1
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Tao M, Chen J, Cui C, Xu Y, Xu J, Shi Z, Yun J, Zhang J, Ou GZ, Liu C, Chen Y, Zhu ZR, Pan R, Xu S, Chen XX, Rokas A, Zhao Y, Wang S, Huang J, Shen XX. Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. NATURE AGING 2024:10.1038/s43587-024-00641-z. [PMID: 38834883 DOI: 10.1038/s43587-024-00641-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/02/2024] [Indexed: 06/06/2024]
Abstract
Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.
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Affiliation(s)
- Mei Tao
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China
| | - Jiani Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chunlai Cui
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yandong Xu
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Jingxiu Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zheyi Shi
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiaqi Yun
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junwei Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Zheng Ou
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeng-Rong Zhu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Suhong Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xue-Xin Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yang Zhao
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Sibao Wang
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Jianhua Huang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China.
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China.
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2
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Ma F, Zheng C. Single-cell phylotranscriptomics of developmental and cell type evolution. Trends Genet 2024; 40:495-510. [PMID: 38490933 DOI: 10.1016/j.tig.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/17/2024]
Abstract
Single-cell phylotranscriptomics is an emerging tool to reveal the molecular and cellular mechanisms of evolution. We summarize its utility in studying the hourglass pattern of ontogenetic evolution and for understanding the evolutionary history of cell types. The developmental hourglass model suggests that the mid-embryonic stage is the most conserved period of development across species, which is supported by morphological and molecular studies. Single-cell phylotranscriptomic analysis has revealed previously underappreciated heterogeneity in transcriptome ages among lineages and cell types throughout development, and has identified the lineages and tissues that drive the whole-organism hourglass pattern. Single-cell transcriptome age analyses also provide important insights into the origin of germ layers, the different selective forces on tissues during adaptation, and the evolutionary relationships between cell types.
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Affiliation(s)
- Fuqiang Ma
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
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3
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Chien JF, Liu H, Wang BA, Luo C, Bartlett A, Castanon R, Johnson ND, Nery JR, Osteen J, Li J, Altshul J, Kenworthy M, Valadon C, Liem M, Claffey N, O'Connor C, Seeker LA, Ecker JR, Behrens MM, Mukamel EA. Cell-type-specific effects of age and sex on human cortical neurons. Neuron 2024:S0896-6273(24)00360-X. [PMID: 38838671 DOI: 10.1016/j.neuron.2024.05.013] [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: 11/29/2023] [Revised: 03/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
Altered transcriptional and epigenetic regulation of brain cell types may contribute to cognitive changes with advanced age. Using single-nucleus multi-omic DNA methylation and transcriptome sequencing (snmCT-seq) in frontal cortex from young adult and aged donors, we found widespread age- and sex-related variation in specific neuron types. The proportion of inhibitory SST- and VIP-expressing neurons was reduced in aged donors. Excitatory neurons had more profound age-related changes in their gene expression and DNA methylation than inhibitory cells. Hundreds of genes involved in synaptic activity, including EGR1, were less expressed in aged adults. Genes located in subtelomeric regions increased their expression with age and correlated with reduced telomere length. We further mapped cell-type-specific sex differences in gene expression and X-inactivation escape genes. Multi-omic single-nucleus epigenomes and transcriptomes provide new insight into the effects of age and sex on human neurons.
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Affiliation(s)
- Jo-Fan Chien
- Department of Physics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Bang-An Wang
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Rosa Castanon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Nicholas D Johnson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Julia Osteen
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Cynthia Valadon
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA
| | - Michelle Liem
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Caz O'Connor
- Flow Cytometry Core Facility, Salk Institute, La Jolla, CA 92037, USA
| | - Luise A Seeker
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA.
| | - M Margarita Behrens
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA; Computational Neurobiology Laboratory, Salk Institute, La Jolla, CA 92037, USA.
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA.
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4
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Gao SM, Qi Y, Zhang Q, Guan Y, Lee YT, Ding L, Wang L, Mohammed AS, Li H, Fu Y, Wang MC. Aging atlas reveals cell-type-specific effects of pro-longevity strategies. NATURE AGING 2024:10.1038/s43587-024-00631-1. [PMID: 38816550 DOI: 10.1038/s43587-024-00631-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/10/2024] [Indexed: 06/01/2024]
Abstract
Organismal aging involves functional declines in both somatic and reproductive tissues. Multiple strategies have been discovered to extend lifespan across species. However, how age-related molecular changes differ among various tissues and how those lifespan-extending strategies slow tissue aging in distinct manners remain unclear. Here we generated the transcriptomic Cell Atlas of Worm Aging (CAWA, http://mengwanglab.org/atlas ) of wild-type and long-lived strains. We discovered cell-specific, age-related molecular and functional signatures across all somatic and germ cell types. We developed transcriptomic aging clocks for different tissues and quantitatively determined how three different pro-longevity strategies slow tissue aging distinctively. Furthermore, through genome-wide profiling of alternative polyadenylation (APA) events in different tissues, we discovered cell-type-specific APA changes during aging and revealed how these changes are differentially affected by the pro-longevity strategies. Together, this study offers fundamental molecular insights into both somatic and reproductive aging and provides a valuable resource for in-depth understanding of the diversity of pro-longevity mechanisms.
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Affiliation(s)
- Shihong Max Gao
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yanyan Qi
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Qinghao Zhang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Youchen Guan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Molecular and Cellular Biology Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Yi-Tang Lee
- Integrative Program of Molecular and Biochemical Science, Baylor College of Medicine, Houston, TX, USA
| | - Lang Ding
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Graduate Program in Chemical, Physical & Structural Biology, Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Aaron S Mohammed
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA
| | - Hongjie Li
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Yusi Fu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, USA.
| | - Meng C Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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5
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Miyamoto T, Hedjazi S, Miyamoto C, Amrein H. Drosophila Neuronal Glucose 6 Phosphatase is a Modulator of Neuropeptide Release that Regulates Muscle Glycogen Stores via FMRFamide Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.28.568950. [PMID: 38077084 PMCID: PMC10705280 DOI: 10.1101/2023.11.28.568950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Neuropeptides (NPs) and their cognate receptors are critical effectors of diverse physiological processes and behaviors. We recently reported of a non-canonical function of the Drosophila Glucose-6-Phosphatase ( G6P ) gene in a subset of neurosecretory cells in the CNS that governs systemic glucose homeostasis in food deprived flies. Here, we show that G6P expressing neurons define 6 groups of neuropeptide secreting cells, 4 in the brain and 2 in the thoracic ganglion. Using the glucose homeostasis phenotype as a screening tool, we find that neurons located in the thoracic ganglion expressing FMRFamide neuropeptides ( FMRFa G6P neurons) are necessary and sufficient to maintain systemic glucose homeostasis in starved flies. We further show that G6P is essential in FMRFa G6P neurons for attaining a prominent Golgi apparatus and secreting neuropeptides efficiently. Finally, we establish that G6P dependent FMRFa signaling is essential for the build-up of glycogen stores in the jump muscle which expresses the receptor for FMRFamides. We propose a general model in which the main role of G6P is to counteract glycolysis in peptidergic neurons for the purpose of optimizing the intracellular environment best suited for the expansion of the Golgi apparatus, boosting release of neuropeptides and enhancing signaling to respective target tissues expressing cognate receptors. SIGNIFICANCE STATEMENT Glucose-6-phosphtase (G6P) is a critical enzyme in sugar synthesis and catalyzes the final step in glucose production. In Drosophila - and insects in general - where trehalose is the circulating sugar and Trehalose phosphate synthase, and not G6P, is used for sugar production, G6P has adopted a novel and unique role in peptidergic neurons in the CNS. Interestingly, flies lacking G6P show diminished Neuropeptide secretions and have a smaller Golgi apparatus in peptidergic neurons. It is hypothesized that the role of G6P is to counteract glycolysis, thereby creating a cellular environment that is more amenable to efficient neuropeptide secretion.
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6
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Park YJ, Lu TC, Jackson T, Goodman LD, Ran L, Chen J, Liang CY, Harrison E, Ko C, Hsu AL, Yamamoto S, Qi Y, Bellen HJ, Li H. Whole organism snRNA-seq reveals systemic peripheral changes in Alzheimer's Disease fly models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.10.584317. [PMID: 38559164 PMCID: PMC10979927 DOI: 10.1101/2024.03.10.584317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Peripheral tissues become disrupted in Alzheimer's Disease (AD). However, a comprehensive understanding of how the expression of AD-associated toxic proteins, Aβ42 and Tau, in neurons impacts the periphery is lacking. Using Drosophila, a prime model organism for studying aging and neurodegeneration, we generated the Alzheimer's Disease Fly Cell Atlas (AD-FCA): whole-organism single-nucleus transcriptomes of 219 cell types from adult flies neuronally expressing human Aβ42 or Tau. In-depth analyses and functional data reveal impacts on peripheral sensory neurons by Aβ42 and on various non-neuronal peripheral tissues by Tau, including the gut, fat body, and reproductive system. This novel AD atlas provides valuable insights into potential biomarkers and the intricate interplay between the nervous system and peripheral tissues in response to AD-associated proteins.
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Affiliation(s)
- Ye-Jin Park
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tzu-Chiao Lu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tyler Jackson
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Cancer Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsey D Goodman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Lindsey Ran
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiaye Chen
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chung-Yi Liang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Erin Harrison
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christina Ko
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ao-Lin Hsu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan, Ann Arbor, MI 28109, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yanyan Qi
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongjie Li
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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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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8
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat Methods 2024:10.1038/s41592-024-02191-z. [PMID: 38366243 DOI: 10.1038/s41592-024-02191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA.
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9
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [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: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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10
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Qian Q, Niwa R. Endocrine Regulation of Aging in the Fruit Fly Drosophila melanogaster. Zoolog Sci 2024; 41:4-13. [PMID: 38587512 DOI: 10.2108/zs230056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/16/2023] [Indexed: 04/09/2024]
Abstract
The past few decades have witnessed increasing research clarifying the role of endocrine signaling in the regulation of aging in both vertebrates and invertebrates. Studies using the model organism fruit fly Drosophila melanogaster have largely advanced our understanding of evolutionarily conserved mechanisms in the endocrinology of aging and anti-aging. Mutations in single genes involved in endocrine signaling modify lifespan, as do alterations of endocrine signaling in a tissue- or cell-specific manner, highlighting a central role of endocrine signaling in coordinating the crosstalk between tissues and cells to determine the pace of aging. Here, we review the current landscape of research in D. melanogaster that offers valuable insights into the endocrine-governed mechanisms which influence lifespan and age-related physiology.
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Affiliation(s)
- Qingyin Qian
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryusuke Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan,
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11
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Wen Y, Chen H, Wang Y, Sun Y, Dou F, Du X, Liu T, Chen C. Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging. Hereditas 2024; 161:3. [PMID: 38173016 PMCID: PMC10763334 DOI: 10.1186/s41065-023-00306-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Vascular aging is an important pathophysiological basis for the senescence of various organs and systems in the human body, and it is a common pathogenetic trigger for many chronic diseases in the elderly. METHODS The extracellular vesicles (EVs) from young and aged umbilical vein endothelial cells were isolated and identified by qPCR the differential expression levels of 47 mRNAs of genes closely related to aging in the two groups. RESULTS There were significant differences in the expression levels of 18 genes (we noted upregulation in PLA2G12A, TP53BP1, CD144, PDE11A, FPGT, SERPINB4, POLD1, and PPFIBP2 and downregulation in ATP2C2, ROBO2, RRM2, GUCY1B1, NAT1-14, VEGFR2, WTAPP1, CD146, DMC1, and GRIK2). Subsequent qPCR identification of the above-mentioned genes in PBMCs and plasma-EVs from the various age groups revealed that the trend in expression levels in peripheral blood plasma-EVs of the different age groups was approximately the same as that in PBMCs. Of these mRNAs, the expression of four genes-PLA2G12A, TP53BP1, OPRL1, and KIAA0895-was commensurate with increasing age. In contradistinction, the expression trend of four genes (CREG1, PBX1, CD34, and SLIT2) was inversely proportional to the increase in age. Finally, by taking their intersection, we determined that the expression of TP53BP1 was upregulated with increasing human age and that CD34 and PBX1 were downregulated with increasing age. CONCLUSION Our study indicates that human peripheral blood plasma-EV-derived TP53BP1, CD34, and PBX1 potentially comprise a noninvasive biomarker for assessing and predicting vascular aging.
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Affiliation(s)
- Yichao Wen
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China
| | - Haiyang Chen
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China
| | - Yu Wang
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Yiqing Sun
- Eberly College of Science, Penn State University, University Park, PA, USA
| | - Fangfang Dou
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China
| | - Xiling Du
- School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Te Liu
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China.
| | - Chuan Chen
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, Shanghai, 200031, China.
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12
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Zhou C, Guo Q, Lin J, Wang M, Zeng Z, Li Y, Li X, Xiang Y, Liang Q, Liu J, Wu T, Zeng Y, He S, Wang S, Zeng H, Liang X. Single-Cell Atlas of Human Ovaries Reveals The Role Of The Pyroptotic Macrophage in Ovarian Aging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305175. [PMID: 38036420 PMCID: PMC10811476 DOI: 10.1002/advs.202305175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/10/2023] [Indexed: 12/02/2023]
Abstract
Female fecundity declines in a nonlinear manner with age during the reproductive years, even as ovulatory cycles continue, which reduces female fertility, disrupts metabolic homeostasis, and eventually induces various chronic diseases. Despite this, the aging-related cellular and molecular changes in human ovaries that occur during these reproductive years have not been elucidated. Here, single-cell RNA sequencing (scRNA-seq) of human ovaries is performed from different childbearing ages and reveals that the activation of the pyroptosis pathway increased with age, mainly in macrophages. The enrichment of pyroptotic macrophages leads to a switch from a tissue-resident macrophage (TRM)-involve immunoregulatory microenvironment in young ovaries to a pyroptotic monocyte-derived macrophage (MDM)-involved proinflammatory microenvironment in middle-aged ovaries. This remolded ovarian immuno-microenvironment further promotes stromal cell senescence and accelerated reproductive decline. This hypothesis is validated in a series of cell and animal experiments using GSDMD-KO mice. In conclusion, the work expands the current understanding of the ovarian aging process by illustrating a pyroptotic macrophage-involved immune mechanism, which has important implications for the development of novel strategies to delay senescence and promote reproductive health.
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Affiliation(s)
- Chuanchuan Zhou
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Qi Guo
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Jiayu Lin
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- Department of Obstetrics and GynaecologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong S.A.R.999077China
| | - Meng Wang
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- Reproductive Medicine CenterThe First People's Hospital of FoshanFoshan528000China
| | - Zhi Zeng
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Yujie Li
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Xiaolan Li
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
| | - Yuting Xiang
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- Department of Obstetrics and GynecologyAffiliated Dongguan HospitalSouthern Medical UniversityDongguan523795China
| | - Qiqi Liang
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Jiawen Liu
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Taibao Wu
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Yanyan Zeng
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Shanyang He
- Department of GynecologyGuangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhou519041China
| | - Sanfeng Wang
- Department of GynecologyGuangdong Women and Children Hospital521 Xing Nan RoadGuangzhouGuangdong511400China
| | - Haitao Zeng
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
| | - Xiaoyan Liang
- Center of Reproductive MedicineThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
- GuangDong Engineering Technology Research Center of Fertility PreservationGuangzhouGuangdong510080China
- Biomedical Innovation CenterThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510080China
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13
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Han JDJ. The ticking of aging clocks. Trends Endocrinol Metab 2024; 35:11-22. [PMID: 37880054 DOI: 10.1016/j.tem.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Computational models that measure biological age and aging rate regardless of chronological age are called aging clocks. The underlying counting mechanisms of the intrinsic timers of these clocks are still unclear. Molecular mediators and determinants of aging rate point to the key roles of DNA damage, epigenetic drift, and inflammation. Persistent DNA damage leads to cellular senescence and the senescence-associated secretory phenotype (SASP), which induces cytotoxic immune cell infiltration; this further induces DNA damage through reactive oxygen and nitrogen species (RONS). I discuss the possibility that DNA damage (or the response to it, including epigenetic changes) is the fundamental counting unit of cell cycles and cellular senescence, that ultimately accounts for cell composition changes and functional decline in tissues, as well as the key intervention points.
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Affiliation(s)
- Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China; Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China; International Center for Aging and Cancer (ICAC), The First Affiliated Hospital, Hainan Medical University, Haikou, China.
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14
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Tower J. Markers and mechanisms of death in Drosophila. FRONTIERS IN AGING 2023; 4:1292040. [PMID: 38149028 PMCID: PMC10749947 DOI: 10.3389/fragi.2023.1292040] [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: 09/10/2023] [Accepted: 11/30/2023] [Indexed: 12/28/2023]
Abstract
Parameters correlated with age and mortality in Drosophila melanogaster include decreased negative geotaxis and centrophobism behaviors, decreased climbing and walking speed, and darkened pigments in oenocytes and eye. Cessation of egg laying predicts death within approximately 5 days. Endogenous green fluorescence in eye and body increases hours prior to death. Many flies exhibit erratic movement hours before death, often leading to falls. Loss of intestinal barrier integrity (IBI) is assayed by feeding blue dye ("Smurf" phenotype), and Smurf flies typically die within 0-48 h. Some studies report most flies exhibit Smurf, whereas multiple groups report most flies die without exhibiting Smurf. Transgenic reporters containing heat shock gene promoters and innate immune response gene promoters progressively increase expression with age, and partly predict remaining life span. Innate immune reporters increase with age in every fly, prior to any Smurf phenotype, in presence or absence of antibiotics. Many flies die on their side or supine (on their back) position. The data suggest three mechanisms for death of Drosophila. One is loss of IBI, as revealed by Smurf assay. The second is nervous system malfunction, leading to erratic behavior, locomotor malfunction, and falls. The aged fly is often unable to right itself after a fall to a side-ways or supine position, leading to inability to access the food and subsequent dehydration/starvation. Finally, some flies die upright without Smurf phenotype, suggesting a possible third mechanism. The frequency of these mechanisms varies between strains and culture conditions, which may affect efficacy of life span interventions.
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Affiliation(s)
- John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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15
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Katheder NS, Browder KC, Chang D, De Maziere A, Kujala P, van Dijk S, Klumperman J, Lu TC, Li H, Lai Z, Sangaraju D, Jasper H. Nicotinic acetylcholine receptor signaling maintains epithelial barrier integrity. eLife 2023; 12:e86381. [PMID: 38063293 PMCID: PMC10764009 DOI: 10.7554/elife.86381] [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: 01/23/2023] [Accepted: 10/31/2023] [Indexed: 01/04/2024] Open
Abstract
Disruption of epithelial barriers is a common disease manifestation in chronic degenerative diseases of the airways, lung, and intestine. Extensive human genetic studies have identified risk loci in such diseases, including in chronic obstructive pulmonary disease (COPD) and inflammatory bowel diseases. The genes associated with these loci have not fully been determined, and functional characterization of such genes requires extensive studies in model organisms. Here, we report the results of a screen in Drosophila melanogaster that allowed for rapid identification, validation, and prioritization of COPD risk genes that were selected based on risk loci identified in human genome-wide association studies (GWAS). Using intestinal barrier dysfunction in flies as a readout, our results validate the impact of candidate gene perturbations on epithelial barrier function in 56% of the cases, resulting in a prioritized target gene list. We further report the functional characterization in flies of one family of these genes, encoding for nicotinic acetylcholine receptor (nAchR) subunits. We find that nAchR signaling in enterocytes of the fly gut promotes epithelial barrier function and epithelial homeostasis by regulating the production of the peritrophic matrix. Our findings identify COPD-associated genes critical for epithelial barrier maintenance, and provide insight into the role of epithelial nAchR signaling for homeostasis.
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Affiliation(s)
- Nadja S Katheder
- Regenerative Medicine, Genentech, South San Francisco, United States
| | - Kristen C Browder
- Regenerative Medicine, Genentech, South San Francisco, United States
| | - Diana Chang
- Human Genetics, Genentech, South San Francisco, United States
| | - Ann De Maziere
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Pekka Kujala
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Suzanne van Dijk
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Tzu-Chiao Lu
- Huffington Center on Aging, Baylor College of Medicine, Houston, United States
| | - Hongjie Li
- Huffington Center on Aging, Baylor College of Medicine, Houston, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Zijuan Lai
- Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, United States
| | - Dewakar Sangaraju
- Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, United States
| | - Heinrich Jasper
- Regenerative Medicine, Genentech, South San Francisco, United States
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16
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Sun X, Shen J, Perrimon N, Kong X, Wang D. The endoribonuclease Arlr is required to maintain lipid homeostasis by downregulating lipolytic genes during aging. Nat Commun 2023; 14:6254. [PMID: 37803019 PMCID: PMC10558556 DOI: 10.1038/s41467-023-42042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
While disorders in lipid metabolism have been associated with aging and age-related diseases, how lipid metabolism is regulated during aging is poorly understood. Here, we characterize the Drosophila endoribonuclease CG2145, an ortholog of mammalian EndoU that we named Age-related lipid regulator (Arlr), as a regulator of lipid homeostasis during aging. In adult adipose tissues, Arlr is necessary for maintenance of lipid storage in lipid droplets (LDs) as flies age, a phenotype that can be rescued by either high-fat or high-glucose diet. Interestingly, RNA-seq of arlr mutant adipose tissues and RIP-seq suggest that Arlr affects lipid metabolism through the degradation of the mRNAs of lipolysis genes - a model further supported by the observation that knockdown of Lsd-1, regucalcin, yip2 or CG5162, which encode genes involved in lipolysis, rescue the LD defects of arlr mutants. In addition, we characterize DendoU as a functional paralog of Arlr and show that human ENDOU can rescue arlr mutants. Altogether, our study reveals a role of ENDOU-like endonucleases as negative regulator of lipolysis.
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Affiliation(s)
- Xiaowei Sun
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Xue Kong
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Dan Wang
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China.
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17
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Izquierdo JM. Chromatin-transcription interface: The secret of eternal youth? Aging Cell 2023; 22:e13927. [PMID: 37427688 PMCID: PMC10497848 DOI: 10.1111/acel.13927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2023] Open
Abstract
In their recent study in Nature, Debès et al. report an increase in RNA polymerase II (Pol II)-mediated transcriptional elongation speed associated with chromatin remodeling during aging in four metazoan animals, two human cell lines, and human blood. Their findings might help us understand why we age through evolutionarily conserved essential processes, and open a window to the molecular and physiological mechanisms influencing healthspan, lifespan and/or longevity.
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Affiliation(s)
- José M. Izquierdo
- Centro de Biología Molecular Severo OchoaConsejo Superior de Investigaciones Científicas‐Universidad Autónoma de Madrid (CSIC‐UAM)MadridSpain
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18
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Wang M, Ho MS. Profiling neurotransmitter-evoked glial responses by RNA-sequencing analysis. Front Neural Circuits 2023; 17:1252759. [PMID: 37645568 PMCID: PMC10461064 DOI: 10.3389/fncir.2023.1252759] [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: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Fundamental properties of neurons and glia are distinctively different. Neurons are excitable cells that transmit information, whereas glia have long been considered as passive bystanders. Recently, the concept of tripartite synapse is proposed that glia are structurally and functionally incorporated into the synapse, the basic unit of information processing in the brains. It has then become intriguing how glia actively communicate with the presynaptic and postsynaptic compartments to influence the signal transmission. Here we present a thorough analysis at the transcriptional level on how glia respond to different types of neurotransmitters. Adult fly glia were purified from brains incubated with different types of neurotransmitters ex vivo. Subsequent RNA-sequencing analyses reveal distinct and overlapping patterns for these transcriptomes. Whereas Acetylcholine (ACh) and Glutamate (Glu) more vigorously activate glial gene expression, GABA retains its inhibitory effect. All neurotransmitters fail to trigger a significant change in the expression of their synthesis enzymes, yet Glu triggers increased expression of neurotransmitter receptors including its own and nAChRs. Expressions of transporters for GABA and Glutamate are under diverse controls from DA, GABA, and Glu, suggesting that the evoked intracellular pathways by these neurotransmitters are interconnected. Furthermore, changes in the expression of genes involved in calcium signaling also functionally predict the change in the glial activity. Finally, neurotransmitters also trigger a general metabolic suppression in glia except the DA, which upregulates a number of genes involved in transporting nutrients and amino acids. Our findings fundamentally dissect the transcriptional change in glia facing neuronal challenges; these results provide insights on how glia and neurons crosstalk in a synaptic context and underlie the mechanism of brain function and behavior.
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Affiliation(s)
| | - Margaret S. Ho
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
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