1
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Brümmer A, Bergmann S. Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs. Nat Commun 2024; 15:3786. [PMID: 38710690 DOI: 10.1038/s41467-024-48244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 04/23/2024] [Indexed: 05/08/2024] Open
Abstract
Expression quantitative trait loci (eQTL) studies typically consider exon expression of genes and discard intronic RNA sequencing reads despite their information on RNA metabolism. Here, we quantify genetic effects on exon and intron levels of genes and their ratio in lymphoblastoid cell lines, revealing thousands of cis-QTLs of each type. While genetic effects are often shared between cis-QTL types, 7814 (47%) are not detected as top cis-QTLs at exon levels. We show that exon levels preferentially capture genetic effects on transcriptional regulation, while exon-intron-ratios better detect those on co- and post-transcriptional processes. Considering all cis-QTL types substantially increases (by 71%) the number of colocalizing variants identified by genome-wide association studies (GWAS). It further allows dissecting the potential gene regulatory processes underlying GWAS associations, suggesting comparable contributions by transcriptional (50%) and co- and post-transcriptional regulation (46%) to complex traits. Overall, integrating intronic RNA sequencing reads in eQTL studies expands our understanding of genetic effects on gene regulatory processes.
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Affiliation(s)
- Anneke Brümmer
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland.
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
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2
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Soheili-Nezhad S, Ibáñez-Solé O, Izeta A, Hoeijmakers JHJ, Stoeger T. Time is ticking faster for long genes in aging. Trends Genet 2024; 40:299-312. [PMID: 38519330 PMCID: PMC11003850 DOI: 10.1016/j.tig.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 03/24/2024]
Abstract
Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.
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Affiliation(s)
- Sourena Soheili-Nezhad
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Olga Ibáñez-Solé
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ander Izeta
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Tecnun-University of Navarra, 20018 Donostia-San Sebastian, Spain.
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands; University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany; Princess Maxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands.
| | - Thomas Stoeger
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA; Potocsnak Longevity Institute, Northwestern University, Chicago, IL, USA; Simpson Querrey Lung Institute for Translational Science, Chicago, IL, USA.
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3
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Wei J, Zhang W, Jiang A, Peng H, Zhang Q, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L, Chen K, Dong B. Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids. Nat Commun 2024; 15:2395. [PMID: 38493164 PMCID: PMC10944513 DOI: 10.1038/s41467-024-46780-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Zygotic genome activation (ZGA) is a universal process in early embryogenesis of metazoan, when the quiescent zygotic nucleus initiates global transcription. However, the mechanisms related to massive genome activation and allele-specific expression (ASE) remain not well understood. Here, we develop hybrids from two deeply diverged (120 Mya) ascidian species to symmetrically document the dynamics of ZGA. We identify two coordinated ZGA waves represent early developmental and housekeeping gene reactivation, respectively. Single-cell RNA sequencing reveals that the major expression wave exhibits spatial heterogeneity and significantly correlates with cell fate. Moreover, allele-specific expression occurs in a species- rather than parent-related manner, demonstrating the divergence of cis-regulatory elements between the two species. These findings provide insights into ZGA in chordates.
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Affiliation(s)
- Jiankai Wei
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wei Zhang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - An Jiang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hongzhe Peng
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Yuting Li
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jianqing Bi
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Linting Wang
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Penghui Liu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jing Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yonghang Ge
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Liya Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Haiyan Yu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Lei Li
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shi Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119 Haibin Rd, Nansha Dist., Guangzhou, 511458, China.
| | - Bo Dong
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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4
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Baralle M, Romano M. Age-Related Alternative Splicing: Driver or Passenger in the Aging Process? Cells 2023; 12:2819. [PMID: 38132139 PMCID: PMC10742131 DOI: 10.3390/cells12242819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy;
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
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5
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Harries LW. Dysregulated RNA processing and metabolism: a new hallmark of ageing and provocation for cellular senescence. FEBS J 2023; 290:1221-1234. [PMID: 35460337 DOI: 10.1111/febs.16462] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022]
Abstract
The human genome is capable of producing hundreds of thousands of different proteins and non-coding RNAs from <20 000 genes, in a co-ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence-associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
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6
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Wang X, Guo S, Zhou H, Sun Y, Gan J, Zhang Y, Zheng W, Zhang C, Wang P, Zhi H, Gao Y, Chen X, Ning S. Pan-cancer transcriptomic analysis identified six classes of immunosenescence genes revealed molecular links between aging, immune system and cancer. Genes Immun 2023. [PMID: 36807625 DOI: 10.1038/s41435-023-00197-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 02/19/2023]
Abstract
Aging is a complex process that significantly impacts the immune system. The aging-related decline of the immune system, termed immunosenescence, can lead to disease development, including cancer. The perturbation of immunosenescence genes may characterize the associations between cancer and aging. However, the systematical characterization of immunosenescence genes in pan-cancer remains largely unexplored. In this study, we comprehensively investigated the expression of immunosenescence genes and their roles in 26 types of cancer. We developed an integrated computational pipeline to identify and characterize immunosenescence genes in cancer based on the expression profiles of immune genes and clinical information of patients. We identified 2218 immunosenescence genes that were significantly dysregulated in a wide variety of cancers. These immunosenescence genes were divided into six categories based on their relationships with aging. Besides, we assessed the importance of immunosenescence genes in clinical prognosis and identified 1327 genes serving as prognostic markers in cancers. BTN3A1, BTN3A2, CTSD, CYTIP, HIF1AN, and RASGRP1 were associated with ICB immunotherapy response and served as prognostic factors after ICB immunotherapy in melanoma. Collectively, our results furthered the understanding of the relationship between immunosenescence and cancer and provided insights into immunotherapy for patients.
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7
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Chang C, Yang Y, Zhou L, Baiyin B, Liu Z, Guo L, Ma F, Wang J, Chai Y, Shi C, Zhang W. Candidate Genes and Gene Networks Change with Age in Japanese Black Cattle by Blood Transcriptome Analysis. Genes (Basel) 2023; 14:504. [PMID: 36833431 PMCID: PMC9956108 DOI: 10.3390/genes14020504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Age is an important physiological factor that affects the metabolism and immune function of beef cattle. While there have been many studies using the blood transcriptome to study the effects of age on gene expression, few have been reported on beef cattle. To this end, we used the blood transcriptomes of Japanese black cattle at different ages as the study subjects and screened 1055, 345, and 1058 differential expressed genes (DEGs) in the calf vs. adult, adult vs. old, and calf vs. old comparison groups, respectively. The weighted co-expression network consisted of 1731 genes. Finally, blue, brown, and yellow age-specific modules were obtained, in which genes were enriched in signaling pathways related to growth and development and immune metabolic dysfunction, respectively. Protein-protein interaction (PPI) analysis showed gene interactions in each specific module, and 20 of the highest connectivity genes were chosen as potential hub genes. Finally, we identified 495, 244, and 1007 genes by exon-wide selection signature (EWSS) analysis of different comparison groups. Combining the results of hub genes, we found that VWF, PARVB, PRKCA, and TGFB1I1 could be used as candidate genes for growth and development stages of beef cattle. CORO2B and SDK1 could be used as candidate marker genes associated with aging. In conclusion, by comparing the blood transcriptome of calves, adult cattle, and old cattle, the candidate genes related to immunity and metabolism affected by age were identified, and the gene co-expression network of different age stages was constructed. It provides a data basis for exploring the growth, development, and aging of beef cattle.
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Affiliation(s)
- Chencheng Chang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yanda Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Le Zhou
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Batu Baiyin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zaixia Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lili Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Fengying Ma
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jie Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yuan Chai
- College of Agronomy Animal Husbandry and Bioengineering, Xing’an Vocational and Technical College, Ulanhot 137400, China
| | - Caixia Shi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
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8
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Resztak JA, Choe J, Nirmalan S, Wei J, Bruinsma J, Houpt R, Alazizi A, Mair-Meijers HE, Wen X, Slatcher RB, Zilioli S, Pique-Regi R, Luca F. Analysis of transcriptional changes in the immune system associated with pubertal development in a longitudinal cohort of children with asthma. Nat Commun 2023; 14:230. [PMID: 36646693 PMCID: PMC9842661 DOI: 10.1038/s41467-022-35742-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Puberty is an important developmental period marked by hormonal, metabolic and immune changes. Puberty also marks a shift in sex differences in susceptibility to asthma. Yet, little is known about the gene expression changes in immune cells that occur during pubertal development. Here we assess pubertal development and leukocyte gene expression in a longitudinal cohort of 251 children with asthma. We identify substantial gene expression changes associated with age and pubertal development. Gene expression changes between pre- and post-menarcheal females suggest a shift from predominantly innate to adaptive immunity. We show that genetic effects on gene expression change dynamically during pubertal development. Gene expression changes during puberty are correlated with gene expression changes associated with asthma and may explain sex differences in prevalence. Our results show that molecular data used to study the genetics of early onset diseases should consider pubertal development as an important factor that modifies the transcriptome.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Jane Choe
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Shreya Nirmalan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Julian Bruinsma
- Department of Psychology, Wayne State University, Detroit, MI, USA
| | - Russell Houpt
- Department of Psychology, Wayne State University, Detroit, MI, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | | | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | | | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, MI, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.
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9
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García-Pérez R, Ramirez JM, Ripoll-Cladellas A, Chazarra-Gil R, Oliveros W, Soldatkina O, Bosio M, Rognon PJ, Capella-Gutierrez S, Calvo M, Reverter F, Guigó R, Aguet F, Ferreira PG, Ardlie KG, Melé M. The landscape of expression and alternative splicing variation across human traits. Cell Genom 2022; 3:100244. [PMID: 36777183 PMCID: PMC9903719 DOI: 10.1016/j.xgen.2022.100244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022]
Abstract
Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.
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Affiliation(s)
- Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Jose Miguel Ramirez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Aida Ripoll-Cladellas
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Ruben Chazarra-Gil
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Winona Oliveros
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Oleksandra Soldatkina
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Mattia Bosio
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Paul Joris Rognon
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Department of Economics and Business, Universitat Pompeu Fabra, Barcelona, Catalonia 08005, Spain,Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia 08034, Spain
| | - Salvador Capella-Gutierrez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Miquel Calvo
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Ferran Reverter
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalonia 08003, Spain
| | | | - Pedro G. Ferreira
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal,Laboratory of Artificial Intelligence and Decision Support, INESC TEC, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal,Institute of Molecular Pathology and Immunology of the University of Porto, Institute for Research and Innovation in Health (i3s), R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | | | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Corresponding author
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10
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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. Nat Aging 2022; 2:1191-1206. [PMID: 37118543 PMCID: PMC10154227 DOI: 10.1038/s43587-022-00317-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Balashova EE, Maslov DL, Trifonova OP, Lokhov PG, Archakov AI. Metabolome Profiling in Aging Studies. Biology 2022; 11:1570. [DOI: 10.3390/biology11111570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Organism aging is closely related to systemic metabolic changes. However, due to the multilevel and network nature of metabolic pathways, it is difficult to understand these connections. Today, scientists are trying to solve this problem using one of the main approaches of metabolomics—untargeted metabolome profiling. The purpose of this publication is to review metabolomic studies based on such profiling, both in animal models and in humans. This review describes metabolites that vary significantly across age groups and include carbohydrates, amino acids, carnitines, biogenic amines, and lipids. Metabolic pathways associated with the aging process are also shown, including those associated with amino acid, lipid, and energy metabolism. The presented data reveal the mechanisms of aging and can be used as a basis for monitoring biological age and predicting age-related diseases in the early stages of their development.
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12
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Yamamoto R, Chung R, Vazquez JM, Sheng H, Steinberg PL, Ioannidis NM, Sudmant PH. Tissue-specific impacts of aging and genetics on gene expression patterns in humans. Nat Commun 2022; 13:5803. [PMID: 36192477 DOI: 10.1038/s41467-022-33509-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Age is the primary risk factor for many common human diseases. Here, we quantify the relative contributions of genetics and aging to gene expression patterns across 27 tissues from 948 humans. We show that the predictive power of expression quantitative trait loci is impacted by age in many tissues. Jointly modelling the contributions of age and genetics to transcript level variation we find expression heritability (h2) is consistent among tissues while the contribution of aging varies by >20-fold with [Formula: see text] in 5 tissues. We find that while the force of purifying selection is stronger on genes expressed early versus late in life (Medawar's hypothesis), several highly proliferative tissues exhibit the opposite pattern. These non-Medawarian tissues exhibit high rates of cancer and age-of-expression-associated somatic mutations. In contrast, genes under genetic control are under relaxed constraint. Together, we demonstrate the distinct roles of aging and genetics on expression phenotypes.
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13
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Xu J, Lan Y, Wang X, Shang K, Liu X, Wang J, Li J, Yue B, Shao M, Fan Z. Multi-omics analysis reveals the host–microbe interactions in aged rhesus macaques. Front Microbiol 2022; 13:993879. [PMID: 36238598 PMCID: PMC9551614 DOI: 10.3389/fmicb.2022.993879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Aging is a complex multifactorial process that greatly affects animal health. Multi-omics analysis is widely applied in evolutionary biology and biomedical research. However, whether multi-omics can provide sufficient information to reveal comprehensive changes in aged non-human primates remains unclear. Here, we explored changes in host–microbe interactions with aging in Chinese rhesus macaques (Macaca mulatta lasiota, CRs) using multi-omics analysis. Results showed marked changes in the oral and gut microbiomes between young and aged CRs, including significantly reduced probiotic abundance and increased pathogenic bacterial abundance in aged CRs. Notably, the abundance of Lactobacillus, which can metabolize tryptophan to produce aryl hydrocarbon receptor (AhR) ligands, was decreased in aged CRs. Consistently, metabolomics detected a decrease in the plasma levels of AhR ligands. In addition, free fatty acid, acyl carnitine, heparin, 2-(4-hydroxyphenyl) propionic acid, and docosahexaenoic acid ethyl ester levels were increased in aged CRs, which may contribute to abnormal fatty acid metabolism and cardiovascular disease. Transcriptome analysis identified changes in the expression of genes associated with tryptophan metabolism and inflammation. In conclusion, many potential links among different omics were found, suggesting that aged CRs face multiple metabolic problems, immunological disorders, and oral and gut diseases. We determined that tryptophan metabolism is critical for the physiological health of aged CRs. Our findings demonstrate the value of multi-omics analyses in revealing host–microbe interactions in non-human primates and suggest that similar approaches could be applied in evolutionary and ecological research of other species.
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Affiliation(s)
- Jue Xu
- West China School of Public Health and West China Fourth Hospital, Chengdu, Sichuan, China
| | - Yue Lan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinqi Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Ke Shang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Xu Liu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiao Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Meiying Shao
- West China School of Public Health and West China Fourth Hospital, Chengdu, Sichuan, China
- *Correspondence: Meiying Shao,
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Zhenxin Fan,
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14
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Han Y, Wennersten SA, Wright JM, Ludwig RW, Lau E, Lam MPY. Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging. Am J Physiol Heart Circ Physiol 2022; 323:H538-H558. [PMID: 35930447 PMCID: PMC9448281 DOI: 10.1152/ajpheart.00244.2022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/20/2022] [Accepted: 07/31/2022] [Indexed: 01/24/2023]
Abstract
The risks of heart diseases are significantly modulated by age and sex, but how these factors influence baseline cardiac gene expression remains incompletely understood. Here, we used RNA sequencing and mass spectrometry to compare gene expression in female and male young adult (4 mo) and early aging (20 mo) mouse hearts, identifying thousands of age- and sex-dependent gene expression signatures. Sexually dimorphic cardiac genes are broadly distributed, functioning in mitochondrial metabolism, translation, and other processes. In parallel, we found over 800 genes with differential aging response between male and female, including genes in cAMP and PKA signaling. Analysis of the sex-adjusted aging cardiac transcriptome revealed a widespread remodeling of exon usage patterns that is largely independent from differential gene expression, concomitant with upstream changes in RNA-binding protein and splice factor transcripts. To evaluate the impact of the splicing events on cardiac proteoform composition, we applied an RNA-guided proteomics computational pipeline to analyze the mass spectrometry data and detected hundreds of putative splice variant proteins that have the potential to rewire the cardiac proteome. Taken together, the results here suggest that cardiac aging is associated with 1) widespread sex-biased aging genes and 2) a rewiring of RNA splicing programs, including sex- and age-dependent changes in exon usages and splice patterns that have the potential to influence cardiac protein structure and function. These changes contribute to the emerging evidence for considerable sexual dimorphism in the cardiac aging process that should be considered in the search for disease mechanisms.NEW & NOTEWORTHY Han et al. used proteogenomics to compare male and female mouse hearts at 4 and 20 mo. Sex-biased cardiac genes function in mitochondrial metabolism, translation, autophagy, and other processes. Hundreds of cardiac genes show sex-by-age interactions, that is, sex-biased aging genes. Cardiac aging is accompanied with a remodeling of exon usage in functionally coordinated genes, concomitant with differential expression of RNA-binding proteins and splice factors. These features represent an underinvestigated aspect of cardiac aging that may be relevant to the search for disease mechanisms.
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Grants
- R21-HL150456 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R00-HL144829 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R00 HL127302 NHLBI NIH HHS
- R03-OD032666 HHS | NIH | NIH Office of the Director (OD)
- R01 HL141278 NHLBI NIH HHS
- F32 HL149191 NHLBI NIH HHS
- F32-HL149191 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R00-HL127302 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R21 HL150456 NHLBI NIH HHS
- R03 OD032666 NIH HHS
- R00 HL144829 NHLBI NIH HHS
- R01-HL141278 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- University of Colorado
- University of Colorado School of Medicine, Anschutz Medical Campus
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Affiliation(s)
- Yu Han
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
| | - Sara A Wennersten
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
| | - Julianna M Wright
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
| | - R W Ludwig
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
| | | | - Maggie P Y Lam
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
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15
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Tong X, Li WX, Liang J, Zheng Y, Dai SX. Two different aging paths in human blood revealed by integrated analysis of gene Expression, mutation and alternative splicing. Gene 2022; 829:146501. [PMID: 35452709 DOI: 10.1016/j.gene.2022.146501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 11/04/2022]
Abstract
Aging is a complex life process that human organs and tissues steadily and continuously decline. Aging has huge heterogeneity, which shows different aging rates among different individuals and in different tissues of the same individual. Many studies of aging are often contradictory and show little common signature. The integrated analysis of these transcriptome datasets will provide an unbiased global view of the aging process. Here, we integrated 8 transcriptome datasets including 757 samples from healthy human blood to study aging from three aspects of gene expression, mutations, and alternative splicing. Surprisingly, we found that transcriptome changes in blood are relatively independent of the chronological age. Further pseudotime analysis revealed two different aging paths (AgingPath1 and AgingPath2) in human blood. The differentially expressed genes (DEGs) along the two paths showed a limited overlap and are enriched in different biological processes. The mutations of DEGs in AgingPath1 are significantly increased in the aging process, while the opposite trend was observed in AgingPath2. Expression quantitative trait loci (eQTL) and splicing quantitative trait loci (sQTL) analysis identified 304 important mutations that can affect both gene expression and alternative splicing during aging. Finally, by comparison between aging and Alzheimer's disease, we identified 37 common DEGs in AgingPath1, AgingPath2 and Alzheimer's disease. These genes may contribute to the shift from aging state to Alzheimer's disease. In summary, this study revealed the two aging paths and the related genes and mutations, which provides a new insight into aging and aging-related disease.
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Affiliation(s)
- Xin Tong
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Wen-Xing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jihao Liang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yang Zheng
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Shao-Xing Dai
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
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16
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Henrich M, Ha P, Wang Y, Ting K, Stodieck L, Soo C, Adams JS, Chun R. Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight. Skelet Muscle 2022; 12:11. [PMID: 35642060 DOI: 10.1186/s13395-022-00294-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As the interest in manned spaceflight increases, so does the requirement to understand the transcriptomic mechanisms that underlay the detrimental physiological adaptations of skeletal muscle to microgravity. While microgravity-induced differential gene expression (DGE) has been extensively investigated, the contribution of differential alternative splicing (DAS) to the plasticity and functional status of the skeletal muscle transcriptome has not been studied in an animal model. Therefore, by evaluating both DGE and DAS across spaceflight, we set out to provide the first comprehensive characterization of the transcriptomic landscape of skeletal muscle during exposure to microgravity. METHODS RNA-sequencing, immunohistochemistry, and morphological analyses were conducted utilizing total RNA and tissue sections isolated from the gastrocnemius and quadriceps muscles of 30-week-old female BALB/c mice exposed to microgravity or ground control conditions for 9 weeks. RESULTS In response to microgravity, the skeletal muscle transcriptome was remodeled via both DGE and DAS. Importantly, while DGE showed variable gene network enrichment, DAS was enriched in structural and functional gene networks of skeletal muscle, resulting in the expression of alternatively spliced transcript isoforms that have been associated with the physiological changes to skeletal muscle in microgravity, including muscle atrophy and altered fiber type function. Finally, RNA-binding proteins, which are required for regulation of pre-mRNA splicing, were themselves differentially spliced but not differentially expressed, an upstream event that is speculated to account for the downstream splicing changes identified in target skeletal muscle genes. CONCLUSIONS Our work serves as the first investigation of coordinate changes in DGE and DAS in large limb muscles across spaceflight. It opens up a new opportunity to understand (i) the molecular mechanisms by which splice variants of skeletal muscle genes regulate the physiological adaptations of skeletal muscle to microgravity and (ii) how small molecule splicing regulator therapies might thwart muscle atrophy and alterations to fiber type function during prolonged spaceflight.
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17
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Sándor S, Jónás D, Tátrai K, Czeibert K, Kubinyi E. Poly(A) RNA sequencing reveals age-related differences in the prefrontal cortex of dogs. GeroScience 2022; 44:1269-1293. [PMID: 35288843 PMCID: PMC9213612 DOI: 10.1007/s11357-022-00533-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/17/2022] [Indexed: 12/02/2022] Open
Abstract
Dogs may possess a unique translational potential to investigate neural aging and dementia because they are prone to age-related cognitive decline, including an Alzheimer’s disease–like pathological condition. Yet very little is known about the molecular mechanisms underlying canine cognitive decline. The goal of the current study was to explore the transcriptomic differences between young and old dogs’ frontal cortex, which is a brain region often affected by various forms of age-related dementia in humans. RNA isolates from the frontal cortical brain area of 13 pet dogs, which represented 7 different breeds and crossbreds, were analyzed. The dogs were euthanized for medical reasons, and their bodies had been donated by their owners for scientific purposes. The poly(A) tail RNA subfraction of the total transcriptome was targeted in the sequencing analysis. Cluster analyses, differential gene expression analyses, and gene ontology analyses were carried out to assess which genes and genetic regulatory mechanisms were mostly affected by aging. Age was the most prominent factor in the clustering of the animals, indicating the presence of distinct gene expression patterns related to aging in a genetically variable population. A total of 3436 genes were found to be differentially expressed between the age groups, many of which were linked to neural function, immune system, and protein synthesis. These findings are in accordance with previous human brain aging RNA sequencing studies. Some genes were found to behave more similarly to humans than to rodents, further supporting the applicability of dogs in translational aging research.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.
| | - Dávid Jónás
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kitti Tátrai
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary.,Department of Genetics, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Kálmán Czeibert
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, 1/c Pázmány Péter sétány, Budapest, 1117, Hungary
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18
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Ogawa T, Schermann H, Kobayashi H, Fushimi K, Okawa A, Jinno T. Age and clinical outcomes after hip fracture surgery: do octogenarian, nonagenarian and centenarian classifications matter? Age Ageing 2021; 50:1952-1960. [PMID: 34228781 DOI: 10.1093/ageing/afab137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND older patients with hip fractures are arbitrarily classified as octogenarians, nonagenarians and centenarians. We have designed this study to quantify in-hospital mortality and complications among each of these groups. We hypothesised that the associations between age and in-hospital mortality and complications are continuously increasing, and that these risks increase rapidly when patients reach a certain age. METHODS this research is a retrospective cohort study using nationwide database between 2010 and 2018. Patients undergoing hip fracture surgery, and aged 60 or older, were included. The associations between patient age, in-hospital mortality and complications were visualised using the restricted cubic spline models, and were analysed employing multivariable regression models. Then, octogenarians, nonagenarians and centenarians were compared. RESULTS among a total of 565,950 patients, 48.7% (n = 275,775) were octogenarians, 23.0% (n = 129,937) were nonagenarians and 0.7% (n = 4,093) were centenarians. The models presented three types of association between age, in-hospital mortality and complications: (i) a continuous increase (mortality and respiratory complications); (ii) a mild increase followed by a steep rise (intensive care unit admission, heart failure, renal failure and surgical site hematoma) and (iii) a steep increase followed by a limited change (coronary heart disease, stroke and pulmonary embolisms). CONCLUSION we identified three types of association between age and clinical outcomes. Patients aged 85-90 may constitute the upper threshold for age categorisations, because the risk of in-hospital complications changed dramatically at that stage. This information can improve clinical awareness of various complications and support collective decision-making.
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Affiliation(s)
- Takahisa Ogawa
- Department of Orthopaedic Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Haggai Schermann
- Division of Orthopedic Surgery, Tel Aviv Sourasky Medical Center, Affiliated with Tel Aviv University, Tel Aviv, Israel
| | - Hiroki Kobayashi
- Department of Medicine, Harvard Medical School, Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, USA
| | - Kiyohide Fushimi
- Department of Health Policy and Informatics, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Atsushi Okawa
- Department of Orthopaedic Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Tetsuya Jinno
- Department of Orthopaedic Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
- Department of Orthopaedic Surgery, Dokkyo Medical University, Saitama Medical Center, Saitama, Japan
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19
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Gupta K, Yadav P, Maryam S, Ahuja G, Sengupta D. Quantification of Age-Related Decline in Transcriptional Homeostasis. J Mol Biol 2021; 433:167179. [PMID: 34339725 DOI: 10.1016/j.jmb.2021.167179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Age-dependent dysregulation of transcription regulatory machinery triggers modulations in the gene expression levels leading to the decline in cellular fitness. Tracking of these transcripts along the temporal axis in multiple species revealed a spectrum of evolutionarily conserved pathways, such as electron transport chain, translation regulation, DNA repair, etc. Recent shreds of evidence suggest that aging deteriorates the transcription machinery itself, indicating the hidden complexity of the aging transcriptomes. This reinforces the need for devising novel computational methods to view aging through the lens of transcriptomics. Here, we present Homeostatic Divergence Score (HDS) to quantify the extent of messenger RNA (mRNA) homeostasis by assessing the balance between spliced and unspliced mRNA repertoire in single cells. We validated its utility in two independent aging datasets, and identified sets of genes undergoing age-related breakdown of transcriptional homeostasis. Moreover, testing of our method on a subpopulation of human embryonic stem cells revealed a set of differentially processed transcripts segregating these subpopulations. Our preliminary analyses in this direction suggest that mRNA processing level information offered by single-cell RNA sequencing (scRNA-seq) data is a superior determinant of chronological age as compared to transcriptional noise.
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Affiliation(s)
- Krishan Gupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Princey Yadav
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Sidrah Maryam
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India.
| | - Debarka Sengupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Institute of Health and Biomedical Innovation, Queensland University of Technology, Australia.
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20
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Abstract
Diploidy has profound implications for population genetics and susceptibility to genetic diseases. Although two copies are present for most genes in the human genome, they are not necessarily both active or active at the same level in a given individual. Genomic imprinting, resulting in exclusive or biased expression in favor of the allele of paternal or maternal origin, is now believed to affect hundreds of human genes. A far greater number of genes display unequal expression of gene copies due to cis-acting genetic variants that perturb gene expression. The availability of data generated by RNA sequencing applied to large numbers of individuals and tissue types has generated unprecedented opportunities to assess the contribution of genetic variation to allelic imbalance in gene expression. Here we review the insights gained through the analysis of these data about the extent of the genetic contribution to allelic expression imbalance, the tools and statistical models for gene expression imbalance, and what the results obtained reveal about the contribution of genetic variants that alter gene expression to complex human diseases and phenotypes.
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Affiliation(s)
- Siobhan Cleary
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
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21
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Pagiatakis C, Musolino E, Gornati R, Bernardini G, Papait R. Epigenetics of aging and disease: a brief overview. Aging Clin Exp Res 2021; 33:737-745. [PMID: 31811572 PMCID: PMC8084772 DOI: 10.1007/s40520-019-01430-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022]
Abstract
Aging is an important risk factor for several human diseases such as cancer, cardiovascular disease and neurodegenerative disorders, resulting from a combination of genetic and environmental factors (e.g., diet, smoking, obesity and stress), which, at molecular level, cause changes in gene expression underlying the decline of physiological function. Epigenetics, which include mechanisms regulating gene expression independently of changes to DNA sequence, regulate gene expression by modulating the structure of chromatin or by regulating the binding of transcriptional machinery to DNA. Several studies showed that an impairment of epigenetic mechanisms promotes alteration of gene expression underlying several aging-related diseases. Alteration of these mechanisms is also linked with changes of gene expression that occurs during aging processes of different tissues. In this review, we will outline the potential role of epigenetics in the onset of two age-related pathologies, cancer and cardiovascular diseases.
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22
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Goldman E, Reich E, Roshihotzki B, Saketkhou M, Wald S, Goldstein A, Klein Y, Abramovitz I, Klutstein M. A Mouse Model for Studying the Development of Apical Periodontitis with Age. Cells 2021; 10:671. [PMID: 33802950 DOI: 10.3390/cells10030671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 01/15/2023] Open
Abstract
Older age is associated with reduced immune function. Our aim was to study how age affects the development of apical periodontitis (AP). AP was induced in two age groups of mice (young vs. adult). Histological samples were stained by Hematoxylin Eosin, Brown and Brenn, and Tartrate-Resistant Acid Phosphatase. In addition, the samples were scanned by Micro-Computerized-Tomography (micro-CT) to evaluate apical constriction and periapical lesion size. Cell density in the periapical region was computationally assessed. Moreover, lesion immune cell populations were characterized by flow cytometry and immunofluorescence. The young group presented more canals with necrotic radicular pulp compared to the adults. There was no difference in bacteria location in the canals between the groups. Apical constriction size was larger in the young mice compared to the adults. The periapical cell density was higher in the young group, while the dominant immune cells in the lesions were neutrophils, which also exhibited the highest young/adult ratio. Immunofluorescence demonstrated neutrophils in the lesion. More osteoclasts were present in the lesions of the young mice, in correlation to the higher volume of bone resorption in this group. Overall, we conclude that the immune reaction to AP stimuli was attenuated in the adult mice compared to the young.
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Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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24
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. Wiley Interdiscip Rev RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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25
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Abstract
Most disease-associated variants, although located in putatively regulatory regions, do not have detectable effects on gene expression. One explanation could be that we have not examined gene expression in the cell types or conditions that are most relevant for disease. Even large-scale efforts to study gene expression across tissues are limited to human samples obtained opportunistically or postmortem, mostly from adults. In this review we evaluate recent findings and suggest an alternative strategy, drawing on the dynamic and highly context-specific nature of gene regulation. We discuss new technologies that can extend the standard regulatory mapping framework to more diverse, disease-relevant cell types and states.
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Affiliation(s)
- Benjamin D Umans
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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26
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Asplund O, Rung J, Groop L, Prasad B R, Hansson O. MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle. Database (Oxford) 2020; 2020:baaa111. [PMID: 33338203 PMCID: PMC7747357 DOI: 10.1093/database/baaa111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/13/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023]
Abstract
MuscleAtlasExplorer is a freely available web application that allows for the exploration of gene expression data from human skeletal muscle. It draws from an extensive publicly available dataset of 1654 skeletal muscle expression microarray samples. Detailed, manually curated, patient phenotype data, with information such as age, sex, BMI and disease status, are combined with skeletal muscle gene expression to provide insights into gene function in skeletal muscle. It aims to facilitate easy exploration of the data using powerful data visualization functions, while allowing for sample selection, in-depth inspection and further analysis using external tools. Availability: MuscleAtlasExplorer is available at https://mae.crc.med.lu.se/mae2 (username 'muscle' and password 'explorer' pre-publication).
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Affiliation(s)
- Olof Asplund
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, Malmö 20502, Sweden
| | - Johan Rung
- SciLifeLab, BMC, Husargatan 3, Uppsala University, Uppsala 751 22, Sweden
| | - Leif Groop
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, Malmö 20502, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 800290 Helsinki, Finland
| | - Rashmi Prasad B
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, Malmö 20502, Sweden
| | - Ola Hansson
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenströms gata 35, Malmö 20502, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 800290 Helsinki, Finland
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27
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Lee JR, Choe SH, Kim YH, Cho HM, Park HR, Lee HE, Jin YB, Kim JS, Jeong KJ, Park SJ, Huh JW. Longitudinal profiling of the blood transcriptome in an African green monkey aging model. Aging (Albany NY) 2020; 13:846-864. [PMID: 33290253 PMCID: PMC7834999 DOI: 10.18632/aging.202190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
African green monkeys (AGMs, Chlorocebus aethiops) are Old World monkeys which are used as experimental models in biomedical research. Recent technological advances in next generation sequencing are useful for unraveling the genetic mechanisms underlying senescence, aging, and age-related disease. To elucidate the normal aging mechanisms in older age, the blood transcriptomes of nine healthy, aged AGMs (15‒23 years old), were analyzed over two years. We identified 910‒1399 accumulated differentially expressed genes (DEGs) in each individual, which increased with age. Aging-related DEGs were sorted across the three time points. A major proportion of the aging-related DEGs belonged to gene ontology (GO) categories involved in translation and rRNA metabolic processes. Next, we sorted common aging-related DEGs across three time points over two years. Common aging-related DEGs belonged to GO categories involved in translation, cellular component biogenesis, rRNA metabolic processes, cellular component organization, biogenesis, and RNA metabolic processes. Furthermore, we identified 29 candidate aging genes that were upregulated across the time series analysis. These candidate aging genes were linked to protein synthesis. This study describes a changing gene expression pattern in AGMs during aging using longitudinal transcriptome sequencing. The candidate aging genes identified here may be potential targets for the treatment of aging.
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Affiliation(s)
- Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56216, Republic of Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Hye-Ri Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee-Eun Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Yeung Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Ji-Su Kim
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56216, Republic of Korea
| | - Kang Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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28
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Ram DR, Kroll K, Reeves RK. Skipped Over: Tuning Natural Killer Cells Toward HIV Through Alternative Splicing. AIDS Res Hum Retroviruses 2020; 36:969-972. [PMID: 32862656 PMCID: PMC7703092 DOI: 10.1089/aid.2020.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural killer (NK) cells provide some of the earliest immune responses to infection, but when viruses manipulate or perturb the immune environment to alter NK cell function, this places the host at a disadvantage. Indeed, others and we observe that in the context of HIV/simian immunodeficiency virus (SIV) infection, although NK cells are not infected, they can become dysfunctional over time. Several studies have characterized protein and transcriptional profiles of NK cells during HIV/SIV infection, but none have examined whether the production of alternative transcripts and corresponding isoforms is modulated. This phenomenon occurs broadly in normal biology and in other disease states, and could provide a novel avenue of investigation that may yield better targets to restore or augment NK cell responses to HIV/SIV. Herein, we briefly summarize published and new data that may provide a perspective on how to target NK cell splice variants.
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Affiliation(s)
- Daniel R. Ram
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kyle Kroll
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - R. Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, Massachusetts, USA
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29
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Schmidt M, Hopp L, Arakelyan A, Kirsten H, Engel C, Wirkner K, Krohn K, Burkhardt R, Thiery J, Loeffler M, Loeffler-Wirth H, Binder H. The Human Blood Transcriptome in a Large Population Cohort and Its Relation to Aging and Health. Front Big Data 2020; 3:548873. [PMID: 33693414 PMCID: PMC7931910 DOI: 10.3389/fdata.2020.548873] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Background: The blood transcriptome is expected to provide a detailed picture of an organism's physiological state with potential outcomes for applications in medical diagnostics and molecular and epidemiological research. We here present the analysis of blood specimens of 3,388 adult individuals, together with phenotype characteristics such as disease history, medication status, lifestyle factors, and body mass index (BMI). The size and heterogeneity of this data challenges analytics in terms of dimension reduction, knowledge mining, feature extraction, and data integration. Methods: Self-organizing maps (SOM)-machine learning was applied to study transcriptional states on a population-wide scale. This method permits a detailed description and visualization of the molecular heterogeneity of transcriptomes and of their association with different phenotypic features. Results: The diversity of transcriptomes is described by personalized SOM-portraits, which specify the samples in terms of modules of co-expressed genes of different functional context. We identified two major blood transcriptome types where type 1 was found more in men, the elderly, and overweight people and it upregulated genes associated with inflammation and increased heme metabolism, while type 2 was predominantly found in women, younger, and normal weight participants and it was associated with activated immune responses, transcriptional, ribosomal, mitochondrial, and telomere-maintenance cell-functions. We find a striking overlap of signatures shared by multiple diseases, aging, and obesity driven by an underlying common pattern, which was associated with the immune response and the increase of inflammatory processes. Conclusions: Machine learning applications for large and heterogeneous omics data provide a holistic view on the diversity of the human blood transcriptome. It provides a tool for comparative analyses of transcriptional signatures and of associated phenotypes in population studies and medical applications.
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Affiliation(s)
- Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Lydia Hopp
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Arsen Arakelyan
- BIG, Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Holger Kirsten
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Christoph Engel
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Kerstin Wirkner
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Knut Krohn
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Ralph Burkhardt
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Joachim Thiery
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Markus Loeffler
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany.,IMISE, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany.,Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
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