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Burn A, Roy F, Freeman M, Coffin JM. Widespread expression of the ancient HERV-K (HML-2) provirus group in normal human tissues. PLoS Biol 2022; 20:e3001826. [PMID: 36256614 PMCID: PMC9578601 DOI: 10.1371/journal.pbio.3001826] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/13/2022] [Indexed: 11/11/2022] Open
Abstract
Human endogenous retrovirus (HERV) transcripts are known to be highly expressed in cancers, yet their activity in nondiseased tissue is largely unknown. Using the GTEx RNA-seq dataset from normal tissue sampled at autopsy, we characterized individual expression of the recent HERV-K (HML-2) provirus group across 13,000 different samples of 54 different tissues from 948 individuals. HML-2 transcripts could be identified in every tissue sampled and were elevated in the cerebellum, pituitary, testis, and thyroid. A total of 37 different individual proviruses were expressed in 1 or more tissues, representing all 3 LTR5 subgroups. Nine proviruses were identified as having long terminal repeat (LTR)-driven transcription, 7 of which belonged to the most recent LTR5HS subgroup. Proviruses of different subgroups displayed a bias in tissue expression, which may be associated with differences in transcription factor binding sites in their LTRs. Provirus expression was greater in evolutionarily older proviruses with an earliest shared ancestor of gorilla or older. HML-2 expression was significantly affected by biological sex in 1 tissue, while age and timing of death (Hardy score) had little effect. Proviruses containing intact gag, pro, and env open reading frames (ORFs) were expressed in the dataset, with almost every tissue measured potentially expressing at least 1 intact ORF (gag). Human endogenous retrovirus (HERV) transcripts are known to be highly expressed in cancers, but what is their activity in normal tissue? This study uses unique patterns of HERV-K RNA expression in the large GEx dataset from non-diseased tissue sites to provide new insights into both the coevolution of HERV-K with our primate ancestors and their current role in human biology.
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Affiliation(s)
- Aidan Burn
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Farrah Roy
- Immuneering Corporation, Cambridge, Massachusetts, United States of America
| | - Michael Freeman
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - John M. Coffin
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
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52
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Morales A, Andrews MG. Approaches to investigating metabolism in human neurodevelopment using organoids: insights from intestinal and cancer studies. Development 2022; 149:dev200506. [PMID: 36255366 PMCID: PMC9720749 DOI: 10.1242/dev.200506] [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] [Indexed: 06/16/2023]
Abstract
Interrogating the impact of metabolism during development is important for understanding cellular and tissue formation, organ and systemic homeostasis, and dysregulation in disease states. To evaluate the vital functions metabolism coordinates during human brain development and disease, pluripotent stem cell-derived models, such as organoids, provide tractable access to neurodevelopmental processes. Despite many strengths of neural organoid models, the extent of their replication of endogenous metabolic programs is currently unclear and requires direct investigation. Studies in intestinal and cancer organoids that functionally evaluate dynamic bioenergetic changes provide a framework that can be adapted for the study of neural metabolism. Validation of in vitro models remains a significant challenge; investigation using in vivo models and primary tissue samples is required to improve our in vitro model systems and, concomitantly, improve our understanding of human development.
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Affiliation(s)
- Alexandria Morales
- Schoolof Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
- Biomedical Engineering Graduate Program, Arizona State University, Tempe, AZ 85281, USA
| | - Madeline G. Andrews
- Schoolof Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
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53
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Zlomuzica A, Plank L, Dere E. A new path to mental disorders: Through gap junction channels and hemichannels. Neurosci Biobehav Rev 2022; 142:104877. [PMID: 36116574 DOI: 10.1016/j.neubiorev.2022.104877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/20/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022]
Abstract
Behavioral disturbances related to emotional regulation, reward processing, cognition, sleep-wake regulation and activity/movement represent core symptoms of most common mental disorders. Increasing empirical and theoretical evidence suggests that normal functioning of these behavioral domains relies on fine graded coordination of neural and glial networks which are maintained and modulated by intercellular gap junction channels and unapposed pannexin or connexin hemichannels. Dysfunctions in these networks might contribute to the development and maintenance of psychopathological and neurobiological features associated with mental disorders. Here we review and discuss the evidence indicating a prominent role of gap junction channel and hemichannel dysfunction in core symptoms of mental disorders. We further discuss how the increasing knowledge on intercellular gap junction channels and unapposed pannexin or connexin hemichannels in the brain might lead to deeper mechanistic insight in common mental disorders and to the development of novel treatment approaches. We further attempt to exemplify what type of future research on this topic could be integrated into multidimensional approaches to understand and cure mental disorders.
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Affiliation(s)
- Armin Zlomuzica
- Department of Behavioral and Clinical Neuroscience, Ruhr-University Bochum (RUB), Massenbergstraße 9-13, D-44787 Bochum, Germany.
| | - Laurin Plank
- Department of Behavioral and Clinical Neuroscience, Ruhr-University Bochum (RUB), Massenbergstraße 9-13, D-44787 Bochum, Germany
| | - Ekrem Dere
- Department of Behavioral and Clinical Neuroscience, Ruhr-University Bochum (RUB), Massenbergstraße 9-13, D-44787 Bochum, Germany; Sorbonne Université. Institut de Biologie Paris-Seine, (IBPS), Département UMR 8256: Adaptation Biologique et Vieillissement, UFR des Sciences de la Vie, Campus Pierre et Marie Curie, Bâtiment B, 9 quai Saint Bernard, F-75005 Paris, France.
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54
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Voloudakis G, Vicari JM, Venkatesh S, Hoffman GE, Dobrindt K, Zhang W, Beckmann ND, Higgins CA, Argyriou S, Jiang S, Hoagland D, Gao L, Corvelo A, Cho K, Lee KM, Bian J, Lee JS, Iyengar SK, Luoh SW, Akbarian S, Striker R, Assimes TL, Schadt EE, Lynch JA, Merad M, tenOever BR, Charney AW, Brennand KJ, Fullard JF, Roussos P. A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility. NPJ Genom Med 2022; 7:52. [PMID: 36064543 PMCID: PMC9441828 DOI: 10.1038/s41525-022-00324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/19/2022] [Indexed: 02/06/2023] Open
Abstract
Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes that reduce COVID-19 host susceptibility is a critical next step. Using a translational genomics approach that integrates COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX), and perturbagen signatures, we identified IL10RB as the top candidate gene target for COVID-19 host susceptibility. In a series of validation steps, we show that predicted GReX upregulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes and that in vitro IL10RB overexpression is associated with increased viral load and activation of disease-relevant molecular pathways.
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Affiliation(s)
- Georgios Voloudakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
| | - James M Vicari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanan Venkatesh
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Gabriel E Hoffman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristina Dobrindt
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Wen Zhang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christina A Higgins
- Department of Microbiology, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Medicine, Grossman School of Medicine, New York University, New York, NY, USA
- Vilcek Institute of Graduate Biomedical Sciences, New York University, New York, NY, USA
| | - Stathis Argyriou
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | | | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kyung Min Lee
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Jiantao Bian
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Jennifer S Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Sudha K Iyengar
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- VA Northeast Ohio Healthcare System, Cleveland VA Medical Center, Cleveland, OH, USA
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, OR, USA
- Department of Medicine, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Striker
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Julie A Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Medicine, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - John F Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
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Hollis HC, Francis JN, Anafi RC. Multi-tissue transcriptional changes and core circadian clock disruption following intensive care. Front Physiol 2022; 13:942704. [PMID: 36045754 PMCID: PMC9420996 DOI: 10.3389/fphys.2022.942704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Both critical illness and current care have been hypothesized to upset daily rhythms and impair molecular circadian function. However, the influence of critical illness on clock function in different tissues and on circadian output genes are unknown. Here we evaluate the effect of critical care and illness on transcription, focusing on the functional organization of the core circadian oscillator. Methods: We downloaded RNAseq count data from the Genotype-Tissue Expression (GTEx) project. Treating mechanical ventilation as a marker for intensive care, we stratified samples into acute death (AD) and intensive care (IC) groups based on the documented Hardy Death Scale. We restricted our analysis to the 25 tissues with >50 samples in each group. Using the edgeR package and controlling for collection center, gender, and age, we identified transcripts differentially expressed between the AD and IC groups. Overrepresentation and enrichment methods were used to identify gene sets modulated by intensive care across tissues. For each tissue, we then calculated the delta clock correlation distance (ΔCCD), a comparative measure of the functional organization of the core circadian oscillator, in the both the AD and IC groups. The statistical significance of the ΔCCD was assessed by permutation, modifying a pre-existing R package to control for confounding variables. Results: Intensive care, as marked by ventilation, significantly modulated the expression of thousands of genes. Transcripts that were modulated in ≥75% of tissues were enriched for genes involved in mitochondrial energetics, cellular stress, metabolism, and notably circadian regulation. Transcripts that were more markedly affected, in ≥10 tissues, were enriched for inflammation, complement and immune pathways. Oscillator organization, as assessed by ΔCCD, was significantly reduced in the intensive care group in 11/25 tissues. Conclusion: Our findings support the hypothesis that patients in intensive care have impaired molecular circadian rhythms. Tissues involved in metabolism and energetics demonstrated the most marked changes in oscillator organization. In adipose tissue, there was a significant overlap between transcripts previously established to be modulated by sleep deprivation and fasting with those modulated by critical care. This work suggests that intensive care protocols that restore sleep/wake and nutritional rhythms may be of benefit.
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Affiliation(s)
- Henry C. Hollis
- School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, United States
| | - Julian N. Francis
- Department of Mathematics, Howard University, Washington, DC, United States
| | - Ron C. Anafi
- Division of Sleep Medicine and Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, PA, United States,*Correspondence: Ron C. Anafi,
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56
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Brusletto BS, Hellerud BC, Olstad OK, Øvstebø R, Brandtzaeg P. Transcriptomic changes in the large organs in lethal meningococcal shock are reflected in a porcine shock model. Front Cell Infect Microbiol 2022; 12:908204. [PMID: 36034711 PMCID: PMC9413276 DOI: 10.3389/fcimb.2022.908204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fulminant meningococcal sepsis with shock and multiple organ failure is associated with a massive systemic inflammatory response involving solid organs. We have previously established a porcine model of the disease to study pathophysiologic and possible therapeutic strategies. Objective This study examined whether the organ specific gene expression profile in such a large animal model reflects the profile seen in patients with fulminant meningococcal sepsis. Patients and methods Data from gene expression profiles induced in organs from patients (n=5) and the porcine model (n=8) were imported into the Ingenuity pathway analysis (IPA) software for comparison analysis. The number of meningococci in the organs were quantified by real time-PCR. Results The all-over transcriptional activation between different organs revealed a striking concordance between the patients and the pigs regarding the pattern of transcriptional activation and activated pathways. Comparison analysis demonstrated similar pattern of upregulation of genes being associated with a large range of inflammatory biofunctions in the patients and the porcine model. Genes associated with biofunctions such as organismal death, morbidity and mortality were similarly downregulated in the patients and the porcine model. Comparison analysis of main predicted canonical pathways also demonstrated a high degree of similarity regarding up- and downregulation in both groups. Core analysis revealed different top-upstream regulators in the different organs in the patients. In the patients pro-inflammatory regulators were most activated in the lungs. In the other organs up-stream factors that regulate signaling pathways involved in development, growth, repair and homeostasis and triglyceride synthesis were most activated. In the porcine model, the top-upstream regulators were pro-inflammatory in all organs. The difference may reflect the shorter duration of the porcine experiment than the duration of the patient’s infection before death. Conclusion The inflammatory responses measured on the transcriptomic level in organs in patients with fulminant meningococcal sepsis is reproduced in the porcine model of the disease, although some differences may exist regarding the top-upregulated factors in individual organs. Thus, this large animal model reproduces important immunological features of meningococcal sepsis and can be a valuable tool in further investigations of inflammatory aspects and possible treatment options
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Affiliation(s)
- Berit Sletbakk Brusletto
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- *Correspondence: Berit Sletbakk Brusletto,
| | | | | | - Reidun Øvstebø
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Petter Brandtzaeg
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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57
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Andrijevic D, Vrselja Z, Lysyy T, Zhang S, Skarica M, Spajic A, Dellal D, Thorn SL, Duckrow RB, Ma S, Duy PQ, Isiktas AU, Liang D, Li M, Kim SK, Daniele SG, Banu K, Perincheri S, Menon MC, Huttner A, Sheth KN, Gobeske KT, Tietjen GT, Zaveri HP, Latham SR, Sinusas AJ, Sestan N. Cellular recovery after prolonged warm ischaemia of the whole body. Nature 2022; 608:405-412. [PMID: 35922506 PMCID: PMC9518831 DOI: 10.1038/s41586-022-05016-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 06/23/2022] [Indexed: 02/05/2023]
Abstract
After cessation of blood flow or similar ischaemic exposures, deleterious molecular cascades commence in mammalian cells, eventually leading to their death1,2. Yet with targeted interventions, these processes can be mitigated or reversed, even minutes or hours post mortem, as also reported in the isolated porcine brain using BrainEx technology3. To date, translating single-organ interventions to intact, whole-body applications remains hampered by circulatory and multisystem physiological challenges. Here we describe OrganEx, an adaptation of the BrainEx extracorporeal pulsatile-perfusion system and cytoprotective perfusate for porcine whole-body settings. After 1 h of warm ischaemia, OrganEx application preserved tissue integrity, decreased cell death and restored selected molecular and cellular processes across multiple vital organs. Commensurately, single-nucleus transcriptomic analysis revealed organ- and cell-type-specific gene expression patterns that are reflective of specific molecular and cellular repair processes. Our analysis comprises a comprehensive resource of cell-type-specific changes during defined ischaemic intervals and perfusion interventions spanning multiple organs, and it reveals an underappreciated potential for cellular recovery after prolonged whole-body warm ischaemia in a large mammal.
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Affiliation(s)
- David Andrijevic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,These authors contributed equally: David Andrijevic, Zvonimir Vrselja, Taras Lysyy, Shupei Zhang
| | - Zvonimir Vrselja
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,These authors contributed equally: David Andrijevic, Zvonimir Vrselja, Taras Lysyy, Shupei Zhang
| | - Taras Lysyy
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Department of Surgery, Yale School of Medicine New Haven, New Haven, CT, USA.,These authors contributed equally: David Andrijevic, Zvonimir Vrselja, Taras Lysyy, Shupei Zhang
| | - Shupei Zhang
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,These authors contributed equally: David Andrijevic, Zvonimir Vrselja, Taras Lysyy, Shupei Zhang
| | - Mario Skarica
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Ana Spajic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - David Dellal
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Stephanie L. Thorn
- Yale Translational Research Imaging Center, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Robert B. Duckrow
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Phan Q. Duy
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.,Medical Scientist Training Program (MD-PhD), Yale School of Medicine, New Haven, CT, USA
| | - Atagun U. Isiktas
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Dan Liang
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mingfeng Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Suel-Kee Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Stefano G. Daniele
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Medical Scientist Training Program (MD-PhD), Yale School of Medicine, New Haven, CT, USA
| | - Khadija Banu
- Department of Nephrology, Yale School of Medicine, New Haven, CT, USA
| | - Sudhir Perincheri
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Madhav C. Menon
- Department of Nephrology, Yale School of Medicine, New Haven, CT, USA
| | - Anita Huttner
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Kevin N. Sheth
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA.,Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Kevin T. Gobeske
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Gregory T. Tietjen
- Department of Surgery, Yale School of Medicine New Haven, New Haven, CT, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Hitten P. Zaveri
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephen R. Latham
- Interdisciplinary Center for Bioethics, Yale University, New Haven, CT, USA
| | - Albert J. Sinusas
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT, USA.,Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA.,Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA. .,Department of Genetics, Yale School of Medicine, New Haven, CT, USA. .,Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA. .,Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA. .,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, USA. .,Yale Child Study Center, New Haven, CT, USA.
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58
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Wei Y, Wang J, Wang Q, Cong B, Li S. The estimation of bloodstain age utilizing circRNAs and mRNAs biomarkers. Forensic Sci Int 2022; 338:111408. [PMID: 35901585 DOI: 10.1016/j.forsciint.2022.111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/19/2022]
Abstract
Determining the time since deposition (TsD) of bloodstains can provide forensic investigators with additional clues, as it can corroborate eyewitness accounts, limit the number of suspects, and help confirm alibis. Bloodstains are the most common bodily fluid stains at crime scenes. In this study, we examined the relative expression levels (REs) of circRNAs and mRNAs data in bloodstains over ten time points by Real-time quantitative polymerase chain reaction (qPCR), to determine the utility of the relative expression levels of RNA markers for TsD estimation. Forensic samples more than just appear in indoor settings, we also evaluated the use of RNA degradation rate to indicate the age of bloodstains in different environments including indoor and outdoor conditions. The expression levels of six blood-specific mRNA markers (GYPA, CD93, ALAS2, SPTB, HBB, HBA), three highly expressed circRNAs in human peripheral blood (hsa_circ_0001445, hsa_circ_0000972, hsa_circ_0000095) and three reference genes (18 S, ACTB and U6) were analyzed across numerous ageing time points. Analysis of the degradation rates of individual RNAs under indoor and outdoor conditions showed that they exhibited a unique degradation profile during the four-month storage interval, with both circRNAs and mRNAs linearly showing continuous degradation, while U6 is more stable than other reference gene markers. In the current study, we firstly used circRNAs as additional novel biomarkers for bloodstain age estimation, and at the same time proved that different environments had a significant impact on the REs of certain blood biomarkers, and sex differences did not affect the age estimation of bloodstains. The REs of the selected RNA molecules in this study showed a non-linear relationship with bloodstain age and the mathematical formula for estimating the bloodstain age based on the relative expression levels of hsa_circ_0001445, ALAS2 and HBB can be used to estimate the TsD of bloodstains from the REs of bloodstains of unknown age, which represent a potentially effective approach to looking for time-dependent changes and TsD estimation.
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Affiliation(s)
- Yangyan Wei
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Junyan Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
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59
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Pressler MP, Horvath A, Entcheva E. Sex-dependent transcription of cardiac electrophysiology and links to acetylation modifiers based on the GTEx database. Front Cardiovasc Med 2022; 9:941890. [PMID: 35935618 PMCID: PMC9354462 DOI: 10.3389/fcvm.2022.941890] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Development of safer drugs based on epigenetic modifiers, e.g., histone deacetylase inhibitors (HDACi), requires better understanding of their effects on cardiac electrophysiology. Using RNAseq data from the genotype-tissue-expression database (GTEx), we created models that link the abundance of acetylation enzymes (HDAC/SIRT/HATs), and the gene expression of ion channels (IC) via select cardiac transcription factors (TFs) in male and female adult human hearts (left ventricle, LV). Gene expression data (transcripts per million, TPM) from GTEx donors (21–70 y.o.) were filtered, normalized and transformed to Euclidian space to allow quantitative comparisons in 84 female and 158 male LVs. Sex-specific partial least-square (PLS) regression models, linking gene expression data for HDAC/SIRT/HATs to TFs and to ICs gene expression, revealed tight co-regulation of cardiac ion channels by HDAC/SIRT/HATs, with stronger clustering in the male LV. Co-regulation of genes encoding excitatory and inhibitory processes in cardiac tissue by the acetylation modifiers may help explain their predominantly net-neutral effects on cardiac electrophysiology. ATP1A1, encoding for the Na/K pump, represented an outlier—with orthogonal regulation by the acetylation modifiers to most of the ICs. The HDAC/SIRT/HAT effects were mediated by strong (+) TF regulators of ICs, e.g., MEF2A and TBX5, in both sexes. Furthermore, for male hearts, PLS models revealed a stronger (+/-) mediatory role on ICs for NKX25 and TGF1B/KLF4, respectively, while RUNX1 exhibited larger (-) TF effects on ICs in females. Male-trained PLS models of HDAC/SIRT/HAT effects on ICs underestimated the effects on some ICs in females. Insights from the GTEx dataset about the co-expression and transcriptional co-regulation of acetylation-modifying enzymes, transcription factors and key cardiac ion channels in a sex-specific manner can help inform safer drug design.
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Affiliation(s)
- Michael P. Pressler
- Department of Biomedical Engineering, George Washington University, Washington, DC, United States
| | - Anelia Horvath
- Department of Biochemistry and Molecular Medicine, McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Emilia Entcheva
- Department of Biomedical Engineering, George Washington University, Washington, DC, United States
- *Correspondence: Emilia Entcheva,
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60
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Molecular landscapes of human hippocampal immature neurons across lifespan. Nature 2022; 607:527-533. [PMID: 35794479 PMCID: PMC9316413 DOI: 10.1038/s41586-022-04912-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/26/2022] [Indexed: 01/18/2023]
Abstract
Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity and unique brain functions in rodents1,2 and are dysregulated in multiple human neurological disorders3-5. Little is known about the molecular characteristics of adult human hippocampal imGCs, and even their existence is under debate1,6-8. Here we performed single-nucleus RNA sequencing aided by a validated machine learning-based analytic approach to identify imGCs and quantify their abundance in the human hippocampus at different stages across the lifespan. We identified common molecular hallmarks of human imGCs across the lifespan and observed age-dependent transcriptional dynamics in human imGCs that suggest changes in cellular functionality, niche interactions and disease relevance, that differ from those in mice9. We also found a decreased number of imGCs with altered gene expression in Alzheimer's disease. Finally, we demonstrated the capacity for neurogenesis in the adult human hippocampus with the presence of rare dentate granule cell fate-specific proliferating neural progenitors and with cultured surgical specimens. Together, our findings suggest the presence of a substantial number of imGCs in the adult human hippocampus via low-frequency de novo generation and protracted maturation, and our study reveals their molecular properties across the lifespan and in Alzheimer's disease.
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61
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Wilk LS, Edelman GJ, Aalders MCG. Next-generation time of death estimation: combining surrogate model-based parameter optimization and numerical thermodynamics. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220162. [PMID: 35911202 PMCID: PMC9326290 DOI: 10.1098/rsos.220162] [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: 02/08/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
The postmortem interval (PMI), i.e. the time since death, plays a key role in forensic investigations, as it aids in the reconstruction of the timeline of events. Currently, the standard method for PMI estimation empirically correlates rectal temperatures and PMIs, frequently necessitating subjective correction factors. To address this shortcoming, numerical thermodynamic algorithms have recently been developed, providing rigorous methods to simulate postmortem body temperatures. Comparing these with measured body temperatures then allows non-subjective PMI determination. This approach, however, hinges on knowledge of two thermodynamic input parameters, which are often irretrievable in forensic practice: the ambient temperature prior to discovery of the body and the body temperature at the time of death (perimortem). Here, we overcome this critical limitation by combining numerical thermodynamic modelling with surrogate model-based parameter optimization. This hybrid computational framework predicts the two unknown parameters directly from the measured postmortem body temperatures. Moreover, by substantially reducing computation times (compared with conventional optimization algorithms), this powerful approach is uniquely suited for use directly at the crime scene. Crucially, we validated this method on deceased human bodies and achieved the lowest PMI estimation errors to date (0.18 h ± 0.77 h). Together, these aspects fundamentally expand the applicability of numerical thermodynamic PMI estimation.
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Affiliation(s)
- Leah S. Wilk
- Department of Biomedical Engineering and Physics, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
- Co van Ledden Hulsebosch Center, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Gerda J. Edelman
- Netherlands Forensic Institute, Divisie Bijzondere Dienstverlening en Expertise, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
| | - Maurice C. G. Aalders
- Department of Biomedical Engineering and Physics, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
- Co van Ledden Hulsebosch Center, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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62
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Liu CL, Chien MN, Hsu YC, Cheng SP. Transcriptomic Characteristics Associated With Aging in the Thyroid Gland. Front Nutr 2022; 9:859702. [PMID: 35694164 PMCID: PMC9174607 DOI: 10.3389/fnut.2022.859702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
The aging thyroid is associated with a plethora of morphological and functional changes. Limited studies have addressed the gene expression signature in the aging thyroid, except for sporadic reports using data from postmortem samples in the Genotype-Tissue Expression (GTEx) project. In this investigation, we analyzed the RNA sequencing data of 58 samples of normal-appearing counterpart thyroid tissues from The Cancer Genome Atlas. Aging-correlated genes were identified by determining the Spearman rank-order correlation between patient age and gene expression level. Additionally, we performed gene set enrichment analysis and conducted a weighted correlation network analysis. The results were compared with those analyzed using the GTEx data. The over-represented protein class of aging-correlated genes is mainly metabolite interconversion enzymes. Our analyses identified alterations in immune and inflammatory responses, mitochondrial functions, cytoskeletal proteins, as well as amino acid and cytochrome P450 metabolism. There was no significant association between thyroid differentiation and age. Our findings may shed molecular light on thyroid disorders in the geriatric population.
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Affiliation(s)
- Chien-Liang Liu
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Ming-Nan Chien
- Division of Endocrinology and Metabolism, Department of Internal Medicine, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Yi-Chiung Hsu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City, Taiwan
| | - Shih-Ping Cheng
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- *Correspondence: Shih-Ping Cheng
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63
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Jones RC, Karkanias J, Krasnow MA, Pisco AO, Quake SR, Salzman J, Yosef N, Bulthaup B, Brown P, Harper W, Hemenez M, Ponnusamy R, Salehi A, Sanagavarapu BA, Spallino E, Aaron KA, Concepcion W, Gardner JM, Kelly B, Neidlinger N, Wang Z, Crasta S, Kolluru S, Morri M, Pisco AO, Tan SY, Travaglini KJ, Xu C, Alcántara-Hernández M, Almanzar N, Antony J, Beyersdorf B, Burhan D, Calcuttawala K, Carter MM, Chan CKF, Chang CA, Chang S, Colville A, Crasta S, Culver RN, Cvijović I, D'Amato G, Ezran C, Galdos FX, Gillich A, Goodyer WR, Hang Y, Hayashi A, Houshdaran S, Huang X, Irwin JC, Jang S, Juanico JV, Kershner AM, Kim S, Kiss B, Kolluru S, Kong W, Kumar ME, Kuo AH, Leylek R, Li B, Loeb GB, Lu WJ, Mantri S, Markovic M, McAlpine PL, de Morree A, Morri M, Mrouj K, Mukherjee S, Muser T, Neuhöfer P, Nguyen TD, Perez K, Phansalkar R, Pisco AO, Puluca N, Qi Z, Rao P, Raquer-McKay H, Schaum N, Scott B, Seddighzadeh B, Segal J, Sen S, Sikandar S, Spencer SP, Steffes LC, Subramaniam VR, Swarup A, Swift M, Travaglini KJ, Van Treuren W, Trimm E, Veizades S, Vijayakumar S, Vo KC, Vorperian SK, Wang W, Weinstein HNW, Winkler J, Wu TTH, Xie J, Yung AR, Zhang Y, Detweiler AM, Mekonen H, Neff NF, Sit RV, Tan M, Yan J, Bean GR, Charu V, Forgó E, Martin BA, Ozawa MG, Silva O, Tan SY, Toland A, Vemuri VNP, Afik S, Awayan K, Botvinnik OB, Byrne A, Chen M, Dehghannasiri R, Detweiler AM, Gayoso A, Granados AA, Li Q, Mahmoudabadi G, McGeever A, de Morree A, Olivieri JE, Park M, Pisco AO, Ravikumar N, Salzman J, Stanley G, Swift M, Tan M, Tan W, Tarashansky AJ, Vanheusden R, Vorperian SK, Wang P, Wang S, Xing G, Xu C, Yosef N, Alcántara-Hernández M, Antony J, Chan CKF, Chang CA, Colville A, Crasta S, Culver R, Dethlefsen L, Ezran C, Gillich A, Hang Y, Ho PY, Irwin JC, Jang S, Kershner AM, Kong W, Kumar ME, Kuo AH, Leylek R, Liu S, Loeb GB, Lu WJ, Maltzman JS, Metzger RJ, de Morree A, Neuhöfer P, Perez K, Phansalkar R, Qi Z, Rao P, Raquer-McKay H, Sasagawa K, Scott B, Sinha R, Song H, Spencer SP, Swarup A, Swift M, Travaglini KJ, Trimm E, Veizades S, Vijayakumar S, Wang B, Wang W, Winkler J, Xie J, Yung AR, Artandi SE, Beachy PA, Clarke MF, Giudice LC, Huang FW, Huang KC, Idoyaga J, Kim SK, Krasnow M, Kuo CS, Nguyen P, Quake SR, Rando TA, Red-Horse K, Reiter J, Relman DA, Sonnenburg JL, Wang B, Wu A, Wu SM, Wyss-Coray T. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science 2022; 376:eabl4896. [PMID: 35549404 PMCID: PMC9812260 DOI: 10.1126/science.abl4896] [Citation(s) in RCA: 286] [Impact Index Per Article: 143.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.
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64
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Rodríguez-Lorenzo S, van Olst L, Rodriguez-Mogeda C, Kamermans A, van der Pol SMA, Rodríguez E, Kooij G, de Vries HE. Single-cell profiling reveals periventricular CD56 bright NK cell accumulation in multiple sclerosis. eLife 2022; 11:73849. [PMID: 35536009 PMCID: PMC9135404 DOI: 10.7554/elife.73849] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 04/29/2022] [Indexed: 11/21/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic demyelinating disease characterised by immune cell infiltration resulting in lesions that preferentially affect periventricular areas of the brain. Despite research efforts to define the role of various immune cells in MS pathogenesis, the focus has been on a few immune cell populations while full-spectrum analysis, encompassing others such as natural killer (NK) cells, has not been performed. Here, we used single-cell mass cytometry (CyTOF) to profile the immune landscape of brain periventricular areas – septum and choroid plexus – and of the circulation from donors with MS, dementia and controls without neurological disease. Using a 37-marker panel, we revealed the infiltration of T cells and antibody-secreting cells in periventricular brain regions and identified a novel NK cell signature specific to MS. CD56bright NK cells were accumulated in the septum of MS donors and displayed an activated and migratory phenotype, similar to that of CD56bright NK cells in the circulation. We validated this signature by multiplex immunohistochemistry and found that the number of NK cells with high expression of granzyme K, typical of the CD56bright subset, was increased in both periventricular lesions and the choroid plexus of donors with MS. Together, our multi-tissue single-cell data shows that CD56bright NK cells accumulate in the periventricular brain regions of MS patients, bringing NK cells back to the spotlight of MS pathology.
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Affiliation(s)
- Sabela Rodríguez-Lorenzo
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
| | - Lynn van Olst
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
| | - Carla Rodriguez-Mogeda
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
| | - Alwin Kamermans
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
| | - Susanne M A van der Pol
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
| | - Ernesto Rodríguez
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
| | - Gijs Kooij
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
| | - Helga E de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location VUmc, Amsterdam, Netherlands
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65
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Somekh J, Lotan N, Sussman E, Yehuda GA. Predicting mechanical ventilation effects on six human tissue transcriptomes. PLoS One 2022; 17:e0264919. [PMID: 35271646 PMCID: PMC8912236 DOI: 10.1371/journal.pone.0264919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 02/21/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mechanical ventilation (MV) is a lifesaving therapy used for patients with respiratory failure. Nevertheless, MV is associated with numerous complications and increased mortality. The aim of this study is to define the effects of MV on gene expression of direct and peripheral human tissues. METHODS Classification models were applied to Genotype-Tissue Expression Project (GTEx) gene expression data of six representative tissues-liver, adipose, skin, nerve-tibial, muscle and lung, for performance comparison and feature analysis. We utilized 18 prediction models using the Random Forest (RF), XGBoost (eXtreme Gradient Boosting) decision tree and ANN (Artificial Neural Network) methods to classify ventilation and non-ventilation samples and to compare their prediction performance for the six tissues. In the model comparison, the AUC (area under receiver operating curve), accuracy, precision, recall, and F1 score were used to evaluate the predictive performance of each model. We then conducted feature analysis per each tissue to detect MV marker genes followed by pathway enrichment analysis for these genes. RESULTS XGBoost outperformed the other methods and predicted samples had undergone MV with an average accuracy for the six tissues of 0.951 and average AUC of 0.945. The feature analysis detected a combination of MV marker genes per each tested tissue, some common across several tissues. MV marker genes were mainly related to inflammation and fibrosis as well as cell development and movement regulation. The MV marker genes were significantly enriched in inflammatory and viral pathways. CONCLUSION The XGBoost method demonstrated clear enhanced performance and feature analysis compared to the other models. XGBoost was helpful in detecting the tissue-specific marker genes for identifying transcriptomic changes related to MV. Our results show that MV is associated with reduced development and movement in the tissues and higher inflammation and injury not only in direct tissues such as the lungs but also in peripheral tissues and thus should be carefully considered before being implemented.
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Affiliation(s)
- Judith Somekh
- Department of Information Systems, University of Haifa, Haifa, Israel
- * E-mail:
| | - Nir Lotan
- Department of Information Systems, University of Haifa, Haifa, Israel
| | - Ehud Sussman
- Department of Information Systems, University of Haifa, Haifa, Israel
| | - Gur Arye Yehuda
- Department of Information Systems, University of Haifa, Haifa, Israel
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66
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Zhang Z, Zamojski M, Smith GR, Willis TL, Yianni V, Mendelev N, Pincas H, Seenarine N, Amper MAS, Vasoya M, Cheng WS, Zaslavsky E, Nair VD, Turgeon JL, Bernard DJ, Troyanskaya OG, Andoniadou CL, Sealfon SC, Ruf-Zamojski F. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms. Cell Rep 2022; 38:110467. [PMID: 35263594 PMCID: PMC8957708 DOI: 10.1016/j.celrep.2022.110467] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/23/2021] [Accepted: 02/09/2022] [Indexed: 01/07/2023] Open
Abstract
Despite their importance in tissue homeostasis and renewal, human pituitary stem cells (PSCs) are incompletely characterized. We describe a human single nucleus RNA-seq and ATAC-seq resource from pediatric, adult, and aged postmortem pituitaries (snpituitaryatlas.princeton.edu) and characterize cell-type-specific gene expression and chromatin accessibility programs for all major pituitary cell lineages. We identify uncommitted PSCs, committing progenitor cells, and sex differences. Pseudotime trajectory analysis indicates that early-life PSCs are distinct from the other age groups. Linear modeling of same-cell multiome data identifies regulatory domain accessibility sites and transcription factors that are significantly associated with gene expression in PSCs compared with other cell types and within PSCs. We identify distinct deterministic mechanisms that contribute to heterogeneous marker expression within PSCs. These findings characterize human stem cell lineages and reveal diverse mechanisms regulating key PSC genes and cell type identity. This study profiles the gene expression and chromatin accessibility landscapes in postmortem male and female pituitaries of different ages using single nucleus multiomics technologies. Zhang et al. characterize the pituitary stem cell population and develop computational methods, which allow us to elucidate regulatory mechanisms underlying pituitary stem cell identity.
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Affiliation(s)
- Zidong Zhang
- Lewis-Sigler Institute for Integrative Genomics and Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA
| | - Michel Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Thea L Willis
- Center for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Val Yianni
- Center for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Natalia Mendelev
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Nitish Seenarine
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Mary Anne S Amper
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Mital Vasoya
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Wan Sze Cheng
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Judith L Turgeon
- Department of Internal Medicine, University of California, Davis, Davis, CA, USA
| | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics and Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA; Department of Computer Science, Princeton University, Princeton, NJ, USA; Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Cynthia L Andoniadou
- Center for Craniofacial and Regenerative Biology, King's College London, London, UK; Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA.
| | - Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA.
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67
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Post mortem computed tomography meets radiomics: a case series on fractal analysis of post mortem changes in the brain. Int J Legal Med 2022; 136:719-727. [PMID: 35239030 PMCID: PMC9005394 DOI: 10.1007/s00414-022-02801-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/14/2022] [Indexed: 10/26/2022]
Abstract
Estimating the post-mortem interval is a fundamental, albeit challenging task in forensic sciences. To this aim, forensic practitioners need to assess post-mortem changes through a plethora of different methods, most of which are inherently qualitative, thus providing broad time intervals rather than precise determinations. This challenging problem is further complicated by the influence of environmental factors, which modify the temporal dynamics of post-mortem changes, sometimes in a rather unpredictable fashion. In this context, the search for quantitative and objective descriptors of post-mortem changes is highly demanded. In this study, we used computed tomography (CT) to assess the post-mortem anatomical modifications occurring in the time interval 0-4 days after death in the brain of four corpses. Our results show that fractal analysis of CT brain slices provides a set of quantitative descriptors able to map post-mortem changes over time throughout the whole brain. Although incapable of producing a direct estimation of the PMI, these descriptors could be used in combination with other more established methods to improve the accuracy and reliability of PMI determination.
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68
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Hu Y, Tian L, Ma K, Han L, Li W, Hu L, Fei G, Zhang T, Yu D, Xu L, Wang F, Xiao B, Chen L. ER stress-related protein, CHOP, may serve as a biomarker of mechanical asphyxia: a primary study. Int J Legal Med 2022; 136:1091-1104. [PMID: 35122137 DOI: 10.1007/s00414-021-02770-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/20/2021] [Indexed: 11/30/2022]
Abstract
The precise authentication of death from mechanical asphyxia (DMA) has been a complex problem in forensic medicine. Besides the traditional methods that concern the superficial characterization of the body, researchers are now paying more attention to the biomarkers that may help the identification of DMA. It has been reported that the extremely hypoxic environment created by DMA can cause the specific expression of mitochondria-related protein, which may sever as the biomarkers of DMA authentication. Since endoplasmic reticulum stress (ER stress) has been found to be related to the dysfunction of mitochondria, it is promising to look for the biomarkers of DMA among ER stress-related proteins. In this article, animal and cell experiments were conducted to examine how ER-mitochondria interaction may be influenced in the hypoxic condition caused by DMA primarily. Human samples were then used to verify the possible biomarkers of DMA. We found that ER stress-related protein CHOP was significantly up-regulated within a short-term postmortem interval (PMI) in brain tissue of DMA samples, which may interact with a series of ER stress- and mitochondria-related protein, leading to the apoptosis of the cells. It was also verified in human samples that the expression level of CHOP can sever as a potential biomarker of DMA within a specific PMI.
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Affiliation(s)
- Yikai Hu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Lu Tian
- Forensic Lab, Criminal Science and Technology Institute, Pudong Branch, Shanghai Public Security Bureau, 255 Yanzhong Road, Shanghai, 200125, People's Republic of China
| | - Kaijun Ma
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai, 200082, People's Republic of China
| | - Liujun Han
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Wencan Li
- Forensic Lab, Criminal Science and Technology Institute, Pudong Branch, Shanghai Public Security Bureau, 255 Yanzhong Road, Shanghai, 200125, People's Republic of China
| | - Luyuyan Hu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Geng Fei
- Department of Criminal Science and Technology, Shanghai Police College, 100 Chongjing Road, Shanghai, 200137, People's Republic of China
| | - Tianye Zhang
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai, 200082, People's Republic of China
| | - Delun Yu
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai, 200082, People's Republic of China
| | - Luyi Xu
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai, 200082, People's Republic of China
| | - Feng Wang
- Forensic Lab, Criminal Science and Technology Institute, Qianjiang Public Security Bureau, 27 Nanpu Road, Qianjiang, 433199, People's Republic of China
| | - Bi Xiao
- Forensic Lab, Criminal Science and Technology Institute, Shanghai Public Security Bureau, 803 North Zhongshan Road, Shanghai, 200082, People's Republic of China.
| | - Long Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai, 200032, People's Republic of China.
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69
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Wucher V, Sodaei R, Amador R, Irimia M, Guigó R. Day-night and seasonal variation of human gene expression across tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.02.28.433266. [PMID: 33688644 PMCID: PMC7941615 DOI: 10.1101/2021.02.28.433266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues. Overall, most variation across tissues during day-night and among seasons was unique to each cycle. Although all tissues remodeled their transcriptomes, brain and gonadal tissues exhibited the highest seasonality, whereas those in the thoracic cavity showed stronger day-night regulation. Core clock genes displayed marked day-night differences across multiple tissues, which were largely conserved in baboon and mouse, but adapted to their nocturnal or diurnal habits. Seasonal variation of expression affected multiple pathways and it was enriched among genes associated with the immune response, consistent with the seasonality of viral infections. Furthermore, they unveiled cytoarchitectural changes in brain regions. Altogether, our results provide the first combined atlas of how transcriptomes from human tissues adapt to major cycling environmental conditions.
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Affiliation(s)
- Valentin Wucher
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- NeuroMyogene Institute, SynatAc Team, INSERM U1217/UMR CNRS 5310, Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndrome, Hospices Civils de Lyon, Lyon, France
- University of Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Reza Sodaei
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raziel Amador
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
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70
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Chighine A, Porcu M, Ferino G, Lenigno N, Trignano C, d'Aloja E, Locci E. Infant urinary metabolomic profile in a fatal acute methadone intoxication. Int J Legal Med 2022; 136:569-575. [PMID: 35018499 PMCID: PMC8847265 DOI: 10.1007/s00414-021-02772-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/29/2021] [Indexed: 11/25/2022]
Abstract
A case report suspicious for a Sudden Infant Death Syndrome is here described. Pathological findings were consistent with an acute respiratory failure while toxicological analysis revealed an elevated blood methadone concentration. Death was then ascribed to an acute methadone intoxication. In addition to the routinary approach, the urinary sample collected at autopsy was investigated with a 1H NMR metabolomic approach and the identified metabolomic profile was challenged with the urinary metabolomic profiles previously obtained from 10 newborns who experienced perinatal asphyxia and 16 healthy control newborns. Intriguingly, the urinary profile of the methadone intoxicated infant was very similar to those belonging to the perinatal asphyxia newborns, especially to those belonging to the newborns characterised by the worst outcome. The results offer several hints on a shared metabolic derangement between different mechanisms of asphyxia/hypoxia. To the best of the authors’ knowledge, this is the first report of the use of a metabolomic approach in a pathological case, in which metabolomics offers useful additional information regarding the mechanism and the cause of death.
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Affiliation(s)
- Alberto Chighine
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria Di Monserrato, 09042, Monserrato, Cagliari, Italy.
| | - Michele Porcu
- Department of Medical Sciences and Public Health, Section of Radiology, University of Cagliari, Cagliari, Italy
| | - Giulio Ferino
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria Di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Nicola Lenigno
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria Di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Claudia Trignano
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ernesto d'Aloja
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria Di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Emanuela Locci
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria Di Monserrato, 09042, Monserrato, Cagliari, Italy
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71
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Cieśla J, Tomsia M. Cadaveric Stem Cells: Their Research Potential and Limitations. Front Genet 2022; 12:798161. [PMID: 35003228 PMCID: PMC8727551 DOI: 10.3389/fgene.2021.798161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/30/2021] [Indexed: 12/28/2022] Open
Abstract
In the era of growing interest in stem cells, the availability of donors for transplantation has become a problem. The isolation of embryonic and fetal cells raises ethical controversies, and the number of adult donors is deficient. Stem cells isolated from deceased donors, known as cadaveric stem cells (CaSCs), may alleviate this problem. So far, it was possible to isolate from deceased donors mesenchymal stem cells (MSCs), adipose delivered stem cells (ADSCs), neural stem cells (NSCs), retinal progenitor cells (RPCs), induced pluripotent stem cells (iPSCs), and hematopoietic stem cells (HSCs). Recent studies have shown that it is possible to collect and use CaSCs from cadavers, even these with an extended postmortem interval (PMI) provided proper storage conditions (like cadaver heparinization or liquid nitrogen storage) are maintained. The presented review summarizes the latest research on CaSCs and their current therapeutic applications. It describes the developments in thanatotranscriptome and scaffolding for cadaver cells, summarizes their potential applications in regenerative medicine, and lists their limitations, such as donor’s unknown medical condition in criminal cases, limited differentiation potential, higher risk of carcinogenesis, or changing DNA quality. Finally, the review underlines the need to develop procedures determining the safe CaSCs harvesting and use.
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Affiliation(s)
- Julia Cieśla
- School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Marcin Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Medical University of Silesia, Katowice, Poland
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72
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Grima N, Henden L, Watson O, Blair IP, Williams KL. Simultaneous Isolation of High-Quality RNA and DNA From Postmortem Human Central Nervous System Tissues for Omics Studies. J Neuropathol Exp Neurol 2021; 81:135-145. [PMID: 34939123 DOI: 10.1093/jnen/nlab129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multi-omics approaches are increasingly being adopted to understand the complex networks underlying disease. The coisolation of high-quality nucleotides from affected tissues is paramount for the parallel analysis of transcriptomic, genomic, and epigenomic data sets. Although nucleotides extracted from postmortem central nervous system (CNS) tissue are widely used in the study of neurodegenerative disease, assessment of methods for the simultaneous isolation of DNA and RNA is limited. Herein, we describe a strategy for the isolation of high-quality DNA and RNA from postmortem human tissue from 7 CNS regions. Motor cortex, frontal cortex, hippocampus, occipital cortex, anterior cingulate cortex, cerebellum, and spinal cord tissues were obtained from 22 individuals diagnosed with motor neuron disease (MND) and 13 neurologically normal controls (n = 245 tissues). We demonstrated that the Qiagen AllPrep DNA/RNA kit consistently isolated DNA and RNA of high yield and quality from all 6 brain regions. Importantly, phenol-chloroform-based extraction was required to isolate high-yield RNA from spinal cord. RNA sequencing using RNA extracted from 6 CNS regions (n = 60) generated high-quality transcriptomes. Hierarchical clustering of data from motor cortex, using an MND susceptibility gene panel and marker genes of disease-associated microglia, demonstrated that MND-specific gene expression signatures could be detected in the transcriptome data.
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Affiliation(s)
- Natalie Grima
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Lyndal Henden
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Owen Watson
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P Blair
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
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73
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Storm CS, Kia DA, Almramhi MM, Bandres-Ciga S, Finan C, Hingorani AD, Wood NW. Finding genetically-supported drug targets for Parkinson's disease using Mendelian randomization of the druggable genome. Nat Commun 2021; 12:7342. [PMID: 34930919 PMCID: PMC8688480 DOI: 10.1038/s41467-021-26280-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 09/14/2021] [Indexed: 12/30/2022] Open
Abstract
Parkinson's disease is a neurodegenerative movement disorder that currently has no disease-modifying treatment, partly owing to inefficiencies in drug target identification and validation. We use Mendelian randomization to investigate over 3,000 genes that encode druggable proteins and predict their efficacy as drug targets for Parkinson's disease. We use expression and protein quantitative trait loci to mimic exposure to medications, and we examine the causal effect on Parkinson's disease risk (in two large cohorts), age at onset and progression. We propose 23 drug-targeting mechanisms for Parkinson's disease, including four possible drug repurposing opportunities and two drugs which may increase Parkinson's disease risk. Of these, we put forward six drug targets with the strongest Mendelian randomization evidence. There is remarkably little overlap between our drug targets to reduce Parkinson's disease risk versus progression, suggesting different molecular mechanisms. Drugs with genetic support are considerably more likely to succeed in clinical trials, and we provide compelling genetic evidence and an analysis pipeline to prioritise Parkinson's disease drug development.
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Affiliation(s)
- Catherine S Storm
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| | - Demis A Kia
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| | - Mona M Almramhi
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London WC1E 6BT, UK
- University College London British Heart Foundation Research Accelerator Centre, New Delhi, India
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX Utrecht, the Netherlands
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London WC1E 6BT, UK
- University College London British Heart Foundation Research Accelerator Centre, New Delhi, India
- Health Data Research UK, 222 Euston Road, London, UK
| | - Nicholas W Wood
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK.
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74
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Perez MF, Sarkies P. Malignancy and NF-κB signalling strengthen coordination between expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes. Genome Biol 2021; 22:328. [PMID: 34857014 PMCID: PMC8638269 DOI: 10.1186/s13059-021-02541-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. The mammalian mitochondrial genome encodes for 13 mitochondrial proteins, and the remaining mitochondrial proteins are encoded by the nuclear genome. Little is known about how coordination between the expression of the two sets of genes is achieved. RESULTS Correlation analysis of RNA-seq expression data from large publicly available datasets is a common method to leverage genetic diversity to infer gene co-expression modules. Here we use this method to investigate nuclear-mitochondrial gene expression coordination. We identify a pitfall in correlation analysis that results from the large variation in the proportion of transcripts from the mitochondrial genome in RNA-seq data. Commonly used normalisation techniques based on total read counts, such as FPKM or TPM, produce artefactual negative correlations between mitochondrial- and nuclear-encoded transcripts. This also results in artefactual correlations between pairs of nuclear-encoded genes, with important consequences for inferring co-expression modules beyond mitochondria. We show that these effects can be overcome by normalizing using the median-ratio normalisation (MRN) or trimmed mean of M values (TMM) methods. Using these normalisations, we find only weak and inconsistent correlations between mitochondrial and nuclear-encoded mitochondrial genes in the majority of healthy human tissues from the GTEx database. CONCLUSIONS We show that a subset of healthy tissues with high expression of NF-κB show significant coordination, suggesting a role for NF-κB in ensuring balanced expression between mitochondrial and nuclear genes. Contrastingly, most cancer types show robust coordination of nuclear and mitochondrial OXPHOS gene expression, identifying this as a feature of gene regulation in cancer.
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Affiliation(s)
- Marcos Francisco Perez
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
- Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
- Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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75
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Abstract
BACKGROUND Electroencephalography (EEG) findings following cardiovascular collapse in death are uncertain. We aimed to characterize EEG changes immediately preceding and following cardiac death. METHODS We retrospectively analyzed EEGs of patients who died from cardiac arrest while undergoing standard EEG monitoring in an intensive care unit. Patients with brain death preceding cardiac death were excluded. Three events during fatal cardiovascular failure were investigated: (1) last recorded QRS complex on electrocardiogram (QRS0), (2) cessation of cerebral blood flow (CBF0) estimated as the time that blood pressure and heart rate dropped below set thresholds, and (3) electrocerebral silence on EEG (EEG0). We evaluated EEG spectral power, coherence, and permutation entropy at these time points. RESULTS Among 19 patients who died while undergoing EEG monitoring, seven (37%) had a comfort-measures-only status and 18 (95%) had a do-not-resuscitate status in place at the time of death. EEG0 occurred at the time of QRS0 in five patients and after QRS0 in two patients (cohort median - 2.0, interquartile range - 8.0 to 0.0), whereas EEG0 was seen at the time of CBF0 in six patients and following CBF0 in 11 patients (cohort median 2.0 min, interquartile range - 1.5 to 6.0). After CBF0, full-spectrum log power (p < 0.001) and coherence (p < 0.001) decreased on EEG, whereas delta (p = 0.007) and theta (p < 0.001) permutation entropy increased. CONCLUSIONS Rarely may patients have transient electrocerebral activity following the last recorded QRS (less than 5 min) and estimated cessation of cerebral blood flow. These results may have implications for discussions around cardiopulmonary resuscitation and organ donation.
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76
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Wang S, Yao X, Ma S, Ping Y, Fan Y, Sun S, He Z, Shi Y, Sun L, Xiao S, Song M, Cai J, Li J, Tang R, Zhao L, Wang C, Wang Q, Zhao L, Hu H, Liu X, Sun G, Chen L, Pan G, Chen H, Li Q, Zhang P, Xu Y, Feng H, Zhao GG, Wen T, Yang Y, Huang X, Li W, Liu Z, Wang H, Wu H, Hu B, Ren Y, Zhou Q, Qu J, Zhang W, Liu GH, Bian XW. A single-cell transcriptomic landscape of the lungs of patients with COVID-19. Nat Cell Biol 2021; 23:1314-1328. [PMID: 34876692 PMCID: PMC8650955 DOI: 10.1038/s41556-021-00796-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 10/18/2021] [Indexed: 02/08/2023]
Abstract
The lung is the primary organ targeted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), making respiratory failure a leading coronavirus disease 2019 (COVID-19)-related mortality. However, our cellular and molecular understanding of how SARS-CoV-2 infection drives lung pathology is limited. Here we constructed multi-omics and single-nucleus transcriptomic atlases of the lungs of patients with COVID-19, which integrate histological, transcriptomic and proteomic analyses. Our work reveals the molecular basis of pathological hallmarks associated with SARS-CoV-2 infection in different lung and infiltrating immune cell populations. We report molecular fingerprints of hyperinflammation, alveolar epithelial cell exhaustion, vascular changes and fibrosis, and identify parenchymal lung senescence as a molecular state of COVID-19 pathology. Moreover, our data suggest that FOXO3A suppression is a potential mechanism underlying the fibroblast-to-myofibroblast transition associated with COVID-19 pulmonary fibrosis. Our work depicts a comprehensive cellular and molecular atlas of the lungs of patients with COVID-19 and provides insights into SARS-CoV-2-related pulmonary injury, facilitating the identification of biomarkers and development of symptomatic treatments.
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Affiliation(s)
- Si Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Xiaohong Yao
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yifang Ping
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhicheng He
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yu Shi
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Liang Sun
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The NHC Key Laboratory of Drug Addiction Medicine, Kunming Medical University, Kunming, China
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatric, Beijing Hospital, National Center of Gerontology, National Health Commission, Beijing, China
| | - Shiqi Xiao
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Cai
- Department of Pathology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Tang
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Liyun Zhao
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Zhao
- Department of Pathology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huifang Hu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xindong Liu
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Guoqiang Sun
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lu Chen
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Guoqing Pan
- The NHC Key Laboratory of Drug Addiction Medicine, Kunming Medical University, Kunming, China
| | - Huaiyong Chen
- Tianjin Key Laboratory of Lung Regenerative Medicine, Tianjin Institute of Respiratory Diseases, Haihe Hospital, Tianjin University, Tianjin, China
| | - Qingrui Li
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Peipei Zhang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Intelligent Pathology Institute, The First Hospital Affiliated to University of Science and Technology of China, Hefei, China
| | - Yuanyuan Xu
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Huyi Feng
- Chongqing Renji Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Guo-Guang Zhao
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing, China
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Tianzi Wen
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China
| | - Yungui Yang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuequan Huang
- Center of Minimally Invasive Intervention, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Wei Li
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhenhua Liu
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hongmei Wang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Haibo Wu
- Intelligent Pathology Institute, The First Hospital Affiliated to University of Science and Technology of China, Hefei, China
| | - Baoyang Hu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yong Ren
- Department of Pathology, General Hospital of Central Theater Command of PLA, Wuhan, China
| | - Qi Zhou
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Weiqi Zhang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China.
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatric, Beijing Hospital, National Center of Gerontology, National Health Commission, Beijing, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, International Center for Aging and Cancer, Xuanwu Hospital Capital Medical University, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xiu-Wu Bian
- Institute of Pathology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Chongqing, China.
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77
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Zhang Q, Tombline G, Ablaeva J, Zhang L, Zhou X, Smith Z, Zhao Y, Xiaoli AM, Wang Z, Lin JR, Jabalameli MR, Mitra J, Nguyen N, Vijg J, Seluanov A, Gladyshev VN, Gorbunova V, Zhang ZD. Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation. Cell Rep 2021; 37:109965. [PMID: 34758328 PMCID: PMC8656434 DOI: 10.1016/j.celrep.2021.109965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 06/07/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
The North American beaver is an exceptionally long-lived and cancer-resistant rodent species. Here, we report the evolutionary changes in its gene coding sequences, copy numbers, and expression. We identify changes that likely increase its ability to detoxify aldehydes, enhance tumor suppression and DNA repair, and alter lipid metabolism, potentially contributing to its longevity and cancer resistance. Hpgd, a tumor suppressor gene, is uniquely duplicated in beavers among rodents, and several genes associated with tumor suppression and longevity are under positive selection in beavers. Lipid metabolism genes show positive selection signals, changes in copy numbers, or altered gene expression in beavers. Aldh1a1, encoding an enzyme for aldehydes detoxification, is particularly notable due to its massive expansion in beavers, which enhances their cellular resistance to ethanol and capacity to metabolize diverse aldehyde substrates from lipid oxidation and their woody diet. We hypothesize that the amplification of Aldh1a1 may contribute to the longevity of beavers. Zhang et al. examine the genome of North American beavers and find evolutionary changes that could contribute to beavers’ longevity. In particular, Aldh1a1, encoding an enzyme for aldehyde detoxification, is massively expanded in the beaver genome, protecting them against exposure to aldehydes from lipid oxidation and their woody diet.
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Affiliation(s)
- Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zachary Smith
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alus M Xiaoli
- Departments of Medicine and Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhen Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nha Nguyen
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
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78
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Li B, Ritchie MD. From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries. Front Genet 2021; 12:713230. [PMID: 34659337 PMCID: PMC8515949 DOI: 10.3389/fgene.2021.713230] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Since their inception, genome-wide association studies (GWAS) have identified more than a hundred thousand single nucleotide polymorphism (SNP) loci that are associated with various complex human diseases or traits. The majority of GWAS discoveries are located in non-coding regions of the human genome and have unknown functions. The valley between non-coding GWAS discoveries and downstream affected genes hinders the investigation of complex disease mechanism and the utilization of human genetics for the improvement of clinical care. Meanwhile, advances in high-throughput sequencing technologies reveal important genomic regulatory roles that non-coding regions play in the transcriptional activities of genes. In this review, we focus on data integrative bioinformatics methods that combine GWAS with functional genomics knowledge to identify genetically regulated genes. We categorize and describe two types of data integrative methods. First, we describe fine-mapping methods. Fine-mapping is an exploratory approach that calibrates likely causal variants underneath GWAS signals. Fine-mapping methods connect GWAS signals to potentially causal genes through statistical methods and/or functional annotations. Second, we discuss gene-prioritization methods. These are hypothesis generating approaches that evaluate whether genetic variants regulate genes via certain genetic regulatory mechanisms to influence complex traits, including colocalization, mendelian randomization, and the transcriptome-wide association study (TWAS). TWAS is a gene-based association approach that investigates associations between genetically regulated gene expression and complex diseases or traits. TWAS has gained popularity over the years due to its ability to reduce multiple testing burden in comparison to other variant-based analytic approaches. Multiple types of TWAS methods have been developed with varied methodological designs and biological hypotheses over the past 5 years. We dive into discussions of how TWAS methods differ in many aspects and the challenges that different TWAS methods face. Overall, TWAS is a powerful tool for identifying complex trait-associated genes. With the advent of single-cell sequencing, chromosome conformation capture, gene editing technologies, and multiplexing reporter assays, we are expecting a more comprehensive understanding of genomic regulation and genetically regulated genes underlying complex human diseases and traits in the future.
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Affiliation(s)
- Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, United States
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, United States
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79
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Wilk LS, Edelman GJ, Roos M, Clerkx M, Dijkman I, Melgar JV, Oostra RJ, Aalders MCG. Individualised and non-contact post-mortem interval determination of human bodies using visible and thermal 3D imaging. Nat Commun 2021; 12:5997. [PMID: 34650046 PMCID: PMC8517003 DOI: 10.1038/s41467-021-26318-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
Abstract
Determining the time since death, i.e., post-mortem interval (PMI), often plays a key role in forensic investigations. The current standard PMI-estimation method empirically correlates rectal temperatures and PMIs, frequently necessitating subjective correction factors. To overcome this, we previously developed a thermodynamic finite-difference (TFD) algorithm, providing a rigorous method to simulate post-mortem temperatures of bodies assuming a straight posture. However, in forensic practice, bodies are often found in non-straight postures, potentially limiting applicability of this algorithm in these cases. Here, we develop an individualised approach, enabling PMI reconstruction for bodies in arbitrary postures, by combining photogrammetry and TFD modelling. Utilising thermal photogrammetry, this approach also represents the first non-contact method for PMI reconstruction. The performed lab and crime scene validations reveal PMI reconstruction accuracies of 0.26 h ± 1.38 h for true PMIs between 2 h and 35 h and total procedural durations of ~15 min. Together, these findings broaden the potential applicability of TFD-based PMI reconstruction. Establishing the time since death (TSD) is vital in many forensic investigations. By combining thermometry, photogrammetry and numerical thermodynamic modelling, the TSD can be determined non-invasively for bodies of arbitrary shape and posture with an unprecedented accuracy of 0.26 h ± 1.38 h.
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Affiliation(s)
- Leah S Wilk
- Department of Biomedical Engineering and Physics, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Co van Ledden Hulsebosch Center, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands
| | - Gerda J Edelman
- Netherlands Forensic Institute, Divisie Bijzondere Dienstverlening en Expertise, Laan van Ypenburg 6, 2497 GB, The Hague, The Netherlands
| | - Martin Roos
- Netherlands Forensic Institute, Divisie Bijzondere Dienstverlening en Expertise, Laan van Ypenburg 6, 2497 GB, The Hague, The Netherlands
| | - Mara Clerkx
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Inge Dijkman
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Jordi Vera Melgar
- Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Roelof-Jan Oostra
- Co van Ledden Hulsebosch Center, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands.,Department of Medical Biology, Section Clinical Anatomy and Embryology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Maurice C G Aalders
- Department of Biomedical Engineering and Physics, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands. .,Co van Ledden Hulsebosch Center, University of Amsterdam, Science Park 904, 1098XH, Amsterdam, The Netherlands.
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80
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Chen N, Wu H, Deng Z, Liao Z, Feng S, Luo Z, Chu Y, Qiu G, Li X, Jin Y, Rong S, Wang F, Gan L, Chen R, Zhao L. [An optimized protocol of meniscus cell extraction for single-cell RNA sequencing]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1310-1318. [PMID: 34658344 DOI: 10.12122/j.issn.1673-4254.2021.09.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To optimize the protocol of meniscus cell extraction to enhance the efficiency of cell suspension preparation and maintain a high cell viability for single-cell RNA sequencing. METHODS We compared the efficiency of the routine cell extraction methods (short-time digestion and long-time digestion) and the optimized protocol for obtaining meniscus cell suspensions by evaluating the cell number obtained and the cell viability. Single-cell RNA sequencing datasets were analyzed to evaluate the stability of the cell suspension prepared using the optimized protocol. The reliability of the optimized protocol was assessed by comparing the single-cell RNA sequencing dataset obtained by the optimized protocol with published single-cell RNA sequencing datasets of the meniscus. RESULTS The optimized protocol harvested a greater number of cells (over 1×105) than the routine protocols. The cell suspension prepared with the optimized protocol showed a cell viability higher than 80%, the highest among the 3 methods. Analysis of single-cell RNA sequencing datasets showed that the ratio of the mitochondrial genes was below 20% in over 80% of the cells. CD34+ cells, MCAM+ cells and COL1A1+ cells were identified in the datasets. Comparison with the publish datasets showed that the optimized protocol was capable of harvesting COL3A1+, COL1A1+, MYLK+, BMP2+, CD93+ and CDK1+ cells. CONCLUSION Single-cell suspension prepared from the meniscus can be stably obtained using the optimized protocol for single-cell RNA sequencing using the 10× Genomics platform.
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Affiliation(s)
- N Chen
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - H Wu
- Zhujiang Hospital, Southern Medical University, Guangzhou 510080, China
| | - Z Deng
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Z Liao
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - S Feng
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Z Luo
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Y Chu
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - G Qiu
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - X Li
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Y Jin
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - S Rong
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - F Wang
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - L Gan
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - R Chen
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - L Zhao
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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81
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Antiga LG, Sibbens L, Abakkouy Y, Decorte R, Van Den Bogaert W, Van de Voorde W, Bekaert B. Cell survival and DNA damage repair are promoted in the human blood thanatotranscriptome shortly after death. Sci Rep 2021; 11:16585. [PMID: 34400689 PMCID: PMC8368024 DOI: 10.1038/s41598-021-96095-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/30/2021] [Indexed: 11/09/2022] Open
Abstract
RNA analysis of post-mortem tissues, or thanatotranscriptomics, has become a topic of interest in forensic science due to the essential information it can provide in forensic investigations. Several studies have previously investigated the effect of death on gene transcription, but it has never been conducted with samples of the same individual. For the first time, a longitudinal mRNA expression analysis study was performed with post-mortem human blood samples from individuals with a known time of death. The results reveal that, after death, two clearly differentiated groups of up- and down-regulated genes can be detected. Pathway analysis suggests active processes that promote cell survival and DNA damage repair, rather than passive degradation, are the source of early post-mortem changes of gene expression in blood. In addition, a generalized linear model with an elastic net restriction predicted post-mortem interval with a root mean square error of 4.75 h. In conclusion, we demonstrate that post-mortem gene expression data can be used as biomarkers to estimate the post-mortem interval though further validation using independent sample sets is required before use in forensic casework.
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Affiliation(s)
- Laura G Antiga
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Department of Experimental and Health Sciences (CEXS), University Pompeu Fabra (UPF), Barcelona, Spain
| | - Lode Sibbens
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
| | - Yasmina Abakkouy
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Wouter Van Den Bogaert
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Wim Van de Voorde
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Bram Bekaert
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium.
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium.
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82
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Sierra B, Magalhães AC, Soares D, Cavadas B, Perez AB, Alvarez M, Aguirre E, Bracho C, Pereira L, Guzman MG. Multi-Tissue Transcriptomic-Informed In Silico Investigation of Drugs for the Treatment of Dengue Fever Disease. Viruses 2021; 13:v13081540. [PMID: 34452405 PMCID: PMC8402662 DOI: 10.3390/v13081540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 12/19/2022] Open
Abstract
Transcriptomics, proteomics and pathogen-host interactomics data are being explored for the in silico–informed selection of drugs, prior to their functional evaluation. The effectiveness of this kind of strategy has been put to the test in the current COVID-19 pandemic, and it has been paying off, leading to a few drugs being rapidly repurposed as treatment against SARS-CoV-2 infection. Several neglected tropical diseases, for which treatment remains unavailable, would benefit from informed in silico investigations of drugs, as performed in this work for Dengue fever disease. We analyzed transcriptomic data in the key tissues of liver, spleen and blood profiles and verified that despite transcriptomic differences due to tissue specialization, the common mechanisms of action, “Adrenergic receptor antagonist”, “ATPase inhibitor”, “NF-kB pathway inhibitor” and “Serotonin receptor antagonist”, were identified as druggable (e.g., oxprenolol, digoxin, auranofin and palonosetron, respectively) to oppose the effects of severe Dengue infection in these tissues. These are good candidates for future functional evaluation and clinical trials.
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Affiliation(s)
- Beatriz Sierra
- Virology Department, PAHO/WHO Collaborating Center for the Study of Dengue and its Vector, Pedro Kourí Institute of Tropical Medicine (IPK), Havana 11400, Cuba; (B.S.); (A.B.P.); (M.A.); (E.A.); (C.B.); (M.G.G.)
| | - Ana Cristina Magalhães
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (D.S.); (B.C.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Daniel Soares
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (D.S.); (B.C.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (D.S.); (B.C.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ana B. Perez
- Virology Department, PAHO/WHO Collaborating Center for the Study of Dengue and its Vector, Pedro Kourí Institute of Tropical Medicine (IPK), Havana 11400, Cuba; (B.S.); (A.B.P.); (M.A.); (E.A.); (C.B.); (M.G.G.)
| | - Mayling Alvarez
- Virology Department, PAHO/WHO Collaborating Center for the Study of Dengue and its Vector, Pedro Kourí Institute of Tropical Medicine (IPK), Havana 11400, Cuba; (B.S.); (A.B.P.); (M.A.); (E.A.); (C.B.); (M.G.G.)
| | - Eglis Aguirre
- Virology Department, PAHO/WHO Collaborating Center for the Study of Dengue and its Vector, Pedro Kourí Institute of Tropical Medicine (IPK), Havana 11400, Cuba; (B.S.); (A.B.P.); (M.A.); (E.A.); (C.B.); (M.G.G.)
| | - Claudia Bracho
- Virology Department, PAHO/WHO Collaborating Center for the Study of Dengue and its Vector, Pedro Kourí Institute of Tropical Medicine (IPK), Havana 11400, Cuba; (B.S.); (A.B.P.); (M.A.); (E.A.); (C.B.); (M.G.G.)
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.C.M.); (D.S.); (B.C.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-22-607-4900
| | - Maria G. Guzman
- Virology Department, PAHO/WHO Collaborating Center for the Study of Dengue and its Vector, Pedro Kourí Institute of Tropical Medicine (IPK), Havana 11400, Cuba; (B.S.); (A.B.P.); (M.A.); (E.A.); (C.B.); (M.G.G.)
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83
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De Paoli-Iseppi R, Gleeson J, Clark MB. Isoform Age - Splice Isoform Profiling Using Long-Read Technologies. Front Mol Biosci 2021; 8:711733. [PMID: 34409069 PMCID: PMC8364947 DOI: 10.3389/fmolb.2021.711733] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/19/2021] [Indexed: 01/12/2023] Open
Abstract
Alternative splicing (AS) of RNA is a key mechanism that results in the expression of multiple transcript isoforms from single genes and leads to an increase in the complexity of both the transcriptome and proteome. Regulation of AS is critical for the correct functioning of many biological pathways, while disruption of AS can be directly pathogenic in diseases such as cancer or cause risk for complex disorders. Current short-read sequencing technologies achieve high read depth but are limited in their ability to resolve complex isoforms. In this review we examine how long-read sequencing (LRS) technologies can address this challenge by covering the entire RNA sequence in a single read and thereby distinguish isoform changes that could impact RNA regulation or protein function. Coupling LRS with technologies such as single cell sequencing, targeted sequencing and spatial transcriptomics is producing a rapidly expanding suite of technological approaches to profile alternative splicing at the isoform level with unprecedented detail. In addition, integrating LRS with genotype now allows the impact of genetic variation on isoform expression to be determined. Recent results demonstrate the potential of these techniques to elucidate the landscape of splicing, including in tissues such as the brain where AS is particularly prevalent. Finally, we also discuss how AS can impact protein function, potentially leading to novel therapeutic targets for a range of diseases.
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Affiliation(s)
| | | | - Michael B. Clark
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
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84
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Tissue-specific expression of p73 and p63 isoforms in human tissues. Cell Death Dis 2021; 12:745. [PMID: 34315849 PMCID: PMC8316356 DOI: 10.1038/s41419-021-04017-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022]
Abstract
p73 and p63 are members of the p53 family that exhibit overlapping and distinct functions in development and homeostasis. The evaluation of p73 and p63 isoform expression across human tissue can provide greater insight to the functional interactions between family members. We determined the mRNA isoform expression patterns of TP73 and TP63 across a panel of 36 human tissues and protein expression within the highest-expressing tissues. TP73 and TP63 expression significantly correlated across tissues. In tissues with concurrent mRNA expression, nuclear co-expression of both proteins was observed in a majority of cells. Using GTEx data, we quantified p73 and p63 isoform expression in human tissue and identified that the α-isoforms of TP73 and TP63 were the predominant isoform expressed in nearly all tissues. Further, we identified a previously unreported p73 mRNA product encoded by exons 4 to 14. In sum, these data provide the most comprehensive tissue-specific atlas of p73 and p63 protein and mRNA expression patterns in human and murine samples, indicating coordinate expression of these transcription factors in the majority of tissues in which they are expressed.
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Abstract
Cell atlases are essential companions to the genome as they elucidate how genes are used in a cell type-specific manner or how the usage of genes changes over the lifetime of an organism. This review explores recent advances in whole-organism single-cell atlases, which enable understanding of cell heterogeneity and tissue and cell fate, both in health and disease. Here we provide an overview of recent efforts to build cell atlases across species and discuss the challenges that the field is currently facing. Moreover, we propose the concept of having a knowledgebase that can scale with the number of experiments and computational approaches and a new feedback loop for development and benchmarking of computational methods that includes contributions from the users. These two aspects are key for community efforts in single-cell biology that will help produce a comprehensive annotated map of cell types and states with unparalleled resolution.
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Affiliation(s)
| | - Bruno Tojo
- Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Aaron McGeever
- Chan Zuckerberg Biohub, San Francisco, California 94103, USA;
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86
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Chighine A, Locci E, Nioi M, d'Aloja E. Looking for Post-Mortem Metabolomic Standardization: Waiting for Godot-The Importance of Post-Mortem Interval in Forensic Metabolomics. Chem Res Toxicol 2021; 34:1946-1947. [PMID: 34283584 DOI: 10.1021/acs.chemrestox.1c00211] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A growing body of evidence suggests that the post-mortem interval exerts a strong effect on the metabolome, independently of the biological matrix or the cause of death. A sound and shared approach in standardization is mandatory.
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Affiliation(s)
- Alberto Chighine
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, 09042, Italy
| | - Emanuela Locci
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, 09042, Italy
| | - Matteo Nioi
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, 09042, Italy
| | - Ernesto d'Aloja
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, 09042, Italy
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87
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Morgan S, Malatras A, Duguez S, Duddy W. Optimized Molecular Interaction Networks for the Study of Skeletal Muscle. J Neuromuscul Dis 2021; 8:S223-S239. [PMID: 34308911 DOI: 10.3233/jnd-210680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Molecular interaction networks (MINs) aim to capture the complex relationships between interacting molecules within a biological system. MINs can be constructed from existing knowledge of molecular functional associations, such as protein-protein binding interactions (PPI) or gene co-expression, and these different sources may be combined into a single MIN. A given MIN may be more or less optimal in its representation of the important functional relationships of molecules in a tissue. OBJECTIVE The aim of this study was to establish whether a combined MIN derived from different types of functional association could better capture muscle-relevant biology compared to its constituent single-source MINs. METHODS MINs were constructed from functional association databases for both protein-binding and gene co-expression. The networks were then compared based on the capture of muscle-relevant genes and gene ontology (GO) terms, tested in two different ways using established biological network clustering algorithms. The top performing MINs were combined to test whether an optimal MIN for skeletal muscle could be constructed. RESULTS The STRING PPI network was the best performing single-source MIN among those tested. Combining STRING with interactions from either the MyoMiner or CoXPRESSdb gene co-expression sources resulted in a combined network with improved performance relative to its constituent networks. CONCLUSION MINs constructed from multiple types of functional association can better represent the functional relationships of molecules in a given tissue. Such networks may be used to improve the analysis and interpretation of functional genomics data in the study of skeletal muscle and neuromuscular diseases. Networks and clusters described by this study, including the combinations of STRING with MyoMiner or with CoXPRESSdb, are available for download from https://www.sys-myo.com/myominer/download.php.
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Affiliation(s)
- Stephen Morgan
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
| | - Apostolos Malatras
- Department of Biological Sciences, Molecular Medicine Research Center, University of Cyprus, University Avenue, Nicosia, Cyprus
| | - Stephanie Duguez
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
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88
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Bonadio RS, Nunes LB, Moretti PNS, Mazzeu JF, Cagnin S, Pic-Taylor A, de Oliveira SF. Insights into how environment shapes post-mortem RNA transcription in mouse brain. Sci Rep 2021; 11:13008. [PMID: 34155272 PMCID: PMC8217559 DOI: 10.1038/s41598-021-92268-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/27/2021] [Indexed: 02/05/2023] Open
Abstract
Most biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.
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Affiliation(s)
- Raphael Severino Bonadio
- grid.7632.00000 0001 2238 5157Department of Genetics and Morphology, University of Brasilia, Brasilia, Brazil ,grid.5608.b0000 0004 1757 3470Department of Biology and CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Larissa Barbosa Nunes
- grid.7632.00000 0001 2238 5157Department of Genetics and Morphology, University of Brasilia, Brasilia, Brazil
| | | | - Juliana Forte Mazzeu
- grid.7632.00000 0001 2238 5157Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Stefano Cagnin
- grid.5608.b0000 0004 1757 3470Department of Biology and CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Aline Pic-Taylor
- grid.7632.00000 0001 2238 5157Department of Genetics and Morphology, University of Brasilia, Brasilia, Brazil
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89
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Zadka Ł, Chrabaszcz K, Buzalewicz I, Wiercigroch E, Glatzel-Plucińska N, Szleszkowski Ł, Gomułkiewicz A, Piotrowska A, Kurnol K, Dzięgiel P, Jurek T, Malek K. Molecular profiling of the intestinal mucosa and immune cells of the colon by multi-parametric histological techniques. Sci Rep 2021; 11:11309. [PMID: 34050214 PMCID: PMC8163794 DOI: 10.1038/s41598-021-90761-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
The impact of the post-mortem interval (PMI) on the optical molecular characteristics of the colonic mucosa and the gut-associated lymphoid tissue (GALT) were examined by multi-parametric measurements techniques. Inflammatory cells were identified by immunohistochemical staining. Molecular parameters were estimated using the Raman spectroscopy (RS) and Fourier Transform Infrared (FTIR) spectroscopic imaging. The 3D refractive index (3D-RI) distributions of samples were determined using the digital holographic tomography. The distribution of immune cells between post-mortem (PM) and normal controls did show significant differences for CD4 (P = 0.0016) or CD8 (P < 0.0001), whose expression level was decreased in PM cases. No association was found between individual PMI values and inflammatory cell distribution. However, there was a tendency for a negative correlation between CD4+ cells and PMI (r = - 0.542, P = 0.032). The alterations ongoing in post-mortem tissue may suggest that PMI has a suppressive effect on the effector properties of the cell-mediated immunity. Moreover, it was confirmed that spectroscopic and digital holotomographic histology are also a useful technique for characterization of the differences in inflammation of varying intensity and in GALT imaging in a solid tissue. Anatomical location of immune cells and methods of tissue fixation determine the molecular and optical parameters of the examined cases.
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Affiliation(s)
- Łukasz Zadka
- grid.4495.c0000 0001 1090 049XHistology and Embryology Division, Department of Human Morphology and Embryology, Wroclaw Medical University, Chałubińskiego 6a, 50-368 Wrocław, Poland
| | - Karolina Chrabaszcz
- grid.5522.00000 0001 2162 9631Faculty of Chemistry, Jagiellonian University in Krakow, Krakow, Poland
| | - Igor Buzalewicz
- grid.7005.20000 0000 9805 3178Bio-Optics Group, Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, 27 Wybrzeże S. Wyspiańskiego St., 50-370, Wroclaw, Poland
| | - Ewelina Wiercigroch
- grid.5522.00000 0001 2162 9631Faculty of Chemistry, Jagiellonian University in Krakow, Krakow, Poland
| | - Natalia Glatzel-Plucińska
- grid.4495.c0000 0001 1090 049XHistology and Embryology Division, Department of Human Morphology and Embryology, Wroclaw Medical University, Chałubińskiego 6a, 50-368 Wrocław, Poland
| | - Łukasz Szleszkowski
- grid.4495.c0000 0001 1090 049XDepartment of Forensic Medicine, Forensic Medicine Unit, Wroclaw Medical University, Wroclaw, Poland
| | - Agnieszka Gomułkiewicz
- grid.4495.c0000 0001 1090 049XHistology and Embryology Division, Department of Human Morphology and Embryology, Wroclaw Medical University, Chałubińskiego 6a, 50-368 Wrocław, Poland
| | - Aleksandra Piotrowska
- grid.4495.c0000 0001 1090 049XHistology and Embryology Division, Department of Human Morphology and Embryology, Wroclaw Medical University, Chałubińskiego 6a, 50-368 Wrocław, Poland
| | - Krzysztof Kurnol
- grid.4495.c0000 0001 1090 049XHistology and Embryology Division, Department of Human Morphology and Embryology, Wroclaw Medical University, Chałubińskiego 6a, 50-368 Wrocław, Poland ,grid.4495.c0000 0001 1090 049XDepartment of General and Oncological Surgery, Wroclaw Medical University, Wrocław, Poland
| | - Piotr Dzięgiel
- grid.4495.c0000 0001 1090 049XHistology and Embryology Division, Department of Human Morphology and Embryology, Wroclaw Medical University, Chałubińskiego 6a, 50-368 Wrocław, Poland
| | - Tomasz Jurek
- grid.4495.c0000 0001 1090 049XDepartment of Forensic Medicine, Forensic Medicine Unit, Wroclaw Medical University, Wroclaw, Poland
| | - Kamilla Malek
- grid.5522.00000 0001 2162 9631Faculty of Chemistry, Jagiellonian University in Krakow, Krakow, Poland
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90
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Lam S, Kommadath A, López-Campos Ó, Prieto N, Aalhus J, Juárez M, Dugan MER, Vahmani P. Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem. PLoS One 2021; 16:e0251868. [PMID: 34033656 PMCID: PMC8148330 DOI: 10.1371/journal.pone.0251868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/04/2021] [Indexed: 11/19/2022] Open
Abstract
Evaluating RNA quality and transcriptomic profile of beef muscle over time post-mortem may provide insight into RNA degradation and underlying biological and functional mechanisms that accompany biochemical changes occurring post-mortem during transformation of muscle to meat. RNA was extracted from longissimus thoracis (LT) sampled from British Continental crossbred heifer carcasses (n = 7) stored at 4°C in an abattoir drip cooler at 5 time points post-mortem, i.e., 45 min (0 h), 6 h, 24 h, 48 h, and 72 h. Following RNA-Sequencing, processed reads were aligned to the ARS-UCD1.2 bovine genome assembly. Subsequent differential expression (DE) analysis identified from 51 to 1434 upregulated and 27 to 2256 downregulated DE genes at individual time points compared to time 0 h, showing a trend for increasing counts of both upregulated and downregulated genes over time. Gene ontology and biological pathway term enrichment analyses on sets of DE genes revealed several processes and their timelines of activation/deactivation that accompanied or were involved with muscle transformation to meat. Although the quality of RNA in refrigerated LT remained high for several days post-mortem, the expression levels of several known biomarker genes for meat quality began to change from 24 h onwards. Therefore, to ensure accuracy of predictions on meat quality traits based on the expression levels of those biomarker genes in refrigerated beef muscle tissue, it is crucial that those expression measurements be made on RNA sampled within 24 h post-mortem. The present study also highlighted the need for more research on the roles of mitochondrial genes and non-coding genes in orchestrating muscle tissue processes after death, and how pre-mortem immune status might influence post-mortem meat quality.
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Affiliation(s)
- Stephanie Lam
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Arun Kommadath
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Óscar López-Campos
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Nuria Prieto
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Jennifer Aalhus
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Manuel Juárez
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Michael E. R. Dugan
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Payam Vahmani
- Department of Animal Science, University of California Davis, Davis, California, United States of America
- * E-mail:
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91
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Shi J, Fok KL, Dai P, Qiao F, Zhang M, Liu H, Sang M, Ye M, Liu Y, Zhou Y, Wang C, Sun F, Xie G, Chen H. Spatio-temporal landscape of mouse epididymal cells and specific mitochondria-rich segments defined by large-scale single-cell RNA-seq. Cell Discov 2021; 7:34. [PMID: 34001862 PMCID: PMC8129088 DOI: 10.1038/s41421-021-00260-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/08/2021] [Indexed: 02/03/2023] Open
Abstract
Spermatozoa acquire their fertilizing ability and forward motility during epididymal transit, suggesting the importance of the epididymis. Although the cell atlas of the epididymis was reported recently, the heterogeneity of the cells and the gene expression profile in the epididymal tube are still largely unknown. Considering single-cell RNA sequencing results, we thoroughly studied the cell composition, spatio-temporal differences in differentially expressed genes (DEGs) in epididymal segments and mitochondria throughout the epididymis with sufficient cell numbers. In total, 40,623 cells were detected and further clustered into 8 identified cell populations. Focused analyses revealed the subpopulations of principal cells, basal cells, clear/narrow cells, and halo/T cells. Notably, two subtypes of principal cells, the Prc7 and Prc8 subpopulations were enriched as stereocilia-like cells according to GO analysis. Further analysis demonstrated the spatially specific pattern of the DEGs in each cell cluster. Unexpectedly, the abundance of mitochondria and mitochondrial transcription (MT) was found to be higher in the corpus and cauda epididymis than in the caput epididymis by scRNA-seq, immunostaining, and qPCR validation. In addition, the spatio-temporal profile of the DEGs from the P42 and P56 epididymis, including transiting spermatozoa, was depicted. Overall, our study presented the single-cell transcriptome atlas of the mouse epididymis and revealed the novel distribution pattern of mitochondria and key genes that may be linked to sperm functionalities in the first wave and subsequent wave of sperm, providing a roadmap to be emulated in efforts to achieve sperm maturation regulation in the epididymis.
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Affiliation(s)
- Jianwu Shi
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Kin Lam Fok
- grid.10784.3a0000 0004 1937 0482School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Pengyuan Dai
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Feng Qiao
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Mengya Zhang
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Huage Liu
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Mengmeng Sang
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Mei Ye
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Yang Liu
- grid.16821.3c0000 0004 0368 8293Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Yiwen Zhou
- grid.16821.3c0000 0004 0368 8293Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chengniu Wang
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Fei Sun
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Gangcai Xie
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
| | - Hao Chen
- grid.260483.b0000 0000 9530 8833Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, Jiangsu 226019 China
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92
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Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M, Dopazo J. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Comput Struct Biotechnol J 2021; 19:2968-2978. [PMID: 34136096 PMCID: PMC8170118 DOI: 10.1016/j.csbj.2021.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Genome-scale mechanistic models of pathways are gaining importance for genomic data interpretation because they provide a natural link between genotype measurements (transcriptomics or genomics data) and the phenotype of the cell (its functional behavior). Moreover, mechanistic models can be used to predict the potential effect of interventions, including drug inhibitions. Here, we present the implementation of a mechanistic model of cell signaling for the interpretation of transcriptomic data as an R/Bioconductor package, a Cytoscape plugin and a web tool with enhanced functionality which includes building interpretable predictors, estimation of the effect of perturbations and assessment of the effect of mutations in complex scenarios.
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Affiliation(s)
- Kinza Rian
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Laboratory of Innovative Technologies (LTI), National School of Applied Sciences in Tangier, UAE, Morocco
| | - Marta R. Hidalgo
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain
| | - Cankut Çubuk
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Matias M. Falco
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Marina Esteban-Medina
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Inmaculada Alamo-Alvarez
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in RareDiseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla 41013, Spain
- Computational Systems Medicine. Institute of Biomedicine of Seville (IBiS), Sevilla 41013, Spain
- Functional Genomics Node (INB-ELIXIR-es), Sevilla, Spain
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93
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Martínez-Rivera V, Cárdenas-Monroy CA, Millan-Catalan O, González-Corona J, Huerta-Pacheco NS, Martínez-Gutiérrez A, Villavicencio-Queijeiro A, Pedraza-Lara C, Hidalgo-Miranda A, Bravo-Gómez ME, Pérez-Plasencia C, Guardado-Estrada M. Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats. PeerJ 2021; 9:e11102. [PMID: 33986977 PMCID: PMC8086579 DOI: 10.7717/peerj.11102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/22/2021] [Indexed: 01/01/2023] Open
Abstract
Background The post-mortem interval (PMI) is the time elapsed since the dead of an individual until the body is found, which is relevant for forensic purposes. The miRNAs regulate the expression of some genes; and due to their small size, they can better support degradation, which makes them suitable for forensic analysis. In the present work, we evaluated the gene expression of miR-381-3p, miR-23b-3p, and miR-144-3p in skeletal muscle in a murine model at the early PMI. Methods We designed a rat model to evaluate the early PMI under controlled conditions. This model consisted in 25 rats divided into five groups of rats, that correspond to the 0, 3, 6, 12 and 24 hours of PMI. The 0 h-PMI was considered as the control group. Muscle samples were taken from each rat to analyze the expression of miR-381-3p, miR-23b-3p, and miR-144-3p by quantitative RT-PCR. The gene expression of each miRNA was expressed as Fold Change (FC) and compared among groups. To find the targets of these miRNAs and the pathways where they participate, we performed an in-silico analysis. From the gene targets of miR-381-3p identified in the silico analysis, the EPC1 gene was selected for gene expression analysis by quantitative RT-PCR in these samples. Also, to evaluate if miR-381-3p could predict the early PMI, a mixed effects model was calculated using its gene expression. Results An upregulation of miR-381-3p was found at 24 h-PMI compared with the control group of 0 h-PMI and (FC = 1.02 vs. FC = 1.96; p = 0.0079). This was the opposite for miR-23b-3p, which had a down-regulation at 24 h-PMI compared to 0 h-PMI (FC = 1.22 vs. FC = 0.13; p = 0.0079). Moreover, the gene expression of miR-381-3p increased throughout the first 24 h of PMI, contrary to miR-23b-3p. The targets of these two miRNAs, participate in biological pathways related to hypoxia, apoptosis, and RNA metabolism. The gene expression of EPC1 was found downregulated at 3 and 12 h of PMI, whereas it remained unchanged at 6 h and 24 h of PMI. Using a multivariate analysis, it was possible to predict the FC of miR-381-3p of all but 6 h-PMI analyzed PMIs. Discussion The present results suggest that miR-23b-3p and miR-381-3p participate at the early PMI, probably regulating the expression of some genes related to the autolysis process as EPC1 gene. Although the miR-381-3p gene expression is a potential estimator of PMI, further studies will be required to obtain better estimates.
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Affiliation(s)
- Vanessa Martínez-Rivera
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Christian A Cárdenas-Monroy
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Oliver Millan-Catalan
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México.,Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jessica González-Corona
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - N Sofia Huerta-Pacheco
- Cátedras CONACYT-Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Antonio Martínez-Gutiérrez
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México
| | - Alexa Villavicencio-Queijeiro
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carlos Pedraza-Lara
- Laboratorio de Entomología, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Nacional de Medicina Genomica, Ciudad de México, México
| | - María Elena Bravo-Gómez
- Laboratorio de Toxicología, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carlos Pérez-Plasencia
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituo Nacional de Cancerologia, Ciudad de México, México.,Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mariano Guardado-Estrada
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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94
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Zhang J, Wang M, Qi X, Shi L, Zhang J, Zhang X, Yang T, Ren J, Liu F, Zhang G, Yan J. Predicting the postmortem interval of burial cadavers based on microbial community succession. Forensic Sci Int Genet 2021; 52:102488. [PMID: 33667880 DOI: 10.1016/j.fsigen.2021.102488] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 01/22/2023]
Abstract
Previous studies have demonstrated that microbial community succession during the decomposition of cadavers could be used to estimate the postmortem interval (PMI). However, the vast majority of the existing studies focused on exposed cadavers. In fact, burial cadavers are common scenarios for forensic investigations. In this study, the microbial communities from gravesoil, rectum and skin of burial SD rat cadavers during decomposition were characterized using 16S rRNA gene high-throughput sequencing. We predicted PMI based on the microbial community succession. Obvious differences in microbial community structures were observed between different stages of decomposition. Later decay stages had a lower alpha diversity compared to earlier decay stages. Significant linear relationships between similarities of the microbial communities and postmortem intervals were observed, manifesting regular succession over the course of decomposition. Furthermore, we combined random forest models with postmortem microbial features to predict PMI. The model explained 86.83%, 84.55% and 81.67% of the variation in the microbial community, with a mean absolute error of 1.82, 2.06 and 2.13 days within 60 days of decomposition for gravesoil, rectum and skin of burial cadavers, respectively. Overall, our results suggested that postmortem microbial community data could serve as a potential forensic tool to estimate accurate PMI of burial cadavers.
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Affiliation(s)
- Jun Zhang
- Shanxi Medical University, Taiyuan 030009, PR China
| | | | - Xiaoqin Qi
- Shanxi Medical University, Taiyuan 030009, PR China
| | - Linyu Shi
- Shanxi Medical University, Taiyuan 030009, PR China
| | | | | | | | - Jianbo Ren
- Shanxi Medical University, Taiyuan 030009, PR China
| | - Feng Liu
- Shanxi Medical University, Taiyuan 030009, PR China
| | | | - Jiangwei Yan
- Shanxi Medical University, Taiyuan 030009, PR China.
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95
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Fathi M, Ross CT, Hosseinzadeh Z. Functional 3-Dimensional Retinal Organoids: Technological Progress and Existing Challenges. Front Neurosci 2021; 15:668857. [PMID: 33958988 PMCID: PMC8095320 DOI: 10.3389/fnins.2021.668857] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Stem cell scientists have developed methods for the self-formation of artificial organs, often referred to as organoids. Organoids can be used as model systems for research in multiple biological disciplines. Yoshiki Sasai’s innovation for deriving mammalian retinal tissue from in vitro stem cells has had a large impact on the study of the biology of vision. New developments in retinal organoid technology provide avenues for in vitro models of human retinal diseases, studies of pathological mechanisms, and development of therapies for retinal degeneration, including electronic retinal implants and gene therapy. Moreover, these innovations have played key roles in establishing models for large-scale drug screening, studying the stages of retinal development, and providing a human model for personalized therapeutic approaches, like cell transplants to replace degenerated retinal cells. Here, we first discuss the importance of human retinal organoids to the biomedical sciences. Then, we review various functional features of retinal organoids that have been developed. Finally, we highlight the current limitations of retinal organoid technologies.
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Affiliation(s)
- Meimanat Fathi
- Department of Cell Techniques and Applied Stem Cell Biology, Faculty of Medicine, Center for Biotechnology and Biomedicine (BBZ), University of Leipzig, Leipzig, Germany.,Physiology and Pathophysiology of the Retina Group, Department of Molecular and Cellular Mechanisms of Neurodegeneration, Paul Flechsig Institute of Brain Research, University of Leipzig, Leipzig, Germany
| | - Cody T Ross
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Zohreh Hosseinzadeh
- Physiology and Pathophysiology of the Retina Group, Department of Molecular and Cellular Mechanisms of Neurodegeneration, Paul Flechsig Institute of Brain Research, University of Leipzig, Leipzig, Germany
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96
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Abstract
Proteomics, the large-scale study of all proteins of an organism or system, is a powerful tool for studying biological systems. It can provide a holistic view of the physiological and biochemical states of given samples through identification and quantification of large numbers of peptides and proteins. In forensic science, proteomics can be used as a confirmatory and orthogonal technique for well-built genomic analyses. Proteomics is highly valuable in cases where nucleic acids are absent or degraded, such as hair and bone samples. It can be used to identify body fluids, ethnic group, gender, individual, and estimate post-mortem interval using bone, muscle, and decomposition fluid samples. Compared to genomic analysis, proteomics can provide a better global picture of a sample. It has been used in forensic science for a wide range of sample types and applications. In this review, we briefly introduce proteomic methods, including sample preparation techniques, data acquisition using liquid chromatography-tandem mass spectrometry, and data analysis using database search, spectral library search, and de novo sequencing. We also summarize recent applications in the past decade of proteomics in forensic science with a special focus on human samples, including hair, bone, body fluids, fingernail, muscle, brain, and fingermark, and address the challenges, considerations, and future developments of forensic proteomics.
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97
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Hade AC, Philips MA, Reimann E, Jagomäe T, Eskla KL, Traks T, Prans E, Kõks S, Vasar E, Väli M. Chronic Alcohol Use Induces Molecular Genetic Changes in the Dorsomedial Thalamus of People with Alcohol-Related Disorders. Brain Sci 2021; 11:435. [PMID: 33805312 PMCID: PMC8066746 DOI: 10.3390/brainsci11040435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 01/12/2023] Open
Abstract
The Mediodorsal (MD) thalamus that represents a fundamental subcortical relay has been underrepresented in the studies focusing on the molecular changes in the brains of subjects with alcohol use disorder (AUD). In the current study, MD thalamic regions from AUD subjects and controls were analyzed with Affymetrix Clariom S human microarray. Long-term alcohol use induced a significant (FDR ≤ 0.05) upregulation of 2802 transcripts and downregulation of 1893 genes in the MD thalamus of AUD subjects. A significant upregulation of GRIN1 (glutamate receptor NMDA type 1) and FTO (alpha-ketoglutarate dependent dioxygenase) was confirmed in western blot analysis. Immunohistochemical staining revealed similar heterogenous distribution of GRIN1 in the thalamic nuclei of both AUD and control subjects. The most prevalent functional categories of upregulated genes were related to glutamatergic and GABAergic neurotransmission, cellular metabolism, and neurodevelopment. The prevalent gene cluster among down-regulated genes was immune system mediators. Forty-two differentially expressed genes, including FTO, ADH1B, DRD2, CADM2, TCF4, GCKR, DPP6, MAPT and CHRH1, have been shown to have strong associations (FDR p < 10-8) with AUD or/and alcohol use phenotypes in recent GWA studies. Despite a small number of subjects, we were able to detect robust molecular changes in the mediodorsal thalamus caused by alcohol emphasizing the importance of deeper brain structures such as diencephalon, in the development of AUD-related dysregulation of neurocircuitry.
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Affiliation(s)
- Andreas-Christian Hade
- Department of Pathological Anatomy and Forensic Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (A.-C.H.); (M.V.)
- Forensic Medical Examination Department, Estonian Forensic Science Institute, 30 Tervise Street, 13419 Tallinn, Estonia
| | - Mari-Anne Philips
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Ene Reimann
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia;
| | - Toomas Jagomäe
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Kattri-Liis Eskla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Tanel Traks
- Department of Dermatology and Venerology, Institute of Clinical Medicine, University of Tartu, 51010 Tartu, Estonia;
| | - Ele Prans
- Department of Anaesthesiology and Intensive Care, Tartu University Hospital, 50406 Tartu, Estonia;
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia;
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia; (T.J.); (K.-L.E.); (E.V.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Marika Väli
- Department of Pathological Anatomy and Forensic Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (A.-C.H.); (M.V.)
- Forensic Medical Examination Department, Estonian Forensic Science Institute, 30 Tervise Street, 13419 Tallinn, Estonia
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98
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Furey NB, Bass AL, Miller KM, Li S, Lotto AG, Healy SJ, Drenner SM, Hinch SG. Infected juvenile salmon can experience increased predation during freshwater migration. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201522. [PMID: 33959321 PMCID: PMC8074935 DOI: 10.1098/rsos.201522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/03/2021] [Indexed: 05/07/2023]
Abstract
Predation risk for animal migrants can be impacted by physical condition. Although size- or condition-based selection is often observed, observing infection-based predation is rare due to the difficulties in assessing infectious agents in predated samples. We examined predation of outmigrating sockeye salmon (Oncorhynchus nerka) smolts by bull trout (Salvelinus confluentus) in south-central British Columbia, Canada. We used a high-throughput quantitative polymerase chain reaction (qPCR) platform to screen for the presence of 17 infectious agents found in salmon and assess 14 host genes associated with viral responses. In one (2014) of the two years assessed (2014 and 2015), the presence of infectious haematopoietic necrosis virus (IHNv) resulted in 15-26 times greater chance of predation; in 2015 IHNv was absent among all samples, predated or not. Thus, we provide further evidence that infection can impact predation risk in migrants. Some smolts with high IHNv loads also exhibited gene expression profiles consistent with a virus-induced disease state. Nine other infectious agents were observed between the two years, none of which were associated with increased selection by bull trout. In 2014, richness of infectious agents was also associated with greater predation risk. This is a rare demonstration of predator consumption resulting in selection for prey that carry infectious agents. The mechanism by which this selection occurs is not yet determined. By culling infectious agents from migrant populations, fish predators could provide an ecological benefit to prey.
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Affiliation(s)
- Nathan B. Furey
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Arthur L. Bass
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Kristi M. Miller
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, Canada
| | - Shaorong Li
- Fisheries and Oceans Canada, Molecular Genetics Section, Pacific Biological Station, Nanaimo, Canada
| | - Andrew G. Lotto
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Stephen J. Healy
- Fisheries and Oceans Canada, Science Branch, Pacific Region, 4160 Marine Dr., West Vancouver, British Columbia, Canada
| | - S. Matthew Drenner
- Stillwater Sciences, 555 W. Fifth St, 35th floor, Los Angeles, CA, USA
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Scott G. Hinch
- Pacific Salmon Ecology and Conservation Laboratory, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
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99
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Dachet F, Brown JB, Valyi-Nagy T, Narayan KD, Serafini A, Boley N, Gingeras TR, Celniker SE, Mohapatra G, Loeb JA. Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Sci Rep 2021; 11:6078. [PMID: 33758256 PMCID: PMC7988150 DOI: 10.1038/s41598-021-85801-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
As a means to understand human neuropsychiatric disorders from human brain samples, we compared the transcription patterns and histological features of postmortem brain to fresh human neocortex isolated immediately following surgical removal. Compared to a number of neuropsychiatric disease-associated postmortem transcriptomes, the fresh human brain transcriptome had an entirely unique transcriptional pattern. To understand this difference, we measured genome-wide transcription as a function of time after fresh tissue removal to mimic the postmortem interval. Within a few hours, a selective reduction in the number of neuronal activity-dependent transcripts occurred with relative preservation of housekeeping genes commonly used as a reference for RNA normalization. Gene clustering indicated a rapid reduction in neuronal gene expression with a reciprocal time-dependent increase in astroglial and microglial gene expression that continued to increase for at least 24 h after tissue resection. Predicted transcriptional changes were confirmed histologically on the same tissue demonstrating that while neurons were degenerating, glial cells underwent an outgrowth of their processes. The rapid loss of neuronal genes and reciprocal expression of glial genes highlights highly dynamic transcriptional and cellular changes that occur during the postmortem interval. Understanding these time-dependent changes in gene expression in post mortem brain samples is critical for the interpretation of research studies on human brain disorders.
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Affiliation(s)
- Fabien Dachet
- University of Illinois at Chicago, Chicago, IL, 60612, USA.
| | - James B Brown
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | | | - Anna Serafini
- University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Nathan Boley
- University of California, Berkeley, CA, 94720, USA
| | | | | | | | - Jeffrey A Loeb
- University of Illinois at Chicago, Chicago, IL, 60612, USA.
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100
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Baker SA, Kwok S, Berry GJ, Montine TJ. Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiring mechanical ventilation. PLoS One 2021; 16:e0247060. [PMID: 33592054 PMCID: PMC7886150 DOI: 10.1371/journal.pone.0247060] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/30/2021] [Indexed: 01/08/2023] Open
Abstract
Mortality due to Covid-19 is highly associated with advanced age, owing in large part to severe lower respiratory tract infection. SARS-CoV-2 utilizes the host ACE2 receptor for infection. Whether ACE2 abundance in the lung contributes to age-associated vulnerability is currently unknown. We set out to characterize the RNA and protein expression profiles of ACE2 in aging human lung in the context of phenotypic parameters likely to affect lung physiology. Examining publicly available RNA sequencing data, we discovered that mechanical ventilation is a critical variable affecting lung ACE2 levels. Therefore, we investigated ACE2 protein abundance in patients either requiring mechanical ventilation or spontaneously breathing. ACE2 distribution and expression were determined in archival lung samples by immunohistochemistry (IHC). Tissues were selected from the specimen inventory at a large teaching hospital collected between 2010-2020. Twelve samples were chosen from patients receiving mechanical ventilation for acute hypoxic respiratory failure (AHRF). Twenty samples were selected from patients not requiring ventilation. We compared samples across age, ranging from 40-83 years old in the ventilated cohort and 14-80 years old in the non-ventilated cohort. Within the alveolated parenchyma, ACE2 expression is predominantly observed in type II pneumocytes (or alveolar type II / AT2 cells) and alveolar macrophages. All 12 samples from our ventilated cohort showed histologic features of diffuse alveolar damage including reactive, proliferating AT2 cells. In these cases, ACE2 was strongly upregulated with age when normalized to lung area (p = 0.004) or cellularity (p = 0.003), associated with prominent expression in AT2 cells. In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly.
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Affiliation(s)
- Steven Andrew Baker
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shirley Kwok
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gerald J. Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Thomas J. Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
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