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Adekunbi DA, Huber HF, Li C, Nathanielsz PW, Cox LA, Salmon AB. Differential mitochondrial bioenergetics and cellular resilience in astrocytes, hepatocytes, and fibroblasts from aging baboons. GeroScience 2024; 46:4443-4459. [PMID: 38607532 PMCID: PMC11335705 DOI: 10.1007/s11357-024-01155-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Biological resilience, broadly defined as the ability to recover from an acute challenge and return to homeostasis, is of growing importance to the biology of aging. At the cellular level, there is variability across tissue types in resilience and these differences are likely to contribute to tissue aging rate disparities. However, there are challenges in addressing these cell-type differences at regional, tissue, and subject level. To address this question, we established primary cells from aged male and female baboons between 13.3 and 17.8 years spanning across different tissues, tissue regions, and cell types including (1) fibroblasts from skin and from the heart separated into the left ventricle (LV), right ventricle (RV), left atrium (LA), and right atrium (RA); (2) astrocytes from the prefrontal cortex and hippocampus; and (3) hepatocytes. Primary cells were characterized by their cell surface markers and their cellular respiration was assessed with Seahorse XFe96. Cellular resilience was assessed by modifying a live-cell imaging approach; we previously reported that monitors proliferation of dividing cells following response and recovery to oxidative (50 µM-H2O2), metabolic (1 mM-glucose), and proteostasis (0.1 µM-thapsigargin) stress. We noted significant differences even among similar cell types that are dependent on tissue source and the diversity in cellular response is stressor-specific. For example, astrocytes had a higher oxygen consumption rate and exhibited greater resilience to oxidative stress (OS) than both fibroblasts and hepatocytes. RV and RA fibroblasts were less resilient to OS compared with LV and LA, respectively. Skin fibroblasts were less impacted by proteostasis stress compared to astrocytes and cardiac fibroblasts. Future studies will test the functional relationship of these outcomes to the age and developmental status of donors as potential predictive markers.
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Affiliation(s)
- Daniel A Adekunbi
- Department of Molecular Medicine and Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Hillary F Huber
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Cun Li
- Department of Animal Science, Texas Pregnancy and Life-Course Health Research Center, University of Wyoming, Laramie, WY, USA
| | - Peter W Nathanielsz
- Department of Animal Science, Texas Pregnancy and Life-Course Health Research Center, University of Wyoming, Laramie, WY, USA
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Adam B Salmon
- Department of Molecular Medicine and Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA.
- Geriatric Research Education and Clinical Center, Audie L. Murphy Hospital, Southwest Veterans Health Care System, San Antonio, TX, USA.
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2
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Hu Y, Wan S, Luo Y, Li Y, Wu T, Deng W, Jiang C, Jiang S, Zhang Y, Liu N, Yang Z, Chen F, Li B, Qu K. Benchmarking algorithms for single-cell multi-omics prediction and integration. Nat Methods 2024:10.1038/s41592-024-02429-w. [PMID: 39322753 DOI: 10.1038/s41592-024-02429-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/19/2024] [Indexed: 09/27/2024]
Abstract
The development of single-cell multi-omics technology has greatly enhanced our understanding of biology, and in parallel, numerous algorithms have been proposed to predict the protein abundance and/or chromatin accessibility of cells from single-cell transcriptomic information and to integrate various types of single-cell multi-omics data. However, few studies have systematically compared and evaluated the performance of these algorithms. Here, we present a benchmark study of 14 protein abundance/chromatin accessibility prediction algorithms and 18 single-cell multi-omics integration algorithms using 47 single-cell multi-omics datasets. Our benchmark study showed overall totalVI and scArches outperformed the other algorithms for predicting protein abundance, and LS_Lab was the top-performing algorithm for the prediction of chromatin accessibility in most cases. Seurat, MOJITOO and scAI emerge as leading algorithms for vertical integration, whereas totalVI and UINMF excel beyond their counterparts in both horizontal and mosaic integration scenarios. Additionally, we provide a pipeline to assist researchers in selecting the optimal multi-omics prediction and integration algorithm.
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Affiliation(s)
- Yinlei Hu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- School of Mathematical Science, University of Science and Technology of China, Hefei, China
| | - Siyuan Wan
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- School of Artificial Intelligence and Data Science, University of Science and Technology of China, Hefei, China
| | - Yuanhanyu Luo
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Yuanzhe Li
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- School of Artificial Intelligence and Data Science, University of Science and Technology of China, Hefei, China
| | - Tong Wu
- National Institute of Biological Sciences, Beijing, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wentao Deng
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Chen Jiang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Shan Jiang
- National Institute of Biological Sciences, Beijing, China
| | - Yueping Zhang
- School of Artificial Intelligence and Data Science, University of Science and Technology of China, Hefei, China
| | - Nianping Liu
- School of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China
| | - Zongcheng Yang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Falai Chen
- School of Mathematical Science, University of Science and Technology of China, Hefei, China.
- School of Artificial Intelligence and Data Science, University of Science and Technology of China, Hefei, China.
| | - Bin Li
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
- National Institute of Biological Sciences, Beijing, China.
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China.
- School of Artificial Intelligence and Data Science, University of Science and Technology of China, Hefei, China.
- School of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China.
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Avila JA, Benthal JT, Schafer JC, Southard-Smith EM. Single Cell Profiling in the Sox10 Dom/+ Hirschsprung Mouse Implicates Hoxa6 in Enteric Neuron Lineage Allocation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613729. [PMID: 39345473 PMCID: PMC11429920 DOI: 10.1101/2024.09.18.613729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Background & Aims Enteric nervous system (ENS) development requires migration, proliferation, and appropriate neuronal diversification from progenitors to enable normal gastrointestinal (GI) motility. Sox10 deficit causes aganglionosis, modeling Hirschsprung disease, and disrupts ratios of postnatal enteric neurons in proximal ganglionated bowel. How Sox10 deficiency alters ratios of enteric neuron subtypes is unclear. Sox10's prominent expression in enteric neural crest-derived progenitors (ENCP) and lack of this gene in enteric neurons led us to examine Sox10 Dom effects ENS progenitors and early differentiating enteric neurons. Methods ENS progenitors, developing neurons, and enteric glia were isolated from Sox10 +/+ and Sox10 Dom/+ littermates for single-cell RNA sequencing (scRNA-seq). scRNA-seq data was processed to identify cell type-specific markers, differentially expressed genes, cell fate trajectories, and gene regulatory network activity between genotypes. Hybridization chain reaction (HCR) validated expression changes detected in scRNA-seq. Results scRNA-seq profiles revealed three neuronal lineages emerging from cycling progenitors via two transition pathways accompanied by elevated activity of Hox gene regulatory networks (GRN) as progenitors transition to neuronal fates. Sox10 Dom/+ scRNA-seq profiles exhibited a novel progenitor cluster, decreased abundance of cells in transitional states, and shifts in cell distributions between two neuronal trajectories. Hoxa6 was differentially expressed in the neuronal lineages impacted in Sox10 Dom/+ mutants and HCR identified altered Hoxa6 expression in early developing neurons of Sox10 Dom/+ ENS. Conclusions Sox10 Dom/+ mutation shifts enteric neuron types by altering neuronal trajectories during early ENS lineage segregation. Multiple neurogenic transcription factors are reduced in Sox10 Dom/+ scRNA-seq profiles including multiple Hox genes. This is the first report that implicates Hox genes in lineage diversification of enteric neurons.
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Mulenge F, Gern OL, Busker LM, Aringo A, Ghita L, Waltl I, Pavlou A, Kalinke U. Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis. J Neuroinflammation 2024; 21:203. [PMID: 39153993 PMCID: PMC11330067 DOI: 10.1186/s12974-024-03197-2] [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: 04/24/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
Microglia serve as a front-line defense against neuroinvasive viral infection, however, determination of their actual transcriptional profiles under conditions of health and disease is challenging. Here, we used various experimental approaches to delineate the transcriptional landscape of microglia during viral infection. Intriguingly, multiple activation genes were found to be artificially induced in sorted microglia and we demonstrated that shear stress encountered during cell sorting was one of the key inducers. Post-hoc analysis revealed that publicly available large-scale single-cell RNA sequencing datasets were significantly tainted by aberrant signatures that are associated with cell sorting. By exploiting the ribosomal tagging approach, we developed a strategy to enrich microglia-specific transcripts by comparing immunoprecipitated RNA with total RNA. Such enriched transcripts were instrumental in defining bona fide signatures of microglia under conditions of health and virus infection. These unified microglial signatures may serve as a benchmark to retrospectively assess ex vivo artefacts from available atlases. Leveraging the microglial translatome, we found enrichment of genes implicated in T-cell activation and cytokine production during the course of VSV infection. These data linked microglia with T-cell re-stimulation and further underscored that microglia are involved in shaping antiviral T-cell responses in the brain. Collectively, our study defines the transcriptional landscape of microglia under steady state and during viral encephalitis and highlights cellular interactions between microglia and T cells that contribute to the control of virus dissemination.
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Affiliation(s)
- Felix Mulenge
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Olivia Luise Gern
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Lena Mareike Busker
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
- Department of Pathology, University of Veterinary Medicine Hannover, 30559, Foundation, Hannover, Germany
| | - Angela Aringo
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Luca Ghita
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
- , Genentech, South San Francisco, CA, 94080, USA
| | - Inken Waltl
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany.
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5
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Castro JP, Shindyapina AV, Barbieri A, Ying K, Strelkova OS, Paulo JA, Tyshkovskiy A, Meinl R, Kerepesi C, Petrashen AP, Mariotti M, Meer MV, Hu Y, Karamyshev A, Losyev G, Galhardo M, Logarinho E, Indzhykulian AA, Gygi SP, Sedivy JM, Manis JP, Gladyshev VN. Age-associated clonal B cells drive B cell lymphoma in mice. NATURE AGING 2024:10.1038/s43587-024-00671-7. [PMID: 39117982 DOI: 10.1038/s43587-024-00671-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 06/19/2024] [Indexed: 08/10/2024]
Abstract
Although cancer is an age-related disease, how the processes of aging contribute to cancer progression is not well understood. In this study, we uncovered how mouse B cell lymphoma develops as a consequence of a naturally aged system. We show here that this malignancy is associated with an age-associated clonal B cell (ACBC) population that likely originates from age-associated B cells. Driven by c-Myc activation, promoter hypermethylation and somatic mutations, IgM+ ACBCs clonally expand independently of germinal centers and show increased biological age. ACBCs become self-sufficient and support malignancy when transferred into young recipients. Inhibition of mTOR or c-Myc in old mice attenuates pre-malignant changes in B cells during aging. Although the etiology of mouse and human B cell lymphomas is considered distinct, epigenetic changes in transformed mouse B cells are enriched for changes observed in human B cell lymphomas. Together, our findings characterize the spontaneous progression of cancer during aging through both cell-intrinsic and microenvironmental changes and suggest interventions for its prevention.
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Affiliation(s)
- José P Castro
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Aging and Aneuploidy Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | | | | | - Kejun Ying
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Olga S Strelkova
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - João A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Rico Meinl
- Retro Biosciences, Redwood City, CA, USA
| | - Csaba Kerepesi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Computer Science and Control (SZTAKI), Loránd Eötvös Research Network, Budapest, Hungary
| | - Anna P Petrashen
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Marco Mariotti
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Margarita V Meer
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- San Diego Institute of Sciences, Altos Labs, San Diego, CA, USA
| | - Yan Hu
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Grigoriy Losyev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mafalda Galhardo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Elsa Logarinho
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Artur A Indzhykulian
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - John P Manis
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Liu L, Zhu L, Liang Q, Yu L, Hu L, Yu Y, Cheng X, Bao H. Tissue-resident C1q + macrophages exert anti-aging potential through the Sirt1 pathway. Inflamm Res 2024; 73:1069-1080. [PMID: 38724770 DOI: 10.1007/s00011-024-01883-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/03/2024] [Accepted: 04/08/2024] [Indexed: 07/01/2024] Open
Abstract
OBJECTIVE Resident immune cells are at the forefront of sensory organ-specific signals, and changes in these cells are closely related to the aging process. The Sirt pathway can regulate NAD + metabolism during aging, thereby affecting the accumulation of ROS. However, the role of the Sirt pathway in resident immune cells in aged tissues is currently unclear. METHODS We investigated Sirt1 signalling in resident immune cells during chronic inflammation in an aged mouse model. Integrated single-cell RNA sequencing data from young and aged mice were used to refine the characterization of immune cells in aged tissues RESULTS: We found that C1q + macrophages could affect chronic inflammation during aging. C1q + macrophages acted in an opposing manner to Il1b + macrophages and were responsible for anti-inflammatory effects during aging. Sirt1 agonists inhibited the decrease in C1qb in macrophages during aging, and anti-aging drugs could affect the expression of C1qb in macrophages via the Sirt1 pathway. CONCLUSIONS In this study, we first identified the relevance of C1q + macrophages in chronic inflammation during aging. The potential anti-aging effect of C1q + macrophages was mediated by the Sirt1 pathway, suggesting new strategies for aging immunotherapy.
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Affiliation(s)
- Liang Liu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China
- Jiangxi Provincial Cardiovascular Disease Clinical Medical Research Center, Nanchang, 330000, China
- Jiangxi Sub-Center of National Clinical Research Center for Cardiovascular Diseases, Nanchang, 330000, China
| | - Lingjuan Zhu
- Center for Prevention and Treatment of Cardiovascular Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China
- Jiangxi Provincial Cardiovascular Disease Clinical Medical Research Center, Nanchang, 330000, China
- Jiangxi Sub-Center of National Clinical Research Center for Cardiovascular Diseases, Nanchang, 330000, China
| | - Qian Liang
- Department of Science and Technology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China
| | - Lingling Yu
- Department of Rehabilitation, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China
| | - Longlong Hu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China
| | - Yun Yu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China
| | - Xiaoshu Cheng
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China.
- Center for Prevention and Treatment of Cardiovascular Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China.
- Jiangxi Provincial Cardiovascular Disease Clinical Medical Research Center, Nanchang, 330000, China.
- Jiangxi Sub-Center of National Clinical Research Center for Cardiovascular Diseases, Nanchang, 330000, China.
| | - Huihui Bao
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China.
- Center for Prevention and Treatment of Cardiovascular Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330000, China.
- Jiangxi Provincial Cardiovascular Disease Clinical Medical Research Center, Nanchang, 330000, China.
- Jiangxi Sub-Center of National Clinical Research Center for Cardiovascular Diseases, Nanchang, 330000, China.
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Bai H, Liu X, Lin M, Meng Y, Tang R, Guo Y, Li N, Clarke MF, Cai S. Progressive senescence programs induce intrinsic vulnerability to aging-related female breast cancer. Nat Commun 2024; 15:5154. [PMID: 38886378 PMCID: PMC11183265 DOI: 10.1038/s41467-024-49106-2] [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: 06/16/2023] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Cancer incidence escalates exponentially with advancing age; however, the underlying mechanism remains unclear. In this study, we build a chronological molecular clock at single-cell transcription level with a mammary stem cell-enriched population to depict physiological aging dynamics in female mice. We find that the mammary aging process is asynchronous and progressive, initiated by an early senescence program, succeeded by an entropic late senescence program with elevated cancer associated pathways, vulnerable to cancer predisposition. The transition towards senescence program is governed by a stem cell factor Bcl11b, loss of which accelerates mammary ageing with enhanced DMBA-induced tumor formation. We have identified a drug TPCA-1 that can rejuvenate mammary cells and significantly reduce aging-related cancer incidence. Our findings establish a molecular portrait of progressive mammary cell aging and elucidate the transcriptional regulatory network bridging mammary aging and cancer predisposition, which has potential implications for the management of cancer prevalence in the aged.
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Affiliation(s)
- Huiru Bai
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaoqin Liu
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Meizhen Lin
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Yuan Meng
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Ruolan Tang
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Yajing Guo
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Li
- Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Michael F Clarke
- Institute of Stem Cell and Regenerative Medicine, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Shang Cai
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China.
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Tao X, Zhu Z, Wang L, Li C, Sun L, Wang W, Gong W. Biomarkers of Aging and Relevant Evaluation Techniques: A Comprehensive Review. Aging Dis 2024; 15:977-1005. [PMID: 37611906 PMCID: PMC11081160 DOI: 10.14336/ad.2023.00808-1] [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: 06/03/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
The risk of developing chronic illnesses and disabilities is increasing with age. To predict and prevent aging, biomarkers relevant to the aging process must be identified. This paper reviews the known molecular, cellular, and physiological biomarkers of aging. Moreover, we discuss the currently available technologies for identifying these biomarkers, and their applications and potential in aging research. We hope that this review will stimulate further research and innovation in this emerging and fast-growing field.
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Affiliation(s)
- Xue Tao
- Department of Research, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
| | - Ziman Zhu
- Beijing Rehabilitation Medicine Academy, Capital Medical University, Beijing, China.
| | - Liguo Wang
- Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
| | - Chunlin Li
- School of Biomedical Engineering, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China.
| | - Liwei Sun
- School of Biomedical Engineering, Capital Medical University, Beijing, China.
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China.
| | - Wei Wang
- Department of Rehabilitation Radiology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
| | - Weijun Gong
- Department of Neurological Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China.
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9
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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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10
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Zhang K, Kan H, Mao A, Yu F, Geng L, Zhou T, Feng L, Ma X. Integrated Single-Cell Transcriptomic Atlas of Human Kidney Endothelial Cells. J Am Soc Nephrol 2024; 35:578-593. [PMID: 38351505 PMCID: PMC11149048 DOI: 10.1681/asn.0000000000000320] [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: 07/20/2023] [Accepted: 02/09/2024] [Indexed: 03/23/2024] Open
Abstract
Key Points We created a comprehensive reference atlas of normal human kidney endothelial cells. We confirmed that endothelial cell types in the human kidney were also highly conserved in the mouse kidney. Background Kidney endothelial cells are exposed to different microenvironmental conditions that support specific physiologic processes. However, the heterogeneity of human kidney endothelial cells has not yet been systematically described. Methods We reprocessed and integrated seven human kidney control single-cell/single-nucleus RNA sequencing datasets of >200,000 kidney cells in the same process. Results We identified five major cell types, 29,992 of which were endothelial cells. Endothelial cell reclustering identified seven subgroups that differed in molecular characteristics and physiologic functions. Mapping new data to a normal kidney endothelial cell atlas allows rapid data annotation and analysis. We confirmed that endothelial cell types in the human kidney were also highly conserved in the mouse kidney and identified endothelial marker genes that were conserved in humans and mice, as well as differentially expressed genes between corresponding subpopulations. Furthermore, combined analysis of single-cell transcriptome data with public genome-wide association study data showed a significant enrichment of endothelial cells, especially arterial endothelial cells, in BP heritability. Finally, we identified M1 and M12 from coexpression networks in endothelial cells that may be deeply involved in BP regulation. Conclusions We created a comprehensive reference atlas of normal human kidney endothelial cells that provides the molecular foundation for understanding how the identity and function of kidney endothelial cells are altered in disease, aging, and between species. Finally, we provide a publicly accessible online tool to explore the datasets described in this work (https://vascularmap.jiangnan.edu.cn ).
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Affiliation(s)
- Ka Zhang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Kan
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Aiqin Mao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Fan Yu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Li Geng
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Tingting Zhou
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Lei Feng
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Xin Ma
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
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11
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Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. eLife 2024; 12:RP90579. [PMID: 38517750 PMCID: PMC10959535 DOI: 10.7554/elife.90579] [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] [Indexed: 03/24/2024] Open
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Ludger JE Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Julie Y Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kerry A Pierce
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Clary B Clish
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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12
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Mella A, Calvetti R, Barreca A, Congiu G, Biancone L. Kidney transplants from elderly donors: what we have learned 20 years after the Crystal City consensus criteria meeting. J Nephrol 2024:10.1007/s40620-024-01888-w. [PMID: 38446386 DOI: 10.1007/s40620-024-01888-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 01/03/2024] [Indexed: 03/07/2024]
Abstract
Based on the current projection of the general population and the combined increase in end-stage kidney disease with age, the number of elderly donors and recipients is increasing, raising crucial questions about how to minimize the discard rate of organs from elderly donors and improve graft and patient outcomes. In 2002, extended criteria donors were the focus of a meeting in Crystal City (VA, USA), with a goal of maximizing the use of organs from deceased donors. Since then, extended criteria donors have progressively contributed to a large number of transplanted grafts worldwide, posing specific issues for allocation systems, recipient management, and therapeutic approaches. This review analyzes what we have learned in the last 20 years about extended criteria donor utilization, the promising innovations in immunosuppressive management, and the molecular pathways involved in the aging process, which constitute potential targets for novel therapies.
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Affiliation(s)
- Alberto Mella
- Renal Transplant Center" A. Vercellone," Nephrology, Dialysis, and Renal Transplant Division, "Città Della Salute e Della Scienza" Hospital, Department of Medical Sciences, University of Turin, Corso Bramante, 88, 10126, Turin, Italy
| | - Ruggero Calvetti
- Renal Transplant Center" A. Vercellone," Nephrology, Dialysis, and Renal Transplant Division, "Città Della Salute e Della Scienza" Hospital, Department of Medical Sciences, University of Turin, Corso Bramante, 88, 10126, Turin, Italy
| | - Antonella Barreca
- Division of Pathology, "Città Della Salute e Della Scienza" Hospital, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Giovanni Congiu
- Renal Transplant Center" A. Vercellone," Nephrology, Dialysis, and Renal Transplant Division, "Città Della Salute e Della Scienza" Hospital, Department of Medical Sciences, University of Turin, Corso Bramante, 88, 10126, Turin, Italy
| | - Luigi Biancone
- Renal Transplant Center" A. Vercellone," Nephrology, Dialysis, and Renal Transplant Division, "Città Della Salute e Della Scienza" Hospital, Department of Medical Sciences, University of Turin, Corso Bramante, 88, 10126, Turin, Italy.
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13
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Zhang Z, Schaefer C, Jiang W, Lu Z, Lee J, Sziraki A, Abdulraouf A, Wick B, Haeussler M, Li Z, Molla G, Satija R, Zhou W, Cao J. A Panoramic View of Cell Population Dynamics in Mammalian Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.583001. [PMID: 38496474 PMCID: PMC10942312 DOI: 10.1101/2024.03.01.583001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different life stages, sexes, and genotypes. This comprehensive dataset allowed us to identify more than 3,000 unique cellular states and catalog over 200 distinct aging-associated cell populations experiencing significant depletion or expansion. Our panoramic analysis uncovered temporally structured, organ- and lineage-specific shifts of cellular dynamics during lifespan progression. Moreover, we investigated aging-associated alterations in immune cell populations, revealing both widespread shifts and organ-specific changes. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte-dependent. The breadth and depth of our 'cell-omics' methodology not only enhance our comprehension of cellular aging but also lay the groundwork for exploring the complex regulatory networks among varied cell types in the context of aging and aging-associated diseases.
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Affiliation(s)
- Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Chloe Schaefer
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Weirong Jiang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Abdulraouf Abdulraouf
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional M.D-Ph.D Program, New York, NY, USA
| | - Brittney Wick
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Zhuoyan Li
- New York Genome Center, New York, NY, USA
| | | | - Rahul Satija
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
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14
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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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15
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Adekunbi DA, Huber HF, Li C, Nathanielsz PW, Cox LA, Salmon AB. Differential mitochondrial bioenergetics and cellular resilience in astrocytes, hepatocytes, and fibroblasts from aging baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579010. [PMID: 38370705 PMCID: PMC10871288 DOI: 10.1101/2024.02.06.579010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Biological resilience, broadly defined as ability to recover from acute challenge and return to homeostasis, is of growing importance to the biology of aging. At the cellular level, there is variability across tissue types in resilience and these differences likely to contribute to tissue aging rate disparities. However, there are challenges in addressing these cell-type differences at regional, tissue and subject level. To address this question, we established primary cells from aged male and female baboons between 13.3-17.8 years spanning across different tissues, tissue regions, and cell types including: (1) fibroblasts from skin and from heart separated into left ventricle (LV), right ventricle (RV), left atrium (LA) and right atrium (RA), (2) astrocytes from the prefrontal cortex and hippocampus and (3) hepatocytes. Primary cells were characterized by their cell surface markers and their cellular respiration assessed with Seahorse XFe96. Cellular resilience was assessed by modifying a live-cell imaging approach we previously reported that monitors proliferation of dividing cells following response and recovery to oxidative (50µM-H2O2), metabolic (1mM-glucose) and proteostasis (0.1µM-thapsigargin) stress. We noted significant differences even among similar cell types that are dependent on tissue source and the diversity in cellular response is stressor specific. For example, astrocytes were more energetic and exhibited greater resilience to oxidative stress (OS) than both fibroblasts and hepatocytes. RV and RA fibroblasts were less resilient to OS compared with LV and LA respectively. Skin fibroblasts were less impacted by proteostasis stress compared to astrocytes and cardiac fibroblasts. Future studies will test the functional relationship of these outcomes to age and developmental status of donors as potential predictive markers.
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Affiliation(s)
- Daniel A Adekunbi
- Department of Molecular Medicine and Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Hillary F Huber
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Cun Li
- Texas Pregnancy and Life-course Health Research Center, Department of Animal Science, University of Wyoming, Laramie, Wyoming, USA
| | - Peter W Nathanielsz
- Texas Pregnancy and Life-course Health Research Center, Department of Animal Science, University of Wyoming, Laramie, Wyoming, USA
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Adam B Salmon
- Department of Molecular Medicine and Barshop Institute for Longevity and Aging Studies, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- Geriatric Research Education and Clinical Center, Audie L. Murphy Hospital, Southwest Veterans Health Care System, San Antonio, Texas, USA
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16
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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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17
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Bekhbat M, Drake J, Reed EC, Lauten TH, Natour T, Vladimirov VI, Case AJ. Repeated social defeat stress leads to immunometabolic shifts in innate immune cells of the spleen. Brain Behav Immun Health 2023; 34:100690. [PMID: 37791319 PMCID: PMC10543777 DOI: 10.1016/j.bbih.2023.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/05/2023] Open
Abstract
Psychosocial stress has been shown to prime peripheral innate immune cells, which take on hyper-inflammatory phenotypes and are implicated in depressive-like behavior in mouse models. However, the impact of stress on cellular metabolic states that are thought to fuel inflammatory phenotypes in immune cells are unknown. Using single cell RNA-sequencing, we investigated mRNA enrichment of immunometabolic pathways in innate immune cells of the spleen in mice subjected to repeated social defeat stress (RSDS) or no stress (NS). RSDS mice displayed a significant increase in the number of splenic macrophages and granulocytes (p < 0.05) compared to NS littermates. RSDS-upregulated genes in macrophages, monocytes, and granulocytes significantly enriched immunometabolic pathways thought to play a role in myeloid-driven inflammation (glycolysis, HIF-1 signaling, MTORC1 signaling) as well as pathways related to oxidative phosphorylation (OXPHOS) and oxidative stress (p < 0.05 and FDR<0.1). These results suggest that the metabolic enhancement reflected by upregulation of glycolytic and OXPHOS pathways may be important for cellular proliferation of splenic macrophages and granulocytes following repeated stress exposure. A better understanding of these intracellular metabolic mechanisms may ultimately help develop novel strategies to reverse the impact of stress and associated peripheral immune changes on the brain and behavior.
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Affiliation(s)
- Mandakh Bekhbat
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30322, USA
| | - John Drake
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX, 77807, USA
| | - Emily C. Reed
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX, 77807, USA
- Department of Medical Physiology, Texas A&M University, Bryan, TX, 77807, USA
| | - Tatlock H. Lauten
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX, 77807, USA
- Department of Medical Physiology, Texas A&M University, Bryan, TX, 77807, USA
| | - Tamara Natour
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX, 77807, USA
- Department of Medical Physiology, Texas A&M University, Bryan, TX, 77807, USA
| | - Vladimir I. Vladimirov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX, 77807, USA
- Department of Psychiatry, University of Arizona, Phoenix, AZ, 85004, USA
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Adam J. Case
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX, 77807, USA
- Department of Medical Physiology, Texas A&M University, Bryan, TX, 77807, USA
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18
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Tyrrell DJ, Wragg KM, Chen J, Wang H, Song J, Blin MG, Bolding C, Vardaman D, Giles K, Tidwell H, Ali MA, Janappareddi A, Wood SC, Goldstein DR. Clonally expanded memory CD8 + T cells accumulate in atherosclerotic plaques and are pro-atherogenic in aged mice. NATURE AGING 2023; 3:1576-1590. [PMID: 37996758 DOI: 10.1038/s43587-023-00515-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/27/2023] [Indexed: 11/25/2023]
Abstract
Aging is a strong risk factor for atherosclerosis and induces accumulation of memory CD8+ T cells in mice and humans. Biological changes that occur with aging lead to enhanced atherosclerosis, yet the role of aging on CD8+ T cells during atherogenesis is unclear. In this study, using femle mice, we found that depletion of CD8+ T cells attenuated atherogenesis in aged, but not young, animals. Furthermore, adoptive transfer of splenic CD8+ T cells from aged wild-type, but not young wild-type, donor mice significantly enhanced atherosclerosis in recipient mice lacking CD8+ T cells. We also characterized T cells in healthy and atherosclerotic young and aged mice by single-cell RNA sequencing. We found specific subsets of age-associated CD8+ T cells, including a Granzyme K+ effector memory subset, that accumulated and was clonally expanded within atherosclerotic plaques. These had transcriptomic signatures of T cell activation, migration, cytotoxicity and exhaustion. Overall, our study identified memory CD8+ T cells as therapeutic targets for atherosclerosis in aging.
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Affiliation(s)
- Daniel J Tyrrell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
| | - Kathleen M Wragg
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Judy Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Program in Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Hui Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jianrui Song
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Muriel G Blin
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Chase Bolding
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Donald Vardaman
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kara Giles
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Harrison Tidwell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Md Akkas Ali
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Sherri C Wood
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Daniel R Goldstein
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Program in Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
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19
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Lercher A, Cheong JG, Jiang C, Hoffmann HH, Ashbrook AW, Yin YS, Quirk C, DeGrace EJ, Chiriboga L, Rosenberg BR, Josefowicz SZ, Rice CM. Antiviral innate immune memory in alveolar macrophages following SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.24.568354. [PMID: 38076887 PMCID: PMC10705235 DOI: 10.1101/2023.11.24.568354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Pathogen encounter results in long-lasting epigenetic imprinting that shapes diseases caused by heterologous pathogens. The breadth of this innate immune memory is of particular interest in the context of respiratory pathogens with increased pandemic potential and wide-ranging impact on global health. Here, we investigated epigenetic imprinting across cell lineages in a disease relevant murine model of SARS-CoV-2 recovery. Past SARS-CoV-2 infection resulted in increased chromatin accessibility of type I interferon (IFN-I) related transcription factors in airway-resident macrophages. Mechanistically, establishment of this innate immune memory required viral pattern recognition and canonical IFN-I signaling and augmented secondary antiviral responses. Past SARS-CoV-2 infection ameliorated disease caused by the heterologous respiratory pathogen influenza A virus. Insights into innate immune memory and how it affects subsequent infections with heterologous pathogens to influence disease pathology could facilitate the development of broadly effective therapeutic strategies.
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Affiliation(s)
- Alexander Lercher
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jin-Gyu Cheong
- Department of Pathology and Laboratory Medicine, Laboratory of Epigenetics and Immunity, Weill Cornell Medicine, New York, NY, 10065, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chenyang Jiang
- Department of Pathology and Laboratory Medicine, Laboratory of Epigenetics and Immunity, Weill Cornell Medicine, New York, NY, 10065, USA
- BCMB Allied Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alison W. Ashbrook
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Yue S. Yin
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Corrine Quirk
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Emma J. DeGrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Luis Chiriboga
- Department of Pathology, New York University Medical Center, New York, NY, 10016, USA
- Center for Biospecimen Research and Development, New York, NY, 10016, USA
| | - Brad R. Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Steven Z. Josefowicz
- Department of Pathology and Laboratory Medicine, Laboratory of Epigenetics and Immunity, Weill Cornell Medicine, New York, NY, 10065, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
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20
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Lagger C, Ursu E, Equey A, Avelar RA, Pisco AO, Tacutu R, de Magalhães JP. scDiffCom: a tool for differential analysis of cell-cell interactions provides a mouse atlas of aging changes in intercellular communication. NATURE AGING 2023; 3:1446-1461. [PMID: 37919434 PMCID: PMC10645595 DOI: 10.1038/s43587-023-00514-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 09/27/2023] [Indexed: 11/04/2023]
Abstract
Dysregulation of intercellular communication is a hallmark of aging. To better quantify and explore changes in intercellular communication, we present scDiffCom and scAgeCom. scDiffCom is an R package, relying on approximately 5,000 curated ligand-receptor interactions, that performs differential intercellular communication analysis between two conditions from single-cell transcriptomics data. Built upon scDiffCom, scAgeCom is an atlas of age-related cell-cell communication changes covering 23 mouse tissues from 58 single-cell RNA sequencing datasets from Tabula Muris Senis and the Calico murine aging cell atlas. It offers a comprehensive resource of tissue-specific and sex-specific aging dysregulations and highlights age-related intercellular communication changes widespread across the whole body, such as the upregulation of immune system processes and inflammation, the downregulation of developmental processes, angiogenesis and extracellular matrix organization and the deregulation of lipid metabolism. Our analysis emphasizes the relevance of the specific ligands, receptors and cell types regulating these processes. The atlas is available online ( https://scagecom.org ).
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Affiliation(s)
- Cyril Lagger
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
- Altos Labs, San Diego, CA, USA
| | - Eugen Ursu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Anaïs Equey
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Roberto A Avelar
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Angela Oliveira Pisco
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Insitro, Inc., South San Francisco, USA
| | - Robi Tacutu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK.
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK.
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21
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Zhang W, Xia S, Xiao W, Song Y, Tang L, Cao M, Yang J, Wang S, Li Z, Xu C, Liu J, Zhao S, Yang C, Wang J. A single-cell transcriptomic landscape of mouse testicular aging. J Adv Res 2023; 53:219-234. [PMID: 36528294 PMCID: PMC10658307 DOI: 10.1016/j.jare.2022.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Advanced paternal age of reproduction is an increasing trend, especially in developed countries and areas. This trend results in elevated risks of adverse reproductive outcomes such as reduced fertility rates, increased pregnancy loss, and poor childhood health. Yet, a systematic profiling of aging-associated molecular and cellular alterations in testicular tissue is still missing. OBJECTIVES We aimed to dissect aging-associated molecular characteristics in testes of mice. METHODS Single-cell transcriptomic sequencing and analysis were conducted in testes of young (2 months old) and old mice (24 months old). Immunofluorescences and immunochemistry were used to characterize aging-associated phenotypes and verify single cell sequence results. RESULTS Here, we constructed the first single-cell transcriptomic atlases of testes of young and old mice. In-depth dissection of aging-dependent transcriptional alterations in specific cell types revealed multiple dysregulated biological processes such as increased 'senescence-associated secretory phenotype' and 'inflammation', which were major aging-associated characteristics. Further analysis of aging-related differentially expressed genes uncovered a disrupted balance of undifferentiated and differentiated spermatogonia stem cells in spermatogonia, indicative of a potential role of spermatogonia stem cells in aging-associated subfertility. Importantly, for the first time, our results identified an increased subtype of aging-specific macrophages, which may contribute to a hostile proinflammatory microenvironment during testicular aging. CONCLUSION Taken together, our findings depict the distinct single-cell transcriptional features of the aged mouse testes and provide enormous resources for a comprehensive understanding of the cell-type-specific molecular mechanisms underlying mouse testicular aging, which may shed light on developing novel potential diagnostic biomarkers and therapeutic targets for age-associated male subfertility.
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Affiliation(s)
- Wei Zhang
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Siyu Xia
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Wei Xiao
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yali Song
- Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan 523000, China
| | - Li Tang
- Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan 523000, China
| | - Min Cao
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Jing Yang
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Shuang Wang
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Zhijie Li
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Chengchao Xu
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Jianqiao Liu
- Key Laboratory for Reproductive Medicine of Guangdong Province, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China.
| | - Shanchao Zhao
- Department of Urology, the Third Affiliated Hospital of Southern Medical University, and Nanfang Hospital, Southern Medical University, Guangzhou, 510500, China.
| | - Chuanbin Yang
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China.
| | - Jigang Wang
- Department of Nephrology, and Shenzhen key Laboratory of Kidney Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, Shenzhen 518020, China; Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan 523000, China; Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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22
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Dos Santos GA, Chatsirisupachai K, Avelar RA, de Magalhães JP. Transcriptomic analysis reveals a tissue-specific loss of identity during ageing and cancer. BMC Genomics 2023; 24:644. [PMID: 37884865 PMCID: PMC10604446 DOI: 10.1186/s12864-023-09756-w] [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: 02/20/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
INTRODUCTION Understanding changes in cell identity in cancer and ageing is of great importance. In this work, we analyzed how gene expression changes in human tissues are associated with tissue specificity during cancer and ageing using transcriptome data from TCGA and GTEx. RESULTS We found significant downregulation of tissue-specific genes during ageing in 40% of the tissues analyzed, which suggests loss of tissue identity with age. For most cancer types, we have noted a consistent pattern of downregulation in genes that are specific to the tissue from which the tumor originated. Moreover, we observed in cancer an activation of genes not usually expressed in the tissue of origin as well as an upregulation of genes specific to other tissues. These patterns in cancer were associated with patient survival. The age of the patient, however, did not influence these patterns. CONCLUSION We identified loss of cellular identity in 40% of the tissues analysed during human ageing, and a clear pattern in cancer, where during tumorigenesis cells express genes specific to other organs while suppressing the expression of genes from their original tissue. The loss of cellular identity observed in cancer is associated with prognosis and is not influenced by age, suggesting that it is a crucial stage in carcinogenesis.
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Affiliation(s)
- Gabriel Arantes Dos Santos
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2WB, UK
| | - Kasit Chatsirisupachai
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
| | - Roberto A Avelar
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
| | - João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2WB, UK.
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23
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Angarola BL, Sharma S, Katiyar N, Gu Kang H, Nehar-Belaid D, Park S, Gott R, Eryilmaz GN, LaBarge MA, Palucka K, Chuang JH, Korstanje R, Ucar D, Anczukow O. Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563147. [PMID: 37961129 PMCID: PMC10634680 DOI: 10.1101/2023.10.20.563147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. We investigate how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory, or cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveal co-localization of aged immune and epithelial cells in situ. Lastly, transcriptional signatures of aging mammary cells are found in human breast tumors, suggesting mechanistic links between aging and cancer. Together, these data uncover that epithelial, immune, and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment, and neoplasia risk.
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Affiliation(s)
| | | | - Neerja Katiyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hyeon Gu Kang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Giray N Eryilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
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24
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Colville A, Liu JY, Rodriguez-Mateo C, Thomas S, Ishak HD, Zhou R, Klein JDD, Morgens DW, Goshayeshi A, Salvi JS, Yao D, Spees K, Dixon SJ, Liu C, Rhee JW, Lai C, Wu JC, Bassik MC, Rando TA. Death-seq identifies regulators of cell death and senolytic therapies. Cell Metab 2023; 35:1814-1829.e6. [PMID: 37699398 PMCID: PMC10597643 DOI: 10.1016/j.cmet.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
Selectively ablating damaged cells is an evolving therapeutic approach for age-related disease. Current methods for genome-wide screens to identify genes whose deletion might promote the death of damaged or senescent cells are generally underpowered because of the short timescales of cell death as well as the difficulty of scaling non-dividing cells. Here, we establish "Death-seq," a positive-selection CRISPR screen optimized to identify enhancers and mechanisms of cell death. Our screens identified synergistic enhancers of cell death induced by the known senolytic ABT-263. The screen also identified inducers of cell death and senescent cell clearance in models of age-related diseases by a related compound, ABT-199, which alone is not senolytic but exhibits less toxicity than ABT-263. Death-seq enables the systematic screening of cell death pathways to uncover molecular mechanisms of regulated cell death subroutines and identifies drug targets for the treatment of diverse pathological states such as senescence, cancer, and fibrosis.
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Affiliation(s)
- Alex Colville
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jie-Yu Liu
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cristina Rodriguez-Mateo
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samantha Thomas
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heather D Ishak
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ronghao Zhou
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julian D D Klein
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David W Morgens
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Armon Goshayeshi
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jayesh S Salvi
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David Yao
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Chun Liu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - June-Wha Rhee
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Celine Lai
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Thomas A Rando
- Paul F. Glenn Center for the Biology of Aging and Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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25
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Groves SM, Quaranta V. Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics. FRONTIERS IN NETWORK PHYSIOLOGY 2023; 3:1225736. [PMID: 37731743 PMCID: PMC10507267 DOI: 10.3389/fnetp.2023.1225736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
Phenotypic plasticity of cancer cells can lead to complex cell state dynamics during tumor progression and acquired resistance. Highly plastic stem-like states may be inherently drug-resistant. Moreover, cell state dynamics in response to therapy allow a tumor to evade treatment. In both scenarios, quantifying plasticity is essential for identifying high-plasticity states or elucidating transition paths between states. Currently, methods to quantify plasticity tend to focus on 1) quantification of quasi-potential based on the underlying gene regulatory network dynamics of the system; or 2) inference of cell potency based on trajectory inference or lineage tracing in single-cell dynamics. Here, we explore both of these approaches and associated computational tools. We then discuss implications of each approach to plasticity metrics, and relevance to cancer treatment strategies.
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Affiliation(s)
- Sarah M. Groves
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Vito Quaranta
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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26
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Billimoria R, Bhatt P. Senescence in cancer: Advances in detection and treatment modalities. Biochem Pharmacol 2023; 215:115739. [PMID: 37562510 DOI: 10.1016/j.bcp.2023.115739] [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: 06/22/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Senescence is a form of irreversible cell cycle arrest. Senescence plays a dual role in cancer, as both a tumor suppressor by preventing the growth of damaged cells and a cancer promoter by creating an inflammatory milieu. Stress-induced premature senescence (SIPS) and replicative senescence are the two major sub-types of senescence. Senescence plays a dual role in cancer, depending on the context and kind of senescence involved. SIPS can cause cancer by nurturing an inflammatory environment, whereas replicative senescence may prevent cancer. Major pathways that are involved in senescence are the p53-p21, p16INK4A-Rb pathway along with mTOR, MAPK, and PI3K pathways. The lack of universal senescence markers makes it difficult to identify senescent cells in vivo. A combination of reliable detection methods of senescent cells in vivo is of utmost importance and will help in early detection and open new avenues for future treatment. New strategies that are being developed in order to tackle these shortcomings are in the field of fluorescent probes, nanoparticles, positron emission tomography probes, biosensors, and the detection of cell-free DNA from liquid biopsies. Along with detection, eradication of these senescent cells is also important to prevent cancer reoccurrence. Recently, the field of nano-senolytic and immunotherapy has also been emerging. This review provides up-to-date information on the various types of advancements made in the field of detection and treatment modalities for senescent cells that hold promise for the future treatment and prognosis of cancer, as well as their limitations and potential solutions.
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Affiliation(s)
- Rezina Billimoria
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Vile Parle (West), Mumbai, India
| | - Purvi Bhatt
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Vile Parle (West), Mumbai, India.
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27
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Zhang Y, Shen J, Cheng W, Roy B, Zhao R, Chai T, Sheng Y, Zhang Z, Chen X, Liang W, Hu W, Liao Q, Pan S, Zhuang W, Zhang Y, Chen R, Mei J, Wei H, Fang X. Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seq. J Genet Genomics 2023; 50:688-701. [PMID: 37156441 DOI: 10.1016/j.jgg.2023.04.012] [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: 01/12/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Gut microbes exhibit complex interactions with their hosts and shape an organism's immune system throughout its lifespan. As the largest secondary lymphoid organ, the spleen has a wide range of immunological functions. To explore the role of microbiota in regulating and shaping the spleen, we employ scRNA-seq and Stereo-seq technologies based on germ-free (GF) mice to detect differences in tissue size, anatomical structure, cell types, functions, and spatial molecular characteristics. We identify 18 cell types, 9 subtypes of T cells, and 7 subtypes of B cells. Gene differential expression analysis reveals that the absence of microorganisms results in alterations in erythropoiesis within the red pulp region and congenital immune deficiency in the white pulp region. Stereo-seq results demonstrate a clear hierarchy of immune cells in the spleen, including marginal zone (MZ) macrophages, MZ B cells, follicular B cells and T cells, distributed in a well-defined pattern from outside to inside. However, this hierarchical structure is disturbed in GF mice. Ccr7 and Cxcl13 chemokines are specifically expressed in the spatial locations of T cells and B cells, respectively. We speculate that the microbiota may mediate the structural composition or partitioning of spleen immune cells by modulating the expression levels of chemokines.
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Affiliation(s)
- Yin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Juan Shen
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Wei Cheng
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bhaskar Roy
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Ruizhen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Tailiang Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yifei Sheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Zhao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xueting Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Weining Hu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qijun Liao
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Wen Zhuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yangrui Zhang
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Rouxi Chen
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Xiaodong Fang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China.
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28
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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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29
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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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30
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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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31
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Li T, Roberts R, Liu Z, Tong W. TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes. Chem Res Toxicol 2023; 36:916-925. [PMID: 37200521 PMCID: PMC10433534 DOI: 10.1021/acs.chemrestox.3c00037] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Indexed: 05/20/2023]
Abstract
Animal studies are required for the evaluation of candidate drugs to ensure patient and volunteer safety. Toxicogenomics is often applied in these studies to gain understanding of the underlying mechanisms of toxicity, which is usually focused on critical organs such as the liver or kidney in young male rats. There is a strong ethical reason to reduce, refine and replace animal use (the 3Rs), where the mapping of data between organs, sexes and ages could reduce the cost and time of drug development. Herein, we proposed a generative adversarial network (GAN)-based framework entitled TransOrGAN that allowed the molecular mapping of gene expression profiles in different rodent organ systems and across sex and age groups. We carried out a proof-of-concept study based on rat RNA-seq data from 288 samples in 9 different organs of both sexes and 4 developmental stages. First, we demonstrated that TransOrGAN could infer transcriptomic profiles between any 2 of the 9 organs studied, yielding an average cosine similarity of 0.984 between synthetic transcriptomic profiles and their corresponding real profiles. Second, we found that TransOrGAN could infer transcriptomic profiles observed in females from males, with an average cosine similarity of 0.984. Third, we found that TransOrGAN could infer transcriptomic profiles in juvenile, adult, and aged animals from adolescent animals with an average cosine similarity of 0.981, 0.983, and 0.989, respectively. Altogether, TransOrGAN is an innovative approach to infer transcriptomic profiles between ages, sexes, and organ systems, offering the opportunity to reduce animal usage and to provide an integrated assessment of toxicity in the whole organism irrespective of sex or age.
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Affiliation(s)
- Ting Li
- National
Center for Toxicological Research, Food
and Drug Administration, Jefferson, Arkansas 72079, United States
| | - Ruth Roberts
- ApconiX Ltd, Alderley Park, Alderley Edge SK10 4TG, United Kingdom
- University
of Birmingham, Edgbaston, Birmingham B15 2TT, United
Kingdom
| | - Zhichao Liu
- Integrative
Toxicology, Nonclinical Drug Safety, Boehringer
Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, United States
| | - Weida Tong
- National
Center for Toxicological Research, Food
and Drug Administration, Jefferson, Arkansas 72079, United States
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32
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Wu S, Ohba S, Matsushita Y. Single-Cell RNA-Sequencing Reveals the Skeletal Cellular Dynamics in Bone Repair and Osteoporosis. Int J Mol Sci 2023; 24:9814. [PMID: 37372962 DOI: 10.3390/ijms24129814] [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: 04/28/2023] [Revised: 05/29/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The bone is an important organ that performs various functions, and the bone marrow inside the skeleton is composed of a complex intermix of hematopoietic, vascular, and skeletal cells. Current single-cell RNA sequencing (scRNA-seq) technology has revealed heterogeneity and sketchy differential hierarchy of skeletal cells. Skeletal stem and progenitor cells (SSPCs) are located upstream of the hierarchy and differentiate into chondrocytes, osteoblasts, osteocytes, and bone marrow adipocytes. In the bone marrow, multiple types of bone marrow stromal cells (BMSCs), which have the potential of SSPCs, are spatiotemporally located in distinct areas, and SSPCs' potential shift of BMSCs may occur with the advancement of age. These BMSCs contribute to bone regeneration and bone diseases, such as osteoporosis. In vivo lineage-tracing technologies show that various types of skeletal lineage cells concomitantly gather and contribute to bone regeneration. In contrast, these cells differentiate into adipocytes with aging, leading to senile osteoporosis. scRNA-seq analysis has revealed that alteration in the cell-type composition is a major cause of tissue aging. In this review, we discuss the cellular dynamics of skeletal cell populations in bone homeostasis, regeneration, and osteoporosis.
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Affiliation(s)
- Sixun Wu
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Shinsuke Ohba
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Osaka 565-0871, Japan
| | - Yuki Matsushita
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
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33
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Walter LD, Orton JL, Hannah Fong EH, Maymi VI, Rudd BD, Elisseeff JH, Cosgrove BD. Single-cell transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states associated with senescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542370. [PMID: 37292698 PMCID: PMC10245980 DOI: 10.1101/2023.05.25.542370] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Skeletal muscle regeneration is driven by the interaction of myogenic and non-myogenic cells. In aging, regeneration is impaired due to dysfunctions of myogenic and non-myogenic cells, but this is not understood comprehensively. We collected an integrated atlas of 273,923 single-cell transcriptomes from muscles of young, old, and geriatric mice (~5, 20, 26 months-old) at six time-points following myotoxin injury. We identified eight cell types, including T and NK cells and macrophage subtypes, that displayed accelerated or delayed response dynamics between ages. Through pseudotime analysis, we observed myogenic cell states and trajectories specific to old and geriatric ages. To explain these age differences, we assessed cellular senescence by scoring experimentally derived and curated gene-lists. This pointed to an elevation of senescent-like subsets specifically within the self-renewing muscle stem cells in aged muscles. This resource provides a holistic portrait of the altered cellular states underlying skeletal muscle regenerative decline across mouse lifespan.
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Affiliation(s)
- Lauren D. Walter
- Genetics, Genomics and Development Graduate Program, Cornell University, Ithaca, NY, USA
| | - Jessica L. Orton
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Viviana I. Maymi
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY, USA
| | - Brian D. Rudd
- Genetics, Genomics and Development Graduate Program, Cornell University, Ithaca, NY, USA
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY, USA
| | - Jennifer H. Elisseeff
- Translational Tissue Engineering Center, Wilmer Eye Institute, and Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin D. Cosgrove
- Genetics, Genomics and Development Graduate Program, Cornell University, Ithaca, NY, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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34
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Delcroix V, Mauduit O, Lee HS, Ivanova A, Umazume T, Knox SM, de Paiva CS, Dartt DA, Makarenkova HP. The First Transcriptomic Atlas of the Adult Lacrimal Gland Reveals Epithelial Complexity and Identifies Novel Progenitor Cells in Mice. Cells 2023; 12:1435. [PMID: 37408269 PMCID: PMC10216974 DOI: 10.3390/cells12101435] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 07/07/2023] Open
Abstract
The lacrimal gland (LG) secretes aqueous tears. Previous studies have provided insights into the cell lineage relationships during tissue morphogenesis. However, little is known about the cell types composing the adult LG and their progenitors. Using scRNAseq, we established the first comprehensive cell atlas of the adult mouse LG to investigate the cell hierarchy, its secretory repertoire, and the sex differences. Our analysis uncovered the complexity of the stromal landscape. Epithelium subclustering revealed myoepithelial cells, acinar subsets, and two novel acinar subpopulations: Tfrchi and Car6hi cells. The ductal compartment contained Wfdc2+ multilayered ducts and an Ltf+ cluster formed by luminal and intercalated duct cells. Kit+ progenitors were identified as: Krt14+ basal ductal cells, Aldh1a1+ cells of Ltf+ ducts, and Sox10+ cells of the Car6hi acinar and Ltf+ epithelial clusters. Lineage tracing experiments revealed that the Sox10+ adult populations contribute to the myoepithelial, acinar, and ductal lineages. Using scRNAseq data, we found that the postnatally developing LG epithelium harbored key features of putative adult progenitors. Finally, we showed that acinar cells produce most of the sex-biased lipocalins and secretoglobins detected in mouse tears. Our study provides a wealth of new data on LG maintenance and identifies the cellular origin of sex-biased tear components.
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Affiliation(s)
- Vanessa Delcroix
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
| | - Olivier Mauduit
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
| | - Hyun Soo Lee
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
- Department of Ophthalmology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Anastasiia Ivanova
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
| | - Takeshi Umazume
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
| | - Sarah M. Knox
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA;
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Cintia S. de Paiva
- The Ocular Surface Center, Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Darlene A. Dartt
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA;
| | - Helen P. Makarenkova
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA 92037, USA; (V.D.); (H.S.L.); (A.I.); (T.U.)
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35
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Barruet E, Striedinger K, Marangoni P, Pomerantz JH. Loss of transcriptional heterogeneity in aged human muscle stem cells. PLoS One 2023; 18:e0285018. [PMID: 37192223 PMCID: PMC10187936 DOI: 10.1371/journal.pone.0285018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/12/2023] [Indexed: 05/18/2023] Open
Abstract
Age-related loss of muscle mass and function negatively impacts healthspan and lifespan. Satellite cells function as muscle stem cells in muscle maintenance and regeneration by self-renewal, activation, proliferation and differentiation. These processes are perturbed in aging at the stem cell population level, contributing to muscle loss. However, how representation of subpopulations within the human satellite cell pool change during aging remains poorly understood. We previously reported a comprehensive baseline of human satellite cell (Hu-MuSCs) transcriptional activity in muscle homeostasis describing functional heterogenous human satellite cell subpopulations such as CAV1+ Hu-MUSCs. Here, we sequenced additional satellite cells from new healthy donors and performed extended transcriptomic analyses with regard to aging. We found an age-related loss of global transcriptomic heterogeneity and identified new markers (CAV1, CXCL14, GPX3) along with previously described ones (FN1, ITGB1, SPRY1) that are altered during aging in human satellite cells. These findings describe new transcriptomic changes that occur during aging in human satellite cells and provide a foundation for understanding functional impact.
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Affiliation(s)
- Emilie Barruet
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, California, United States of America
| | - Katharine Striedinger
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Pauline Marangoni
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, California, United States of America
| | - Jason H. Pomerantz
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
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36
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Ibañez-Solé O, Barrio I, Izeta A. Age or lifestyle-induced accumulation of genotoxicity is associated with a length-dependent decrease in gene expression. iScience 2023; 26:106368. [PMID: 37013186 PMCID: PMC10066539 DOI: 10.1016/j.isci.2023.106368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/26/2023] [Accepted: 03/05/2023] [Indexed: 03/12/2023] Open
Abstract
DNA damage has long been advocated as a molecular driver of aging. DNA damage occurs in a stochastic manner, and is therefore more likely to accumulate in longer genes. The length-dependent accumulation of transcription-blocking damage, unlike that of somatic mutations, should be reflected in gene expression datasets of aging. We analyzed gene expression as a function of gene length in several single-cell RNA sequencing datasets of mouse and human aging. We found a pervasive age-associated length-dependent underexpression of genes across species, tissues, and cell types. Furthermore, we observed length-dependent underexpression associated with UV-radiation and smoke exposure, and in progeroid diseases, Cockayne syndrome, and trichothiodystrophy. Finally, we studied published gene sets showing global age-related changes. Genes underexpressed with aging were significantly longer than overexpressed genes. These data highlight a previously undetected hallmark of aging and show that accumulation of genotoxicity in long genes could lead to reduced RNA polymerase II processivity.
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Affiliation(s)
- Olga Ibañez-Solé
- Tissue Engineering Group; Biodonostia Health Research Institute, 20014 Donostia-San Sebastián, Spain
| | - Irantzu Barrio
- Department of Mathematics, University of the basque Country UPV/EHU, 48940 Leioa, Spain
- Basque Center for Applied Mathematics, BCAM, 48009 Bilbao, Spain
| | - Ander Izeta
- Tissue Engineering Group; Biodonostia Health Research Institute, 20014 Donostia-San Sebastián, Spain
- Tecnun-University of Navarra, 20018 Donostia-San Sebastián, Spain
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37
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Wayman JA, Thomas A, Bejjani A, Katko A, Almanan M, Godarova A, Korinfskaya S, Cazares TA, Yukawa M, Kottyan LC, Barski A, Chougnet CA, Hildeman DA, Miraldi ER. An atlas of gene regulatory networks for memory CD4 + T cells in youth and old age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531590. [PMID: 36945549 PMCID: PMC10028906 DOI: 10.1101/2023.03.07.531590] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Aging profoundly affects immune-system function, promoting susceptibility to pathogens, cancers and chronic inflammation. We previously identified a population of IL-10-producing, T follicular helper-like cells (" Tfh10 "), linked to suppressed vaccine responses in aged mice. Here, we integrate single-cell ( sc )RNA-seq, scATAC-seq and genome-scale modeling to characterize Tfh10 - and the full CD4 + memory T cell ( CD4 + TM ) compartment - in young and old mice. We identified 13 CD4 + TM populations, which we validated through cross-comparison to prior scRNA-seq studies. We built gene regulatory networks ( GRNs ) that predict transcription-factor control of gene expression in each T-cell population and how these circuits change with age. Through integration with pan-cell aging atlases, we identified intercellular-signaling networks driving age-dependent changes in CD4 + TM. Our atlas of finely resolved CD4 + TM subsets, GRNs and cell-cell communication networks is a comprehensive resource of predicted regulatory mechanisms operative in memory T cells, presenting new opportunities to improve immune responses in the elderly.
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38
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Warren WC, Rice ES, Meyer A, Hearn CJ, Steep A, Hunt HD, Monson MS, Lamont SJ, Cheng HH. The immune cell landscape and response of Marek's disease resistant and susceptible chickens infected with Marek's disease virus. Sci Rep 2023; 13:5355. [PMID: 37005445 PMCID: PMC10067856 DOI: 10.1038/s41598-023-32308-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/25/2023] [Indexed: 04/04/2023] Open
Abstract
Genetically resistant or susceptible chickens to Marek's disease (MD) have been widely used models to identify the molecular determinants of these phenotypes. However, these prior studies lacked the basic identification and understanding of immune cell types that could be translated toward improved MD control. To gain insights into specific immune cell types and their responses to Marek's disease virus (MDV) infection, we used single-cell RNA sequencing (scRNAseq) on splenic cells from MD resistant and susceptible birds. In total, 14,378 cells formed clusters that identified various immune cell types. Lymphocytes, specifically T cell subtypes, were the most abundant with significant proportional changes in some subtypes upon infection. The largest number of differentially expressed genes (DEG) response was seen in granulocytes, while macrophage DEGs differed in directionality by subtype and line. Among the most DEG in almost all immune cell types were granzyme and granulysin, both associated with cell-perforating processes. Protein interactive network analyses revealed multiple overlapping canonical pathways within both lymphoid and myeloid cell lineages. This initial estimation of the chicken immune cell type landscape and its accompanying response will greatly aid efforts in identifying specific cell types and improving our knowledge of host response to viral infection.
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Affiliation(s)
- Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
| | - Edward S Rice
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Ashley Meyer
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Cari J Hearn
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Alec Steep
- Department of Human Genetics Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Henry D Hunt
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Melissa S Monson
- Department of Animal Science, Iowa State University, Ames, IA, USA
- Food Safety and Enteric Pathogens Research Unit, USDA, ARS, NADC, Ames, IA, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Hans H Cheng
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA.
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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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40
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Bartz J, Jung H, Wasiluk K, Zhang L, Dong X. Progress in Discovering Transcriptional Noise in Aging. Int J Mol Sci 2023; 24:3701. [PMID: 36835113 PMCID: PMC9966367 DOI: 10.3390/ijms24043701] [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: 12/31/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Increasing stochasticity is a key feature in the aging process. At the molecular level, in addition to genome instability, a well-recognized hallmark of aging, cell-to-cell variation in gene expression was first identified in mouse hearts. With the technological breakthrough in single-cell RNA sequencing, most studies performed in recent years have demonstrated a positive correlation between cell-to-cell variation and age in human pancreatic cells, as well as mouse lymphocytes, lung cells, and muscle stem cells during senescence in vitro. This phenomenon is known as the "transcriptional noise" of aging. In addition to the increasing evidence in experimental observations, progress also has been made to better define transcriptional noise. Traditionally, transcriptional noise is measured using simple statistical measurements, such as the coefficient of variation, Fano factor, and correlation coefficient. Recently, multiple novel methods have been proposed, e.g., global coordination level analysis, to define transcriptional noise based on network analysis of gene-to-gene coordination. However, remaining challenges include a limited number of wet-lab observations, technical noise in single-cell RNA sequencing, and the lack of a standard and/or optimal data analytical measurement of transcriptional noise. Here, we review the recent technological progress, current knowledge, and challenges to better understand transcriptional noise in aging.
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Affiliation(s)
- Josh Bartz
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hannim Jung
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Karen Wasiluk
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lei Zhang
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
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41
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Cohn RL, Gasek NS, Kuchel GA, Xu M. The heterogeneity of cellular senescence: insights at the single-cell level. Trends Cell Biol 2023; 33:9-17. [PMID: 35599179 PMCID: PMC9812642 DOI: 10.1016/j.tcb.2022.04.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 01/07/2023]
Abstract
Senescent cells are highly associated with aging and pathological conditions and could be targeted to slow the aging process. One commonly used marker to examine senescent cells in vivo is p16, which has led to important discoveries. Recent studies have also described new senescence markers beyond p16 and have highlighted the importance of investigating senescence heterogeneity in cell types and tissues. With the development of high-throughput technologies, such as single-cell RNA-seq and single-nucleus RNA-seq, we can examine senescent cells at the single-cell level and potentially uncover new markers. This review emphasizes that there is an urgent need to investigate senescence heterogeneity and discuss how this could be accomplished by using advanced technologies and sequencing datasets.
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Affiliation(s)
- Rachel L Cohn
- UConn Center on Aging, UConn Health, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Nathan S Gasek
- UConn Center on Aging, UConn Health, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | | | - Ming Xu
- UConn Center on Aging, UConn Health, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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42
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Hurvitz N, Elkhateeb N, Sigawi T, Rinsky-Halivni L, Ilan Y. Improving the effectiveness of anti-aging modalities by using the constrained disorder principle-based management algorithms. FRONTIERS IN AGING 2022; 3:1044038. [PMID: 36589143 PMCID: PMC9795077 DOI: 10.3389/fragi.2022.1044038] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
Aging is a complex biological process with multifactorial nature underlined by genetic, environmental, and social factors. In the present paper, we review several mechanisms of aging and the pre-clinically and clinically studied anti-aging therapies. Variability characterizes biological processes from the genome to cellular organelles, biochemical processes, and whole organs' function. Aging is associated with alterations in the degrees of variability and complexity of systems. The constrained disorder principle defines living organisms based on their inherent disorder within arbitrary boundaries and defines aging as having a lower variability or moving outside the boundaries of variability. We focus on associations between variability and hallmarks of aging and discuss the roles of disorder and variability of systems in the pathogenesis of aging. The paper presents the concept of implementing the constrained disease principle-based second-generation artificial intelligence systems for improving anti-aging modalities. The platform uses constrained noise to enhance systems' efficiency and slow the aging process. Described is the potential use of second-generation artificial intelligence systems in patients with chronic disease and its implications for the aged population.
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Affiliation(s)
- Noa Hurvitz
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Narmine Elkhateeb
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Tal Sigawi
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Lilah Rinsky-Halivni
- Braun School of Public Health, Hebrew University of Jerusalem, Jerusalem, Israel,Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Yaron Ilan
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel,*Correspondence: Yaron Ilan,
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43
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Zhang J, He M, Xie Q, Su A, Yang K, Liu L, Liang J, Li Z, Huang X, Hu J, Liu Q, Song B, Hu C, Chen L, Wang Y. Predicting In Vitro and In Vivo Anti-SARS-CoV-2 Activities of Antivirals by Intracellular Bioavailability and Biochemical Activity. ACS OMEGA 2022; 7:45023-45035. [PMID: 36530252 PMCID: PMC9753181 DOI: 10.1021/acsomega.2c05376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Cellular drug response (concentration required for obtaining 50% of a maximum cellular effect, EC50) can be predicted by the intracellular bioavailability (F ic) and biochemical activity (half-maximal inhibitory concentration, IC50) of drugs. In an ideal model, the cellular negative log of EC50 (pEC50) equals the sum of log F ic and the negative log of IC50 (pIC50). Here, we measured F ic's of remdesivir, favipiravir, and hydroxychloroquine in various cells and calculated their anti-SARS-CoV-2 EC50's. The predicted EC50's are close to the observed EC50's in vitro. When the lung concentrations of antiviral drugs are higher than the predicted EC50's in alveolar type 2 cells, the antiviral drugs inhibit virus replication in vivo, and vice versa. Overall, our results indicate that both in vitro and in vivo antiviral activities of drugs can be predicted by their intracellular bioavailability and biochemical activity without using virus. This virus-free strategy can help medicinal chemists and pharmacologists to screen antivirals during early drug discovery, especially for researchers who are not able to work in the high-level biosafety lab.
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Affiliation(s)
- Jinwen Zhang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Mingfeng He
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Qian Xie
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Ailing Su
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Kuangyang Yang
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Lichu Liu
- Institute
of Orthopedics and Traumatology, Foshan Hospital of Traditional Chinese
Medicine, Foshan528000, China
| | - Jianhui Liang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Ziqi Li
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Xiuxin Huang
- The
First Clinical College of Changsha Medical College, Changsha410219, China
| | - Jianshu Hu
- Department
of Pharmacology, University of Oxford, OxfordOX1 3QT, UK
| | - Qian Liu
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Bing Song
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
| | - Chun Hu
- Key
Laboratory of Structure-based Drug Design & Discovery (Ministry
of Education), School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Lei Chen
- School of
Life Science and Technology, Key Laboratory of Developmental Genes
and Human Disease, Southeast University, Nanjing210096, China
| | - Yan Wang
- Center
for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, China
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Stoeger T, Grant RA, McQuattie-Pimentel AC, Anekalla KR, Liu SS, Tejedor-Navarro H, Singer BD, Abdala-Valencia H, Schwake M, Tetreault MP, Perlman H, Balch WE, Chandel NS, Ridge KM, Sznajder JI, Morimoto RI, Misharin AV, Budinger GRS, Nunes Amaral LA. Aging is associated with a systemic length-associated transcriptome imbalance. NATURE AGING 2022; 2:1191-1206. [PMID: 37118543 PMCID: PMC10154227 DOI: 10.1038/s43587-022-00317-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/21/2022] [Indexed: 12/14/2022]
Abstract
Aging is among the most important risk factors for morbidity and mortality. To contribute toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data from multiple studies. Here, we show that transcript length alone explains most transcriptional changes observed with aging in mice and humans. We present three lines of evidence supporting the biological importance of the uncovered transcriptome imbalance. First, in vertebrates the length association primarily displays a lower relative abundance of long transcripts in aging. Second, eight antiaging interventions of the Interventions Testing Program of the National Institute on Aging can counter this length association. Third, we find that in humans and mice the genes with the longest transcripts enrich for genes reported to extend lifespan, whereas those with the shortest transcripts enrich for genes reported to shorten lifespan. Our study opens fundamental questions on aging and the organization of transcriptomes.
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Affiliation(s)
- Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA.
| | - Rogan A Grant
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | | | - Kishore R Anekalla
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Sophia S Liu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | | | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, IL, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Michael Schwake
- Department of Neurology, Northwestern University, Evanston, IL, USA
- Faculty of Chemistry, University of Bielefeld, Bielefeld, Germany
| | - Marie-Pier Tetreault
- Division of Gastroenterology and Hepatology, Northwestern University, Evanston, IL, USA
| | - Harris Perlman
- Division of Rheumatology, Northwestern University, Evanston, IL, USA
| | | | - Navdeep S Chandel
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, USA.
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - Luis A Nunes Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA.
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45
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Maughan EF, Hynds RE, Pennycuick A, Nigro E, Gowers KH, Denais C, Gómez-López S, Lazarus KA, Orr JC, Pearce DR, Clarke SE, Lee DDH, Woodall MN, Masonou T, Case KM, Teixeira VH, Hartley BE, Hewitt RJ, Al Yaghchi C, Sandhu GS, Birchall MA, O’Callaghan C, Smith CM, De Coppi P, Butler CR, Janes SM. Cell-intrinsic differences between human airway epithelial cells from children and adults. iScience 2022; 25:105409. [PMID: 36388965 PMCID: PMC9664344 DOI: 10.1016/j.isci.2022.105409] [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: 02/01/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The airway epithelium is a protective barrier that is maintained by the self-renewal and differentiation of basal stem cells. Increasing age is a principle risk factor for chronic lung diseases, but few studies have explored age-related molecular or functional changes in the airway epithelium. We retrieved epithelial biopsies from histologically normal tracheobronchial sites from pediatric and adult donors and compared their cellular composition and gene expression profile (in laser capture-microdissected whole epithelium, fluorescence-activated cell-sorted basal cells, and basal cells in cell culture). Histologically, pediatric and adult tracheobronchial epithelium was similar in composition. We observed age-associated changes in RNA sequencing studies, including higher interferon-associated gene expression in pediatric epithelium. In cell culture, pediatric cells had higher colony formation ability, sustained in vitro growth, and outcompeted adult cells in a direct competitive proliferation assay. Our results demonstrate cell-intrinsic differences between airway epithelial cells from children and adults in both homeostatic and proliferative states.
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Affiliation(s)
- Elizabeth F. Maughan
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Robert E. Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Adam Pennycuick
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Ersilia Nigro
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Kate H.C. Gowers
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Celine Denais
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Sandra Gómez-López
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Kyren A. Lazarus
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Jessica C. Orr
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - David R. Pearce
- University College London Cancer Institute, University College London, London WC1E 6DD, UK
| | - Sarah E. Clarke
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Dani Do Hyang Lee
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Maximillian N.J. Woodall
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Tereza Masonou
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Katie-Marie Case
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Vitor H. Teixeira
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | | | | | - Chadwan Al Yaghchi
- The National Centre for Airway Reconstruction, Department of Otolaryngology, Charing Cross Hospital, London W6 8RF, UK
| | - Gurpreet S. Sandhu
- The National Centre for Airway Reconstruction, Department of Otolaryngology, Charing Cross Hospital, London W6 8RF, UK
| | - Martin A. Birchall
- University College London Ear Institute, University College London, London WC1X 8EE, UK
| | - Christopher O’Callaghan
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Claire M. Smith
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Paolo De Coppi
- Stem Cell and Regenerative Medicine Section, University College London Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Colin R. Butler
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
- Tracheal Service, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Sam M. Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
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Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X, Ren B. Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain. Cell Res 2022; 32:1008-1021. [PMID: 36207411 PMCID: PMC9652396 DOI: 10.1038/s41422-022-00719-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/21/2022] [Indexed: 01/31/2023] Open
Abstract
Loss of heterochromatin has been implicated as a cause of pre-mature aging and age-associated decline in organ functions in mammals; however, the specific cell types and gene loci affected by this type of epigenetic change have remained unclear. To address this knowledge gap, we probed chromatin accessibility at single-cell resolution in the brains, hearts, skeletal muscles, and bone marrows from young, middle-aged, and old mice, and assessed age-associated changes at 353,126 candidate cis-regulatory elements (cCREs) across 32 major cell types. Unexpectedly, we detected increased chromatin accessibility within specific heterochromatin domains in old mouse excitatory neurons. The gain of chromatin accessibility at these genomic loci was accompanied by the cell-type-specific loss of heterochromatin and activation of LINE1 elements. Immunostaining further confirmed the loss of the heterochromatin mark H3K9me3 in the excitatory neurons but not in inhibitory neurons or glial cells. Our results reveal the cell-type-specific changes in chromatin landscapes in old mice and shed light on the scope of heterochromatin loss in mammalian aging.
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Affiliation(s)
- Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- School of Life Sciences, Westlake University, Hangzhou, China.
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Chenxu Zhu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Steven Francis Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Liqi Tong
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA.
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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47
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Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space. Nat Commun 2022; 13:6118. [PMID: 36253379 PMCID: PMC9574176 DOI: 10.1038/s41467-022-33758-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Computational tools for integrative analyses of diverse single-cell experiments are facing formidable new challenges including dramatic increases in data scale, sample heterogeneity, and the need to informatively cross-reference new data with foundational datasets. Here, we present SCALEX, a deep-learning method that integrates single-cell data by projecting cells into a batch-invariant, common cell-embedding space in a truly online manner (i.e., without retraining the model). SCALEX substantially outperforms online iNMF and other state-of-the-art non-online integration methods on benchmark single-cell datasets of diverse modalities, (e.g., single-cell RNA sequencing, scRNA-seq, single-cell assay for transposase-accessible chromatin use sequencing, scATAC-seq), especially for datasets with partial overlaps, accurately aligning similar cell populations while retaining true biological differences. We showcase SCALEX's advantages by constructing continuously expandable single-cell atlases for human, mouse, and COVID-19 patients, each assembled from diverse data sources and growing with every new data. The online data integration capacity and superior performance makes SCALEX particularly appropriate for large-scale single-cell applications to build upon previous scientific insights.
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48
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Liu S, Iorgulescu JB, Li S, Borji M, Barrera-Lopez IA, Shanmugam V, Lyu H, Morriss JW, Garcia ZN, Murray E, Reardon DA, Yoon CH, Braun DA, Livak KJ, Wu CJ, Chen F. Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response. Immunity 2022; 55:1940-1952.e5. [PMID: 36223726 PMCID: PMC9745674 DOI: 10.1016/j.immuni.2022.09.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/21/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022]
Abstract
T cells mediate antigen-specific immune responses to disease through the specificity and diversity of their clonotypic T cell receptors (TCRs). Determining the spatial distributions of T cell clonotypes in tissues is essential to understanding T cell behavior, but spatial sequencing methods remain unable to profile the TCR repertoire. Here, we developed Slide-TCR-seq, a 10-μm-resolution method, to sequence whole transcriptomes and TCRs within intact tissues. We confirmed the ability of Slide-TCR-seq to map the characteristic locations of T cells and their receptors in mouse spleen. In human lymphoid germinal centers, we identified spatially distinct TCR repertoires. Profiling T cells in renal cell carcinoma and melanoma specimens revealed heterogeneous immune responses: T cell states and infiltration differed intra- and inter-clonally, and adjacent tumor and immune cells exhibited distinct gene expression. Altogether, our method yields insights into the spatial relationships between clonality, neighboring cell types, and gene expression that drive T cell responses.
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Affiliation(s)
- Sophia Liu
- Biophysics Program, Harvard University, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J Bryan Iorgulescu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mehdi Borji
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Vignesh Shanmugam
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Haoxiang Lyu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Julia W Morriss
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zoe N Garcia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David A Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles H Yoon
- Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David A Braun
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Yale Center of Cellular and Molecular Oncology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Stem Cell Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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49
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Harris ZM, Sun Y, Joerns J, Clark B, Hu B, Korde A, Sharma L, Shin HJ, Manning EP, Placek L, Unutmaz D, Stanley G, Chun H, Sauler M, Rajagopalan G, Zhang X, Kang MJ, Koff JL. Epidermal Growth Factor Receptor Inhibition Is Protective in Hyperoxia-Induced Lung Injury. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9518592. [PMID: 36193076 PMCID: PMC9526641 DOI: 10.1155/2022/9518592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 01/01/2023]
Abstract
Aims Studies have linked severe hyperoxia, or prolonged exposure to very high oxygen levels, with worse clinical outcomes. This study investigated the role of epidermal growth factor receptor (EGFR) in hyperoxia-induced lung injury at very high oxygen levels (>95%). Results Effects of severe hyperoxia (100% oxygen) were studied in mice with genetically inhibited EGFR and wild-type littermates. Despite the established role of EGFR in lung repair, EGFR inhibition led to improved survival and reduced acute lung injury, which prompted an investigation into this protective mechanism. Endothelial EGFR genetic knockout did not confer protection. EGFR inhibition led to decreased levels of cleaved caspase-3 and poly (ADP-ribosyl) polymerase (PARP) and decreased terminal dUTP nick end labeling- (TUNEL-) positive staining in alveolar epithelial cells and reduced ERK activation, which suggested reduced apoptosis in vivo. EGFR inhibition decreased hyperoxia (95%)-induced apoptosis and ERK in murine alveolar epithelial cells in vitro, and CRISPR-mediated EGFR deletion reduced hyperoxia-induced apoptosis and ERK in human alveolar epithelial cells in vitro. Innovation. This work defines a protective role of EGFR inhibition to decrease apoptosis in lung injury induced by 100% oxygen. This further characterizes the complex role of EGFR in acute lung injury and outlines a novel hyperoxia-induced cell death pathway that warrants further study. Conclusion In conditions of severe hyperoxia (>95% for >24 h), EGFR inhibition led to improved survival, decreased lung injury, and reduced cell death. These findings further elucidate the complex role of EGFR in acute lung injury.
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Affiliation(s)
- Zachary M. Harris
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Ying Sun
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - John Joerns
- Division of Pulmonary and Critical Care; Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA 75390
| | - Brian Clark
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Buqu Hu
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Asawari Korde
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Hyeon Jun Shin
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Edward P. Manning
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Lindsey Placek
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Derya Unutmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Gail Stanley
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Hyung Chun
- Section of Cardiovascular Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Maor Sauler
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Govindarajan Rajagopalan
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Xuchen Zhang
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Min-Jong Kang
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
| | - Jonathan L. Koff
- Section of Pulmonary, Critical Care, and Sleep Medicine; Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA 06510
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50
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Abstract
Ageing leads to profound alterations in the immune system and increases susceptibility to some chronic, infectious and autoimmune diseases. In recent years, widespread application of single-cell techniques has enabled substantial progress in our understanding of the ageing immune system. These comprehensive approaches have expanded and detailed the current views of ageing and immunity. Here we review a body of recent studies that explored how the immune system ages using unbiased profiling techniques at single-cell resolution. Specifically, we discuss an emergent understanding of age-related alterations in innate and adaptive immune cell populations, antigen receptor repertoires and immune cell-supporting microenvironments of the peripheral tissues. Focusing on the results obtained in mice and humans, we describe the multidimensional data that align with established concepts of immune ageing as well as novel insights emerging from these studies. We further discuss outstanding questions in the field and highlight techniques that will advance our understanding of immune ageing in the future.
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Affiliation(s)
- Denis A Mogilenko
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Irina Shchukina
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
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