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Noble PA, Pozhitkov A, Singh K, Woods E, Liu C, Levin M, Javan G, Wan J, Abouhashem AS, Mathew-Steiner SS, Sen CK. Unraveling the Enigma of Organismal Death: Insights, Implications, and Unexplored Frontiers. Physiology (Bethesda) 2024; 39:0. [PMID: 38624244 DOI: 10.1152/physiol.00004.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/21/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024] Open
Abstract
Significant knowledge gaps exist regarding the responses of cells, tissues, and organs to organismal death. Examining the survival mechanisms influenced by metabolism and environment, this research has the potential to transform regenerative medicine, redefine legal death, and provide insights into life's physiological limits, paralleling inquiries in embryogenesis.
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Affiliation(s)
- Peter A Noble
- Department of Microbiology, University of Alabama Birmingham, Birmingham, Alabama, United States
| | - Alexander Pozhitkov
- Division of Research Informatics, Beckman Research Institute, City of Hope, Duarte, California, United States
| | - Kanhaiya Singh
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Erik Woods
- Ossium Health, Indianapolis, Indiana, United States
| | - Chunyu Liu
- Institute for Human Performance, Upstate Medical University, Syracuse, New York, United States
| | - Michael Levin
- Department of Biology, Tufts University, Medford, Massachusetts, United States
| | - Gulnaz Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, Alabama, United States
| | - Jun Wan
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Ahmed Safwat Abouhashem
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Shomita S Mathew-Steiner
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Chandan K Sen
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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2
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Kulshrestha P, Sharma S, Vishwakarma S, Ali MJ, Dave TV, Kaur I. Quality and applicability of cadaveric donor eyes for molecular biology research: An Indian experience. Indian J Ophthalmol 2024; 72:962-967. [PMID: 38454856 DOI: 10.4103/ijo.ijo_2553_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/04/2024] [Indexed: 03/09/2024] Open
Abstract
PURPOSE Human ocular tissue banking plays an important part in the advancement of translational research for identifying the molecular processes involved in disease etiology and pathogenesis. Timely obtaining a good-quality ocular tissue from a cadaveric donor is exceedingly difficult, especially in remote areas, with a variable transportation time (within 12-24 h), raising concerns about RNA quality and its subsequent applications. Therefore, we assessed the utility of retinal tissues from cadaver donor and enucleated eyes based on the RNA quality and gene expression by real-time polymerase chain reaction (PCR). SETTINGS AND DESIGN Prospective study. METHODS Retina tissues were separated from the donor/enucleated eyes received in the eye bank within 24 h of death (n = 15) and within an hour from OR (n = 3), respectively, and stored immediately at -80 degree. RNA was isolated using trizol, and the quantity and quality were assessed using Qubit and agarose gel electrophoresis, respectively. QPCR was performed for measuring the expression of different retinal-specific genes. The cellular viability of the retina was assessed by establishing explant primary cell cultures. STATISTICAL ANALYSIS The data were calculated as an average of normalised Ct values ± standard error of the mean. RESULTS RNA obtained from cadaveric tissues despite being partially degraded showed a uniform strong gene expression of several retinal-specific genes such as PAX6, RHO, TUBB3, CRX , and ALDH1L1 . The primary cultures established from cadaveric tissues showed viable cells. CONCLUSION The cadaver donor tissues collected within 24 hours of death can be effectively utilized for gene expression profiling.
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Affiliation(s)
- Prerna Kulshrestha
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sarmeela Sharma
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sushma Vishwakarma
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mohammed J Ali
- Govindram Seksaria Institute of Dacryology, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Tarjani V Dave
- Hariram Motumal Nasta and Renu Hariram Nasta Ophthalmic Plastic Surgery Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Inderjeet Kaur
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
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3
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Carbonell-Sala S, Perteghella T, Lagarde J, Nishiyori H, Palumbo E, Arnan C, Takahashi H, Carninci P, Uszczynska-Ratajczak B, Guigó R. CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing. Nat Commun 2024; 15:5278. [PMID: 38937428 PMCID: PMC11211341 DOI: 10.1038/s41467-024-49523-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we develop CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5' capped, full-length transcripts. In our study, we evaluate the performance of CapTrap-seq alongside other widely used RNA-seq library preparation protocols in human and mouse tissues, employing both ONT and PacBio sequencing technologies. To explore the quantitative capabilities of CapTrap-seq and its accuracy in reconstructing full-length RNA molecules, we implement a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5'cap formation. Our benchmarks, incorporating the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) data, demonstrate that CapTrap-seq is a competitive, platform-agnostic RNA library preparation method for generating full-length transcript sequences.
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Affiliation(s)
- Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Tamara Perteghella
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Flomics Biotech, SL, Carrer de Roc Boronat 31, 08005, Barcelona, Catalonia, Spain
| | - Hiromi Nishiyori
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
- Human Technopole, Milan, Italy
| | - Barbara Uszczynska-Ratajczak
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
- Department of Computational Biology of Noncoding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
- Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
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4
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Rodriguez de Los Santos M, Kopell BH, Buxbaum Grice A, Ganesh G, Yang A, Amini P, Liharska LE, Vornholt E, Fullard JF, Dong P, Park E, Zipkowitz S, Kaji DA, Thompson RC, Liu D, Park YJ, Cheng E, Ziafat K, Moya E, Fennessy B, Wilkins L, Silk H, Linares LM, Sullivan B, Cohen V, Kota P, Feng C, Johnson JS, Rieder MK, Scarpa J, Nadkarni GN, Wang M, Zhang B, Sklar P, Beckmann ND, Schadt EE, Roussos P, Charney AW, Breen MS. Divergent landscapes of A-to-I editing in postmortem and living human brain. Nat Commun 2024; 15:5366. [PMID: 38926387 PMCID: PMC11208617 DOI: 10.1038/s41467-024-49268-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) editing is a prevalent post-transcriptional RNA modification within the brain. Yet, most research has relied on postmortem samples, assuming it is an accurate representation of RNA biology in the living brain. We challenge this assumption by comparing A-to-I editing between postmortem and living prefrontal cortical tissues. Major differences were found, with over 70,000 A-to-I sites showing higher editing levels in postmortem tissues. Increased A-to-I editing in postmortem tissues is linked to higher ADAR and ADARB1 expression, is more pronounced in non-neuronal cells, and indicative of postmortem activation of inflammation and hypoxia. Higher A-to-I editing in living tissues marks sites that are evolutionarily preserved, synaptic, developmentally timed, and disrupted in neurological conditions. Common genetic variants were also found to differentially affect A-to-I editing levels in living versus postmortem tissues. Collectively, these discoveries offer more nuanced and accurate insights into the regulatory mechanisms of RNA editing in the human brain.
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Affiliation(s)
| | - Brian H Kopell
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Gauri Ganesh
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andy Yang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pardis Amini
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lora E Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Vornholt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pengfei Dong
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Zipkowitz
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Deepak A Kaji
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donjing Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - You Jeong Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimia Ziafat
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Moya
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hannah Silk
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa M Linares
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brendan Sullivan
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vanessa Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Prashant Kota
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Claudia Feng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Joseph Scarpa
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Minghui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Michael S Breen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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5
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Luo Y, Yang L, Wu H, Xu H, Peng J, Wang Y, Zhou F. Exploring the Molecular Mechanism of Comorbidity of Type 2 Diabetes Mellitus and Colorectal Cancer: Insights from Bulk Omics and Single-Cell Sequencing Validation. Biomolecules 2024; 14:693. [PMID: 38927096 PMCID: PMC11201668 DOI: 10.3390/biom14060693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/06/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The relationship between type 2 diabetes mellitus (T2DM) and colorectal cancer (CRC) has long been extensively recognized, but their crosstalk mechanisms based on gene regulation remain elusive. In our study, for the first time, bulk RNA-seq and single-cell RNA-seq data were used to explore the shared molecular mechanisms between T2DM and CRC. Moreover, Connectivity Map and molecular docking were employed to determine potential drugs targeting the candidate targets. Eight genes (EVPL, TACSTD2, SOX4, ETV4, LY6E, MLXIPL, ENTPD3, UGP2) were identified as characteristic comorbidity genes for T2DM and CRC, with EVPL and ENTPD3 further identified as core comorbidity genes. Our results demonstrated that upregulation of EVPL and downregulation of ENTPD3 were intrinsic molecular features throughout T2DM and CRC and were significantly associated with immune responses, immune processes, and abnormal immune landscapes in both diseases. Single-cell analysis highlighted a cancer-associated fibroblast (CAF) subset that specifically expressed ENTPD3 in CRC, which exhibited high heterogeneity and unique tumor-suppressive features that were completely different from classical cancer-promoting CAFs. Furthermore, ENTPD3+ CAFs could notably predict immunotherapy response in CRC, holding promise to be an immunotherapy biomarker at the single-cell level. Finally, we identified that droperidol may be a novel drug simultaneously targeting EVPL and ENTPD3. In conclusion, previous studies have often focused solely on metabolic alterations common to T2DM and CRC. Our study establishes EVPL and ENTPD3 as characteristic molecules and immune biomarkers of comorbidity in T2DM and CRC patients, and emphasizes the importance of considering immunological mechanisms in the co-development of T2DM and CRC.
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Affiliation(s)
- Yongge Luo
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
| | - Lei Yang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - Han Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - Hui Xu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - Jin Peng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - You Wang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
| | - Fuxiang Zhou
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Wuhan 430071, China
- Hubei Provincial Clinical Research Center for Cancer, Wuhan 430071, China
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6
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Parnia S, Patel J, Bloom BM, Kulstad E, Deakin CD, Spiegel R. Recalled experience of death: Disinhibition not degeneration in relation to death facilitates inner states of lucid hyperconsciousness with novel cognitive insights. Resuscitation 2024; 199:110205. [PMID: 38609063 DOI: 10.1016/j.resuscitation.2024.110205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Affiliation(s)
- Sam Parnia
- Critical Care and Resuscitation Research Program, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
| | - Jignesh Patel
- Division of Pulmonary, Critical Care and Sleep Medicine, Stony Brook University Hospital, Long Island, NY, USA
| | - Benjamin M Bloom
- Department of Emergency Medicine, Royal London Hospital, Barts Health NHS Trust, London, U.K; Department of Emergency Medicine, Whipps Cross Hospital, Barts Health NHS Trust, London, UK; Department of Emergency Medicine, Newham Hospital, Barts Health NHS Trust, London, UK
| | - Erik Kulstad
- Department of Emergency Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Charles D Deakin
- University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Rebecca Spiegel
- Department of Neurology, Stony Brook Level 4 Epilepsy Center at the School of Medicine Stony Brook University, Long Island, NY, USA
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7
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Nieuwenhuis TO, Giles HH, Arking JVA, Patil AH, Shi W, McCall MN, Halushka MK. Patterns of Unwanted Biological and Technical Expression Variation Among 49 Human Tissues. J Transl Med 2024; 104:102069. [PMID: 38670317 DOI: 10.1016/j.labinv.2024.102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/21/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Tissue gene expression studies are impacted by biological and technical sources of variation, which can be broadly classified into wanted and unwanted variation. The latter, if not addressed, results in misleading biological conclusions. Methods have been proposed to reduce unwanted variation, such as normalization and batch correction. A more accurate understanding of all causes of variation could significantly improve the ability of these methods to remove unwanted variation while retaining variation corresponding to the biological question of interest. We used 17,282 samples from 49 human tissues in the Genotype-Tissue Expression data set (v8) to investigate patterns and causes of expression variation. Transcript expression was transformed to z-scores, and only the most variable 2% of transcripts were evaluated and clustered based on coexpression patterns. Clustered gene sets were assigned to different biological or technical causes based on histologic appearances and metadata elements. We identified 522 variable transcript clusters (median: 11 per tissue) among the samples. Of these, 63% were confidently explained, 16% were likely explained, 7% were low confidence explanations, and 14% had no clear cause. Histologic analysis annotated 46 clusters. Other common causes of variability included sex, sequencing contamination, immunoglobulin diversity, and compositional tissue differences. Less common biological causes included death interval (Hardy score), disease status, and age. Technical causes included blood draw timing and harvesting differences. Many of the causes of variation in bulk tissue expression were identifiable in the Tabula Sapiens data set of single-cell expression. This is among the largest explorations of the underlying sources of tissue expression variation. It uncovered expected and unexpected causes of variable gene expression and demonstrated the utility of matched histologic specimens. It further demonstrated the value of acquiring meaningful tissue harvesting metadata elements to use for improved normalization, batch correction, and analysis of both bulk and single-cell RNA-seq data.
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Affiliation(s)
- Tim O Nieuwenhuis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hunter H Giles
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeremy V A Arking
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Arun H Patil
- Lieber Institute for Brain Development, Baltimore, Maryland
| | - Wen Shi
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York; Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York
| | - Marc K Halushka
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio.
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8
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de los Santos MR, Kopell BH, Grice AB, Ganesh G, Yang A, Amini P, Liharska LE, Vornholt E, Fullard JF, Dong P, Park E, Zipkowitz S, Kaji DA, Thompson RC, Liu D, Park YJ, Cheng E, Ziafat K, Moya E, Fennessy B, Wilkins L, Silk H, Linares LM, Sullivan B, Cohen V, Kota P, Feng C, Johnson JS, Rieder MK, Scarpa J, Nadkarni GN, Wang M, Zhang B, Sklar P, Beckmann ND, Schadt EE, Roussos P, Charney AW, Breen MS. Divergent landscapes of A-to-I editing in postmortem and living human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.06.24306763. [PMID: 38765961 PMCID: PMC11100843 DOI: 10.1101/2024.05.06.24306763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Adenosine-to-inosine (A-to-I) editing is a prevalent post-transcriptional RNA modification within the brain. Yet, most research has relied on postmortem samples, assuming it is an accurate representation of RNA biology in the living brain. We challenge this assumption by comparing A-to-I editing between postmortem and living prefrontal cortical tissues. Major differences were found, with over 70,000 A-to-I sites showing higher editing levels in postmortem tissues. Increased A-to-I editing in postmortem tissues is linked to higher ADAR1 and ADARB1 expression, is more pronounced in non-neuronal cells, and indicative of postmortem activation of inflammation and hypoxia. Higher A-to-I editing in living tissues marks sites that are evolutionarily preserved, synaptic, developmentally timed, and disrupted in neurological conditions. Common genetic variants were also found to differentially affect A-to-I editing levels in living versus postmortem tissues. Collectively, these discoveries illuminate the nuanced functions and intricate regulatory mechanisms of RNA editing within the human brain.
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Affiliation(s)
| | - Brian H. Kopell
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Gauri Ganesh
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andy Yang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pardis Amini
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lora E. Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Vornholt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F. Fullard
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pengfei Dong
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Zipkowitz
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Deepak A. Kaji
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C. Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Donjing Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - You Jeong Park
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimia Ziafat
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Moya
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hannah Silk
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa M. Linares
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brendan Sullivan
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vanessa Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Prashant Kota
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Claudia Feng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Joseph Scarpa
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Minghui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D. Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E. Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Michael S. Breen
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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9
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Shen Z, Zhong Y, Wang Y, Zhu H, Liu R, Yu S, Zhang H, Wang M, Yang T, Zhang M. A computational approach to estimate postmortem interval using postmortem computed tomography of multiple tissues based on animal experiments. Int J Legal Med 2024; 138:1093-1107. [PMID: 37999765 DOI: 10.1007/s00414-023-03127-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
The estimation of postmortem interval (PMI) is a complex and challenging problem in forensic medicine. In recent years, many studies have begun to use machine learning methods to estimate PMI. However, research combining postmortem computed tomography (PMCT) with machine learning models for PMI estimation is still in early stages. This study aims to establish a multi-tissue machine learning model for PMI estimation using PMCT data from various tissues. We collected PMCT data of seven tissues, including brain, eyeballs, myocardium, liver, kidneys, erector spinae, and quadriceps femoris from 10 rabbits after death. CT images were taken every 12 h until 192 h after death, and HU values were extracted from the CT images of each tissue as a dataset. Support vector machine, random forest, and K-nearest neighbors were performed to establish PMI estimation models, and after adjusting the parameters of each model, they were used as first-level classification to build a stacking model to further improve the PMI estimation accuracy. The accuracy and generalized area under the receiver operating characteristic curve of the multi-tissue stacking model were able to reach 93% and 0.96, respectively. Results indicated that PMCT detection could be used to obtain postmortem change of different tissue densities, and the stacking model demonstrated strong predictive and generalization abilities. This approach provides new research methods and ideas for the study of PMI estimation.
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Affiliation(s)
- Zefang Shen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
| | - Yue Zhong
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
| | - Yucong Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
| | - Haibiao Zhu
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
| | - Ran Liu
- Forensic Science Center of Beijing Huatong Junjian Science and Technology Company Limited, Beijing, 100016, China
| | - Shengnan Yu
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
| | - Haidong Zhang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
| | - Min Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
| | - Tiantong Yang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China.
| | - Mengzhou Zhang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China.
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10
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Tomaz da Silva P, Zhang Y, Theodorakis E, Martens LD, Yépez VA, Pelechano V, Gagneur J. Cellular energy regulates mRNA degradation in a codon-specific manner. Mol Syst Biol 2024; 20:506-520. [PMID: 38491213 PMCID: PMC11066088 DOI: 10.1038/s44320-024-00026-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/18/2024] Open
Abstract
Codon optimality is a major determinant of mRNA translation and degradation rates. However, whether and through which mechanisms its effects are regulated remains poorly understood. Here we show that codon optimality associates with up to 2-fold change in mRNA stability variations between human tissues, and that its effect is attenuated in tissues with high energy metabolism and amplifies with age. Mathematical modeling and perturbation data through oxygen deprivation and ATP synthesis inhibition reveal that cellular energy variations non-uniformly alter the effect of codon usage. This new mode of codon effect regulation, independent of tRNA regulation, provides a fundamental mechanistic link between cellular energy metabolism and eukaryotic gene expression.
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Affiliation(s)
- Pedro Tomaz da Silva
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Yujie Zhang
- Scilifelab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Evangelos Theodorakis
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Laura D Martens
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Vicente A Yépez
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Vicent Pelechano
- Scilifelab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
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11
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dos Santos GA, Magdaleno GDV, de Magalhães JP. Evidence of a pan-tissue decline in stemness during human aging. Aging (Albany NY) 2024; 16:5796-5810. [PMID: 38604248 PMCID: PMC11042951 DOI: 10.18632/aging.205717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/02/2024] [Indexed: 04/13/2024]
Abstract
Despite their biological importance, the role of stem cells in human aging remains to be elucidated. In this work, we applied a machine learning methodology to GTEx transcriptome data and assigned stemness scores to 17,382 healthy samples from 30 human tissues aged between 20 and 79 years. We found that ~60% of the studied tissues exhibit a significant negative correlation between the subject's age and stemness score. The only significant exception was the uterus, where we observed an increased stemness with age. Moreover, we observed that stemness is positively correlated with cell proliferation and negatively correlated with cellular senescence. Finally, we also observed a trend that hematopoietic stem cells derived from older individuals might have higher stemness scores. In conclusion, we assigned stemness scores to human samples and show evidence of a pan-tissue loss of stemness during human aging, which adds weight to the idea that stem cell deterioration may contribute to human aging.
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Affiliation(s)
- Gabriel Arantes dos Santos
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo 01246 903, Brazil
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, United Kingdom
| | | | - João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, United Kingdom
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12
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De-Giorgio F, Bergamin E, Baldi A, Gatta R, Pascali VL. Immunohistochemical expression of HMGB1 and related proteins in the skin as a possible tool for determining post-mortem interval: a preclinical study. Forensic Sci Med Pathol 2024; 20:149-165. [PMID: 37490201 PMCID: PMC10944391 DOI: 10.1007/s12024-023-00634-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2023] [Indexed: 07/26/2023]
Abstract
Determining the post-mortem interval (PMI) is one of forensic pathology's primary objectives and one of its most challenging tasks. Numerous studies have demonstrated the accuracy of histomorphology and immunohistochemical investigations in determining the time of death. Nevertheless, the skin, a robust and easy-to-remove tissue, has only been partially analyzed so far. By studying 20 adult male mice, we tried to determine whether post-mortem immunohistochemical detection in the skin of HMGB1 proteins and associated components (Beclin1 and RAGE) could be used for this purpose. We discovered that nuclear HMGB1 overexpression indicates that death occurred within the previous 12 h, nuclear HMGB1 negativization with high cytoplasmic HMGB1 intensity indicates that death occurred between 12 and 36 h earlier and cytoplasmic HMGB1 negativization indicates that more than 48 h have passed since death. RAGE and Beclin1 levels in the cytoplasm also decreased with time. The latter proteins' negativization might indicate that more than 24 and 36 h, respectively, have passed from the time of death. These indicators might potentially be helpful in forensic practice for determining the PMI using immunohistochemistry.
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Affiliation(s)
- Fabio De-Giorgio
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
- Department of Healthcare Surveillance and Bioethics, Section of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Eva Bergamin
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Department of Healthcare Surveillance and Bioethics, Section of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alfonso Baldi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania Luigi Vanvitelli, Caserta, Italy
| | - Roberto Gatta
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Vincenzo L Pascali
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Department of Healthcare Surveillance and Bioethics, Section of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
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13
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Lahmer T, Weirich G, Porubsky S, Rasch S, Kammerstetter FA, Schustetter C, Schüffler P, Erber J, Dibos M, Delbridge C, Kuhn PH, Jeske S, Steinhardt M, Chaker A, Heim M, Heemann U, Schmid RM, Weichert W, Stock KF, Slotta-Huspenina J. Postmortem Minimally Invasive Autopsy in Critically Ill COVID-19 Patients at the Bedside: A Proof-of-Concept Study at the ICU. Diagnostics (Basel) 2024; 14:294. [PMID: 38337812 PMCID: PMC10854968 DOI: 10.3390/diagnostics14030294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Economic restrictions and workforce cuts have continually challenged conventional autopsies. Recently, the COVID-19 pandemic has added tissue quality and safety requirements to the investigation of this disease, thereby launching efforts to upgrade autopsy strategies. METHODS In this proof-of-concept study, we performed bedside ultrasound-guided minimally invasive autopsy (US-MIA) in the ICU of critically ill COVID-19 patients using a structured protocol to obtain non-autolyzed tissue. Biopsies were assessed for their quality (vitality) and length of biopsy (mm) and for diagnosis. The efficiency of the procedure was monitored in five cases by recording the time of each step and safety issues by swabbing personal protective equipment and devices for viral contamination. FINDINGS Ultrasound examination and tissue procurement required a mean time period of 13 min and 54 min, respectively. A total of 318 multiorgan biopsies were obtained from five patients. Quality and vitality standards were fulfilled, which not only allowed for specific histopathological diagnosis but also the reliable detection of SARS-CoV-2 virions in unexpected organs using electronic microscopy and RNA-expressing techniques. INTERPRETATION Bedside multidisciplinary US-MIA allows for the fast and efficient acquisition of autolytic-free tissue and offers unappreciated potential to overcome the limitations of research in postmortem studies.
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Affiliation(s)
- Tobias Lahmer
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany; (S.R.); (J.E.); (M.D.); (R.M.S.)
| | - Gregor Weirich
- Institute of Pathology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (G.W.); (F.A.K.); (C.S.); (P.S.); (C.D.); (P.H.K.); (W.W.); (J.S.-H.)
| | - Stefan Porubsky
- Institut für Pathologie, Universitätsklinikum Mainz, Langenbeckstraße 1, 55131 Mainz, Germany;
| | - Sebastian Rasch
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany; (S.R.); (J.E.); (M.D.); (R.M.S.)
| | - Florian A. Kammerstetter
- Institute of Pathology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (G.W.); (F.A.K.); (C.S.); (P.S.); (C.D.); (P.H.K.); (W.W.); (J.S.-H.)
| | - Christian Schustetter
- Institute of Pathology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (G.W.); (F.A.K.); (C.S.); (P.S.); (C.D.); (P.H.K.); (W.W.); (J.S.-H.)
| | - Peter Schüffler
- Institute of Pathology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (G.W.); (F.A.K.); (C.S.); (P.S.); (C.D.); (P.H.K.); (W.W.); (J.S.-H.)
| | - Johanna Erber
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany; (S.R.); (J.E.); (M.D.); (R.M.S.)
| | - Miriam Dibos
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany; (S.R.); (J.E.); (M.D.); (R.M.S.)
| | - Claire Delbridge
- Institute of Pathology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (G.W.); (F.A.K.); (C.S.); (P.S.); (C.D.); (P.H.K.); (W.W.); (J.S.-H.)
| | - Peer Hendrik Kuhn
- Institute of Pathology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (G.W.); (F.A.K.); (C.S.); (P.S.); (C.D.); (P.H.K.); (W.W.); (J.S.-H.)
| | - Samuel Jeske
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Zentrum München, Trogerstraße 30, 81675 Munich, Germany;
| | - Manuel Steinhardt
- Department of Diagnostic and Interventional Radiology, School of Medicine, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany;
| | - Adam Chaker
- Department of Otorhinolaryngology, University Hospital Klinikum Rechts der Isar, Ismaninger Straße 22, 81675 Munich, Germany;
| | - Markus Heim
- Department of Anesthesiology and Intensive Medicine, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany;
| | - Uwe Heemann
- Department of Nephrology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (U.H.); (K.F.S.)
| | - Roland M. Schmid
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany; (S.R.); (J.E.); (M.D.); (R.M.S.)
| | - Wilko Weichert
- Institute of Pathology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (G.W.); (F.A.K.); (C.S.); (P.S.); (C.D.); (P.H.K.); (W.W.); (J.S.-H.)
| | - Konrad Friedrich Stock
- Department of Nephrology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (U.H.); (K.F.S.)
| | - Julia Slotta-Huspenina
- Institute of Pathology, School of Medicine, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany; (G.W.); (F.A.K.); (C.S.); (P.S.); (C.D.); (P.H.K.); (W.W.); (J.S.-H.)
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14
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Lücke J, Böttcher M, Nawrocki M, Meins N, Schnell J, Heinrich F, Bertram F, Sabihi M, Seeger P, Pfaff M, Notz S, Blankenburg T, Zhang T, Kempski J, Reeh M, Wolter S, Mann O, Lütgehetmann M, Hackert T, Izbicki JR, Duprée A, Huber S, Ondruschka B, Giannou AD. Obesity and diabetes mellitus are associated with SARS-CoV-2 outcomes without influencing signature genes of extrapulmonary immune compartments at the RNA level. Heliyon 2024; 10:e24508. [PMID: 38298642 PMCID: PMC10828091 DOI: 10.1016/j.heliyon.2024.e24508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is responsible for eliciting Coronavirus disease 2019 (COVID-19) still challenges healthcare services worldwide. While many patients only suffer from mild symptoms, patients with some pre-existing medical conditions are at a higher risk for a detrimental course of disease. However, the underlying mechanisms determining disease course are only partially understood. One key factor influencing disease severity is described to be immune-mediated. In this report, we describe a post-mortem analysis of 45 individuals who died from SARS-CoV-2 infection. We could show that although sociodemographic factors and premedical conditions such as obesity and diabetes mellitus reduced survival time in our cohort, they were not associated with changes in the expression of immune-related signature genes at the RNA level in the blood, the gut, or the liver between these different groups. Our data indicate that obesity and diabetes mellitus influence SARS-CoV-2-related mortality, without influencing the extrapulmonary gene expression of immunity-related signature genes at the RNA level.
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Affiliation(s)
- Jöran Lücke
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Marius Böttcher
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Mikolaj Nawrocki
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Nicholas Meins
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Josa Schnell
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Fabian Heinrich
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Butenfeld 34, 22529, Hamburg, Germany
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franziska Bertram
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Morsal Sabihi
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Philipp Seeger
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Marie Pfaff
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Sara Notz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Tom Blankenburg
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Tao Zhang
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Jan Kempski
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- The Calcium Signaling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Matthias Reeh
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Stefan Wolter
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Oliver Mann
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Jakob R. Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Anna Duprée
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Samuel Huber
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Benjamin Ondruschka
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Butenfeld 34, 22529, Hamburg, Germany
| | - Anastasios D. Giannou
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
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15
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Caldas P, Luz M, Baseggio S, Andrade R, Sobral D, Grosso AR. Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features. Commun Biol 2024; 7:100. [PMID: 38225287 PMCID: PMC10789751 DOI: 10.1038/s42003-024-05779-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Transcription termination is a crucial step in the production of conforming mRNAs and functional proteins. Under cellular stress conditions, the transcription machinery fails to identify the termination site and continues transcribing beyond gene boundaries, a phenomenon designated as transcription readthrough. However, the prevalence and impact of this phenomenon in healthy human tissues remain unexplored. Here, we assessed transcription readthrough in almost 3000 transcriptome profiles representing 23 human tissues and found that 34% of the expressed protein-coding genes produced readthrough transcripts. The production of readthrough transcripts was restricted in genomic regions with high transcriptional activity and was associated with inefficient splicing and increased chromatin accessibility in terminal regions. In addition, we showed that these transcripts contained several binding sites for the same miRNA, unravelling a potential role as miRNA sponges. Overall, this work provides evidence that transcription readthrough is pervasive and non-stochastic, not only in abnormal conditions but also in healthy tissues. This suggests a potential role for such transcripts in modulating normal cellular functions.
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Affiliation(s)
- Paulo Caldas
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Mariana Luz
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Simone Baseggio
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Rita Andrade
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Daniel Sobral
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Ana Rita Grosso
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
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Javan GT, Singh K, Finley SJ, Green RL, Sen CK. Complexity of human death: its physiological, transcriptomic, and microbiological implications. Front Microbiol 2024; 14:1345633. [PMID: 38282739 PMCID: PMC10822681 DOI: 10.3389/fmicb.2023.1345633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Human death is a complex, time-governed phenomenon that leads to the irreversible cessation of all bodily functions. Recent molecular and genetic studies have revealed remarkable experimental evidence of genetically programmed cellular death characterized by several physiological processes; however, the basic physiological function that occurs during the immediate postmortem period remains inadequately described. There is a paucity of knowledge connecting necrotic pathologies occurring in human organ tissues to complete functional loss of the human organism. Cells, tissues, organs, and organ systems show a range of differential resilience and endurance responses that occur during organismal death. Intriguingly, a persistent ambiguity in the study of postmortem physiological systems is the determination of the trajectory of a complex multicellular human body, far from life-sustaining homeostasis, following the gradual or sudden expiry of its regulatory systems. Recent groundbreaking investigations have resulted in a paradigm shift in understanding the cell biology and physiology of death. Two significant findings are that (i) most cells in the human body are microbial, and (ii) microbial cell abundance significantly increases after death. By addressing the physiological as well as the microbiological aspects of death, future investigations are poised to reveal innovative insights into the enigmatic biological activities associated with death and human decomposition. Understanding the elaborate crosstalk of abiotic and biotic factors in the context of death has implications for scientific discoveries important to informing translational knowledge regarding the transition from living to the non-living. There are important and practical needs for a transformative reestablishment of accepted models of biological death (i.e., artificial intelligence, AI) for more precise determinations of when the regulatory mechanisms for homeostasis of a living individual have ceased. In this review, we summarize mechanisms of physiological, genetic, and microbiological processes that define the biological changes and pathways associated with human organismal death and decomposition.
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Affiliation(s)
- Gulnaz T. Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Kanhaiya Singh
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sheree J. Finley
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Robert L. Green
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Chandan K. Sen
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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17
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Pait MC, Kaye SD, Su Y, Kumar A, Singh S, Gironda SC, Vincent S, Anwar M, Carroll CM, Snipes JA, Lee J, Furdui CM, Deep G, Macauley SL. Novel method for collecting hippocampal interstitial fluid extracellular vesicles (EV ISF ) reveals sex-dependent changes in microglial EV proteome in response to Aβ pathology. J Extracell Vesicles 2024; 13:e12398. [PMID: 38191961 PMCID: PMC10774707 DOI: 10.1002/jev2.12398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024] Open
Abstract
Brain-derived extracellular vesicles (EVs) play an active role in Alzheimer's disease (AD), relaying important physiological information about their host tissues. The internal cargo of EVs is protected from degradation, making EVs attractive AD biomarkers. However, it is unclear how circulating EVs relate to EVs isolated from disease-vulnerable brain regions. We developed a novel method for collecting EVs from the hippocampal interstitial fluid (ISF) of live mice. EVs (EVISF ) were isolated via ultracentrifugation and characterized by nanoparticle tracking analysis, immunogold labelling, and flow cytometry. Mass spectrometry and proteomic analyses were performed on EVISF cargo. EVISF were 40-150 nm in size and expressed CD63, CD9, and CD81. Using a model of cerebral amyloidosis (e.g., APPswe, PSEN1dE9 mice), we found protein concentration increased but protein diversity decreased with Aβ deposition. Genotype, age, and Aβ deposition modulated proteostasis- and immunometabolic-related pathways. Changes in the microglial EVISF proteome were sexually dimorphic and associated with a differential response of plaque associated microglia. We found that female APP/PS1 mice have more amyloid plaques, less plaque associated microglia, and a less robust- and diverse- EVISF microglial proteome. Thus, in vivo microdialysis is a novel technique for collecting EVISF and offers a unique opportunity to explore the role of EVs in AD.
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Affiliation(s)
- Morgan C. Pait
- Department of Physiology & PharmacologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Sarah D. Kaye
- Department of Physiology & PharmacologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Yixin Su
- Department of Cancer BiologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Ashish Kumar
- Department of Cancer BiologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Sangeeta Singh
- Department of Cancer BiologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Stephen C. Gironda
- Department of Physiology & PharmacologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Samantha Vincent
- Department of Physiology & PharmacologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Maria Anwar
- Department of Physiology & PharmacologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Caitlin M. Carroll
- Department of Physiology & PharmacologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - James Andy Snipes
- Department of Physiology & PharmacologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Jingyun Lee
- Department of Internal MedicineSection on Molecular MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Proteomics and Metabolomics Shared ResourceWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Cristina M. Furdui
- Department of Internal MedicineSection on Molecular MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Proteomics and Metabolomics Shared ResourceWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Atrium Health Wake Forest Baptist Comprehensive Cancer CenterWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Gagan Deep
- Department of Cancer BiologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Atrium Health Wake Forest Baptist Comprehensive Cancer CenterWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Center for Research on Substance Use and AddictionWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- J Paul Sticht Center for Healthy Aging and Alzheimer's PreventionWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Shannon L. Macauley
- Department of Physiology & PharmacologyWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- J Paul Sticht Center for Healthy Aging and Alzheimer's PreventionWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Internal MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Alzheimer's Disease Research CenterWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Center for Diabetes and MetabolismWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Cardiovascular Sciences CenterWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
- Department of PhysiologyUniversity of KentuckyLexingtonKentuckyUSA
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18
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Lahmer T, Stock K, Rasch S, Porubsky S, Jeske S, Schustetter C, Protzer U, Heemann U, Schmid R, Weichert W, Weirich G, Slotta-Huspenina J. [Interdisciplinary ultrasound-guided, minimally invasive autopsy in COVID-19-deceased patients in the intensive care unit of a university hospital : A proof-of-concept study]. PATHOLOGIE (HEIDELBERG, GERMANY) 2023; 44:193-197. [PMID: 38051339 PMCID: PMC10739551 DOI: 10.1007/s00292-023-01248-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/06/2023] [Indexed: 12/07/2023]
Abstract
In this feasibility study, we carried out in an interdisciplinary team standardised, ultrasound-guided, minimally invasive autopsy (US-MIA) directly at the bedside of patients who died of COVID-19 in the intensive care unit of the Rechts der Isar Hospital of the Technical University Munich (TUM). The aim of the study was to verify the feasibility, time efficiency and infection hygiene aspects of the process, as well as the quality of the tissue samples. Our results show that bedside US-MIA is suitable for obtaining tissue samples before the onset of postmortem autolysis, and that it can also be carried out quickly and safely. The potential of US-MIA, which has gained little recognition so far, deserves special attention in the context of postmortem diagnosis, research and quality assurance. In the future, these strengths of US-MIA could help to lead postmortem diagnosis into the modern age of pathological deep analytics ("omics").
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Affiliation(s)
- T Lahmer
- Klinik und Poliklinik für Innere Medizin II, Klinikum Rechts der Isar, Technische Universität München, München, Deutschland
| | - K Stock
- Abteilung für Nephrologie - Nierenheilkunde, Klinikum Rechts der Isar, Technische Universität München, München, Deutschland
| | - S Rasch
- Klinik und Poliklinik für Innere Medizin II, Klinikum Rechts der Isar, Technische Universität München, München, Deutschland
| | - S Porubsky
- Institut für allgemeine Pathologie, Johannes Gutenberg-Universität Mainz, Mainz, Deutschland
| | - S Jeske
- Institut für Virologie, Technische Universität München, München, Deutschland
| | - C Schustetter
- Institut für Allgemeine Pathologie und Pathologische Anatomie, TUM School of Medicine and Health, Technische Universität München, München, Deutschland, Trogerstr. 18, 81675
| | - U Protzer
- Institut für Virologie, Technische Universität München, München, Deutschland
| | - U Heemann
- Abteilung für Nephrologie - Nierenheilkunde, Klinikum Rechts der Isar, Technische Universität München, München, Deutschland
| | - R Schmid
- Klinik und Poliklinik für Innere Medizin II, Klinikum Rechts der Isar, Technische Universität München, München, Deutschland
| | - W Weichert
- Institut für Allgemeine Pathologie und Pathologische Anatomie, TUM School of Medicine and Health, Technische Universität München, München, Deutschland, Trogerstr. 18, 81675
| | - G Weirich
- Institut für Allgemeine Pathologie und Pathologische Anatomie, TUM School of Medicine and Health, Technische Universität München, München, Deutschland, Trogerstr. 18, 81675
| | - J Slotta-Huspenina
- Institut für Allgemeine Pathologie und Pathologische Anatomie, TUM School of Medicine and Health, Technische Universität München, München, Deutschland, Trogerstr. 18, 81675.
- Pathologie Starnberg MVZ GmbH, Starnberg, Deutschland.
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Collado-Torres L, Klei L, Liu C, Kleinman JE, Hyde TM, Geschwind DH, Gandal MJ, Devlin B, Weinberger DR. Comparison of gene expression in living and postmortem human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.08.23298172. [PMID: 37986747 PMCID: PMC10659492 DOI: 10.1101/2023.11.08.23298172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Molecular mechanisms of neuropsychiatric disorders are challenging to study in human brain. For decades, the preferred model has been to study postmortem human brain samples despite the limitations they entail. A recent study generated RNA sequencing data from biopsies of prefrontal cortex from living patients with Parkinson's Disease and compared gene expression to postmortem tissue samples, from which they found vast differences between the two. This led the authors to question the utility of postmortem human brain studies. Through re-analysis of the same data, we unexpectedly found that the living brain tissue samples were of much lower quality than the postmortem samples across multiple standard metrics. We also performed simulations that illustrate the effects of ignoring RNA degradation in differential gene expression analyses, showing the effects can be substantial and of similar magnitude to what the authors find. For these reasons, we believe the authors' conclusions are unjustified. To the contrary, while opportunities to study gene expression in the living brain are welcome, evidence that this eclipses the value of postmortem analyses is not apparent.
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Affiliation(s)
- Leonardo Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Daniel H Geschwind
- Intellectual and Developmental Disabilities Research Center, Department of Psychiatry, Department of Human Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, Center for Autism Research and Treatment, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
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20
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Chighine A, Stocchero M, Ferino G, De-Giorgio F, Conte C, Nioi M, d'Aloja E, Locci E. Metabolomics investigation of post-mortem human pericardial fluid. Int J Legal Med 2023; 137:1875-1885. [PMID: 37402012 PMCID: PMC10567860 DOI: 10.1007/s00414-023-03050-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
INTRODUCTION Due to its peculiar anatomy and physiology, the pericardial fluid is a biological matrix of particular interest in the forensic field. Despite this, the available literature has mainly focused on post-mortem biochemistry and forensic toxicology, while to the best of authors' knowledge post-mortem metabolomics has never been applied. Similarly, estimation of the time since death or post-mortem interval based on pericardial fluids has still rarely been attempted. OBJECTIVES We applied a metabolomic approach based on 1H nuclear magnetic resonance spectroscopy to ascertain the feasibility of monitoring post-mortem metabolite changes on human pericardial fluids with the aim of building a multivariate regression model for post-mortem interval estimation. METHODS Pericardial fluid samples were collected in 24 consecutive judicial autopsies, in a time frame ranging from 16 to 170 h after death. The only exclusion criterion was the quantitative and/or qualitative alteration of the sample. Two different extraction protocols were applied for low molecular weight metabolites selection, namely ultrafiltration and liquid-liquid extraction. Our metabolomic approach was based on the use of 1H nuclear magnetic resonance and multivariate statistical data analysis. RESULTS The pericardial fluid samples treated with the two experimental protocols did not show significant differences in the distribution of the metabolites detected. A post-mortem interval estimation model based on 18 pericardial fluid samples was validated with an independent set of 6 samples, giving a prediction error of 33-34 h depending on the experimental protocol used. By narrowing the window to post-mortem intervals below 100 h, the prediction power of the model was significantly improved with an error of 13-15 h depending on the extraction protocol. Choline, glycine, ethanolamine, and hypoxanthine were the most relevant metabolites in the prediction model. CONCLUSION The present study, although preliminary, shows that PF samples collected from a real forensic scenario represent a biofluid of interest for post-mortem metabolomics, with particular regard to the estimation of the time since death.
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Affiliation(s)
- Alberto Chighine
- Cittadella Universitaria di Monserrato, 09042, Monserrato (CA), Italy.
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy.
| | - Matteo Stocchero
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Giulio Ferino
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | - Fabio De-Giorgio
- Department of Health Care Surveillance and Bioethics, Section of Legal Medicine, Catholic University of Rome, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Celeste Conte
- Department of Health Care Surveillance and Bioethics, Section of Legal Medicine, Catholic University of Rome, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Matteo Nioi
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | - Ernesto d'Aloja
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | - Emanuela Locci
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
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21
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Klontzas ME, Leventis D, Spanakis K, Karantanas AH, Kranioti EF. Post-mortem CT radiomics for the prediction of time since death. Eur Radiol 2023; 33:8387-8395. [PMID: 37329460 DOI: 10.1007/s00330-023-09746-2] [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: 02/15/2023] [Revised: 03/27/2023] [Accepted: 04/22/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVES Post-mortem interval (PMI) estimation has long been relying on sequential post-mortem changes on the body as a function of extrinsic, intrinsic, and environmental factors. Such factors are difficult to account for in complicated death scenes; thus, PMI estimation can be compromised. Herein, we aimed to evaluate the use of post-mortem CT (PMCT) radiomics for the differentiation between early and late PMI. METHODS Consecutive whole-body PMCT examinations performed between 2016 and 2021 were retrospectively included (n = 120), excluding corpses without an accurately reported PMI (n = 23). Radiomics data were extracted from liver and pancreas tissue and randomly split into training and validation sets (70:30%). Following data preprocessing, significant features were selected (Boruta selection) and three XGBoost classifiers were built (liver, pancreas, combined) to differentiate between early (< 12 h) and late (> 12 h) PMI. Classifier performance was assessed with receiver operating characteristics (ROC) curves and areas under the curves (AUC), which were compared by bootstrapping. RESULTS A total of 97 PMCTs were included, representing individuals (23 females and 74 males) with a mean age of 47.1 ± 23.38 years. The combined model achieved the highest AUC reaching 75% (95%CI 58.4-91.6%) (p = 0.03 compared to liver and p = 0.18 compared to pancreas). The liver-based and pancreas-based XGBoost models achieved AUCs of 53.6% (95%CI 34.8-72.3%) and 64.3% (95%CI 46.7-81.9%) respectively (p > 0.05 for the comparison between liver- and pancreas-based models). CONCLUSION The use of radiomics analysis on PMCT examinations differentiated early from late PMI, unveiling a novel image-based method with important repercussions in forensic casework. CLINICAL RELEVANCE STATEMENT This paper introduces the employment of radiomics in forensic diagnosis by presenting an effective automated alternative method of estimating post-mortem interval from targeted tissues, thus paving the way for improvement in speed and quality of forensic investigations. KEY POINTS • A combined liver-pancreas radiomics model differentiated early from late post-mortem intervals (using a 12-h threshold) with an area under the curve of 75% (95%CI 58.4-91.6%). • XGBoost models based on liver-only or pancreas-only radiomics demonstrated inferior performance to the combined model in predicting the post-mortem interval.
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Affiliation(s)
- Michail E Klontzas
- Department of Medical Imaging, University Hospital of Heraklion, Voutes, Heraklion, 71110, Crete, Greece
- Department of Radiology, Medical School, University of Crete, Voutes, Heraklion, 71110, Crete, Greece
- Advanced Hybrid Imaging Systems, Institute of Computer Science - FORTH, Voutes, Heraklion, 71110, Crete, Greece
| | - Dimitrios Leventis
- Department of Medical Imaging, University Hospital of Heraklion, Voutes, Heraklion, 71110, Crete, Greece
| | - Konstantinos Spanakis
- Department of Medical Imaging, University Hospital of Heraklion, Voutes, Heraklion, 71110, Crete, Greece
| | - Apostolos H Karantanas
- Department of Medical Imaging, University Hospital of Heraklion, Voutes, Heraklion, 71110, Crete, Greece.
- Department of Radiology, Medical School, University of Crete, Voutes, Heraklion, 71110, Crete, Greece.
- Advanced Hybrid Imaging Systems, Institute of Computer Science - FORTH, Voutes, Heraklion, 71110, Crete, Greece.
| | - Elena F Kranioti
- Forensic Medicine Unit, Department of Forensic Sciences, Faculty of Medicine, University of Crete, Voutes, Heraklion, 71110, Greece.
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Heinrich F, Mertz KD, Glatzel M, Beer M, Krasemann S. Using autopsies to dissect COVID-19 pathogenesis. Nat Microbiol 2023; 8:1986-1994. [PMID: 37798476 DOI: 10.1038/s41564-023-01488-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 09/04/2023] [Indexed: 10/07/2023]
Abstract
The emergence of SARS-CoV-2 has resulted in millions of deaths as a result of COVID-19. Suitable models were missing at the beginning of the pandemic, and studies investigating disease pathogenesis relied on patients who had succumbed to COVID-19. Since then, autopsies of patients have substantially contributed to our understanding of the pathogenesis of COVID-19 and associated major organ complications. Here we summarize how autopsies have complemented experimental studies, mainly in animal models, and how they have facilitated critical knowledge of COVID-19 to improve daily clinical practice and develop therapeutic interventions. Employing advanced histopathologic and molecular genetic methods in post-mortem tissues, the COVID-19 pandemic has highlighted the importance of autopsies for virology research and clinical practice in current and emerging infectious diseases.
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Affiliation(s)
- Fabian Heinrich
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten D Mertz
- Institute of Pathology, Kantonsspital Baselland, Liestal, Switzerland
- University of Basel, Basel, Switzerland
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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23
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Dos Santos GA, Chatsirisupachai K, Avelar RA, de Magalhães JP. Transcriptomic analysis reveals a tissue-specific loss of identity during ageing and cancer. BMC Genomics 2023; 24:644. [PMID: 37884865 PMCID: PMC10604446 DOI: 10.1186/s12864-023-09756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
INTRODUCTION Understanding changes in cell identity in cancer and ageing is of great importance. In this work, we analyzed how gene expression changes in human tissues are associated with tissue specificity during cancer and ageing using transcriptome data from TCGA and GTEx. RESULTS We found significant downregulation of tissue-specific genes during ageing in 40% of the tissues analyzed, which suggests loss of tissue identity with age. For most cancer types, we have noted a consistent pattern of downregulation in genes that are specific to the tissue from which the tumor originated. Moreover, we observed in cancer an activation of genes not usually expressed in the tissue of origin as well as an upregulation of genes specific to other tissues. These patterns in cancer were associated with patient survival. The age of the patient, however, did not influence these patterns. CONCLUSION We identified loss of cellular identity in 40% of the tissues analysed during human ageing, and a clear pattern in cancer, where during tumorigenesis cells express genes specific to other organs while suppressing the expression of genes from their original tissue. The loss of cellular identity observed in cancer is associated with prognosis and is not influenced by age, suggesting that it is a crucial stage in carcinogenesis.
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Affiliation(s)
- Gabriel Arantes Dos Santos
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2WB, UK
| | - Kasit Chatsirisupachai
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
| | - Roberto A Avelar
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
| | - João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2WB, UK.
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Abstract
Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of transcripts of multiple types. Among these, a small set of protein-coding mRNAs play a disproportionately large role in defining phenotypes. Due to their sequence conservation, orthology can be established, making it possible to define the universal catalog of eukaryotic protein-coding genes. This catalog should substantially contribute to uncovering the genomic events underlying the emergence of eukaryotic phenotypes. This piece briefly reviews the basics of protein-coding gene prediction, discusses challenges in finalizing annotation of the human genome, and proposes strategies for producing annotations across the eukaryotic Tree of Life. This lays the groundwork for obtaining the catalog of all genes-the Earth's code of life.
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Affiliation(s)
- Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Catalonia
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia
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25
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Sorokin M, Buzdin AA, Guryanova A, Efimov V, Suntsova MV, Zolotovskaia MA, Koroleva EV, Sekacheva MI, Tkachev VS, Garazha A, Kremenchutckaya K, Drobyshev A, Seryakov A, Gudkov A, Alekseenko IV, Rakitina O, Kostina MB, Vladimirova U, Moisseev A, Bulgin D, Radomskaya E, Shestakov V, Baklaushev VP, Prassolov V, Shegay PV, Li X, Poddubskaya EV, Gaifullin N. Large-scale assessment of pros and cons of autopsy-derived or tumor-matched tissues as the norms for gene expression analysis in cancers. Comput Struct Biotechnol J 2023; 21:3964-3986. [PMID: 37635765 PMCID: PMC10448432 DOI: 10.1016/j.csbj.2023.07.040] [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: 03/05/2023] [Revised: 07/17/2023] [Accepted: 07/30/2023] [Indexed: 08/29/2023] Open
Abstract
Normal tissues are essential for studying disease-specific differential gene expression. However, healthy human controls are typically available only in postmortal/autopsy settings. In cancer research, fragments of pathologically normal tissue adjacent to tumor site are frequently used as the controls. However, it is largely underexplored how cancers can systematically influence gene expression of the neighboring tissues. Here we performed a comprehensive pan-cancer comparison of molecular profiles of solid tumor-adjacent and autopsy-derived "healthy" normal tissues. We found a number of systemic molecular differences related to activation of the immune cells, intracellular transport and autophagy, cellular respiration, telomerase activation, p38 signaling, cytoskeleton remodeling, and reorganization of the extracellular matrix. The tumor-adjacent tissues were deficient in apoptotic signaling and negative regulation of cell growth including G2/M cell cycle transition checkpoint. We also detected an extensive rearrangement of the chemical perception network. Molecular targets of 32 and 37 cancer drugs were over- or underexpressed, respectively, in the tumor-adjacent norms. These processes may be driven by molecular events that are correlated between the paired cancer and adjacent normal tissues, that mostly relate to inflammation and regulation of intracellular molecular pathways such as the p38, MAPK, Notch, and IGF1 signaling. However, using a model of macaque postmortal tissues we showed that for the 30 min - 24-hour time frame at 4ºC, an RNA degradation pattern in lung biosamples resulted in an artifact "differential" expression profile for 1140 genes, although no differences could be detected in liver. Thus, such concerns should be addressed in practice.
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Affiliation(s)
- Maksim Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Omicsway Corp., Walnut, CA 91789, USA
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anton A. Buzdin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
| | - Anastasia Guryanova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Victor Efimov
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maria V. Suntsova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Marianna A. Zolotovskaia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- Omicsway Corp., Walnut, CA 91789, USA
| | - Elena V. Koroleva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Marina I. Sekacheva
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Victor S. Tkachev
- Omicsway Corp., Walnut, CA 91789, USA
- Oncobox Ltd., Moscow 121205, Russia
| | - Andrew Garazha
- Omicsway Corp., Walnut, CA 91789, USA
- Oncobox Ltd., Moscow 121205, Russia
| | | | - Aleksey Drobyshev
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | | | - Alexander Gudkov
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Irina V. Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", 2, Kurchatov Square, Moscow 123182, Russian
- FSBI "National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov" Ministry of Healthcare of the Russian Federation, Moscow 117198, Russia
| | - Olga Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Maria B. Kostina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Uliana Vladimirova
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Oncobox Ltd., Moscow 121205, Russia
| | - Aleksey Moisseev
- I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Dmitry Bulgin
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | - Elena Radomskaya
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | - Viktor Shestakov
- Research Institute of Medical Primatology, 177 Mira str., Veseloye, Sochi 354376, Russia
| | | | - Vladimir Prassolov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str., Moscow 119991, Russia
| | - Petr V. Shegay
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, 249036 Obninsk, Russia
| | - Xinmin Li
- UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA
| | | | - Nurshat Gaifullin
- Department of Physiology and General Pathology, Faculty of Medicine, Lomonosov Moscow State University, Moscow 119991, Russia
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Zhang Q, Zhang Y, Xie B, Liu D, Wang Y, Zhou Z, Zhang Y, King E, Tse G, Liu T. Resveratrol activation of SIRT1/MFN2 can improve mitochondria function, alleviating doxorubicin‐induced myocardial injury. CANCER INNOVATION 2023; 2:253-264. [DOI: 10.1002/cai2.64] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/08/2023] [Indexed: 10/11/2023]
Abstract
AbstractBackgroundDoxorubicin is a widely used cytotoxic chemotherapy agent for treating different malignancies. However, its use is associated with dose‐dependent cardiotoxicity, causing irreversible myocardial damage and significantly reducing the patient's quality of life and survival. In this study, an animal model of doxorubicin‐induced cardiomyopathy was used to investigate the pathogenesis of doxorubicin‐induced myocardial injury. This study also investigated a possible treatment strategy for alleviating myocardial injury through resveratrol therapy in vitro.MethodsAdult male C57BL/6J mice were randomly divided into a control group and a doxorubicin group. Body weight, echocardiography, surface electrocardiogram, and myocardial histomorphology were measured. The mechanisms of doxorubicin cardiotoxicity in H9c2 cell lines were explored by comparing three groups (phosphate‐buffered saline, doxorubicin, and doxorubicin with resveratrol).ResultsCompared to the control group, the doxorubicin group showed a lower body weight and higher systolic arterial pressure, associated with reduced left ventricular ejection fraction and left ventricular fractional shortening, prolonged PR interval, and QT interval. These abnormalities were associated with vacuolation and increased disorder in the mitochondria of cardiomyocytes, increased protein expression levels of α‐smooth muscle actin and caspase 3, and reduced protein expression levels of Mitofusin2 (MFN2) and Sirtuin1 (SIRT1). Compared to the doxorubicin group, doxorubicin + resveratrol treatment reduced caspase 3 and manganese superoxide dismutase, and increased MFN2 and SIRT1 expression levels.ConclusionDoxorubicin toxicity leads to abnormal mitochondrial morphology and dysfunction in cardiomyocytes and induces apoptosis by interfering with mitochondrial fusion. Resveratrol ameliorates doxorubicin‐induced cardiotoxicity by activating SIRT1/MFN2 to improve mitochondria function.
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Affiliation(s)
- Qingling Zhang
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
| | - Yunpeng Zhang
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
| | - Bingxin Xie
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
| | - Daiqi Liu
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
| | - Yueying Wang
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
| | - Zandong Zhou
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
| | - Yue Zhang
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
| | - Emma King
- Epidemiology Research Unit, Cardiovascular Analytics Group China‐UK Collaboration Hong Kong China
| | - Gary Tse
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
- Epidemiology Research Unit, Cardiovascular Analytics Group China‐UK Collaboration Hong Kong China
- Kent and Medway Medical School Canterbury Kent UK
| | - Tong Liu
- Department of Cardiology, Tianjin Key Laboratory of Ionic‐Molecular Function of Cardiovascular Disease, Tianjin Institute of Cardiology The Second Hospital of Tianjin Medical University Tianjin China
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Liharska LE, Park YJ, Ziafat K, Wilkins L, Silk H, Linares LM, Vornholt E, Sullivan B, Cohen V, Kota P, Feng C, Cheng E, Moya E, Thompson RC, Johnson JS, Rieder MK, Huang J, Scarpa J, Hashemi A, Polanco J, Levin MA, Nadkarni GN, Sebra R, Crary J, Schadt EE, Beckmann ND, Kopell BH, Charney AW. A study of gene expression in the living human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.21.23288916. [PMID: 37163086 PMCID: PMC10168405 DOI: 10.1101/2023.04.21.23288916] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A goal of medical research is to determine the molecular basis of human brain health and illness. One way to achieve this goal is through observational studies of gene expression in human brain tissue. Due to the unavailability of brain tissue from living people, most such studies are performed using tissue from postmortem brain donors. An assumption underlying this practice is that gene expression in the postmortem human brain is an accurate representation of gene expression in the living human brain. Here, this assumption - which, until now, had not been adequately tested - is tested by comparing human prefrontal cortex gene expression between 275 living samples and 243 postmortem samples. Expression levels differed significantly for nearly 80% of genes, and a systematic examination of alternative explanations for this observation determined that these differences are not a consequence of cell type composition, RNA quality, postmortem interval, age, medication, morbidity, symptom severity, tissue pathology, sample handling, batch effects, or computational methods utilized. Analyses integrating the data generated for this study with data from earlier landmark studies that used tissue from postmortem brain donors showed that postmortem brain gene expression signatures of neurological and mental illnesses, as well as of normal traits such as aging, may not be accurate representations of these gene expression signatures in the living brain. By using tissue from large cohorts living people, future observational studies of human brain biology have the potential to (1) determine the medical research questions that can be addressed using postmortem tissue as a proxy for living tissue and (2) expand the scope of medical research to include questions about the molecular basis of human brain health and illness that can only be addressed in living people (e.g., "What happens at the molecular level in the brain as a person experiences an emotion?").
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Singh PP, Benayoun BA. Considerations for reproducible omics in aging research. NATURE AGING 2023; 3:921-930. [PMID: 37386258 PMCID: PMC10527412 DOI: 10.1038/s43587-023-00448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
Technical advancements over the past two decades have enabled the measurement of the panoply of molecules of cells and tissues including transcriptomes, epigenomes, metabolomes and proteomes at unprecedented resolution. Unbiased profiling of these molecular landscapes in the context of aging can reveal important details about mechanisms underlying age-related functional decline and age-related diseases. However, the high-throughput nature of these experiments creates unique analytical and design demands for robustness and reproducibility. In addition, 'omic' experiments are generally onerous, making it crucial to effectively design them to eliminate as many spurious sources of variation as possible as well as account for any biological or technical parameter that may influence such measures. In this Perspective, we provide general guidelines on best practices in the design and analysis of omic experiments in aging research from experimental design to data analysis and considerations for long-term reproducibility and validation of such studies.
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Affiliation(s)
- Param Priya Singh
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Aging Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, USA.
- Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
- USC Stem Cell Initiative, Los Angeles, CA, USA.
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29
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Carbonell-Sala S, Lagarde J, Nishiyori H, Palumbo E, Arnan C, Takahashi H, Carninci P, Uszczynska-Ratajczak B, Guigó R. CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.543444. [PMID: 37398314 PMCID: PMC10312720 DOI: 10.1101/2023.06.16.543444] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts remains a challenge for long-read sequencing methods. To address this limitation, we developed CapTrap-seq, a cDNA library preparation method, which combines the Cap-trapping strategy with oligo(dT) priming to detect 5'capped, full-length transcripts, together with the data processing pipeline LyRic. We benchmarked CapTrap-seq and other popular RNA-seq library preparation protocols in a number of human tissues using both ONT and PacBio sequencing. To assess the accuracy of the transcript models produced, we introduced a capping strategy for synthetic RNA spike-in sequences that mimics the natural 5'cap formation in RNA spike-in molecules. We found that the vast majority (up to 90%) of transcript models that LyRic derives from CapTrap-seq reads are full-length. This makes it possible to produce highly accurate annotations with minimal human intervention.
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30
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Tosoni G, Ayyildiz D, Bryois J, Macnair W, Fitzsimons CP, Lucassen PJ, Salta E. Mapping human adult hippocampal neurogenesis with single-cell transcriptomics: Reconciling controversy or fueling the debate? Neuron 2023; 111:1714-1731.e3. [PMID: 37015226 DOI: 10.1016/j.neuron.2023.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/06/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
The notion of exploiting the regenerative potential of the human brain in physiological aging or neurological diseases represents a particularly attractive alternative to conventional strategies for enhancing or restoring brain function. However, a major first question to address is whether the human brain does possess the ability to regenerate. The existence of human adult hippocampal neurogenesis (AHN) has been at the center of a fierce scientific debate for many years. The advent of single-cell transcriptomic technologies was initially viewed as a panacea to resolving this controversy. However, recent single-cell RNA sequencing studies in the human hippocampus yielded conflicting results. Here, we critically discuss and re-analyze previously published AHN-related single-cell transcriptomic datasets. We argue that, although promising, the single-cell transcriptomic profiling of AHN in the human brain can be confounded by methodological, conceptual, and biological factors that need to be consistently addressed across studies and openly discussed within the scientific community.
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Affiliation(s)
- Giorgia Tosoni
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Will Macnair
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Carlos P Fitzsimons
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Paul J Lucassen
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands; Center for Urban Mental Health, University of Amsterdam, 1098 SM, Amsterdam, the Netherlands
| | - Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands.
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Guardado-Estrada M, Cárdenas-Monroy CA, Martínez-Rivera V, Cortez F, Pedraza-Lara C, Millan-Catalan O, Pérez-Plasencia C. A miRNome analysis at the early postmortem interval. PeerJ 2023; 11:e15409. [PMID: 37304870 PMCID: PMC10257396 DOI: 10.7717/peerj.15409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/23/2023] [Indexed: 06/13/2023] Open
Abstract
The postmortem interval (PMI) is the time elapsing since the death of an individual until the body is examined. Different molecules have been analyzed to better estimate the PMI with variable results. The miRNAs draw attention in the forensic field to estimate the PMI as they can better support degradation. In the present work, we analyzed the miRNome at early PMI in rats' skeletal muscle using the Affymetrix GeneChip™ miRNA 4.0 microarrays. We found 156 dysregulated miRNAs in rats' skeletal muscle at 24 h of PMI, out of which 84 were downregulated, and 72 upregulated. The miRNA most significantly downregulated was miR-139-5p (FC = -160, p = 9.97 × 10-11), while the most upregulated was rno-miR-92b-5p (FC = 241.18, p = 2.39 × 10-6). Regarding the targets of these dysregulated miRNAs, the rno-miR-125b-5p and rno-miR-138-5p were the miRNAs with more mRNA targets. The mRNA targets that we found in the present study participate in several biological processes such as interleukin secretion regulation, translation regulation, cell growth, or low oxygen response. In addition, we found a downregulation of SIRT1 mRNA and an upregulation of TGFBR2 mRNA at 24 h of PMI. These results suggest there is an active participation of miRNAs at early PMI which could be further explored to identify potential biomarkers for PMI estimation.
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Affiliation(s)
- Mariano Guardado-Estrada
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Christian A. Cárdenas-Monroy
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vanessa Martínez-Rivera
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Fernanda Cortez
- Computational Genomics Division, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Carlos Pedraza-Lara
- Laboratorio de Entomología, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Oliver Millan-Catalan
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Carlos Pérez-Plasencia
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Instituto Nacional de Cancerología, Mexico City, Mexico
- Unidad de Investigación Biomédica en Cáncer, Laboratorio de Genómica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
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32
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Prawer YDJ, Gleeson J, De Paoli-Iseppi R, Clark MB. Pervasive effects of RNA degradation on Nanopore direct RNA sequencing. NAR Genom Bioinform 2023; 5:lqad060. [PMID: 37305170 PMCID: PMC10251640 DOI: 10.1093/nargab/lqad060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/18/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023] Open
Abstract
Oxford Nanopore direct RNA sequencing (DRS) is capable of sequencing complete RNA molecules and accurately measuring gene and isoform expression. However, as DRS is designed to profile intact RNA, expression quantification may be more heavily dependent upon RNA integrity than alternative RNA sequencing methodologies. It is currently unclear how RNA degradation impacts DRS or whether it can be corrected for. To assess the impact of RNA integrity on DRS, we performed a degradation time series using SH-SY5Y neuroblastoma cells. Our results demonstrate that degradation is a significant and pervasive factor that can bias DRS measurements, including a reduction in library complexity resulting in an overrepresentation of short genes and isoforms. Degradation also biases differential expression analyses; however, we find that explicit correction can almost fully recover meaningful biological signal. In addition, DRS provided less biased profiling of partially degraded samples than Nanopore PCR-cDNA sequencing. Overall, we find that samples with RNA integrity number (RIN) > 9.5 can be treated as undegraded and samples with RIN > 7 can be utilized for DRS with appropriate correction. These results establish the suitability of DRS for a wide range of samples, including partially degraded in vivo clinical and post-mortem samples, while limiting the confounding effect of degradation on expression quantification.
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Affiliation(s)
- Yair D J Prawer
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Josie Gleeson
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ricardo De Paoli-Iseppi
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael B Clark
- To whom correspondence should be addressed. Tel: +61 3 9035 3669;
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Shlobin NA, Aru J, Vicente R, Zemmar A. What happens in the brain when we die? Deciphering the neurophysiology of the final moments in life. Front Aging Neurosci 2023; 15:1143848. [PMID: 37228251 PMCID: PMC10203241 DOI: 10.3389/fnagi.2023.1143848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023] Open
Abstract
When do we die and what happens in the brain when we die? The mystery around these questions has engaged mankind for centuries. Despite the challenges to obtain recordings of the dying brain, recent studies have contributed to better understand the processes occurring during the last moments of life. In this review, we summarize the literature on neurophysiological changes around the time of death. Perhaps the only subjective description of death stems from survivors of near-death experiences (NDEs). Hallmarks of NDEs include memory recall, out-of-body experiences, dreaming, and meditative states. We survey the evidence investigating neurophysiological changes of these experiences in healthy subjects and attempt to incorporate this knowledge into the existing literature investigating the dying brain to provide valuations for the neurophysiological footprint and timeline of death. We aim to identify reasons explaining the variations of data between studies investigating this field and provide suggestions to standardize research and reduce data variability.
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Affiliation(s)
- Nathan A. Shlobin
- Department of Neurosurgery, Henan Provincial People’s Hospital, Henan University School of Medicine, Zhengzhou, China
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Jaan Aru
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Raul Vicente
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ajmal Zemmar
- Department of Neurosurgery, Henan Provincial People’s Hospital, Henan University School of Medicine, Zhengzhou, China
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, United States
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Kocsmár É, Schmid M, Cosenza-Contreras M, Kocsmár I, Föll M, Krey L, Barta BA, Rácz G, Kiss A, Werner M, Schilling O, Lotz G, Bronsert P. Proteome alterations in human autopsy tissues in relation to time after death. Cell Mol Life Sci 2023; 80:117. [PMID: 37020120 PMCID: PMC10075177 DOI: 10.1007/s00018-023-04754-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023]
Abstract
Protein expression is a primary area of interest for routine histological diagnostics and tissue-based research projects, but the limitations of its post-mortem applicability remain largely unclear. On the other hand, tissue specimens obtained during autopsies can provide unique insight into advanced disease states, especially in cancer research. Therefore, we aimed to identify the maximum post-mortem interval (PMI) which is still suitable for characterizing protein expression patterns, to explore organ-specific differences in protein degradation, and to investigate whether certain proteins follow specific degradation kinetics. Therefore, the proteome of human tissue samples obtained during routine autopsies of deceased patients with accurate PMI (6, 12, 18, 24, 48, 72, 96 h) and without specific diseases that significantly affect tissue preservation, from lungs, kidneys and livers, was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For the kidney and liver, significant protein degradation became apparent at 48 h. For the lung, the proteome composition was rather static for up to 48 h and substantial protein degradation was detected only at 72 h suggesting that degradation kinetics appear to be organ specific. More detailed analyses suggested that proteins with similar post-mortem kinetics are not primarily shared in their biological functions. The overrepresentation of protein families with analogous structural motifs in the kidney indicates that structural features may be a common factor in determining similar postmortem stability. Our study demonstrates that a longer post-mortem period may have a significant impact on proteome composition, but sampling within 24 h may be appropriate, as degradation is within acceptable limits even in organs with faster autolysis.
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Affiliation(s)
- Éva Kocsmár
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Marlene Schmid
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miguel Cosenza-Contreras
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ildikó Kocsmár
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Melanie Föll
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
| | - Leah Krey
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bálint András Barta
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Gergely Rácz
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - András Kiss
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Martin Werner
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Gábor Lotz
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Peter Bronsert
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Biobank Comprehensive Cancer Center Freiburg, University Medical Center, Freiburg, Germany.
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Nieuwenhuis TO, Giles HH, McCall MN, Halushka MK. Patterns of unwanted biological and technical expression variation across 49 human tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.531935. [PMID: 36945408 PMCID: PMC10028996 DOI: 10.1101/2023.03.09.531935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
All tissue-based gene expression studies are impacted by biological and technical sources of variation. Numerous methods are used to normalize and batch correct these datasets. A more accurate understanding of all causes of variation could further optimize these approaches. We used 17,282 samples from 49 tissues in the Genotype Tissue Expression (GTEx) dataset (v8) to investigate patterns and causes of expression variation. Transcript expression was normalized to Z-scores and only the most variable 2% of transcripts were evaluated and clustered based on co-expression patterns. Clustered gene sets were solved to different biological or technical causes related to metadata elements and histologic images. We identified 522 variable transcript clusters (median 11 per tissue) across the samples. Of these, 64% were confidently explained, 15% were likely explained, 7% were low confidence explanations and 14% had no clear cause. Common causes included sex, sequencing contamination, immunoglobulin diversity, and compositional tissue differences. Less common biological causes included death interval (Hardy score), muscle atrophy, diabetes status, and menopause. Technical causes included brain pH and harvesting differences. Many of the causes of variation in bulk tissue expression were identifiable in the Tabula Sapiens dataset of single cell expression. This is the largest exploration of the underlying sources of tissue expression variation. It uncovered expected and unexpected causes of variable gene expression. These identified sources of variation will inform which metadata to acquire with tissue harvesting and can be used to improve normalization, batch correction, and analysis of both bulk and single cell RNA-seq data.
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Affiliation(s)
- Tim O Nieuwenhuis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hunter H Giles
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Moreira JD, Gower AC, Xue L, Alekseyev Y, Smith KK, Choi SH, Ayalon N, Farb MG, Tenan K, LeClerc A, Levy D, Benjamin EJ, Lenburg ME, Mitchell RN, Padera RF, Fetterman JL, Gopal DM. Systematic dissection, preservation, and multiomics in whole human and bovine hearts. Cardiovasc Pathol 2023; 63:107495. [PMID: 36334690 PMCID: PMC10031913 DOI: 10.1016/j.carpath.2022.107495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/22/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES We sought to develop a rigorous, systematic protocol for the dissection and preservation of human hearts for biobanking that expands previous success in postmortem transcriptomics to multiomics from paired tissue. BACKGROUND Existing cardiac biobanks consist largely of biopsy tissue or explanted hearts in select diseases and are insufficient for correlating whole organ phenotype with clinical data. METHODS We demonstrate optimal conditions for multiomics interrogation (ribonucleic acid (RNA) sequencing, untargeted metabolomics) in hearts by evaluating the effect of technical variables (storage solution, temperature) and simulated postmortem interval (PMI) on RNA and metabolite stability. We used bovine (n=3) and human (n=2) hearts fixed in PAXgene or snap-frozen with liquid nitrogen. RESULTS Using a paired Wald test, only two of the genes assessed were differentially expressed between left ventricular samples from bovine hearts stored in PAXgene at 0 and 12 hours PMI (FDR q<0.05). We obtained similar findings in human left ventricular samples, suggesting stability of RNA transcripts at PMIs up to 12 hours. Different library preparation methods (mRNA poly-A capture vs. rRNA depletion) resulted in similar quality metrics with both library preparations achieving >95% of reads properly aligning to the reference genomes across all PMIs for bovine and human hearts. PMI had no effect on RNA Integrity Number or quantity of RNA recovered at the time points evaluated. Of the metabolites identified (855 total) using untargeted metabolomics of human left ventricular tissue, 503 metabolites remained stable across PMIs (0, 4, 8, 12 hours). Most metabolic pathways retained several stable metabolites. CONCLUSIONS Our data demonstrate a technically rigorous, reproducible protocol that will enhance cardiac biobanking practices and facilitate novel insights into human CVD. CONDENSED ABSTRACT Cardiovascular disease (CVD) is the leading cause of mortality worldwide. Current biobanking practices insufficiently capture both the diverse array of phenotypes present in CVDs and the spatial heterogeneity across cardiac tissue sites. We have developed a rigorous and systematic protocol for the dissection and preservation of human cardiac biospecimens to enhance the availability of whole organ tissue for multiple applications. When combined with longitudinal clinical phenotyping, our protocol will enable multiomics in hearts to deepen our understanding of CVDs.
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Affiliation(s)
- Jesse D Moreira
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Adam C Gower
- Department of Medicine, Section of Computational Biomedicine, and Clinical and Translational Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Liying Xue
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Yuriy Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Karan K Smith
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Seung H Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nir Ayalon
- Cardiovascular Medicine Section, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Melissa G Farb
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Kenneth Tenan
- BU Microarray and Sequencing Resource, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Ashley LeClerc
- BU Microarray and Sequencing Resource, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Medicine, Preventive Medicine & Epidemiology Section, Boston University Chobanian & Avedisian School of Medicine, Boston University and the National Heart, Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Emelia J Benjamin
- Department of Medicine, Preventive Medicine & Epidemiology Section, Boston University Chobanian & Avedisian School of Medicine, Boston University and the National Heart, Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA; Section of Cardiovascular Medicine, Boston Medical Center/Boston University Chobanian & Avedisian School of Medicine and Department of Epidemiology Boston University School of Public Health, Boston, MA, USA
| | - Marc E Lenburg
- Department of Medicine, Section of Computational Biomedicine, and Clinical and Translational Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Richard N Mitchell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica L Fetterman
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
| | - Deepa M Gopal
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA; Cardiovascular Medicine Section, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
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Arat S, Huynh R, Kumpf S, Qian J, Shoieb A, Virgen-Slane R, Voigt F, Xie Z, Jakubczak JL. Effects of donor source on transcriptomic profiles of human kidney tissue. FASEB J 2023; 37:e22804. [PMID: 36753402 DOI: 10.1096/fj.202201754r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/27/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023]
Abstract
Normal human tissue is a critical reference control in biomedical research. However, the type of tissue donor can significantly affect the underlying biology of the samples. We investigated the impact of tissue donor source type by performing transcriptomic analysis on healthy kidney tissue from three donor source types: cadavers, organ donors, and normal-adjacent tissue from surgical resections of clear cell renal cell carcinomas, and we compared the gene expression profiles to those of clear cell renal cell carcinoma samples. Comparisons among the normal samples revealed general similarity, with notable differences in gene expression pathways involving immune system and inflammatory processes, response to extracellular stimuli, ion transport, and metabolism. When compared to tumors, the transcriptomic profiles of the normal adjacent tissue were highly similar to the profiles from cadaveric and organ donor tissue samples, arguing against the presence of a field cancerization effect in clear cell renal cell carcinoma. We conclude that all three normal source types are suitable for reference kidney control samples, but important differences must be noted for particular research areas and tissue banking strategies.
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Affiliation(s)
- Seda Arat
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Renee Huynh
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Steven Kumpf
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Jessie Qian
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Ahmed Shoieb
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Richard Virgen-Slane
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., La Jolla, California, USA
| | - Frank Voigt
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Zhiyong Xie
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts, USA
| | - John L Jakubczak
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
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Kelly DE, Ramdas S, Ma R, Rawlings-Goss RA, Grant GR, Ranciaro A, Hirbo JB, Beggs W, Yeager M, Chanock S, Nyambo TB, Omar SA, Woldemeskel D, Belay G, Li H, Brown CD, Tishkoff SA. The genetic and evolutionary basis of gene expression variation in East Africans. Genome Biol 2023; 24:35. [PMID: 36829244 PMCID: PMC9951478 DOI: 10.1186/s13059-023-02874-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Mapping of quantitative trait loci (QTL) associated with molecular phenotypes is a powerful approach for identifying the genes and molecular mechanisms underlying human traits and diseases, though most studies have focused on individuals of European descent. While important progress has been made to study a greater diversity of human populations, many groups remain unstudied, particularly among indigenous populations within Africa. To better understand the genetics of gene regulation in East Africans, we perform expression and splicing QTL mapping in whole blood from a cohort of 162 diverse Africans from Ethiopia and Tanzania. We assess replication of these QTLs in cohorts of predominantly European ancestry and identify candidate genes under selection in human populations. RESULTS We find the gene regulatory architecture of African and non-African populations is broadly shared, though there is a considerable amount of variation at individual loci across populations. Comparing our analyses to an equivalently sized cohort of European Americans, we find that QTL mapping in Africans improves the detection of expression QTLs and fine-mapping of causal variation. Integrating our QTL scans with signatures of natural selection, we find several genes related to immunity and metabolism that are highly differentiated between Africans and non-Africans, as well as a gene associated with pigmentation. CONCLUSION Extending QTL mapping studies beyond European ancestry, particularly to diverse indigenous populations, is vital for a complete understanding of the genetic architecture of human traits and can reveal novel functional variation underlying human traits and disease.
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Affiliation(s)
- Derek E Kelly
- Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shweta Ramdas
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Rong Ma
- Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Jibril B Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William Beggs
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Meredith Yeager
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Institutes of Health, Rockville, MD, USA
| | - Thomas B Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, Dar Es Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Dawit Woldemeskel
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial Cellular and Molecular Biology Department, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hongzhe Li
- Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher D Brown
- Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
- Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah A Tishkoff
- Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, USA.
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GSDME-mediated pyroptosis promotes the progression and associated inflammation of atherosclerosis. Nat Commun 2023; 14:929. [PMID: 36807553 PMCID: PMC9938904 DOI: 10.1038/s41467-023-36614-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/09/2023] [Indexed: 02/20/2023] Open
Abstract
Pyroptosis, a type of Gasdermin-mediated cell death, contributes to an exacerbation of inflammation. To test the hypothesis that GSDME-mediated pyroptosis aggravates the progression of atherosclerosis, we generate ApoE and GSDME dual deficiency mice. As compared with the control mice, GSDME-/-/ApoE-/- mice show a reduction of atherosclerotic lesion area and inflammatory response when induced with a high-fat diet. Human atherosclerosis single-cell transcriptome analysis demonstrates that GSDME is mainly expressed in macrophages. In vitro, oxidized low-density lipoprotein (ox-LDL) induces GSDME expression and pyroptosis in macrophages. Mechanistically, ablation of GSDME in macrophages represses ox-LDL-induced inflammation and macrophage pyroptosis. Moreover, the signal transducer and activator of transcription 3 (STAT3) directly correlates with and positively regulates GSDME expression. This study explores the transcriptional mechanisms of GSDME during atherosclerosis development and indicates that GSDME-mediated pyroptosis in the progression of atherosclerosis could be a potential therapeutic approach for atherosclerosis.
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40
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Locci E, Stocchero M, Gottardo R, Chighine A, De-Giorgio F, Ferino G, Nioi M, Demontis R, Tagliaro F, d'Aloja E. PMI estimation through metabolomics and potassium analysis on animal vitreous humour. Int J Legal Med 2023; 137:887-895. [PMID: 36799966 PMCID: PMC10085955 DOI: 10.1007/s00414-023-02975-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/08/2023] [Indexed: 02/18/2023]
Abstract
INTRODUCTION The estimation of post-mortem interval (PMI) remains a major challenge in forensic science. Most of the proposed approaches lack the reliability required to meet the rigorous forensic standards. OBJECTIVES We applied 1H NMR metabolomics to estimate PMI on ovine vitreous humour comparing the results with the actual scientific gold standard, namely vitreous potassium concentrations. METHODS Vitreous humour samples were collected in a time frame ranging from 6 to 86 h after death. Experiments were performed by using 1H NMR metabolomics and ion capillary analysis. Data were submitted to multivariate statistical data analysis. RESULTS A multivariate calibration model was built to estimate PMI based on 47 vitreous humour samples. The model was validated with an independent test set of 24 samples, obtaining a prediction error on the entire range of 6.9 h for PMI < 24 h, 7.4 h for PMI between 24 and 48 h, and 10.3 h for PMI > 48 h. Time-related modifications of the 1H NMR vitreous metabolomic profile could predict PMI better than potassium up to 48 h after death, whilst a combination of the two is better than the single approach for higher PMI estimation. CONCLUSION The present study, although in a proof-of-concept animal model, shows that vitreous metabolomics can be a powerful tool to predict PMI providing a more accurate estimation compared to the widely studied approach based on vitreous potassium concentrations.
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Affiliation(s)
- Emanuela Locci
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Matteo Stocchero
- Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Rossella Gottardo
- Department of Diagnostics and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
| | - Alberto Chighine
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy.
| | - Fabio De-Giorgio
- Department of Health Surveillance and Bioethics, Section of Legal Medicine, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, 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
| | - Matteo Nioi
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Roberto Demontis
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Franco Tagliaro
- Department of Diagnostics and Public Health, Unit of Forensic Medicine, University of Verona, Verona, 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
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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. PLoS Biol 2023; 21:e3001986. [PMID: 36745672 PMCID: PMC9934459 DOI: 10.1371/journal.pbio.3001986] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/16/2023] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
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. This atlas may have multiple applications; for example, drug targets with day-night or seasonal variation in gene expression may benefit from temporally adjusted doses.
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Affiliation(s)
- Valentin Wucher
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- MeLiS, SynatAc Team, UCBL1—CNRS UMR5284—Inserm U1314, 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
- * E-mail: (MI); (RG)
| | - Roderic Guigó
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail: (MI); (RG)
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Talamanca L, Gobet C, Naef F. Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans. Science 2023; 379:478-483. [PMID: 36730411 DOI: 10.1126/science.add0846] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) project with an algorithm that assigns circadian phases to 914 donors, by integrating temporal information from multiple tissues in each individual, to identify messenger RNA (mRNA) rhythms in 46 tissues. Clock transcripts showed conserved timing relationships and tight synchrony across the body. mRNA rhythms varied in breadth, covering global and tissue-specific functions, including metabolic pathways and systemic responses. The clock structure was conserved across sexes and age groups. However, overall gene expression rhythms were highly sex-dimorphic and more sustained in females. Rhythmic programs generally dampened with age across the body.
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Affiliation(s)
- Lorenzo Talamanca
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Cédric Gobet
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Salta E, Lazarov O, Fitzsimons CP, Tanzi R, Lucassen PJ, Choi SH. Adult hippocampal neurogenesis in Alzheimer's disease: A roadmap to clinical relevance. Cell Stem Cell 2023; 30:120-136. [PMID: 36736288 PMCID: PMC10082636 DOI: 10.1016/j.stem.2023.01.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
Adult hippocampal neurogenesis (AHN) drops sharply during early stages of Alzheimer's disease (AD), via unknown mechanisms, and correlates with cognitive status in AD patients. Understanding AHN regulation in AD could provide a framework for innovative pharmacological interventions. We here combine molecular, behavioral, and clinical data and critically discuss the multicellular complexity of the AHN niche in relation to AD pathophysiology. We further present a roadmap toward a better understanding of the role of AHN in AD by probing the promises and caveats of the latest technological advancements in the field and addressing the conceptual and methodological challenges ahead.
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Affiliation(s)
- Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Orly Lazarov
- Department of Anatomy and Cell Biology, College of Medicine, The University of Illinois at Chicago, 808 S Wood St., Chicago, IL 60612, USA
| | - Carlos P Fitzsimons
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Rudolph Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, McCance Center for Brain Health, 114 16th Street, Boston, MA 02129, USA.
| | - Paul J Lucassen
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands; Center for Urban Mental Health, University of Amsterdam, Kruislaan 404, 1098 SM, Amsterdam, The Netherlands.
| | - Se Hoon Choi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, McCance Center for Brain Health, 114 16th Street, Boston, MA 02129, USA.
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Grave-to-cradle: human embryonic lineage tracing from the postmortem body. Exp Mol Med 2023; 55:13-21. [PMID: 36599930 PMCID: PMC9898511 DOI: 10.1038/s12276-022-00912-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/02/2022] [Accepted: 10/13/2022] [Indexed: 01/06/2023] Open
Abstract
Curiosity concerning the process of human creation has been around for a long time. Relevant questions seemed to be resolved with the knowledge of how cells divide after fertilization obtained through in vitro fertilization experiments. However, we still do not know how human life is created at the cellular level. Recently, the value of cadavers as a resource from which to obtain "normal" cells and tissues has been established, and human research using postmortem bodies has attracted growing scientific attention. As the human genome can be analyzed at the level of nucleotides through whole-genome sequencing, individual cells in a postmortem body can be traced back to determine what developmental processes have transpired from fertilization. These retrospective lineage tracing studies have answered several unsolved questions on how humans are created. This review covers the methodologies utilized in lineage tracing research in a historical context and the conceptual basis for reconstructing the division history of cells in a retrospective manner using postzygotic somatic variants in postmortem tissue. We further highlight answers that postmortem research could potentially address and discuss issues that wait to be solved in the future.
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García-Pérez R, Ramirez JM, Ripoll-Cladellas A, Chazarra-Gil R, Oliveros W, Soldatkina O, Bosio M, Rognon PJ, Capella-Gutierrez S, Calvo M, Reverter F, Guigó R, Aguet F, Ferreira PG, Ardlie KG, Melé M. The landscape of expression and alternative splicing variation across human traits. CELL GENOMICS 2022; 3:100244. [PMID: 36777183 PMCID: PMC9903719 DOI: 10.1016/j.xgen.2022.100244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022]
Abstract
Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.
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Affiliation(s)
- Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Jose Miguel Ramirez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Aida Ripoll-Cladellas
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Ruben Chazarra-Gil
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Winona Oliveros
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Oleksandra Soldatkina
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Mattia Bosio
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Paul Joris Rognon
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Department of Economics and Business, Universitat Pompeu Fabra, Barcelona, Catalonia 08005, Spain,Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia 08034, Spain
| | - Salvador Capella-Gutierrez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Miquel Calvo
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Ferran Reverter
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalonia 08003, Spain
| | | | - Pedro G. Ferreira
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal,Laboratory of Artificial Intelligence and Decision Support, INESC TEC, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal,Institute of Molecular Pathology and Immunology of the University of Porto, Institute for Research and Innovation in Health (i3s), R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | | | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Corresponding author
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Kemfack AM, Hernandez-Morato I, Moayedi Y, Pitman MJ. An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model. Sci Rep 2022; 12:21665. [PMID: 36522411 PMCID: PMC9755529 DOI: 10.1038/s41598-022-25643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Challenges related to high-quality RNA extraction from post-mortem tissue have limited RNA-sequencing (RNA-seq) application in certain skeletal muscle groups, including the intrinsic laryngeal muscles (ILMs). The present study identified critical factors contributing to substandard RNA extraction from the ILMs and established a suitable method that permitted high-throughput analysis. Here, standard techniques for tissue processing were adapted, and an effective means to control confounding effects during specimen preparation was determined. The experimental procedure consistently provided sufficient intact total RNA (N = 68) and RIN ranging between 7.0 and 8.6, which was unprecedented using standard RNA purification protocols. This study confirmed the reproducibility of the workflow through repeated trials at different postnatal time points and across the distinctive ILMs. High-throughput diagnostics from 90 RNA samples indicated no sequencing alignment scores below 70%, validating the extraction strategy. Significant differences between the standard and experimental conditions suggest circumvented challenges and broad applicability to other skeletal muscles. This investigation remains ongoing given the prospect of therapeutic insights to voice, swallowing, and airway disorders. The present methodology supports pioneering global transcriptome investigations in the larynx previously unfounded in literature.
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Affiliation(s)
- Angela M Kemfack
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Ignacio Hernandez-Morato
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA.
| | - Yalda Moayedi
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
- Department of Neurology, Irving Medical Center, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Michael J Pitman
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
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Edlow BL, Kinney HC. Defining the boundary between life and death: New insights from neuropathology. J Neuropathol Exp Neurol 2022; 82:3-5. [PMID: 36519398 PMCID: PMC9764079 DOI: 10.1093/jnen/nlac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Brian L Edlow
- Send correspondence to: Brian L. Edlow, MD, Center for Neurotechnology and Neurorecovery, Massachusetts General Hospital, 101 Merrimac Street—Suite 310, Boston, MA 02114, USA; E-mail:
| | - Hannah C Kinney
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Estimation of Early Postmortem Interval from Long Noncoding RNA Gene Expression in the Incised Cutaneous Wound: An Experimental Study. Biomedicines 2022; 10:biomedicines10112919. [PMID: 36428487 PMCID: PMC9687757 DOI: 10.3390/biomedicines10112919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/19/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
The assessment of alteration of postmortem RNA expression has forensic significance in estimating postmortem interval. To evaluate wound healing progression and the effect of different postmortem intervals, histopathological changes, immunohistochemical matrix metalloproteinase-9 (MMP-9) expression, and long noncoding fatty acid oxidation (lncFAO), RNA expression was assessed in the incised cutaneous wound model. A full-thickness cutaneous wound was inflicted on 75 rats. All 15 rats were sacrificed at different post-infliction intervals (0, 2, 4, 8 and 10 days), and the cutaneous wounds (n = 5) were excised at different postmortem intervals (0, 5, and 24 h after euthanasia). The maximal inflammatory healing stage was detected at day 4 post-infliction, while near complete healing, thick mature collagen deposition was detected at day 10 post-infliction. LncFAO expression was significantly over-expressed with increasing wound age. MMP-9 was detectable on injury day with continuous elevation until 8 days post-wounding, which later decreased. Although histopathological and immunohistochemical examinations within 24 h postmortem did not show any remarkable changes, lncFAO RNA expression showed a significant negative correlation with hours passed since death. The combined use of histopathological changes, immunohistochemical expression of MMP-9, and molecular expression of lncFAO could be appropriate in wound dating verification. Among these factors, lncFAO could be a reliable indicator in postmortem interval estimation.
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Dental DNA as an Indicator of Post-Mortem Interval (PMI): A Pilot Research. Int J Mol Sci 2022; 23:ijms232112896. [DOI: 10.3390/ijms232112896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Teeth have proven to be a reliable source of DNA for forensic analysis as the pulp is rich in cells and protected from damaging factors and contamination by dental hard tissues. The pilot study aims to evaluate the feasibility of Next-Generation sequencing analysis on dental pulp to detect genetic mutations in DNA caused by post-mortem cell necrosis. We used a 56-gene oncopanel kit on a sample of 17 teeth extracted from living patients. Time of the tooth avulsion was assumed as death of the individual and Post-mortem Interval (PMI) was the time elapse since the DNA extraction and analysis. Days and Accumulated Degree Days (ADD) were assumed as measures of PMI that ranged between 0 to 34 days. Only 38 of the 56 considered genes proved to be affected by mutations (101), thus being of forensic interest. More specifically, 14 mutations occurred only in a specific range of PMIs/ADD; 67 were detected (alone or as clusters of the same gene) at specific PMI/ADD; 22 occurred at every PMI/ADD, except for some specific intervals. Since dental pulp was not targeted by any oncological diseases and all teeth were intact, vital, and from patients with unremarkable medical history, it could be assumed that mutations were due to post-mortem DNA changes induced by pulp death and the increasing time elapse since death. This pilot study found encouraging results in the application of NGS analysis on dental DNA, especially for PMIs of several days for which the traditional tools for PMI estimation have limitations. Further research on a larger sample of PMI and validation research on a larger sample of PMI and validation of the results are indeed necessary.
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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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