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Thakral S, Purohit P, Mishra R, Gupta V, Setia P. The impact of RNA stability and degradation in different tissues to the determination of post-mortem interval: A systematic review. Forensic Sci Int 2023; 349:111772. [PMID: 37450949 DOI: 10.1016/j.forsciint.2023.111772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/11/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023]
Abstract
Postmortem interval (PMI) in legal medicine is extremely important for both criminal and civil cases, and several sorts of techniques have been recommended. This systematic review solely focuses on approaches linked to RNA analysis, instead of including all proposed methods for determining the PMI. The term PMI will be used in this review to indicate the time between a person's death and the postmortem examination of the body. We adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Guidelines when conducting this systematic review. The majority of studies on various tissues at various time intervals at various temperatures are non-human, and just a small number are on humans. The results are then provided using various statistical approaches. To calculate the PMI, post-mortem RNA degradation was examined using several tissues. The result so obtained had an opposite polarity. While some studies show that RNA stability in various tissues remained constant for several days after death, the other group of studies showed evident RNA degradation over time post-mortem, which was significantly influenced by temperature and other agonal factors. These factors have an impact on the multi-parametric mathematical model of ante and post-mortem factors on RNA degradation, as well as its applicability and feasibility. The estimation of PMI using RNA degradation can prove to be highly objective and efficient after controlling for the various factors and challenges that pose the estimation of RNA in forensic samples difficult.
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Affiliation(s)
- Sahil Thakral
- Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, Bathinda, Punjab 151001, India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - Richa Mishra
- Department of Transfusion Medicine and Blood Bank, All India Institute of Medical Sciences, Bathinda, Punjab 151001, India
| | - Vaibhav Gupta
- Department of Forensic Medicine and Toxicology, Vardhman Mahavir Medical College, New Delhi, India
| | - Puneet Setia
- Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India.
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2
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A Systematic Comparison of Protocols for Recovery of High-Quality RNA from Human Islets Extracted by Laser Capture Microdissection. Biomolecules 2021; 11:biom11050625. [PMID: 33922227 PMCID: PMC8144988 DOI: 10.3390/biom11050625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 12/21/2022] Open
Abstract
The isolation of high-quality RNA from endocrine pancreas sections represents a considerable challenge largely due to the high ribonuclease levels. Laser capture microdissection (LCM) of mammalian islets, in association with RNA extraction protocols, has emerged as a feasible approach to characterizing their genetic and proteomic profiles. However, a validated protocol to obtain high-quality RNA from LCM-derived human pancreas specimens that is appropriate for next-generation sequencing analysis is still lacking. In this study, we applied four methods (Picopure extraction kit, Qiazol protocol, Qiazol + Clean-up kit, and RNeasy Microkit + Carrier) to extract RNA from human islets obtained from both non-diabetic individuals and patients with type 2 diabetes who had undergone partial pancreatectomy, as well as handpicked islets from both non-diabetic and diabetic organ donors. The yield and purity of total RNA were determined by 260/280 absorbance using Nanodrop 100 and the RNA integrity number with a bioanalyzer. The results indicated that among the four methods, the RNeasy MicroKit + Carrier (Qiagen) provides the highest yield and purity.
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Apaolaza PS, Balcacean D, Zapardiel-Gonzalo J, Nelson G, Lenchik N, Akhbari P, Gerling I, Richardson SJ, Rodriguez-Calvo T. Islet expression of type I interferon response sensors is associated with immune infiltration and viral infection in type 1 diabetes. SCIENCE ADVANCES 2021; 7:7/9/eabd6527. [PMID: 33627420 PMCID: PMC7904254 DOI: 10.1126/sciadv.abd6527] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/04/2021] [Indexed: 05/04/2023]
Abstract
Previous results indicate the presence of an interferon (IFN) signature in type 1 diabetes (T1D), capable of inducing chronic inflammation and compromising b cell function. Here, we determined the expression of the IFN response markers MxA, PKR, and HLA-I in the islets of autoantibody-positive and T1D donors. We found that these markers can be coexpressed in the same islet, are more abundant in insulin-containing islets, are highly expressed in islets with insulitis, and their expression levels are correlated with the presence of the enteroviral protein VP1. The expression of these markers was associated with down-regulation of multiple genes in the insulin secretion pathway. The coexistence of an IFN response and a microbial stress response is likely to prime islets for immune destruction. This study highlights the importance of therapeutic interventions aimed at eliminating potentially persistent infections and diminishing inflammation in individuals with T1D.
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Affiliation(s)
- Paola S Apaolaza
- Institute of Diabetes Research, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, 80939, Germany
| | - Diana Balcacean
- Institute of Diabetes Research, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, 80939, Germany
| | - Jose Zapardiel-Gonzalo
- Institute of Diabetes Research, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, 80939, Germany
| | - Grace Nelson
- Department of Medicine, University of Tennessee, Memphis, TN 38163, USA
| | - Nataliya Lenchik
- Department of Medicine, University of Tennessee, Memphis, TN 38163, USA
| | - Pouria Akhbari
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Ivan Gerling
- Department of Medicine, University of Tennessee, Memphis, TN 38163, USA
| | - Sarah J Richardson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Teresa Rodriguez-Calvo
- Institute of Diabetes Research, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, 80939, Germany.
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4
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Yip L, Fuhlbrigge R, Alkhataybeh R, Fathman CG. Gene Expression Analysis of the Pre-Diabetic Pancreas to Identify Pathogenic Mechanisms and Biomarkers of Type 1 Diabetes. Front Endocrinol (Lausanne) 2020; 11:609271. [PMID: 33424774 PMCID: PMC7793767 DOI: 10.3389/fendo.2020.609271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/16/2020] [Indexed: 12/28/2022] Open
Abstract
Type 1 Diabetes (T1D) occurs as a result of the autoimmune destruction of pancreatic β-cells by self-reactive T cells. The etiology of this disease is complex and difficult to study due to a lack of disease-relevant tissues from pre-diabetic individuals. In this study, we performed gene expression analysis on human pancreas tissues obtained from the Network of Pancreatic Organ Donors with Diabetes (nPOD), and showed that 155 genes were differentially expressed by ≥2-fold in the pancreata of autoantibody-positive (AA+) at-risk individuals compared to healthy controls. Only 48 of these genes remained changed by ≥2-fold in the pancreata of established T1D patients. Pathway analysis of these genes showed a significant association with various immune pathways. We were able to validate the differential expression of eight disease-relevant genes by QPCR analysis: A significant upregulation of CADM2, and downregulation of TRPM5, CRH, PDK4, ANGPL4, CLEC4D, RSG16, and FCGR2B was confirmed in the pancreata of AA+ individuals versus controls. Studies have already implicated FCGR2B in the pathogenesis of disease in non-obese diabetic (NOD) mice. Here we showed that CADM2, TRPM5, PDK4, and ANGPL4 were similarly changed in the pancreata of pre-diabetic 12-week-old NOD mice compared to NOD.B10 controls, suggesting a possible role for these genes in the pathogenesis of both T1D and NOD disease. The loss of the leukocyte-specific gene, FCGR2B, in the pancreata of AA+ individuals, is particularly interesting, as it may serve as a potential whole blood biomarker of disease progression. To test this, we quantified FCGR2B expression in peripheral blood samples of T1D patients, and AA+ and AA- first-degree relatives of T1D patients enrolled in the TrialNet Pathway to Prevention study. We showed that FCGR2B was significantly reduced in the peripheral blood of AA+ individuals compared to AA- controls. Together, these findings demonstrate that gene expression analysis of pancreatic tissue and peripheral blood samples can be used to identify disease-relevant genes and pathways and potential biomarkers of disease progression in T1D.
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Esteva-Socias M, Artiga MJ, Bahamonde O, Belar O, Bermudo R, Castro E, Escámez T, Fraga M, Jauregui-Mosquera L, Novoa I, Peiró-Chova L, Rejón JD, Ruiz-Miró M, Vieiro-Balo P, Villar-Campo V, Zazo S, Rábano A, Villena C. In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network. J Transl Med 2019; 17:370. [PMID: 31718661 PMCID: PMC6852937 DOI: 10.1186/s12967-019-2124-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/01/2019] [Indexed: 01/10/2023] Open
Abstract
The purpose of the present work is to underline the importance of obtaining a standardized procedure to ensure and evaluate both clinical and research usability of human tissue samples. The study, which was carried out by the Biospecimen Science Working Group of the Spanish Biobank Network, is based on a general overview of the current situation about quality assurance in human tissue biospecimens. It was conducted an exhaustive review of the analytical techniques used to evaluate the quality of human tissue samples over the past 30 years, as well as their reference values if they were published, and classified them according to the biomolecules evaluated: (i) DNA, (ii) RNA, and (iii) soluble or/and fixed proteins for immunochemistry. More than 130 publications released between 1989 and 2019 were analysed, most of them reporting results focused on the analysis of tumour and biopsy samples. A quality assessment proposal with an algorithm has been developed for both frozen tissue samples and formalin-fixed paraffin-embedded (FFPE) samples, according to the expected quality of sample based on the available pre-analytical information and the experience of the participants in the Working Group. The high heterogeneity of human tissue samples and the wide number of pre-analytic factors associated to quality of samples makes it very difficult to harmonize the quality criteria. However, the proposed method to assess human tissue sample integrity and antigenicity will not only help to evaluate whether stored human tissue samples fit for the purpose of biomarker development, but will also allow to perform further studies, such as assessing the impact of different pre-analytical factors on very well characterized samples or evaluating the readjustment of tissue sample collection, processing and storing procedures. By ensuring the quality of the samples used on research, the reproducibility of scientific results will be guaranteed.
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Affiliation(s)
- Margalida Esteva-Socias
- Centro de Investigación Biomédica en Red Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain.,Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
| | | | | | - Oihana Belar
- Basque Foundation for Health Innovation and Research, Basque Biobank, Barakaldo, Spain
| | - Raquel Bermudo
- Hospital Clínic-IDIBAPS Biobank, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Erika Castro
- Basque Foundation for Health Innovation and Research, Basque Biobank, Barakaldo, Spain
| | - Teresa Escámez
- IMIB Biobank, Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Máximo Fraga
- Depto. de Ciencias Forenses, Anatomía Patolóxica, Xinecología e Obstetricia, e Pediatría, Facultade de Medicina, Universidade de Santiago de Compostela (USC), Santiago, Spain.,Biobanco Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago, Spain
| | | | - Isabel Novoa
- Vall d'Hebron University Hospital Biobank, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | | | - Juan-David Rejón
- Biobanco del Sistema Sanitario Público de Andalucía, Granada, Spain
| | - María Ruiz-Miró
- IRBLleida Biobank, Instituto de Investigaciones Biomédica de Lleida-Fundación Dr. Pifarre, Lérida, Spain
| | - Paula Vieiro-Balo
- Biobanco Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago, Spain
| | | | - Sandra Zazo
- Department of Pathology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Alberto Rábano
- Banco de Tejidos, Fundación CIEN, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Villena
- Centro de Investigación Biomédica en Red Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain. .,Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain.
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Snyder MP, Lin S, Posgai A, Atkinson M, Regev A, Rood J, Rozenblatt-Rosen O, Gaffney L, Hupalowska A, Satija R, Gehlenborg N, Shendure J, Laskin J, Harbury P, Nystrom NA, Silverstein JC, Bar-Joseph Z, Zhang K, Börner K, Lin Y, Conroy R, Procaccini D, Roy AL, Pillai A, Brown M, Galis ZS, Cai L, Shendure J, Trapnell C, Lin S, Jackson D, Snyder MP, Nolan G, Greenleaf WJ, Lin Y, Plevritis S, Ahadi S, Nevins SA, Lee H, Schuerch CM, Black S, Venkataraaman VG, Esplin E, Horning A, Bahmani A, Zhang K, Sun X, Jain S, Hagood J, Pryhuber G, Kharchenko P, Atkinson M, Bodenmiller B, Brusko T, Clare-Salzler M, Nick H, Otto K, Posgai A, Wasserfall C, Jorgensen M, Brusko M, Maffioletti S, Caprioli RM, Spraggins JM, Gutierrez D, Patterson NH, Neumann EK, Harris R, deCaestecker M, Fogo AB, van de Plas R, Lau K, Cai L, Yuan GC, Zhu Q, Dries R, Yin P, Saka SK, Kishi JY, Wang Y, Goldaracena I, Laskin J, Ye D, Burnum-Johnson KE, Piehowski PD, Ansong C, Zhu Y, Harbury P, Desai T, Mulye J, Chou P, Nagendran M, Bar-Joseph Z, Teichmann SA, Paten B, Murphy RF, Ma J, Kiselev VY, Kingsford C, Ricarte A, Keays M, Akoju SA, Ruffalo M, Gehlenborg N, Kharchenko P, Vella M, McCallum C, Börner K, Cross LE, Friedman SH, Heiland R, Herr B, Macklin P, Quardokus EM, Record L, Sluka JP, Weber GM, Nystrom NA, Silverstein JC, Blood PD, Ropelewski AJ, Shirey WE, Scibek RM, Mabee P, Lenhardt WC, Robasky K, Michailidis S, Satija R, Marioni J, Regev A, Butler A, Stuart T, Fisher E, Ghazanfar S, Rood J, Gaffney L, Eraslan G, Biancalani T, Vaishnav ED, Conroy R, Procaccini D, Roy A, Pillai A, Brown M, Galis Z, Srinivas P, Pawlyk A, Sechi S, Wilder E, Anderson J. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature 2019; 574:187-192. [PMID: 31597973 PMCID: PMC6800388 DOI: 10.1038/s41586-019-1629-x] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/09/2019] [Indexed: 12/12/2022]
Abstract
Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions.
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Rodriguez-Calvo T. Enterovirus infection and type 1 diabetes: unraveling the crime scene. Clin Exp Immunol 2018; 195:15-24. [PMID: 30307605 DOI: 10.1111/cei.13223] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/02/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022] Open
Abstract
Enteroviruses (EV) have been historically associated to type 1 diabetes. Definitive proof for their implication in disease development is lacking, but growing evidence suggests that they could be involved in beta cell destruction either directly by killing beta cells or indirectly by creating an exacerbated inflammatory response in the islets, capable of attracting autoreactive T cells to the 'scene of the crime'. Epidemiological and serological studies have been associated with the appearance of islet autoimmunity and EV RNA has been detected in prospective studies. In addition, the EV capsid protein has been detected in the islets of recent-onset type 1 diabetic donors, suggesting the existence of a low-grade EV infection that could become persistent. Increasing evidence in the field shows that a 'viral signature' exists in type 1 diabetes and involves interferon responses that could be sustained during prolonged periods. These include the up-regulation of markers such as protein kinase R (PKR), melanoma differentiation-associated protein 5 (MDA5), retinoic acid inducible gene I (RIG-I), myxovirus resistance protein (MxA) and human leukocyte antigen-I (HLA-I) and the release of chemokines able to attract immune cells to the islets leading to insulitis. In this scenario, the hyperexpression of HLA-I molecules would promote antigen presentation to autoreactive T cells, favoring beta cell recognition and, ultimately, destruction. In this review, an overview is provided of the standing evidence that implicates EVs in beta cell 'murder', the time-line of events is investigated from EV entry in the cell to beta cell death and possible accomplices are highlighted that might be involved in beta cell demise.
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Affiliation(s)
- T Rodriguez-Calvo
- Institute for Diabetes Research, Helmholtz Diabetes Center at Helmholtz Zentrum München, Munich, Germany
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Abstract
PURPOSE OF REVIEW To provide an overview of studies that have detected enteroviruses (EV) in samples from people with type 1 diabetes (T1D), the techniques they have used, and which challenges they have encountered. RECENT FINDINGS Recent studies have detected EVs in serum, blood, stools, nasal swabs, and pancreas of people with T1D before or around clinical onset of disease, indicating that an association between EV infections and T1D exists. However, definitive evidence for its role as disease triggers is lacking. Recent access to human samples is starting to provide the necessary tools to define their role in disease pathogenesis. Emerging evidence suggests that chronic infections take place in the pancreas of diabetic donors. However, the development of sensitive techniques able to detect low amounts of viral protein and RNA still constitute a major challenge for the field. New evidence at the protein, RNA, and host immune response level suggests a role for EV infections in the development of autoimmunity. In the upcoming years, new technologies, collaborative efforts, and therapeutic interventions are likely to find a definitive answer for their role in disease pathogenesis.
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Affiliation(s)
- Teresa Rodriguez-Calvo
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Diabetes Research, Ingolstaedter Landstrasse 1, 85764, Munich-Neuherberg, Germany.
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Marchetti P, Suleiman M, Marselli L. Organ donor pancreases for the study of human islet cell histology and pathophysiology: a precious and valuable resource. Diabetologia 2018; 61:770-774. [PMID: 29354869 PMCID: PMC6449064 DOI: 10.1007/s00125-018-4546-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/06/2017] [Indexed: 12/15/2022]
Abstract
Direct in vivo assessment of pancreatic islet-cells for the study of the pathophysiology of diabetes in humans is hampered by anatomical and technological hurdles. To date, most of the information that has been generated is derived from histological studies performed on pancreatic tissue from autopsy, surgery, in vivo biopsy or organ donation. Each approach has its advantages and disadvantages (as summarised in this commentary); however, in this edition of Diabetologia, Kusmartseva et al ( https://doi.org/10.1007/s00125-017-4494-x ) provide further evidence to support the use of organ donor pancreases for the study of human diabetes. They show that length of terminal hospitalisation of organ donors prior to death does not seem to influence the frequency of inflammatory cells infiltrating the pancreas and the replication of beta cells. These findings are reassuring, demonstrating the reliability of this precious and valuable resource for human islet cells research.
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Affiliation(s)
- Piero Marchetti
- Department of Clinical and Experimental Medicine and University Hospital, University of Pisa, via Paradisa 2, 56121, Pisa, Italy.
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine and University Hospital, University of Pisa, via Paradisa 2, 56121, Pisa, Italy
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine and University Hospital, University of Pisa, via Paradisa 2, 56121, Pisa, Italy
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Kusmartseva I, Beery M, Philips T, Selman S, Jadhav P, Wasserfall C, Muller A, Pugliese A, Longmate JA, Schatz DA, Atkinson MA, Kaddis JS. Hospital time prior to death and pancreas histopathology: implications for future studies. Diabetologia 2018; 61:954-958. [PMID: 29128936 PMCID: PMC5844815 DOI: 10.1007/s00125-017-4494-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/12/2017] [Indexed: 01/06/2023]
Abstract
AIMS/HYPOTHESIS Diabetes research studies routinely rely upon the use of tissue samples from human organ donors. It remains unclear whether the length of hospital stay prior to organ donation affects the presence of cells infiltrating the pancreas or the frequency of replicating beta cells. METHODS To address this, 39 organ donors without diabetes were matched for age, sex, BMI and ethnicity in groups of three. Within each group, donors varied by length of hospital stay immediately prior to organ donation (<3 days, 3 to <6 days, or ≥6 days). Serial sections from tissue blocks in the pancreas head, body and tail regions were immunohistochemically double stained for insulin and CD45, CD68, or Ki67. Slides were electronically scanned and quantitatively analysed for cell positivity. RESULTS No differences in CD45+, CD68+, insulin+, Ki67+ or Ki67+/insulin+ cell frequencies were found when donors were grouped according to duration of hospital stay. Likewise, no interactions were observed between hospitalisation group and pancreas region, age, or both; however, with Ki67 staining, cell frequencies were greater in the body vs the tail region of the pancreas (∆ 0.65 [unadjusted 95% CI 0.25, 1.04]; p = 0.002) from donors <12 year of age. Interestingly, frequencies were less in the body vs tail region of the pancreas for both CD45+ cells (∆ -0.91 [95% CI -1.71, -0.10]; p = 0.024) and insulin+ cells (∆ -0.72 [95% CI -1.10, -0.34]; p < 0.001). CONCLUSIONS/INTERPRETATION This study suggests that immune or replicating beta cell frequencies are not affected by the length of hospital stay prior to donor death in pancreases used for research. DATA AVAILABILITY All referenced macros (adopted and developed), calculations, programming code and numerical dataset files (including individual-level donor data) are freely available on GitHub through Zenodo at https://doi.org/10.5281/zenodo.1034422.
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Affiliation(s)
- Irina Kusmartseva
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Maria Beery
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Tiffany Philips
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Stephen Selman
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Priyanka Jadhav
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Clive Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Axel Muller
- Department of Diabetes and Cancer Discovery Science, Diabetes and Metabolism Research Institute, City of Hope/Beckman Research Institute, 1500 East Duarte Road, Duarte, CA, 91010-3000, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Desmond A Schatz
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, Diabetes and Metabolism Research Institute, City of Hope/Beckman Research Institute, 1500 East Duarte Road, Duarte, CA, 91010-3000, USA.
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Bevilacqua C, Ducos B. Laser microdissection: A powerful tool for genomics at cell level. Mol Aspects Med 2017; 59:5-27. [PMID: 28927943 DOI: 10.1016/j.mam.2017.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022]
Abstract
Laser microdissection (LM) has become widely democratized over the last fifteen years. Instruments have evolved to offer more powerful and efficient lasers as well as new options for sample collection and preparation. Technological evolutions have also focused on the post-microdissection analysis capabilities, opening up investigations in all disciplines of experimental and clinical biology, thanks to the advent of new high-throughput methods of genome analysis, including RNAseq and proteomics, now globally known as microgenomics, i.e. analysis of biomolecules at the cell level. In spite of the advances these rapidly developing methods have allowed, the workflow for sampling and collection by LM remains a critical step in insuring sample integrity in terms of histology (accurate cell identification) and biochemistry (reliable analyzes of biomolecules). In this review, we describe the sample processing as well as the strengths and limiting factors of LM applied to the specific selection of one or more cells of interest from a heterogeneous tissue. We will see how the latest developments in protocols and methods have made LM a powerful and sometimes essential tool for genomic and proteomic analyzes of tiny amounts of biomolecules extracted from few cells isolated from a complex tissue, in their physiological context, thus offering new opportunities for understanding fundamental physiological and/or patho-physiological processes.
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Affiliation(s)
- Claudia Bevilacqua
- GABI, Plateforme @BRIDGE, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, 78350 Jouy en Josas, France.
| | - Bertrand Ducos
- LPS-ENS, CNRS UMR 8550, UPMC, Université Denis Diderot, PSL Research University, 24 Rue Lhomond, 75005 Paris France; High Throughput qPCR Core Facility, IBENS, 46 Rue d'Ulm, 75005 Paris France; Laser Microdissection Facility of Montagne Sainte Geneviève, CIRB Collège de France, Place Marcellin Berthelot, 75005 Paris France.
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