pathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | | | - Augusto Schneider
- Universidade Federal de Pelotas, Faculdade de Nutrição, 96010-610 Pelotas, RS, Brazil
| | - Simon Haas
- German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Division of Stem Cells and Cancer, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Charité - Universitätsmedizin Berlin, Department of Hematology, Oncology and Cancer Immunology, 10115 Berlin, Germany
| | - Duncan T Odom
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Ângela Gonçalves
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany.
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20
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Panier S, Wang S, Schumacher B. Genome Instability and DNA Repair in Somatic and Reproductive Aging. ANNUAL REVIEW OF PATHOLOGY 2024; 19:261-290. [PMID: 37832947 DOI: 10.1146/annurev-pathmechdis-051122-093128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Genetic material is constantly subjected to genotoxic insults and is critically dependent on DNA repair. Genome maintenance mechanisms differ in somatic and germ cells as the soma only requires maintenance during an individual's lifespan, while the germline indefinitely perpetuates its genetic information. DNA lesions are recognized and repaired by mechanistically highly diverse repair machineries. The DNA damage response impinges on a vast array of homeostatic processes and can ultimately result in cell fate changes such as apoptosis or cellular senescence. DNA damage causally contributes to the aging process and aging-associated diseases, most prominently cancer. By causing mutations, DNA damage in germ cells can lead to genetic diseases and impact the evolutionary trajectory of a species. The mechanisms ensuring tight control of germline DNA repair could be highly instructive in defining strategies for improved somatic DNA repair. They may provide future interventions to maintain health and prevent disease during aging.
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Affiliation(s)
- Stephanie Panier
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Siyao Wang
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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21
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Ilan Y. Variability in exercise is linked to improved age-related dysfunctions: A potential role for the constrained-disorder principle-based second-generation artificial intelligence system. RESEARCH SQUARE 2023:rs.3.rs-3671709. [PMID: 38196652 PMCID: PMC10775380 DOI: 10.21203/rs.3.rs-3671709/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Objective: Regular physical activity (PA) promotes mental and physical health. Nevertheless, inactivity is a worldwide pandemic, and methods to augment exercise benefits are required. The constrained disorder principle (CDP) characterizes biological systems based on their inherent variability. We aimed to investigate the association between intra-individual variability in PA and disability among non-athlete adults. Methods: In this retrospective analysis of the longitudinal SHARE survey, we included non-disabled adults aged >50 with at least six visits over 14 years. Self-reported PA frequency was documented bi- to triennially. Low PA intensity was defined as vigorous PA frequency less than once a week. Stable PA was described as an unchanged PA intensity in all consecutive middle observations. The primary outcome was defined as a physical limitation in everyday activities at the end of the survey. Secondary outcomes were cognitive functions, including short-term memory, long-term memory, and verbal fluency. Results: The study included 2,049 non-disabled adults with a mean age of 53 and 49.1% women. In the initially high PA intensity group, variability in PA was associated with increased physical disability prevalence (23.3% vs. 33.2%, stable vs. unstable PA ; P<0.01; adjusted P<0.01). In the initially low PA intensity group, variability was associated with a reduced physical disability (45.6% vs. 33.3%, stable vs. unstable PA ; P=0.02; adjusted P=0.03). There were no statistically significant differences in cognitive parameters between the groups. Among individuals with the same low PA intensity at the beginning and end of follow-up, variability was associated with reduced physical disability (56.9% vs. 36.5%, stable vs. unstable PA ; P=0.02; adjusted P=0.04) and improved short-term memory (score change: -0.28 vs. +0.29, stable vs. unstable PA ; P=0.05). Conclusion: Incorporating variability into PA regimens of inactive adults may enhance their physical and cognitive benefits.
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22
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Tobias GC, Gomes JLP, Fernandes LG, Voltarelli VA, de Almeida NR, Jannig PR, de Souza RWA, Negrão CE, Oliveira EM, Chammas R, Alves CRR, Brum PC. Aerobic exercise training mitigates tumor growth and cancer-induced splenomegaly through modulation of non-platelet platelet factor 4 expression. Sci Rep 2023; 13:21970. [PMID: 38081853 PMCID: PMC10713653 DOI: 10.1038/s41598-023-47217-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Exercise training reduces the incidence of several cancers, but the mechanisms underlying these effects are not fully understood. Exercise training can affect the spleen function, which controls the hematopoiesis and immune response. Analyzing different cancer models, we identified that 4T1, LLC, and CT26 tumor-bearing mice displayed enlarged spleen (splenomegaly), and exercise training reduced spleen mass toward control levels in two of these models (LLC and CT26). Exercise training also slowed tumor growth in melanoma B16F10, colon tumor 26 (CT26), and Lewis lung carcinoma (LLC) tumor-bearing mice, with minor effects in mammary carcinoma 4T1, MDA-MB-231, and MMTV-PyMT mice. In silico analyses using transcriptome profiles derived from these models revealed that platelet factor 4 (Pf4) is one of the main upregulated genes associated with splenomegaly during cancer progression. To understand whether exercise training would modulate the expression of these genes in the tumor and spleen, we investigated particularly the CT26 model, which displayed splenomegaly and had a clear response to the exercise training effects. RT-qPCR analysis confirmed that trained CT26 tumor-bearing mice had decreased Pf4 mRNA levels in both the tumor and spleen when compared to untrained CT26 tumor-bearing mice. Furthermore, exercise training specifically decreased Pf4 mRNA levels in the CT26 tumor cells. Aspirin treatment did not change tumor growth, splenomegaly, and tumor Pf4 mRNA levels, confirming that exercise decreased non-platelet Pf4 mRNA levels. Finally, tumor Pf4 mRNA levels are deregulated in The Cancer Genome Atlas Program (TCGA) samples and predict survival in multiple cancer types. This highlights the potential therapeutic value of exercise as a complementary approach to cancer treatment and underscores the importance of understanding the exercise-induced transcriptional changes in the spleen for the development of novel cancer therapies.
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Affiliation(s)
- Gabriel C Tobias
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil.
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - João L P Gomes
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
| | - Larissa G Fernandes
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
| | - Vanessa A Voltarelli
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Ney R de Almeida
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
| | - Paulo R Jannig
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Rodrigo W Alves de Souza
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Carlos E Negrão
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
- Instituto do Coração (InCor), Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Edilamar M Oliveira
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
| | - Roger Chammas
- Department of Radiology and Oncology, Faculdade de Medicine, Universidade de São Paulo, São Paulo, Brazil
| | - Christiano R R Alves
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil
| | - Patricia C Brum
- School of Physical Education and Sport, Universidade de São Paulo, Avenida Professor Mello Moraes, 65-Butantã, São Paulo, SP, 05508-030, Brazil.
- Department of Physiology & Biophysics, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
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23
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Yang M, Harrison BR, Promislow DEL. Cellular age explains variation in age-related cell-to-cell transcriptome variability. Genome Res 2023; 33:1906-1916. [PMID: 37973195 PMCID: PMC10760448 DOI: 10.1101/gr.278144.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Organs and tissues age at different rates within a single individual. Such asynchrony in aging has been widely observed at multiple levels, from functional hallmarks, such as anatomical structures and physiological processes, to molecular endophenotypes, such as the transcriptome and metabolome. However, we lack a conceptual framework to understand why some components age faster than others. Just as demographic models explain why aging evolves, here we test the hypothesis that demographic differences among cell types, determined by cell-specific differences in turnover rate, can explain why the transcriptome shows signs of aging in some cell types but not others. Through analysis of mouse single-cell transcriptome data across diverse tissues and ages, we find that cellular age explains a large proportion of the variation in the age-related increase in transcriptome variance. We further show that long-lived cells are characterized by relatively high expression of genes associated with proteostasis and that the transcriptome of long-lived cells shows greater evolutionary constraint than short-lived cells. In contrast, in short-lived cell types, the transcriptome is enriched for genes associated with DNA repair. Based on these observations, we develop a novel heuristic model that explains how and why aging rates differ among cell types.
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Affiliation(s)
- Ming Yang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Benjamin R Harrison
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Daniel E L Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington 98195, USA;
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
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24
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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.
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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
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25
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Zheng H, Vijg J, Fard AT, Mar JC. Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging. Genome Biol 2023; 24:238. [PMID: 37864221 PMCID: PMC10588274 DOI: 10.1186/s13059-023-03036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 08/11/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Single-cell RNA-sequencing (scRNA-seq) technologies enable the capture of gene expression heterogeneity and consequently facilitate the study of cell-to-cell variability at the cell type level. Although different methods have been proposed to quantify cell-to-cell variability, it is unclear what the optimal statistical approach is, especially in light of challenging data structures that are unique to scRNA-seq data like zero inflation. RESULTS We systematically evaluate the performance of 14 different variability metrics that are commonly applied to transcriptomic data for measuring cell-to-cell variability. Leveraging simulations and real datasets, we benchmark the metric performance based on data-specific features, sparsity and sequencing platform, biological properties, and the ability to recapitulate true levels of biological variability based on known gene sets. Next, we use scran, the metric with the strongest all-round performance, to investigate changes in cell-to-cell variability that occur during B cell differentiation and the aging processes. The analysis of primary cell types from hematopoietic stem cells (HSCs) and B lymphopoiesis reveals unique gene signatures with consistent patterns of variable and stable expression profiles during B cell differentiation which highlights the significance of these methods. Identifying differentially variable genes between young and old cells elucidates the regulatory changes that may be overlooked by solely focusing on mean expression changes and we investigate this in the context of regulatory networks. CONCLUSIONS We highlight the importance of capturing cell-to-cell gene expression variability in a complex biological process like differentiation and aging and emphasize the value of these findings at the level of individual cell types.
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Affiliation(s)
- Huiwen Zheng
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Atefeh Taherian Fard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.
| | - Jessica Cara Mar
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.
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26
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Sanchez-Quant E, Richter ML, Colomé-Tatché M, Martinez-Jimenez CP. Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge. Genome Biol 2023; 24:234. [PMID: 37848949 PMCID: PMC10583437 DOI: 10.1186/s13059-023-03075-9] [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: 06/08/2022] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes are the gold standard model for the assessment of drug efficacy, safety, and toxicity in the early phases of drug development. Recent advances in single-cell genomics demonstrate liver zonation and ploidy as main drivers of cellular heterogeneity. However, little is known about the impact of hepatocyte specialization on liver function upon metabolic challenge, including hepatic metabolism, detoxification, and protein synthesis. RESULTS Here, we investigate the metabolic capacity of individual human hepatocytes in vitro. We assess how chronic accumulation of lipids enhances cellular heterogeneity and impairs the metabolisms of drugs. Using a phenotyping five-probe cocktail, we identify four functional subgroups of hepatocytes responding differently to drug challenge and fatty acid accumulation. These four subgroups display differential gene expression profiles upon cocktail treatment and xenobiotic metabolism-related specialization. Notably, intracellular fat accumulation leads to increased transcriptional variability and diminishes the drug-related metabolic capacity of hepatocytes. CONCLUSIONS Our results demonstrate that, upon a metabolic challenge such as exposure to drugs or intracellular fat accumulation, hepatocyte subgroups display different and heterogeneous transcriptional responses.
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Affiliation(s)
- Eva Sanchez-Quant
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Maria Lucia Richter
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Maria Colomé-Tatché
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), 85354, Freising, Germany.
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 82152, Munich, Germany.
| | - Celia Pilar Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, 85764, Neuherberg, Germany.
- TUM School of Medicine, Technical University of Munich, Munich (TUM), 80333, Munich, Germany.
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27
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Zhang J, Wu Q, Hu X, Wang Y, Lu J, Chakraborty R, Martin KA, Guo S. Serum Response Factor Reduces Gene Expression Noise and Confers Cell State Stability. Stem Cells 2023; 41:907-915. [PMID: 37386941 PMCID: PMC11009695 DOI: 10.1093/stmcls/sxad051] [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: 10/20/2022] [Accepted: 06/09/2023] [Indexed: 07/01/2023]
Abstract
The role of serum response factor (Srf), a central mediator of actin dynamics and mechanical signaling, in cell identity regulation is debated to be either a stabilizer or a destabilizer. We investigated the role of Srf in cell fate stability using mouse pluripotent stem cells. Despite the fact that serum-containing cultures yield heterogeneous gene expression, deletion of Srf in mouse pluripotent stem cells leads to further exacerbated cell state heterogeneity. The exaggerated heterogeneity is detectible not only as increased lineage priming but also as the developmentally earlier 2C-like cell state. Thus, pluripotent cells explore more variety of cellular states in both directions of development surrounding naïve pluripotency, a behavior that is constrained by Srf. These results support that Srf functions as a cell state stabilizer, providing rationale for its functional modulation in cell fate intervention and engineering.
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Affiliation(s)
- Jian Zhang
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Qiao Wu
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Xiao Hu
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Yadong Wang
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Jun Lu
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Raja Chakraborty
- Department of Medicine, Section of Cardiovascular Medicine, Yale University, New Haven, CT, USA
| | - Kathleen A Martin
- Department of Medicine, Section of Cardiovascular Medicine, Yale University, New Haven, CT, USA
| | - Shangqin Guo
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Yale Stem Cell Center, Yale University, New Haven, CT, USA
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28
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Liu J, Kreimer A, Li WV. Differential variability analysis of single-cell gene expression data. Brief Bioinform 2023; 24:bbad294. [PMID: 37598422 PMCID: PMC10516347 DOI: 10.1093/bib/bbad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/18/2023] [Accepted: 07/29/2023] [Indexed: 08/22/2023] Open
Abstract
The advent of single-cell RNA sequencing (scRNA-seq) technologies has enabled gene expression profiling at the single-cell resolution, thereby enabling the quantification and comparison of transcriptional variability among individual cells. Although alterations in transcriptional variability have been observed in various biological states, statistical methods for quantifying and testing differential variability between groups of cells are still lacking. To identify the best practices in differential variability analysis of single-cell gene expression data, we propose and compare 12 statistical pipelines using different combinations of methods for normalization, feature selection, dimensionality reduction and variability calculation. Using high-quality synthetic scRNA-seq datasets, we benchmarked the proposed pipelines and found that the most powerful and accurate pipeline performs simple library size normalization, retains all genes in analysis and uses denSNE-based distances to cluster medoids as the variability measure. By applying this pipeline to scRNA-seq datasets of COVID-19 and autism patients, we have identified cellular variability changes between patients with different severity status or between patients and healthy controls.
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Affiliation(s)
- Jiayi Liu
- Graduate Programs in Molecular Biosciences, Rutgers, The State University of New Jersey, 604 Allison Rd, Piscataway, 08854, NJ, USA
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, 08854, NJ, USA
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, Piscataway, 08854, NJ, USA
| | - Anat Kreimer
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, 08854, NJ, USA
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, Piscataway, 08854, NJ, USA
| | - Wei Vivian Li
- Department of Statistics, University of California, Riverside, 900 University Ave, Riverside, 92521, CA, USA
- Previous affiliation where part of the work was completed: Department of Biostatistics and Epidemiology, Rutgers, The State University of New Jersey, 683 Hoes Lane West, Piscataway, 08854, NJ, USA
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29
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Xie K, Ehninger D. Ageing-associated phenotypes in mice. Mech Ageing Dev 2023; 214:111852. [PMID: 37454704 DOI: 10.1016/j.mad.2023.111852] [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: 04/21/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Ageing is a continuous process in life featuring progressive damage accumulation that leads to physiological decline, functional deterioration and ultimately death of an organism. Based on the relatively close anatomical and physiological similarity to humans, the mouse has been proven as a valuable model organism in ageing research over the last decades. In this review, we survey methods and tools currently in use to assess ageing phenotypes in mice. We summarize a range of ageing-associated alterations detectable at two major levels of analysis: (1) physiology and pathophysiology and (2) molecular biomarkers. Age-sensitive phenotypes provided in this article may serve to inform future studies targeting various aspects of organismal ageing in mice. In addition, we discuss conceptual and technical challenges faced by previous ageing studies in mice and, where possible, provide recommendations on how to resolve some of these issues.
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Affiliation(s)
- Kan Xie
- Translational Biogerontology Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1/99, 53127 Bonn, Germany
| | - Dan Ehninger
- Translational Biogerontology Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1/99, 53127 Bonn, Germany.
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30
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Roux AE, Yuan H, Podshivalova K, Hendrickson D, Kerr R, Kenyon C, Kelley D. Individual cell types in C. elegans age differently and activate distinct cell-protective responses. Cell Rep 2023; 42:112902. [PMID: 37531250 DOI: 10.1016/j.celrep.2023.112902] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/17/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023] Open
Abstract
Aging is characterized by a global decline in physiological function. However, by constructing a complete single-cell gene expression atlas, we find that Caenorhabditis elegans aging is not random in nature but instead is characterized by coordinated changes in functionally related metabolic, proteostasis, and stress-response genes in a cell-type-specific fashion, with downregulation of energy metabolism being the only nearly universal change. Similarly, the rates at which cells age differ significantly between cell types. In some cell types, aging is characterized by an increase in cell-to-cell variance, whereas in others, variance actually decreases. Remarkably, multiple resilience-enhancing transcription factors known to extend lifespan are activated across many cell types with age; we discovered new longevity candidates, such as GEI-3, among these. Together, our findings suggest that cells do not age passively but instead react strongly, and individualistically, to events that occur during aging. This atlas can be queried through a public interface.
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Affiliation(s)
| | - Han Yuan
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | | | - Rex Kerr
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Cynthia Kenyon
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
| | - David Kelley
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
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31
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Lissek T. Aging, adaptation and maladaptation. FRONTIERS IN AGING 2023; 4:1256844. [PMID: 37701757 PMCID: PMC10493302 DOI: 10.3389/fragi.2023.1256844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
Aging is accompanied by a dysregulation of adaptive processes. On the one hand, physiological adaptation mechanisms such as learning and memory, immune system plasticity and exercise-dependent muscle remodeling are blunted. On the other hand, several maladaptive processes increase with age including cancer, pathological cardiovascular remodeling and metabolic dysregulation. With increasing age the quotient of beneficial adaptation (Ab) to harmful adaptation (Ah), Ab/Ah, decreases. The adaptation-maladaptation framework of aging entails that there are age-related pathological phenotypes that are the result of activation of physiological adaptation mechanisms (e.g., maladaptation as a result of misdirection of adaptive cascades and molecular damage incurred by adaptation processes) and their occurrence over time might, to some degree, be inevitable. Aging might hence result from the organism's inability to solve the adaptation-maladaptation dilemma. The present work explores the concept of counteracting aging through adaptation and proposes that interventions such as exercise, environmental enrichment and dietary restriction work in counteracting aging because they increase the ratio Ab/Ah by both raising Ab (e.g., by inducing metaplasticity in cells, meaning they raise the adaptability of cells to future stimuli) and decreasing Ah (e.g., through desensitizing certain potentially harmful adaptive mechanisms). Molecules whose aging-related expression changes can explain aspects of dysfunctional adaptation such as CREB and certain immediate early genes are examined and it is delineated how a better understanding of the dynamical organization of adaptation cascades could elucidate the seemingly complex role of adaptation in driving aging as well as protecting against it.
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Affiliation(s)
- Thomas Lissek
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
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32
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Liu R, Zhao E, Yu H, Yuan C, Abbas MN, Cui H. Methylation across the central dogma in health and diseases: new therapeutic strategies. Signal Transduct Target Ther 2023; 8:310. [PMID: 37620312 PMCID: PMC10449936 DOI: 10.1038/s41392-023-01528-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 08/26/2023] Open
Abstract
The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control, development, and health. Methylation of DNA, RNAs, histones, and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological processes. Aberrant methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging, necessitating the development of therapies to correct the disease-driver methylation imbalance. In this Review, we summarize the operating system of methylation across the central dogma, which includes writers, erasers, readers, and reader-independent outputs. We then discuss how dysregulation of the system contributes to neurological disorders, cancer, and aging. Current small-molecule compounds that target the modifiers show modest success in certain cancers. The methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity, limiting their therapeutic application, especially for diseases with a monogenic cause or different directions of methylation changes. Emerging tools capable of site-specific methylation manipulation hold great promise to solve this dilemma. With the refinement of delivery vehicles, these new tools are well positioned to advance the basic research and clinical translation of the methylation field.
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Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Huijuan Yu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Chaoyu Yuan
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China.
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33
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Jain A, Sturmlechner I, Weyand CM, Goronzy JJ. Heterogeneity of memory T cells in aging. Front Immunol 2023; 14:1250916. [PMID: 37662959 PMCID: PMC10471982 DOI: 10.3389/fimmu.2023.1250916] [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: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Immune memory is a requisite and remarkable property of the immune system and is the biological foundation of the success of vaccinations in reducing morbidity from infectious diseases. Some vaccines and infections induce long-lasting protection, but immunity to other vaccines and particularly in older adults rarely persists over long time periods. Failed induction of an immune response and accelerated waning of immune memory both contribute to the immuno-compromised state of the older population. Here we review how T cell memory is influenced by age. T cell memory is maintained by a dynamic population of T cells that are heterogeneous in their kinetic parameters under homeostatic condition and their function. Durability of T cell memory can be influenced not only by the loss of a clonal progeny, but also by broader changes in the composition of functional states and transition of T cells to a dysfunctional state. Genome-wide single cell studies on total T cells have started to provide insights on the influence of age on cell heterogeneity over time. The most striking findings were a trend to progressive effector differentiation and the activation of pro-inflammatory pathways, including the emergence of CD4+ and CD8+ cytotoxic subsets. Genome-wide data on antigen-specific memory T cells are currently limited but can be expected to provide insights on how changes in T cell subset heterogeneity and transcriptome relate to durability of immune protection.
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Affiliation(s)
- Abhinav Jain
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Ines Sturmlechner
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Cornelia M. Weyand
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- Department of Medicine, Division of Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Jörg J. Goronzy
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- Department of Medicine, Division of Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
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34
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Mao S, Su J, Wang L, Bo X, Li C, Chen H. A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures. Genome Res 2023; 33:1381-1394. [PMID: 37524436 PMCID: PMC10547252 DOI: 10.1101/gr.277491.122] [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: 11/19/2022] [Accepted: 07/12/2023] [Indexed: 08/02/2023]
Abstract
Accurately measuring biological age is crucial for improving healthcare for the elderly population. However, the complexity of aging biology poses challenges in how to robustly estimate aging and interpret the biological significance of the traits used for estimation. Here we present SCALE, a statistical pipeline that quantifies biological aging in different tissues using explainable features learned from literature and single-cell transcriptomic data. Applying SCALE to the "Mouse Aging Cell Atlas" (Tabula Muris Senis) data, we identified tissue-level transcriptomic aging programs for more than 20 murine tissues and created a multitissue resource of mouse quantitative aging-associated genes. We observe that SCALE correlates well with other age indicators, such as the accumulation of somatic mutations, and can distinguish subtle differences in aging even in cells of the same chronological age. We further compared SCALE with other transcriptomic and methylation "clocks" in data from aging muscle stem cells, Alzheimer's disease, and heterochronic parabiosis. Our results confirm that SCALE is more generalizable and reliable in assessing biological aging in aging-related diseases and rejuvenating interventions. Overall, SCALE represents a valuable advancement in our ability to measure aging accurately, robustly, and interpretably in single cells.
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Affiliation(s)
- Shulin Mao
- Yuanpei College, Peking University, Beijing 100871, China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiayu Su
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Longteng Wang
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
- School of Life Sciences, Joint Graduate Program of Peking-Tsinghua-NIBS, Peking University, Beijing 100871, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China;
- Center for Statistical Science, Peking University, Beijing 100871, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China;
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35
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Senapati P, Miyano M, Sayaman RW, Basam M, Leung A, LaBarge MA, Schones DE. Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells. Genome Res 2023; 33:1229-1241. [PMID: 37463750 PMCID: PMC10547379 DOI: 10.1101/gr.277511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/23/2023] [Indexed: 07/20/2023]
Abstract
A primary function of DNA methylation in mammalian genomes is to repress transposable elements (TEs). The widespread methylation loss that is commonly observed in cancer cells results in the loss of epigenetic repression of TEs. The aging process is similarly characterized by changes to the methylome. However, the impact of these epigenomic alterations on TE silencing and the functional consequences of this have remained unclear. To assess the epigenetic regulation of TEs in aging, we profiled DNA methylation in human mammary luminal epithelial cells (LEps)-a key cell lineage implicated in age-related breast cancers-from younger and older women. We report here that several TE subfamilies function as regulatory elements in normal LEps, and a subset of these display consistent methylation changes with age. Methylation changes at these TEs occurred at lineage-specific transcription factor binding sites, consistent with loss of lineage specificity. Whereas TEs mainly showed methylation loss, CpG islands (CGIs) that are targets of the Polycomb repressive complex 2 (PRC2) show a gain of methylation in aging cells. Many TEs with methylation loss in aging LEps have evidence of regulatory activity in breast cancer samples. We furthermore show that methylation changes at TEs impact the regulation of genes associated with luminal breast cancers. These results indicate that aging leads to DNA methylation changes at TEs that undermine the maintenance of lineage specificity, potentially increasing susceptibility to breast cancer.
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Affiliation(s)
- Parijat Senapati
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143-0981, USA
| | - Mudaser Basam
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
| | - Mark A LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, California 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
- Center for Cancer Biomarker Research, University of Bergen, 5021 Bergen, Norway
| | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, USA;
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010, USA
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36
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Plesa AM, Shadpour M, Boyden E, Church GM. Transcriptomic reprogramming for neuronal age reversal. Hum Genet 2023; 142:1293-1302. [PMID: 37004545 PMCID: PMC10066999 DOI: 10.1007/s00439-023-02529-1] [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: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 04/04/2023]
Abstract
Aging is a progressive multifaceted functional decline of a biological system. Chronic age-related conditions such as neurodegenerative diseases are leading causes of death worldwide, and they are becoming a pressing problem for our society. To address this global challenge, there is a need for novel, safe, and effective rejuvenation therapies aimed at reversing age-related phenotypes and improving human health. With gene expression being a key determinant of cell identity and function, and in light of recent studies reporting rejuvenation effects through genetic perturbations, we propose an age reversal strategy focused on reprogramming the cell transcriptome to a youthful state. To this end, we suggest using transcriptomic data from primary human cells to predict rejuvenation targets and develop high-throughput aging assays, which can be used in large perturbation screens. We propose neural cells as particularly relevant targets for rejuvenation due to substantial impact of neurodegeneration on human frailty. Of all cell types in the brain, we argue that glutamatergic neurons, neuronal stem cells, and oligodendrocytes represent the most impactful and tractable targets. Lastly, we provide experimental designs for anti-aging reprogramming screens that will likely enable the development of neuronal age reversal therapies, which hold promise for dramatically improving human health.
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Affiliation(s)
- Alexandru M. Plesa
- Department of Genetics, Harvard Medical School, Boston, MA USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA USA
| | - Michael Shadpour
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA USA
- Department of Biological Engineering, MIT, Cambridge, MA USA
| | - Ed Boyden
- Department of Biological Engineering, MIT, Cambridge, MA USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA USA
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37
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Singh PP, Benayoun BA. Considerations for reproducible omics in aging research. NATURE AGING 2023; 3:921-930. [PMID: 37386258 PMCID: PMC10527412 DOI: 10.1038/s43587-023-00448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
Technical advancements over the past two decades have enabled the measurement of the panoply of molecules of cells and tissues including transcriptomes, epigenomes, metabolomes and proteomes at unprecedented resolution. Unbiased profiling of these molecular landscapes in the context of aging can reveal important details about mechanisms underlying age-related functional decline and age-related diseases. However, the high-throughput nature of these experiments creates unique analytical and design demands for robustness and reproducibility. In addition, 'omic' experiments are generally onerous, making it crucial to effectively design them to eliminate as many spurious sources of variation as possible as well as account for any biological or technical parameter that may influence such measures. In this Perspective, we provide general guidelines on best practices in the design and analysis of omic experiments in aging research from experimental design to data analysis and considerations for long-term reproducibility and validation of such studies.
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Affiliation(s)
- Param Priya Singh
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Aging Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, USA.
- Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
- USC Stem Cell Initiative, Los Angeles, CA, USA.
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38
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Zhang C, Wang D, Dowell R, Yi R. Single cell analysis of transcriptome and open chromatin reveals the dynamics of hair follicle stem cell aging. FRONTIERS IN AGING 2023; 4:1192149. [PMID: 37465120 PMCID: PMC10350644 DOI: 10.3389/fragi.2023.1192149] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023]
Abstract
Aging is defined as the functional decline of tissues and organisms, leading to many human conditions, such as cancer, neurodegenerative diseases, and hair loss. Although stem cell exhaustion is widely recognized as a hallmark of aging, our understanding of cell state changes-specifically, the dynamics of the transcriptome and open chromatin landscape, and their relationship with aging-remains incomplete. Here we present a longitudinal, single-cell atlas of the transcriptome and open chromatin landscape for epithelia cells of the skin across various hair cycle stages and ages in mice. Our findings reveal fluctuating hair follicle stem cell (HF-SC) states, some of which are associated with the progression of the hair cycle during aging. Conversely, inner bulge niche cells display a more linear progression, seemingly less affected by the hair cycle. Further analysis of the open chromatin landscape, determined by single-cell Assay for Transposase-Accessible Chromatin (ATAC) sequencing, demonstrates that reduced open chromatin regions in HF-SCs are associated with differentiation, whereas gained open chromatin regions in HF-SCs are linked to the transcriptional control of quiescence. These findings enhance our understanding of the transcriptional dynamics in HF-SC aging and lay the molecular groundwork for investigating and potentially reversing the aging process in future experimental studies.
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Affiliation(s)
- Chi Zhang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Dongmei Wang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Robin Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Rui Yi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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39
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Zhu H, Chen J, Liu K, Gao L, Wu H, Ma L, Zhou J, Liu Z, Han JDJ. Human PBMC scRNA-seq-based aging clocks reveal ribosome to inflammation balance as a single-cell aging hallmark and super longevity. SCIENCE ADVANCES 2023; 9:eabq7599. [PMID: 37379396 DOI: 10.1126/sciadv.abq7599] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Quantifying aging rate is important for evaluating age-associated decline and mortality. A blood single-cell RNA sequencing dataset for seven supercentenarians (SCs) was recently generated. Here, we generate a reference 28-sample aging cohort to compute a single-cell level aging clock and to determine the biological age of SCs. Our clock model placed the SCs at a blood biological age to between 80.43 and 102.67 years. Compared to the model-expected aging trajectory, SCs display increased naive CD8+ T cells, decreased cytotoxic CD8+ T cells, memory CD4+ T cells, and megakaryocytes. As the most prominent molecular hallmarks at the single-cell level, SCs contain more cells and cell types with high ribosome level, which is associated with and, according to Bayesian network inference, contributes to a low inflammation state and slow aging of SCs. Inhibiting ribosomal activity or translation in monocytes validates such translation against inflammation balance revealed by our single-cell aging clock.
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Affiliation(s)
- Hongming Zhu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Jiawei Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, P.R. China
| | - Kangping Liu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, P.R. China
| | - Lei Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
- Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui 230001, P.R. China
| | - Haiyan Wu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Liangliang Ma
- Department of Health Management, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Jieru Zhou
- Department of Health Management, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Zhongmin Liu
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, P.R. China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing 100871, P.R. China
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40
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Rosales-Alvarez RE, Rettkowski J, Herman JS, Dumbović G, Cabezas-Wallscheid N, Grün D. VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells. Genome Biol 2023; 24:148. [PMID: 37353813 PMCID: PMC10290360 DOI: 10.1186/s13059-023-02974-1] [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: 09/27/2022] [Accepted: 05/18/2023] [Indexed: 06/25/2023] Open
Abstract
Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential driving force of cellular differentiation. Utilizing single-cell RNA-sequencing, we develop VarID2 for the quantification of biological noise at single-cell resolution. VarID2 reveals enhanced nuclear versus cytoplasmic noise, and distinct regulatory modes stratified by correlation between noise, expression, and chromatin accessibility. Noise levels are minimal in murine hematopoietic stem cells (HSCs) and increase during differentiation and ageing. Differential noise identifies myeloid-biased Dlk1+ long-term HSCs in aged mice with enhanced quiescence and self-renewal capacity. VarID2 reveals noise dynamics invisible to conventional single-cell transcriptome analysis.
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Affiliation(s)
- Reyna Edith Rosales-Alvarez
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics, and Metabolism (IMPRS-IEM), Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jasmin Rettkowski
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Freiburg, Germany
| | - Josip Stefan Herman
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Gabrijela Dumbović
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Nina Cabezas-Wallscheid
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Dominic Grün
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany.
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution. Genome Res 2023; 33:839-856. [PMID: 37442575 PMCID: PMC10519413 DOI: 10.1101/gr.276765.122] [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: 03/17/2022] [Accepted: 06/08/2023] [Indexed: 07/15/2023]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single-cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated peripheral blood mononuclear cells from 96 African American children. We used novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we showed that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and showed widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan 48201, USA
| | - Edward Sendler
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Henriette E Mair-Meijers
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Peijun Wu
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard B Slatcher
- Department of Psychology, University of Georgia, Athens, Georgia 30602, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Biology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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42
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Zhu J, Yang Y. scMEB: a fast and clustering-independent method for detecting differentially expressed genes in single-cell RNA-seq data. BMC Genomics 2023; 24:280. [PMID: 37231345 DOI: 10.1186/s12864-023-09374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Cell clustering is a prerequisite for identifying differentially expressed genes (DEGs) in single-cell RNA sequencing (scRNA-seq) data. Obtaining a perfect clustering result is of central importance for subsequent analyses, but not easy. Additionally, the increase in cell throughput due to the advancement of scRNA-seq protocols exacerbates many computational issues, especially regarding method runtime. To address these difficulties, a new, accurate, and fast method for detecting DEGs in scRNA-seq data is needed. RESULTS Here, we propose single-cell minimum enclosing ball (scMEB), a novel and fast method for detecting single-cell DEGs without prior cell clustering results. The proposed method utilizes a small part of known non-DEGs (stably expressed genes) to build a minimum enclosing ball and defines the DEGs based on the distance of a mapped gene to the center of the hypersphere in a feature space. CONCLUSIONS We compared scMEB to two different approaches that could be used to identify DEGs without cell clustering. The investigation of 11 real datasets revealed that scMEB outperformed rival methods in terms of cell clustering, predicting genes with biological functions, and identifying marker genes. Moreover, scMEB was much faster than the other methods, making it particularly effective for finding DEGs in high-throughput scRNA-seq data. We have developed a package scMEB for the proposed method, which could be available at https://github.com/FocusPaka/scMEB .
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Affiliation(s)
- Jiadi Zhu
- School of Mathematics and Statistics, Xidian University, Xi'an, China
| | - Youlong Yang
- School of Mathematics and Statistics, Xidian University, Xi'an, China.
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43
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Liu L, Kim S, Buckley MT, Reyes JM, Kang J, Tian L, Wang M, Lieu A, Mao M, Rodriguez-Mateo C, Ishak HD, Jeong M, Wu JC, Goodell MA, Brunet A, Rando TA. Exercise reprograms the inflammatory landscape of multiple stem cell compartments during mammalian aging. Cell Stem Cell 2023; 30:689-705.e4. [PMID: 37080206 PMCID: PMC10216894 DOI: 10.1016/j.stem.2023.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 12/02/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023]
Abstract
Exercise has the ability to rejuvenate stem cells and improve tissue regeneration in aging animals. However, the cellular and molecular changes elicited by exercise have not been systematically studied across a broad range of cell types in stem cell compartments. We subjected young and old mice to aerobic exercise and generated a single-cell transcriptomic atlas of muscle, neural, and hematopoietic stem cells with their niche cells and progeny, complemented by whole transcriptome analysis of single myofibers. We found that exercise ameliorated the upregulation of a number of inflammatory pathways associated with old age and restored aspects of intercellular communication mediated by immune cells within these stem cell compartments. Exercise has a profound impact on the composition and transcriptomic landscape of circulating and tissue-resident immune cells. Our study provides a comprehensive view of the coordinated responses of multiple aged stem cells and niche cells to exercise at the transcriptomic level.
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Affiliation(s)
- Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Department of Neurology, UCLA, Los Angeles, CA, USA
| | - Soochi Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jaime M Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jengmin Kang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Lei Tian
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Mingqiang Wang
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Alexander Lieu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Mao
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Cristina Rodriguez-Mateo
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Heather D Ishak
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Mira Jeong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Department of Medicine, Stanford University, Stanford, CA, USA; Greenstone Biosciences, Palo Alto, CA, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Anne Brunet
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Department of Neurology, UCLA, Los Angeles, CA, USA; Neurology Service, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA.
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44
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Sims AA, Gurkar AU. DNA damage-induced stalling of transcription drives aging through gene expression imbalance. DNA Repair (Amst) 2023; 125:103483. [PMID: 36921370 DOI: 10.1016/j.dnarep.2023.103483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Age-related changes in gene expression have long been examined to understand the biology of aging. The hallmarks of aging are biological processes known to be associated with aging, but whether there is a unifying driver of these attributes, is not well understood. With the advent of technology over the last few years, it is quite clear that aging leads to global decline in transcription. In this Perspective, we highlight a new study in Nature Genetics that aimed to determine why global transcription rate reduces with age and how this phenomenon is the driver that interconnects multiple hallmarks of aging. This study recognizes that age-related accumulation of DNA damage, particularly transcription-blocking lesions, stalls RNA polymerase. This phenomenon affects longer genes leading to a gradual loss of transcription and skewing the transcriptome. In order to design a successful aging intervention, future work will be needed to test how some promising therapies in pre-clinical trials target affect transcriptional rate.
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Affiliation(s)
- Austin A Sims
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA 15219, USA
| | - Aditi U Gurkar
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA 15219, USA.
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45
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Guo L, Li X, Gould T, Wang ZY, Cao W. T cell aging and Alzheimer's disease. Front Immunol 2023; 14:1154699. [PMID: 37081887 PMCID: PMC10110977 DOI: 10.3389/fimmu.2023.1154699] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023] Open
Abstract
The brain has long been considered an immune-privileged organ due to the presence of the blood-brain barrier (BBB). However, recent discoveries have revealed the underestimated role of T cells in the brain through the meningeal lymphatic system. Age is the primary risk factor for Alzheimer's disease (AD), resulting in marked age-dependent changes in T cells. Manipulating peripheral T cell immune response has been shown to impact AD, but the relationship between T cell aging and AD remains poorly understood. Given the limited success of targeting amyloid beta (Aβ) and the growing evidence of T cells' involvement in non-lymphoid organ aging, a deeper understanding of the relationship between T cells and AD in the context of aging is crucial for advancing therapeutic progress. In this review, we comprehensively examine existing studies on T cells and AD and offer an integrated perspective on their interconnections in the context of aging. This understanding can inform the development of new interventions to prevent or treat AD.
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Affiliation(s)
- Lin Guo
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang, China
| | - Xiaoting Li
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang, China
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang, China
| | | | - Zhan-You Wang
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang, China
| | - Wenqiang Cao
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang, China
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46
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Debès C, Papadakis A, Grönke S, Karalay Ö, Tain LS, Mizi A, Nakamura S, Hahn O, Weigelt C, Josipovic N, Zirkel A, Brusius I, Sofiadis K, Lamprousi M, Lu YX, Huang W, Esmaillie R, Kubacki T, Späth MR, Schermer B, Benzing T, Müller RU, Antebi A, Partridge L, Papantonis A, Beyer A. Ageing-associated changes in transcriptional elongation influence longevity. Nature 2023; 616:814-821. [PMID: 37046086 PMCID: PMC10132977 DOI: 10.1038/s41586-023-05922-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/07/2023] [Indexed: 04/14/2023]
Abstract
Physiological homeostasis becomes compromised during ageing, as a result of impairment of cellular processes, including transcription and RNA splicing1-4. However, the molecular mechanisms leading to the loss of transcriptional fidelity are so far elusive, as are ways of preventing it. Here we profiled and analysed genome-wide, ageing-related changes in transcriptional processes across different organisms: nematodes, fruitflies, mice, rats and humans. The average transcriptional elongation speed (RNA polymerase II speed) increased with age in all five species. Along with these changes in elongation speed, we observed changes in splicing, including a reduction of unspliced transcripts and the formation of more circular RNAs. Two lifespan-extending interventions, dietary restriction and lowered insulin-IGF signalling, both reversed most of these ageing-related changes. Genetic variants in RNA polymerase II that reduced its speed in worms5 and flies6 increased their lifespan. Similarly, reducing the speed of RNA polymerase II by overexpressing histone components, to counter age-associated changes in nucleosome positioning, also extended lifespan in flies and the division potential of human cells. Our findings uncover fundamental molecular mechanisms underlying animal ageing and lifespan-extending interventions, and point to possible preventive measures.
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Affiliation(s)
- Cédric Debès
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Antonios Papadakis
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Özlem Karalay
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Luke S Tain
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Shuhei Nakamura
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Oliver Hahn
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Carina Weigelt
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Anne Zirkel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Isabell Brusius
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Konstantinos Sofiadis
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Mantha Lamprousi
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Yu-Xuan Lu
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Wenming Huang
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Reza Esmaillie
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Torsten Kubacki
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin R Späth
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Bernhard Schermer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Benzing
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Roman-Ulrich Müller
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Adam Antebi
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Linda Partridge
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, UCL, London, UK.
| | - Argyris Papantonis
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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Burnaevskiy N, Oshima J, Mendenhall AR. Rapid emergence of transcriptional heterogeneity upon molecular stress predisposes cells to two distinct states of senescence. GeroScience 2023; 45:1115-1130. [PMID: 36562924 PMCID: PMC9886721 DOI: 10.1007/s11357-022-00709-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: 07/27/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Slowing aging can reduce the risk of chronic diseases. In particular, eliminating senescent cells is a promising approach to slow aging. Previous studies found that both cells from older animals and senescent cells have noisy gene expression. Here, we performed a large-scale single-cell RNA-sequencing time course to understand how transcriptional heterogeneity develops among senescent cells. We found that cells experiencing senescence-inducing oxidative stress rapidly adopt one of two major transcriptional states. One senescent cell state is associated with stress response, and the other is associated with tissue remodeling. We did not observe increased stochastic gene expression. This data is consistent with the idea that reproducible, limited, distinct, and coherent transcriptional states exist in senescent cell populations. These physiologically distinct senescent cell subtypes may each affect the aging process in unique ways and constitute a source of heterogeneity in aging.
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Affiliation(s)
- Nikolay Burnaevskiy
- Department of Pathology, University of Washington, Seattle, WA, USA
- Present Address: Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Junko Oshima
- Department of Pathology, University of Washington, Seattle, WA, USA
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48
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Molecular Markers of Blood Cell Populations Can Help Estimate Aging of the Immune System. Int J Mol Sci 2023; 24:ijms24065708. [PMID: 36982782 PMCID: PMC10055688 DOI: 10.3390/ijms24065708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Aging of the immune system involves functional changes in individual cell populations, in hematopoietic tissues and at the systemic level. They are mediated by factors produced by circulating cells, niche cells, and at the systemic level. Age-related alterations in the microenvironment of the bone marrow and thymus cause a decrease in the production of naive immune cells and functional immunodeficiencies. Another result of aging and reduced tissue immune surveillance is the accumulation of senescent cells. Some viral infections deplete adaptive immune cells, increasing the risk of autoimmune and immunodeficiency conditions, leading to a general degradation in the specificity and effectiveness of the immune system in old age. During the COVID-19 pandemic, the state-of-the-art application of mass spectrometry, multichannel flow cytometry, and single-cell genetic analysis have provided vast data on the mechanisms of aging of the immune system. These data require systematic analysis and functional verification. In addition, the prediction of age-related complications is a priority task of modern medicine in the context of the increase in the aged population and the risk of premature death during epidemics. In this review, based on the latest data, we discuss the mechanisms of immune aging and highlight some cellular markers as indicators of age-related immune disbalance that increase the risk of senile diseases and infectious complications.
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49
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Decrease in naturally occurring antibodies against epitopes of Alzheimer's disease (AD) risk gene products is associated with cognitive decline in AD. J Neuroinflammation 2023; 20:74. [PMID: 36922858 PMCID: PMC10018846 DOI: 10.1186/s12974-023-02750-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Naturally occurring antibodies (NAbs) are germline-encoded immunoglobulins that can bind to and clear out self-neo-epitopes as well as apoptotic and necrotic cells. However, NAbs pathological relevance in Alzheimer's disease (AD) is not well-understood. METHODS Twenty-eight candidate proteins encoded by AD-associated genes were selected for this study based on a number of selection criteria, including preferential expression in the brain and B-lymphocyte cells. The levels of NAbs in plasma were analyzed according to their epitopes in age- and gender-matched cognitively normal subjects (CN, n = 56), subjects with mild cognitive impairment (MCI, n = 16) and subjects with AD (n = 56). We aimed to study the levels of their NAbs in plasma and their associations with cognitive decline in individuals with AD. RESULTS Of the 28 antigens tested, 17 showed decreased NAbs in individuals with AD; in particular, NAb-TREM2 had an area under the ROC curve of 0.806, with the highest sensitivity (0.370) at 95% specificity among all 28 tests. Further protein-protein interaction networks and functional enrichment analysis suggested that target genes were enriched in AD-related pathological processes classified under "Alzheimer's disease", "neurodegenerative disease" and "amyloidosis". The "Alzheimer's disease" and "neurodegenerative disease" clusters, which converged on the initial "recognition" step of microglial phagocytosis, showed the best diagnostic performance for AD. CONCLUSIONS This study suggests a decline in the function of the adaptive immune system in AD, and the levels of circulating NAbs are likely to serve as biomarkers for surveilling the progression of AD.
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Patras L, Shaashua L, Matei I, Lyden D. Immune determinants of the pre-metastatic niche. Cancer Cell 2023; 41:546-572. [PMID: 36917952 PMCID: PMC10170403 DOI: 10.1016/j.ccell.2023.02.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 03/16/2023]
Abstract
Primary tumors actively and specifically prime pre-metastatic niches (PMNs), the future sites of organotropic metastasis, preparing these distant microenvironments for disseminated tumor cell arrival. While initial studies of the PMN focused on extracellular matrix alterations and stromal reprogramming, it is increasingly clear that the far-reaching effects of tumors are in great part achieved through systemic and local PMN immunosuppression. Here, we discuss recent advances in our understanding of the tumor immune microenvironment and provide a comprehensive overview of the immune determinants of the PMN's spatiotemporal evolution. Moreover, we depict the PMN immune landscape, based on functional pre-clinical studies as well as mounting clinical evidence, and the dynamic, reciprocal crosstalk with systemic changes imposed by cancer progression. Finally, we outline emerging therapeutic approaches that alter the dynamics of the interactions driving PMN formation and reverse immunosuppression programs in the PMN ensuring early anti-tumor immune responses.
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Affiliation(s)
- Laura Patras
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of Molecular Biology and Biotechnology, Center of Systems Biology, Biodiversity and Bioresources, Faculty of Biology and Geology, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Lee Shaashua
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Irina Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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