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Cianci V, Mondello C, Sapienza D, Guerrera MC, Cianci A, Cracò A, Omero F, Gioffrè V, Gualniera P, Asmundo A, Germanà A. Potential Role of mRNA in Estimating Postmortem Interval: A Systematic Review. Int J Mol Sci 2024; 25:8185. [PMID: 39125753 PMCID: PMC11311348 DOI: 10.3390/ijms25158185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/17/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Although the postmortem interval estimation still represents one of the main goals of forensic medicine, there are still several limitations that weigh on the methods most used for its determination: for this reason, even today, precisely estimating the postmortem interval remains one of the most important challenges in the forensic pathology field. To try to overcome these limitations, in recent years, numerous studies have been conducted on the potential use of the mRNA degradation time for reaching a more precise post mortem interval (PMI) estimation. An evidence-based systematic review of the literature has been conducted to evaluate the state of the art of the knowledge focusing on the potential correlation between mRNA degradation and PMI estimation. The research has been performed using the electronic databases PubMed and Scopus. The analysis conducted made it possible to confirm the potential applicability of mRNA for reaching a more precise PMI estimation. The analysis of the results highlighted the usefulness of some mRNAs, such as β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA, especially in short time frames, within a few hours or days of death. The matrices on which these analyses were conducted were also analyzed, resulting in less exposure to the external environment, including the heart, brain, and dental pulp. The major limitations were also reported, including the short time intervals analyzed in most of the articles, the lack of mathematical models, and the failure to report the error rate between the mRNA degradation time and PMI. Given the still small number of published articles, the lack of globally recognized standardized methods, and the numerous techniques used to evaluate the mRNA degradation times, numerous and larger studies are still necessary to reach more solid and shared evidence.
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Affiliation(s)
- Vincenzo Cianci
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Legal Medicine, University of Messina, Via Consolare Valeria, 1, 98125 Messina, Italy; (C.M.); (P.G.); (A.A.)
| | - Cristina Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Legal Medicine, University of Messina, Via Consolare Valeria, 1, 98125 Messina, Italy; (C.M.); (P.G.); (A.A.)
| | - Daniela Sapienza
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Legal Medicine, University of Messina, Via Consolare Valeria, 1, 98125 Messina, Italy; (C.M.); (P.G.); (A.A.)
| | - Maria Cristina Guerrera
- Zebrafish Neuromorphology Lab, Department of Veterinary Sciences, University of Messina, 98168 Messina, Italy; (M.C.G.); (A.G.)
| | - Alessio Cianci
- Department of Cardiovascular Medicine, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy;
| | - Annalisa Cracò
- Diagnostic and Interventional Radiology Unit, Department of Biomedical Sciences and Morphological and Functional Imaging, University Hospital Messina, 98125 Messina, Italy;
| | - Fausto Omero
- Medical Oncology Unit, Department of Human Pathology “G. Barresi”, University of Messina, 98125 Messina, Italy;
| | - Vittorio Gioffrè
- Department of Otorhinolaryngology-Head and Neck Surgery, IRCCS San Raffaele, Vita-Salute San Raffaele University, Via Olgettina 60, 20132 Milan, Italy;
| | - Patrizia Gualniera
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Legal Medicine, University of Messina, Via Consolare Valeria, 1, 98125 Messina, Italy; (C.M.); (P.G.); (A.A.)
| | - Alessio Asmundo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Legal Medicine, University of Messina, Via Consolare Valeria, 1, 98125 Messina, Italy; (C.M.); (P.G.); (A.A.)
| | - Antonino Germanà
- Zebrafish Neuromorphology Lab, Department of Veterinary Sciences, University of Messina, 98168 Messina, Italy; (M.C.G.); (A.G.)
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Farzad N, Enninful A, Bao S, Zhang D, Deng Y, Fan R. Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nat Protoc 2024:10.1038/s41596-024-01013-y. [PMID: 38943021 DOI: 10.1038/s41596-024-01013-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/11/2024] [Indexed: 06/30/2024]
Abstract
Spatial epigenetic mapping of tissues enables the study of gene regulation programs and cellular functions with the dependency on their local tissue environment. Here we outline a complete procedure for two spatial epigenomic profiling methods: spatially resolved genome-wide profiling of histone modifications using in situ cleavage under targets and tagmentation (CUT&Tag) chemistry (spatial-CUT&Tag) and transposase-accessible chromatin sequencing (spatial-ATAC-sequencing) for chromatin accessibility. Both assays utilize in-tissue Tn5 transposition to recognize genomic DNA loci followed by microfluidic deterministic barcoding to incorporate spatial address codes. Furthermore, these two methods do not necessitate prior knowledge of the transcription or epigenetic markers for a given tissue or cell type but permit genome-wide unbiased profiling pixel-by-pixel at the 10 μm pixel size level and single-base resolution. To support the widespread adaptation of these methods, details are provided in five general steps: (1) sample preparation; (2) Tn5 transposition in spatial-ATAC-sequencing or antibody-controlled pA-Tn5 tagmentation in CUT&Tag; (3) library preparation; (4) next-generation sequencing; and (5) data analysis using our customed pipelines available at: https://github.com/dyxmvp/Spatial_ATAC-seq and https://github.com/dyxmvp/spatial-CUT-Tag . The whole procedure can be completed on four samples in 2-3 days. Familiarity with basic molecular biology and bioinformatics skills with access to a high-performance computing environment are required. A rudimentary understanding of pathology and specimen sectioning, as well as deterministic barcoding in tissue-specific skills (e.g., design of a multiparameter barcode panel and creation of microfluidic devices), are also advantageous. In this protocol, we mainly focus on spatial profiling of tissue region-specific epigenetic landscapes in mouse embryos and mouse brains using spatial-ATAC-sequencing and spatial-CUT&Tag, but these methods can be used for other species with no need for species-specific probe design.
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Affiliation(s)
- Negin Farzad
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Shuozhen Bao
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Pennsylvania, PA, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
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3
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Cao J, Zheng Z, Sun D, Chen X, Cheng R, Lv T, An Y, Zheng J, Song J, Wu L, Yang C. Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing. Nat Biotechnol 2024:10.1038/s41587-023-02086-y. [PMID: 38228777 DOI: 10.1038/s41587-023-02086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq), which offers both high sensitivity and high resolution. Decoder-seq combines dendrimeric nanosubstrates with microfluidic coordinate barcoding to generate spatial arrays with a DNA density approximately ten times higher than previously reported methods while maintaining flexibility in resolution. We show that the high RNA capture efficiency of Decoder-seq improved the detection of lowly expressed olfactory receptor (Olfr) genes in mouse olfactory bulbs and contributed to the discovery of a unique layer enrichment pattern for two Olfr genes. The near-cellular resolution provided by Decoder-seq has enabled the construction of a spatial single-cell atlas of the mouse hippocampus, revealing dendrite-enriched mRNAs in neurons. When applying Decoder-seq to human renal cell carcinomas, we dissected the heterogeneous tumor microenvironment across different cancer subtypes and identified spatial gradient-expressed genes related to epithelial-mesenchymal transition with the potential to predict tumor prognosis and progression.
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Affiliation(s)
- Jiao Cao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhong Zheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Di Sun
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Cheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianpeng Lv
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu An
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junhua Zheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jia Song
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemical of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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Matuleviciute R, Akinluyi ET, Muntslag TAO, Dewing JM, Long KR, Vernon AC, Tremblay ME, Menassa DA. Microglial contribution to the pathology of neurodevelopmental disorders in humans. Acta Neuropathol 2023; 146:663-683. [PMID: 37656188 PMCID: PMC10564830 DOI: 10.1007/s00401-023-02629-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
Microglia are the brain's resident macrophages, which guide various developmental processes crucial for brain maturation, activity, and plasticity. Microglial progenitors enter the telencephalic wall by the 4th postconceptional week and colonise the fetal brain in a manner that spatiotemporally tracks key neurodevelopmental processes in humans. However, much of what we know about how microglia shape neurodevelopment comes from rodent studies. Multiple differences exist between human and rodent microglia warranting further focus on the human condition, particularly as microglia are emerging as critically involved in the pathological signature of various cognitive and neurodevelopmental disorders. In this article, we review the evidence supporting microglial involvement in basic neurodevelopmental processes by focusing on the human species. We next concur on the neuropathological evidence demonstrating whether and how microglia contribute to the aetiology of two neurodevelopmental disorders: autism spectrum conditions and schizophrenia. Next, we highlight how recent technologies have revolutionised our understanding of microglial biology with a focus on how these tools can help us elucidate at unprecedented resolution the links between microglia and neurodevelopmental disorders. We conclude by reviewing which current treatment approaches have shown most promise towards targeting microglia in neurodevelopmental disorders and suggest novel avenues for future consideration.
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Affiliation(s)
- Rugile Matuleviciute
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Elizabeth T Akinluyi
- Division of Medical Sciences, University of Victoria, Victoria, Canada
- Department of Pharmacology and Therapeutics, Afe Babalola University, Ado Ekiti, Nigeria
| | - Tim A O Muntslag
- Princess Maxima Centre for Paediatric Oncology, Utrecht, The Netherlands
| | | | - Katherine R Long
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Anthony C Vernon
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - David A Menassa
- Department of Neuropathology & The Queen's College, University of Oxford, Oxford, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.
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5
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Akello JO, Bujaki E, Shaw AG, Khurshid A, Arshad Y, Troman C, Majumdar M, O'Toole Á, Rambaut A, Alam MM, Martin J, Grassly NC. Comparison of Eleven RNA Extraction Methods for Poliovirus Direct Molecular Detection in Stool Samples. Microbiol Spectr 2023; 11:e0425222. [PMID: 36939356 PMCID: PMC10100708 DOI: 10.1128/spectrum.04252-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/27/2023] [Indexed: 03/21/2023] Open
Abstract
Direct detection by PCR of poliovirus RNA in stool samples provides a rapid diagnostic and surveillance tool that can replace virus isolation by cell culture in global polio surveillance. The sensitivity of direct detection methods is likely to depend on the choice of RNA extraction method and sample volume. We report a comparative analysis of 11 nucleic acid extraction methods (7 manual and 4 semiautomated) for poliovirus molecular detection using stool samples (n = 59) that had been previously identified as poliovirus positive by cell culture. To assess the effect of RNA recovery methods, extracted RNA using each of the 11 methods was tested with a poliovirus-specific reverse transcription-quantitative PCR (RT-qPCR), a pan-poliovirus RT-PCR (near-whole-genome amplification), a pan-enterovirus RT-PCR (entire capsid region), and a nested VP1 PCR that is the basis of a direct detection method based on nanopore sequencing. We also assessed extracted RNA integrity and quantity. The overall effect of extraction method on poliovirus PCR amplification assays tested in this study was found to be statistically significant (P < 0.001), thus indicating that the choice of RNA extraction method is an important component that needs to be carefully considered for any diagnostic based on nucleic acid amplification. Performance of the methods was generally consistent across the different assays used. Of the 11 extraction methods tested, the MagMAX viral RNA isolation kit used manually or automatically was found to be the preferable method for poliovirus molecular direct detection considering performance, cost, and processing time. IMPORTANCE Poliovirus, the causative agent of poliomyelitis, is a target of global eradication led by the World Health Organization since 1988. Direct molecular detection and genomic sequencing without virus propagation in cell culture is arguably a critical tool in the final stages of polio eradication. Efficient recovery of good-quality viral RNA from stool samples is a prerequisite for direct detection by nucleic acid amplification. We tested 11 nucleic acid extraction methods to identify those facilitating sensitive, fast, simple, and cost-effective extraction, with flexibility for manual and automated protocols considered. Several different PCR assays were used to compare the recovered viral RNA to test suitability for poliovirus direct molecular detection. Our findings highlight the importance of choosing a suitable RNA extraction protocol and provide useful information to diagnostic laboratories and researchers facing the choice of RNA extraction method for direct molecular virus detection from stool.
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Affiliation(s)
- Joyce Odeke Akello
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Erika Bujaki
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Alexander G. Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Adnan Khurshid
- Department of Virology, National Institute for Health, Islamabad, Pakistan
| | - Yasir Arshad
- Department of Virology, National Institute for Health, Islamabad, Pakistan
| | - Catherine Troman
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Manasi Majumdar
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, United Kingdom
| | | | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control (NIBSC), MHRA, Potters Bar, United Kingdom
| | - Nicholas C. Grassly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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6
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Moffitt JR, Lundberg E, Heyn H. The emerging landscape of spatial profiling technologies. Nat Rev Genet 2022; 23:741-759. [PMID: 35859028 DOI: 10.1038/s41576-022-00515-3] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 01/04/2023]
Abstract
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein profiling methods as a major pillar for cellular atlas building of complex samples, from tissues to full organisms. Emerging methods yield omics measurements at resolutions covering the nano- to microscale, enabling the charting of cellular heterogeneity, complex tissue architectures and dynamic changes during development and disease. We present an overview of the developing landscape of in situ spatial genome, transcriptome and proteome technologies, exemplify their impact on cell biology and translational research, and discuss current challenges for their community-wide adoption. Among many transformative applications, we envision that spatial methods will map entire organs and enable next-generation pathology.
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Affiliation(s)
- Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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7
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Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis. Sci Rep 2022; 12:11876. [PMID: 35831338 PMCID: PMC9279471 DOI: 10.1038/s41598-022-15293-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/22/2022] [Indexed: 11/15/2022] Open
Abstract
B cells play a significant role in established Rheumatoid Arthritis (RA). However, it is unclear to what extent differentiated B cells are present in joint tissue already at the onset of disease. Here, we studied synovial biopsies (n = 8) captured from untreated patients at time of diagnosis. 3414 index-sorted B cells underwent RNA sequencing and paired tissue pieces were subjected to spatial transcriptomics (n = 4). We performed extensive bioinformatics analyses to dissect the local B cell composition. Select plasma cell immunoglobulin sequences were expressed as monoclonal antibodies and tested by ELISA. Memory and plasma cells were found irrespective of autoantibody status of the patients. Double negative memory B cells were prominent, but did not display a distinct transcriptional profile. The tissue architecture implicate both local B cell maturation via T cell help and plasma cell survival niches with a strong CXCL12–CXCR4 axis. The immunoglobulin sequence analyses revealed clonality between the memory B and plasma cell pools further supporting local maturation. One of the plasma cell-derived antibodies displayed citrulline autoreactivity, demonstrating local autoreactive plasma cell differentiation in joint biopsies captured from untreated early RA. Hence, plasma cell niches are not a consequence of chronic inflammation, but are already present at the time of diagnosis.
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8
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Elishaev M, Hodonsky CJ, Ghosh SKB, Finn AV, von Scheidt M, Wang Y. Opportunities and Challenges in Understanding Atherosclerosis by Human Biospecimen Studies. Front Cardiovasc Med 2022; 9:948492. [PMID: 35872917 PMCID: PMC9300954 DOI: 10.3389/fcvm.2022.948492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last few years, new high-throughput biotechnologies and bioinformatic methods are revolutionizing our way of deep profiling tissue specimens at the molecular levels. These recent innovations provide opportunities to advance our understanding of atherosclerosis using human lesions aborted during autopsies and cardiac surgeries. Studies on human lesions have been focusing on understanding the relationship between molecules in the lesions with tissue morphology, genetic risk of atherosclerosis, and future adverse cardiovascular events. This review will highlight ways to utilize human atherosclerotic lesions in translational research by work from large cardiovascular biobanks to tissue registries. We will also discuss the opportunities and challenges of working with human atherosclerotic lesions in the era of next-generation sequencing.
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Affiliation(s)
- Maria Elishaev
- Department of Pathology and Laboratory Medicine, Center for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Chani J. Hodonsky
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | | | - Aloke V. Finn
- Cardiovascular Pathology Institute, Gaithersburg, MD, United States
| | - Moritz von Scheidt
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung, Partner Site Munich Heart Alliance, Munich, Germany
| | - Ying Wang
- Department of Pathology and Laboratory Medicine, Center for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
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9
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Liu X, Jiang Y, Song D, Zhang L, Xu G, Hou R, Zhang Y, Chen J, Cheng Y, Liu L, Xu X, Chen G, Wu D, Chen T, Chen A, Wang X. Clinical challenges of tissue preparation for spatial transcriptome. Clin Transl Med 2022; 12:e669. [PMID: 35083877 PMCID: PMC8792118 DOI: 10.1002/ctm2.669] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/06/2023] Open
Abstract
Spatial transcriptomics is considered as an important part of spatiotemporal molecular images to bridge molecular information with clinical images. Of those potentials and opportunities, the excellent quality of human sample preparation and handling will ensure the precise and reliable information generated from clinical spatial transcriptome. The present study aims at defining potential factors that might influence the quality of spatial transcriptomics in lung cancer, para-cancer, or normal tissues, pathological images of sections and the RNA integrity before spatial transcriptome sequencing. We categorised potential influencing factors from clinical aspects, including patient selection, pathological definition, surgical types, sample harvest, temporary preservation conditions and solutions, frozen approaches, transport and storage conditions and duration. We emphasis on the relationship between the combination of histological scores with RNA integrity number (RIN) and the unique molecular identifier (UMI), which is determines the quality of of spatial transcriptomics; however, we did not find significantly relevance between them. Our results showed that isolated times and dry conditions of sample are critical for the UMI and the quality of spatial transcriptomic samples. Thus, clinical procedures of sample preparation should be furthermore optimised and standardised as new standards of operation performance for clinical spatial transcriptome. Our data suggested that the temporary preservation time and condition of samples at operation room should be within 30 min and in 'dry' status. The direct cryo-preservation within OCT media for human lung sample is recommended. Thus, we believe that clinical spatial transcriptome will be a decisive approach and bridge in the development of spatiotemporal molecular images and provide new insights for understanding molecular mechanisms of diseases at multi-orientations.
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Affiliation(s)
- Xiaoxia Liu
- Department of Pulmonary and Critical Care MedicineInstitute for Clinical ScienceShanghai Institute of Clinical BioinformaticsZhongshan Hospital of Fudan UniversityShanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesShanghaiChina
| | - Yujia Jiang
- BGIShenzhenChina
- BGI College & Henan Institute of Medical and Pharmaceutical SciencesZhengzhou UniversityZhengzhouChina
| | - Dongli Song
- Department of Pulmonary and Critical Care MedicineInstitute for Clinical ScienceShanghai Institute of Clinical BioinformaticsZhongshan Hospital of Fudan UniversityShanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesShanghaiChina
- Jinshan Hospital Centre for Tumor Diagnosis and TherapyFudan University Shanghai Medical CollegeShanghaiChina
| | - Linlin Zhang
- Department of Pulmonary and Critical Care MedicineInstitute for Clinical ScienceShanghai Institute of Clinical BioinformaticsZhongshan Hospital of Fudan UniversityShanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesShanghaiChina
| | - Guang Xu
- Institute of Computer ScienceFudan UniversityShanghaiChina
| | - Rui Hou
- Shanghai Biotechnology CorporationShanghaiChina
| | - Yong Zhang
- Department of Pulmonary and Critical Care MedicineInstitute for Clinical ScienceShanghai Institute of Clinical BioinformaticsZhongshan Hospital of Fudan UniversityShanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesShanghaiChina
| | - Jian Chen
- Shanghai Lung Cancer CenterShanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Yunfeng Cheng
- Jinshan Hospital Centre for Tumor Diagnosis and TherapyFudan University Shanghai Medical CollegeShanghaiChina
| | | | | | - Gang Chen
- Department of PathologyZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Duojiao Wu
- Department of Pulmonary and Critical Care MedicineInstitute for Clinical ScienceShanghai Institute of Clinical BioinformaticsZhongshan Hospital of Fudan UniversityShanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesShanghaiChina
- Jinshan Hospital Centre for Tumor Diagnosis and TherapyFudan University Shanghai Medical CollegeShanghaiChina
| | - Tianxiang Chen
- Shanghai Lung Cancer CenterShanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiChina
| | | | - Xiangdong Wang
- Department of Pulmonary and Critical Care MedicineInstitute for Clinical ScienceShanghai Institute of Clinical BioinformaticsZhongshan Hospital of Fudan UniversityShanghai Engineering Research for AI Technology for Cardiopulmonary DiseasesShanghaiChina
- Jinshan Hospital Centre for Tumor Diagnosis and TherapyFudan University Shanghai Medical CollegeShanghaiChina
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10
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Sankowski R, Monaco G, Prinz M. Evaluating microglial phenotypes using single-cell technologies. Trends Neurosci 2021; 45:133-144. [PMID: 34872773 DOI: 10.1016/j.tins.2021.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/25/2021] [Accepted: 11/07/2021] [Indexed: 12/13/2022]
Abstract
Recent single-cell technologies have enabled researchers to simultaneously assess the transcriptomes and other modalities of thousands of cells within their spatial context. Here, we have summarized available single-cell methods for dissociated tissues and tissue slides with respect to the specifics of microglial biology. We have focused on next-generation-based technologies. We review the potential of these single-cell sequencing methods and newer multiomics approaches to extend the understanding of microglia function beyond the status quo.
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Affiliation(s)
- Roman Sankowski
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Single-Cell Omics Platform Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gianni Monaco
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Single-Cell Omics Platform Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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