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Wright S, Burkholz SR, Zelinsky C, Wittman C, Carback RT, Harris PE, Blankenberg T, Herst CV, Rubsamen RM. Survivin Expression in Luminal Breast Cancer and Adjacent Normal Tissue for Immuno-Oncology Applications. Int J Mol Sci 2023; 24:11827. [PMID: 37511584 PMCID: PMC10380623 DOI: 10.3390/ijms241411827] [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: 06/25/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Survivin (BIRC5) is a tumor-associated antigen (TAA) overexpressed in various tumors but present at low to undetectable levels in normal tissue. Survivin is known to have a high expression in breast cancer (e.g., Ductal Carcinoma in situ (DCIS) and triple negative breast cancer). Previous studies have not compared survivin expression levels in DCIS tumor samples to levels in adjacent, normal breast tissue from the same patient. To ensure the effective use of survivin as a target for T cell immunotherapy of breast cancer, it is essential to ascertain the varying levels of survivin expression between DCIS tumor tissue samples and the adjacent normal breast tissue taken from the same patient simultaneously. Next-generation sequencing of RNA (RNA-seq) in normal breast tissue and tumor breast tissue from five women presenting with DCIS for lumpectomy was used to identify sequence variation and expression levels of survivin. The identity of both tumor and adjacent normal tissue samples were corroborated by histopathology. Survivin was overexpressed in human breast tissue tumor samples relative to the corresponding adjacent human normal breast tissue. Wild-type survivin transcripts were the predominant species identified in all tumor tissue sequenced. This study demonstrates upregulated expression of wild type survivin in DCIS tumor tissue versus normal breast tissue taken from the same patient at the same time, and provides evidence that developing selective cytotoxic T lymphocyte (CTL) immunotherapy for DCIS targeting survivin warrants further study.
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Affiliation(s)
- Sharon Wright
- Saint Mary’s Regional Medical Center, Reno, NV 89503, USA; (S.W.); (C.Z.); (C.W.)
- Western Surgical Group, Reno, NV 89502, USA
| | - Scott R. Burkholz
- Flow Pharma Inc., Warrensville Heights, OH 44128, USA; (S.R.B.); (R.T.C.); (P.E.H.); (T.B.); (C.V.H.)
| | - Cathy Zelinsky
- Saint Mary’s Regional Medical Center, Reno, NV 89503, USA; (S.W.); (C.Z.); (C.W.)
| | - Connor Wittman
- Saint Mary’s Regional Medical Center, Reno, NV 89503, USA; (S.W.); (C.Z.); (C.W.)
| | - Richard T. Carback
- Flow Pharma Inc., Warrensville Heights, OH 44128, USA; (S.R.B.); (R.T.C.); (P.E.H.); (T.B.); (C.V.H.)
| | - Paul E. Harris
- Flow Pharma Inc., Warrensville Heights, OH 44128, USA; (S.R.B.); (R.T.C.); (P.E.H.); (T.B.); (C.V.H.)
| | - Tikoes Blankenberg
- Flow Pharma Inc., Warrensville Heights, OH 44128, USA; (S.R.B.); (R.T.C.); (P.E.H.); (T.B.); (C.V.H.)
- Shasta Pathology Associates, Redding, CA 96001, USA
| | - Charles V. Herst
- Flow Pharma Inc., Warrensville Heights, OH 44128, USA; (S.R.B.); (R.T.C.); (P.E.H.); (T.B.); (C.V.H.)
| | - Reid M. Rubsamen
- Saint Mary’s Regional Medical Center, Reno, NV 89503, USA; (S.W.); (C.Z.); (C.W.)
- Flow Pharma Inc., Warrensville Heights, OH 44128, USA; (S.R.B.); (R.T.C.); (P.E.H.); (T.B.); (C.V.H.)
- Cleveland Medical Center, University Hospitals, Cleveland, OH 44106, USA
- Case Western Reserve School of Medicine, Cleveland, OH 44106, USA
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2
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Servais MD, Galtier F, Nouvel A, Rebuffat S, Laget J, Géan A, Provost N, Lorcy F, Rigau V, Couderc G, Géraud P, Nocca D, Builles N, De Préville N, Lajoix AD. Addressing the quality challenge of a human biospecimen biobank through the creation of a quality management system. PLoS One 2022; 17:e0278780. [PMID: 36584180 PMCID: PMC9803146 DOI: 10.1371/journal.pone.0278780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/22/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The objective of the COMET (COllection of MEtabolic Tissues) biobank project is to create a high-quality collection of insulin-sensitive tissues (liver, muscle, adipose tissues, and epiploic artery) and blood sample derivatives (plasma, serum, DNA and RNA), collected from 270 grade 2-3 obese patients undergoing bariatric surgery. Relevant data on patient such as clinical/biological characteristics and sample handling are also collected. For this, our aim was to establish a Quality Management System (QMS) to meet the reliability and quality requirements necessary for its scientific exploitation. MATERIALS AND METHODS The COMET QMS includes: (1) Quality Assurance to standardize all stages of the biobanking process, (2) Quality Controls on samples from the first patients included in order to validate the sample management process and ensure reproducible quality; and 3) "in process" Quality Controls to ensure the reliability of the storage procedures and the stability of the samples over time. RESULTS For serum and plasma, several corrective actions, such as temperature handling and centrifugation conditions, were made to the protocol and led to improvement of the volume and quality of samples. Regarding DNA, all samples evaluated achieved a satisfactory level of purity and integrity and most of them yielded the required DNA quantity. All frozen tissue samples had RNAs of good purity. RNA quality was confirmed by RIN, achieving values in most cases over 7 and efficient amplification of housekeeping genes by RT-qPCR, with no significant differences among samples from the same tissue type. In the "in process" Quality Controls, DNA, RNA, and histological integrity of tissues showed no differences among samples after different preservation times. CONCLUSION Quality Control results have made it possible to validate the entire biobank process and confirm the utility of implementing QMS to guarantee the quality of a biospecimen collection.
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Affiliation(s)
| | - Florence Galtier
- INSERM, Clinical Investigation Center 1411, St Eloi Hospital, University Hospital of Montpellier, Montpellier, France
- Department of Endocrinology, Lapeyronie Hospital, University Hospital of Montpellier, Montpellier, France
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Agathe Nouvel
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Sandra Rebuffat
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Jonas Laget
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | | | | | - Frédéric Lorcy
- Biological Resources Center, Anatomy and Cytology Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Valérie Rigau
- Biological Resources Center, Anatomy and Cytology Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Guilhem Couderc
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, Montpellier, France
| | - Philippe Géraud
- INSERM, Clinical Investigation Center 1411, St Eloi Hospital, University Hospital of Montpellier, Montpellier, France
| | - David Nocca
- Department of Digestive Surgery, University Hospital of Montpellier, Montpellier, France
| | - Nicolas Builles
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, Montpellier, France
| | | | - Anne-Dominique Lajoix
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
- * E-mail:
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3
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Tian B, Li Q. Single-Cell Sequencing and Its Applications in Liver Cancer. Front Oncol 2022; 12:857037. [PMID: 35574365 PMCID: PMC9097917 DOI: 10.3389/fonc.2022.857037] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
As one of the most lethal cancers, primary liver cancer (PLC) has high tumor heterogeneity, including the heterogeneity between cancer cells. Traditional methods which have been used to identify tumor heterogeneity for a long time are based on large mixed cell samples, and the research results usually show average level of the cell population, ignoring the heterogeneity between cancer cells. In recent years, single-cell sequencing has been increasingly applied to the studies of PLCs. It can detect the heterogeneity between cancer cells, distinguish each cell subgroup in the tumor microenvironment (TME), and also reveal the clonal characteristics of cancer cells, contributing to understand the evolution of tumor. Here, we introduce the process of single-cell sequencing, review the applications of single-cell sequencing in the heterogeneity of cancer cells, TMEs, oncogenesis, and metastatic mechanisms of liver cancer, and discuss some of the current challenges in the field.
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Nouvel A, Laget J, Duranton F, Leroy J, Desmetz C, Servais MD, de Préville N, Galtier F, Nocca D, Builles N, Rebuffat S, Lajoix AD. Optimization of RNA extraction methods from human metabolic tissue samples of the COMET biobank. Sci Rep 2021; 11:20975. [PMID: 34697345 PMCID: PMC8545963 DOI: 10.1038/s41598-021-00355-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
Constitution of biobank of human tissues requires careful handling and storage of biological material, to guarantee the quality of samples. Tissue preparation is also critical for further applications such as transcriptomic profiling. In this study, our aim was to evaluate the impact of different disruption techniques (FastPrep-24 instrument, GentleMACS dissociator, and syringe/needle) and homogenizing buffers (RLT versus QIAzol) on RNA purity and quality of metabolic tissues (adipose tissues, liver and skeletal muscle) present in the COMET Biobank. For all homogenization methods used and tissue types, the A260/280 ratios reached values ≥ 1.8, which are in the range of what is found in human tissues and cell lines, while the A260/230 ratios were however ≤ 1.8, with the lowest value obtained with GentleMACS Dissociator. In addition, GentleMACS Dissociator combined with QIAzol reagent gave the highest RIN value and 28S/18S ratio for all tissues tested, except for muscle. Performing RT-qPCR, Ct values for different housekeeping genes can be influenced by extraction methods and RNA quality of samples. In conclusion, we have demonstrated that different disruption techniques and homogenizing buffers impact the purity and some quality markers of RNA, and can also impact quantification of mRNAs by RT-qPCR in human metabolic tissues.
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Affiliation(s)
- Agathe Nouvel
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Jonas Laget
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Flore Duranton
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France.,RD Néphrologie, 2 rue des Muriers, 34090, Montpellier, France
| | - Jérémy Leroy
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Caroline Desmetz
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | | | | | - Florence Galtier
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France.,Clinical Investigation Center 1411, Hôpital St Eloi, INSERM, University Hospital of Montpellier, 80 Avenue Augustin Fliche, 34295, Montpellier Cedex 5, France.,Department of Endocrinology, Lapeyronie Hospital, University Hospital of Montpellier, 371 avenue du Doyen Gaston Giraud, 34295, Montpellier Cedex 5, France
| | - David Nocca
- Department of Digestive Surgery, University Hospital of Montpellier, 80 Avenue Augustin Fliche, 34295, Montpellier Cedex 5, France
| | - Nicolas Builles
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, 80 Avenue Augustin Fliche, 34295, Montpellier Cedex 5, France
| | - Sandra Rebuffat
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Anne-Dominique Lajoix
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France.
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5
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Neuber AC, Tostes CH, Ribeiro AG, Marczynski GT, Komoto TT, Rogeri CD, da Silva VD, Mauad EC, Reis RM, Marques MMC. The biobank of barretos cancer hospital: 14 years of experience in cancer research. Cell Tissue Bank 2021; 23:271-284. [PMID: 34216325 DOI: 10.1007/s10561-021-09941-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/20/2021] [Indexed: 01/15/2023]
Abstract
Despite the developments in cancer research over years, cancer is still one of the leading causes of death worldwide. In Brazil, the number of cancer cases for the several next years (2020-2022) is expected to increase up to 625,000. Thus, translational research has been vital to determine the potential risk, prognostic, and predictive biomarkers in cancer. Therefore, Barretos Cancer Hospital implemented a biobank (BB-BCH) in 2006, which is responsible for processing, storage, and provision of biological materials from cancer and non-cancer participants. Hence, this article aimed to describe BB-BCH's history, experiences, and outcomes and explore its impact on Brazilian translational oncology research scenario. BB-BCH has a multidisciplinary team who are responsible for guaranteeing the quality of all processes as recommended by international guidelines for biobanks. Furthermore, BB-BCH has ample equipment to ensure the quality of all material requested by researchers as genetic material (DNA and RNA) and/or entire biospecimens. From 2006 to 2019, BB-BCH contained 252,069 samples from 44,933 participants, the whole collection is represented by 15 different types of biospecimens collected from them. According to our data, the most collected and stored topography in men is head and neck (29%); in women is breast (28%); and in children is torso and limb (27%) samples. Finally, we supported national and international consortia and projects such as The Cancer Genome Atlas. BB-BCH is a vital knowledge source for scientific community, enabling the development of high-quality studies, with a wide variety of tumor categories and high national representativeness of Brazilian population.
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Affiliation(s)
| | | | - Adeylson Guimarães Ribeiro
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil
| | | | | | | | - Vinicius Duval da Silva
- Barretos Cancer Hospital Biobank, São Paulo, Brazil.,Department of Pathology, Barretos Cancer Hospital, São Paulo, Brazil
| | - Edmundo Carvalho Mauad
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil
| | - Rui Manuel Reis
- Barretos Cancer Hospital Biobank, São Paulo, Brazil.,Department of Prevention, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Márcia M C Marques
- Barretos Cancer Hospital Biobank, São Paulo, Brazil. .,Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil. .,Barretos School of Health Sciences, Barretos, SP, Brazil.
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6
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Binkley MS, Jeon YJ, Nesselbush M, Moding EJ, Nabet BY, Almanza D, Kunder C, Stehr H, Yoo CH, Rhee S, Xiang M, Chabon JJ, Hamilton E, Kurtz DM, Gojenola L, Owen SG, Ko RB, Shin JH, Maxim PG, Lui NS, Backhus LM, Berry MF, Shrager JB, Ramchandran KJ, Padda SK, Das M, Neal JW, Wakelee HA, Alizadeh AA, Loo BW, Diehn M. KEAP1/NFE2L2 Mutations Predict Lung Cancer Radiation Resistance That Can Be Targeted by Glutaminase Inhibition. Cancer Discov 2020; 10:1826-1841. [PMID: 33071215 PMCID: PMC7710558 DOI: 10.1158/2159-8290.cd-20-0282] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 08/12/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022]
Abstract
Tumor genotyping is not routinely performed in localized non-small cell lung cancer (NSCLC) due to lack of associations of mutations with outcome. Here, we analyze 232 consecutive patients with localized NSCLC and demonstrate that KEAP1 and NFE2L2 mutations are predictive of high rates of local recurrence (LR) after radiotherapy but not surgery. Half of LRs occurred in tumors with KEAP1/NFE2L2 mutations, indicating that they are major molecular drivers of clinical radioresistance. Next, we functionally evaluate KEAP1/NFE2L2 mutations in our radiotherapy cohort and demonstrate that only pathogenic mutations are associated with radioresistance. Furthermore, expression of NFE2L2 target genes does not predict LR, underscoring the utility of tumor genotyping. Finally, we show that glutaminase inhibition preferentially radiosensitizes KEAP1-mutant cells via depletion of glutathione and increased radiation-induced DNA damage. Our findings suggest that genotyping for KEAP1/NFE2L2 mutations could facilitate treatment personalization and provide a potential strategy for overcoming radioresistance conferred by these mutations. SIGNIFICANCE: This study shows that mutations in KEAP1 and NFE2L2 predict for LR after radiotherapy but not surgery in patients with NSCLC. Approximately half of all LRs are associated with these mutations and glutaminase inhibition may allow personalized radiosensitization of KEAP1/NFE2L2-mutant tumors.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Michael S Binkley
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford, California
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | | | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, California
- Stanford Cancer Institute, Stanford, California
| | - Diego Almanza
- Cancer Biology Program, Stanford University, Stanford, California
| | - Christian Kunder
- Department of Pathology, Stanford University, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, California
| | - Christopher H Yoo
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Siyeon Rhee
- Department of Biology, Stanford University, Stanford, California
| | - Michael Xiang
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, California
| | | | - Emily Hamilton
- Cancer Biology Program, Stanford University, Stanford, California
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Linda Gojenola
- Department of Pathology, Stanford University, Stanford, California
| | - Susie Grant Owen
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Ryan B Ko
- Department of Radiation Oncology, Stanford University, Stanford, California
| | | | - Peter G Maxim
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Natalie S Lui
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Leah M Backhus
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Mark F Berry
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Joseph B Shrager
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Kavitha J Ramchandran
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Sukhmani K Padda
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Millie Das
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Joel W Neal
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Heather A Wakelee
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University, Stanford, California
- Stanford Cancer Institute, Stanford, California
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, California.
- Stanford Cancer Institute, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
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7
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Shangguan A, Zhou H, Sun W, Ding R, Li X, Liu J, Zhou Y, Chen X, Ding F, Yang L, Zhang S. Cryopreservation Induces Alterations of miRNA and mRNA Fragment Profiles of Bull Sperm. Front Genet 2020; 11:419. [PMID: 32431726 PMCID: PMC7214931 DOI: 10.3389/fgene.2020.00419] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/03/2020] [Indexed: 11/30/2022] Open
Abstract
Although cryopreservation of bull semen is widely used commercially in the livestock breeding industry, cryopreservation results in low fertility of bull sperm. As an important regulatory factor, the alteration of small non-coding RNA (sncRNA) profile during cryopreservation of bull sperm is not yet completely known. In the present study, we sequenced sncRNAs of frozen and fresh sperm to study the link of alteration of the sncRNA profiles (particularly in miRNAs and mRNA fragments) with low sperm fertility caused by cryopreservation. We identified 55 miRNAs and 526 mRNA fragments differentially expressed (DE) between frozen and fresh sperm. Subsequently, the functional analysis revealed that targeted genes of DE miRNAs in sperm had roles in the fertilization, ATP, and apoptosis. Instead, targeted genes of DE miRNAs in cow metaphase II oocyte were significantly enriched in the MAPK signaling pathway, autophagy-animal pathway, and mitophagy-animal pathway. Additionally, biological processes of DNA repair, spermatid development, response to temperature stimulus, and cellular response to DNA damage stimulus were enriched by mRNA fragments. In conclusion, we found that DE miRNAs or DE mRNA fragments in cryopreservation may influence the fertility of sperm, these findings will provide the reference to improve the cryopreservation technology of bull semen.
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Affiliation(s)
- Aishao Shangguan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hao Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei Sun
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Rui Ding
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Xihe Li
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Jiajia Liu
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xing Chen
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Fengling Ding
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shujun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
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8
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Wilcox MB, Laranjeira SG, Eriksson TM, Jessen KR, Mirsky R, Quick TJ, Phillips JB. Characterising cellular and molecular features of human peripheral nerve degeneration. Acta Neuropathol Commun 2020; 8:51. [PMID: 32303273 PMCID: PMC7164159 DOI: 10.1186/s40478-020-00921-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/26/2020] [Indexed: 12/23/2022] Open
Abstract
Nerve regeneration is a key biological process in those recovering from neural trauma. From animal models it is known that the regenerative capacity of the peripheral nervous system (PNS) relies heavily on the remarkable ability of Schwann cells to undergo a phenotypic shift from a myelinating phenotype to one that is supportive of neural regeneration. In rodents, a great deal is known about the molecules that control this process, such as the transcription factors c-Jun and early growth response protein 2 (EGR2/KROX20), or mark the cells and cellular changes involved, including SOX10 and P75 neurotrophin receptor (p75NTR). However, ethical and practical challenges associated with studying human nerve injury have meant that little is known about human nerve regeneration.The present study addresses this issue, analysing 34 denervated and five healthy nerve samples from 27 patients retrieved during reconstructive nerve procedures. Using immunohistochemistry and Real-Time quantitative Polymerase Chain Reaction (RT-qPCR), the expression of SOX10, c-Jun, p75NTR and EGR2 was assessed in denervated samples and compared to healthy nerve. Nonparametric smoothing linear regression was implemented to better visualise trends in the expression of these markers across denervated samples.It was found, first, that two major genes associated with repair Schwann cells in rodents, c-Jun and p75NTR, are also up-regulated in acutely injured human nerves, while the myelin associated transcription factor EGR2 is down-regulated, observations that encourage the view that rodent models are relevant for learning about human nerve injury. Second, as in rodents, the expression of c-Jun and p75NTR declines during long-term denervation. In rodents, diminishing c-Jun and p75NTR levels mark the general deterioration of repair cells during chronic denervation, a process thought to be a major obstacle to effective nerve repair. The down-regulation of c-Jun and p75NTR reported here provides the first molecular evidence that also in humans, repair cells deteriorate during chronic denervation.
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Affiliation(s)
- Matthew B. Wilcox
- Peripheral Nerve Injury Research Unit, Royal National Orthopaedic Hospital, Stanmore, UK
- Department of Pharmacology, UCL School of Pharmacy, University College London, London, WC1N 1AX UK
- UCL Centre for Nerve Engineering, University College London, London, UK
| | - Simão G Laranjeira
- UCL Centre for Nerve Engineering, University College London, London, UK
- Department of Mechanical Engineering, University College London, London, UK
| | - Tuula M. Eriksson
- Department of Biomaterials and Tissue Engineering, Eastman Dental Institute, University College London, London, UK
| | - Kristjan R. Jessen
- UCL Centre for Nerve Engineering, University College London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Rhona Mirsky
- UCL Centre for Nerve Engineering, University College London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Tom J. Quick
- Peripheral Nerve Injury Research Unit, Royal National Orthopaedic Hospital, Stanmore, UK
- UCL Centre for Nerve Engineering, University College London, London, UK
| | - James B. Phillips
- Department of Pharmacology, UCL School of Pharmacy, University College London, London, WC1N 1AX UK
- UCL Centre for Nerve Engineering, University College London, London, UK
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9
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Chu SG, Poli De Frias S, Sakairi Y, Kelly RS, Chase R, Konishi K, Blau A, Tsai E, Tsoyi K, Padera RF, Sholl LM, Goldberg HJ, Mallidi HR, Camp PC, El-Chemaly SY, Perrella MA, Choi AMK, Washko GR, Raby BA, Rosas IO. Biobanking and cryopreservation of human lung explants for omic analysis. Eur Respir J 2020; 55:13993003.01635-2018. [PMID: 31699836 DOI: 10.1183/13993003.01635-2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/10/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Sarah G Chu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,These authors contributed equally to the manuscript
| | - Sergio Poli De Frias
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,These authors contributed equally to the manuscript
| | - Yuichi Sakairi
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kazuhisa Konishi
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ashley Blau
- Partners Biobank and Translational Genomics Core, Harvard Medical School, Boston, MA, USA
| | - Ellen Tsai
- Partners Biobank and Translational Genomics Core, Harvard Medical School, Boston, MA, USA
| | - Konstantin Tsoyi
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert F Padera
- Dept of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynette M Sholl
- Dept of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hilary J Goldberg
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hari R Mallidi
- Division of Thoracic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Phillip C Camp
- Division of Thoracic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Souheil Y El-Chemaly
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark A Perrella
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dept of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin A Raby
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Respiratory Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ivan O Rosas
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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10
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Bumbat M, Wang M, Liang W, Ye P, Sun W, Liu B. Effects of Me 2SO and Trehalose on the Cell Viability, Proliferation, and Bcl-2 Family Gene ( BCL-2, BAX, and BAD) Expression in Cryopreserved Human Breast Cancer Cells. Biopreserv Biobank 2019; 18:33-40. [PMID: 31800305 DOI: 10.1089/bio.2019.0082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Long-term cryopreservation of the viability and metabolic state of cells in cancer cell/tissue specimens has significant implications for diagnostic verification of disease progression in cancer patients and selection of effective treatment options via development of the patient-derived xenograft (PDX) models for drug screening. The purpose of this study is to investigate the effects of cryoprotectant agents (CPAs) on the expression of BCL-2 family genes (BCL-2, BAX, and BAD) that are involved in the growth and development of breast cancers. MCF-7 cells were cryopreserved in Dulbecco's modified Eagle's medium (DMEM) with 20% (v/v) fetal bovine serum, using 10% (v/v) Me2SO (dimethyl sulfoxide, DMSO) or 7.5% (v/v) Me2SO with 100is-300 mM trehalose as cryoprotectant solutions. After storage at -80°C for 7 days, the cells were thawed for evaluation. The use of Me2SO and trehalose has affected cell survival, proliferation, apoptotic state, as well as BCL-2 family gene expression. The conventional 10% (v/v) Me2SO method yields ∼80% post-thaw cell survival and good cell proliferation, but it drastically alters the pattern of the BCL-2 family gene expression. The antiapoptotic gene BCL-2 is downregulated, whereas two proapoptotic genes BAX and BAD are upregulated. The partial substitution of Me2SO with 200 or 300 mM trehalose enhances cell proliferation of survived cells after cryopreservation. The presence of trehalose upregulates the expression of both the antiapoptotic gene BCL-2 and proapoptotic genes BAX and BAD. Cryopreservation could tip off the checkpoint of the apoptotic pathway regulated by the BCL-2 family members, and the effect may be protectant dependent. The findings of this study demonstrate the importance of paying attention to the potential change of gene expression and metabolic state of cancer cells after cryopreservation in an attempt to development of the PDX models from cryopreserved cancer cells or tissue specimens.
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Affiliation(s)
- Myagmarjav Bumbat
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Meixia Wang
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Wei Liang
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Ping Ye
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Wendell Sun
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Baolin Liu
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
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11
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Fouda MA, Elzefzafy NA, Taha II, Mohemmed OM, Wahab AAA, Farahat IG. Effect of seasonal variation in ambient temperature on RNA quality of breast cancer tissue in a remote biobank setting. Exp Mol Pathol 2019; 112:104334. [PMID: 31726039 DOI: 10.1016/j.yexmp.2019.104334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/01/2019] [Accepted: 11/09/2019] [Indexed: 02/04/2023]
Abstract
Studies involving oncology especially diagnosis, prognosis and therapeutic monitoring are increasingly relying on molecular analyses. These analyses require high quality biomolecules to get accurate and precise results and this requires among others, monitoring for pre-analytical variables. The purpose of our study was to validate the SOPs of the newly established Egyptian National Cancer Institute (ENCI) biobank. We used a panel of 91 fresh frozen breast cancer tissue samples and their matched normal tissues and have investigated the overall quality (integrity and yield) of RNA extracted from fresh frozen breast tumor tissues and matched normal breast tissues. We investigated the effect of several factors including seasonal temperature variation, cold ischemia time, transportation method, and RNA extraction method. The RNA yield and quality were significantly increased with tumor samples collected in winter, transported on wet ice and using an automated RNA extraction platform. No significant effect was observed due to increased cold ischemia time >30 min. The effect of delay in time to cryopreservation on RNA degradation in fresh tissue samples may vary according to the type of tissue, temperature during tissue collection and transportation, and the use of stabilizing agents as RNA later.
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Affiliation(s)
- Merhan A Fouda
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Egypt; ENCI biobank, National Cancer Institute, Cairo University, Egypt.
| | - Nahla A Elzefzafy
- Department of Cancer Biology, National Cancer Institute, Cairo University, Egypt; ENCI biobank, National Cancer Institute, Cairo University, Egypt
| | - Iman I Taha
- ENCI biobank, National Cancer Institute, Cairo University, Egypt
| | - Omar M Mohemmed
- ENCI biobank, National Cancer Institute, Cairo University, Egypt
| | - Abdelhady Ali Abdel Wahab
- Department of Cancer Biology, National Cancer Institute, Cairo University, Egypt; ENCI biobank, National Cancer Institute, Cairo University, Egypt
| | - Iman Gouda Farahat
- Department of Pathology, National Cancer Institute, Cairo University, Egypt; ENCI biobank, National Cancer Institute, Cairo University, Egypt
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12
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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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13
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Mendy M, Caboux E, Wild CP. Centralization of the IARC Biobank: Combining Multiple Sample Collections into a Common Platform. Biopreserv Biobank 2019; 17:433-443. [PMID: 31091138 DOI: 10.1089/bio.2018.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The International Agency for Research on Cancer (IARC) is the World Health Organization's (WHO) cancer research agency. The agency conducts research on cancer with worldwide collaborations, adopting a multidisciplinary approach of epidemiology and laboratory-based studies on cancer causes, as well as preventive interventions. The IARC Biobank stores multiple collections of samples and conducts preanalytical services for studies conducted worldwide in support of the research activities. Traditionally, the multiple collections from these studies were managed by the individual research groups in different project-specific databases. In 2010, a program to centralize sample collections into a single platform was initiated by adopting a common database with the introduction of a minimum dataset for sample collections received at IARC. The process involved checking data files, verifying the storage location of samples, conducting data harmonization, and importing or migrating existing data from project-specific spreadsheets and databases into the common database. In addition to the creation of a common biobank database and an up-to-date inventory of IARC's biological resources, a governance structure was established. The creation of the Biobank Steering Committee and the adoption of an access policy is to facilitate and guide the sharing of IARC's resources in a transparent manner, while taking into account Ethical, Legal, and Social Issues.
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Affiliation(s)
- Maimuna Mendy
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, Lyon, France
| | - Elodie Caboux
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, Lyon, France
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14
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Wilcox M, Quick TJ, Phillips JB. The Effects of Surgical Antiseptics and Time Delays on RNA Isolated From Human and Rodent Peripheral Nerves. Front Cell Neurosci 2019; 13:189. [PMID: 31178696 PMCID: PMC6538796 DOI: 10.3389/fncel.2019.00189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/12/2019] [Indexed: 01/25/2023] Open
Abstract
Peripheral Nerve Injury (PNI) is common following blunt or penetrating trauma with an estimated prevalence of 2% among the trauma population. The resulting economic and societal impacts are significant. Nerve regeneration is a key biological process in those recovering from neural trauma. Real Time-quantitative Polymerase Chain Reaction (RT-qPCR) and RNA sequencing (RNA seq) are investigative methods that are often deployed by researchers to characterize the cellular and molecular mechanisms that underpin this process. However, the ethical and practical challenges associated with studying human nerve injury have meant that studies of nerve injury have largely been limited to rodent models of renervation. In some circumstances it is possible to liberate human nerve tissue for study, for example during reconstructive nerve repair. This complex surgical environment affords numerous challenges for optimizing the yield of RNA in sufficient quantity and quality for downstream RT-qPCR and/or RNA seq applications. This study characterized the effect of: (1) Time delays between surgical liberation and cryopreservation and (2) contact with antiseptic surgical reagents, on the quantity and quality of RNA isolated from human and rodent nerve samples. It was found that time delays of greater than 3 min between surgical liberation and cryopreservation of human nerve samples significantly decreased RNA concentrations to be sub-optimal for downstream RT-qPCR/RNA seq applications (<5 ng/μl). Minimizing the exposure of human nerve samples to antiseptic surgical reagents significantly increased yield of RNA isolated from samples. The detrimental effect of antiseptic reagents on RNA yield was further confirmed in a rodent model where RNA yield was 8.3-fold lower compared to non-exposed samples. In summary, this study has shown that changes to the surgical tissue collection protocol can have significant effects on the yield of RNA isolated from nerve samples. This will enable the optimisation of protocols in future studies, facilitating characterisation of the cellular and molecular mechanisms that underpin the regenerative capacity of the human peripheral nervous system.
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Affiliation(s)
- Matthew Wilcox
- Peripheral Nerve Injury Research Unit, Royal National Orthopaedic Hospital, Stanmore, United Kingdom.,Department of Pharmacology, UCL School of Pharmacy, University College London, London, United Kingdom.,UCL Centre for Nerve Engineering, University College London, London, United Kingdom
| | - Tom J Quick
- Peripheral Nerve Injury Research Unit, Royal National Orthopaedic Hospital, Stanmore, United Kingdom.,Department of Pharmacology, UCL School of Pharmacy, University College London, London, United Kingdom.,UCL Centre for Nerve Engineering, University College London, London, United Kingdom
| | - James B Phillips
- Department of Pharmacology, UCL School of Pharmacy, University College London, London, United Kingdom.,UCL Centre for Nerve Engineering, University College London, London, United Kingdom
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15
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He T, Huang Y, Chak JC, Klar RM. Recommendations for improving accuracy of gene expression data in bone and cartilage tissue engineering. Sci Rep 2018; 8:14874. [PMID: 30291289 PMCID: PMC6173755 DOI: 10.1038/s41598-018-33242-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/26/2018] [Indexed: 12/15/2022] Open
Abstract
Autogenous tissue grafting remains the gold standard in the treatment of critical sized bone and certain cartilage defects, while the translation of tissue engineered osteogenesis or chondrogenesis from the lab bench into clinical practice, utilizing natural or synthetic biomimetic devices, remains challenging. One of the crucial underestimated reasons for non-translatability could be the imprecision and inconsistency of generated gene expression profiles, utilizing improperly optimized and standardized quantitative gene assays. Utilizing GeNorm for downstream qRT-PCR applications, the stability of reference genes in relation to optimal cDNA amounts was assessed on human bone marrow-derived mesenchymal and adipose-derived stem cells neat and made to differentiate into chondrocytes including normal human derived chondrocytes and muscle tissue from rats. Results showed that reference genes can vary substantially across separately and/or combined cell lines and/or tissue types including treatment parameters. The recommendations to all bone and cartilage tissue engineers utilizing qRT-PCR is not to assume that reference gene stability and quantity remain conserved across cell lines or tissue types but to always determine, for each new experiment, the stability and normalization quantity of reference genes anew.
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Affiliation(s)
- Tao He
- Laboratory of Biomechanics and Experimental Orthopaedics, Department of Orthopaedic Surgery, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany.,Department of Orthopaedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yijiang Huang
- Laboratory of Biomechanics and Experimental Orthopaedics, Department of Orthopaedic Surgery, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany
| | - Juy Chi Chak
- Laboratory of Biomechanics and Experimental Orthopaedics, Department of Orthopaedic Surgery, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany
| | - Roland Manfred Klar
- Laboratory of Biomechanics and Experimental Orthopaedics, Department of Orthopaedic Surgery, Physical Medicine and Rehabilitation, University Hospital of Munich (LMU), Munich, Germany.
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16
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Successful Secondary Engraftment of Pancreatic Ductal Adenocarcinoma and Cholangiocarcinoma Patient-Derived Xenografts After Previous Failed Primary Engraftment. Transl Oncol 2018; 12:69-75. [PMID: 30273859 PMCID: PMC6170258 DOI: 10.1016/j.tranon.2018.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND: Patient-derived xenografts (PDX) provide histologically accurate cancer models that recapitulate patient malignant phenotype and allow for highly correlative oncologic in-vivo downstream translational studies. Primary PDX engraftment failure has significant negative consequences on programmatic efficiency and resource utilization and is due to either no tumor growth or development of lymphoproliferative tumors. We aimed to determine if secondary engraftment of previously cryopreserved patient tumor tissues would allow salvage of PDX models that failed previous primary engraftment and increase overall engraftment efficiency. METHODS: Patient hepatobiliary and pancreatic cancers that failed primary engraftment were identified. Previously cryopreserved primary patient cancerous tissues were implanted into immunodeficient mice (NOD/SCID). Mice were monitored, growth metrics calculated, and secondary engraftment outcomes were recorded. Established PDX were verified and compared to original patient tissue through multiple generations by a GI pathologist. RESULTS: We identified 55 patient tumors that previously failed primary engraftment: no tumor growth (n = 46, 84%) or lymphoproliferative tumor (LT) (n = 9, 16%). After secondary implantation using cryopreserved patient tissues, 29 new histologically validated PDX models were generated with an overall secondary engraftment rate of 53% for all tumor types with greatest yield in pancreatic and biliary tract cancers. Of the secondary engraftment failures (n = 26), 21 (38%) were due to no growth and 5 (9%) developed LT. CONCLUSION: Secondary PDX engraftment using cryopreserved primary cancerous is feasible after previous failed engraftment attempts and can result in a 50% increase in overall engraftment efficiency with decreases in LT formation. This technique allows for salvage of critical patient PDX models that would otherwise not exist. SYNOPSIS: Patient-derived xenografts have many important translational applications however can be limited by engraftment failure. We demonstrate optimized methodology utilizing cryopreservation of primary tumor tissue that allows for subsequent successful secondary engraftment and creation of PDX models that failed previous primary engraftment and allowed salvage of patient PDX models that would otherwise not exist.
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17
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Unger FT, Lange N, Krüger J, Compton C, Moore H, Agrawal L, Juhl H, David KA. Nanoproteomic analysis of ischemia-dependent changes in signaling protein phosphorylation in colorectal normal and cancer tissue. J Transl Med 2016; 14:6. [PMID: 26742633 PMCID: PMC4705760 DOI: 10.1186/s12967-015-0752-1] [Citation(s) in RCA: 16] [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: 07/17/2015] [Accepted: 12/02/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Clinical diagnostic research relies upon the collection of tissue samples, and for those samples to be representative of the in vivo situation. Tissue collection procedures, including post-operative ischemia, can impact the molecular profile of the tissue at the genetic and proteomic level. Understanding the influence of factors such as ischemia on tissue samples is imperative in order to develop both markers of tissue quality and ultimately accurate diagnostic tests. METHODS Using NanoPro1000 technology, a rapid and highly sensitive immunoassay platform, the phosphorylation status of clinically relevant cancer-related biomarkers in response to ischemia was quantified in tissue samples from 20 patients with primary colorectal cancer. Tumor tissue and adjacent normal tissue samples were collected and subjected to cold ischemia prior to nanoproteomic analysis of AKT, ERK1/2, MEK1/2, and c-MET. Ischemia-induced relative changes in overall phosphorylation and phosphorylation of individual isoforms were calculated and statistical significance determined. Any differences in baseline levels of phosphorylation between tumor tissue and normal tissue were also analyzed. RESULTS Changes in overall phosphorylation of the selected proteins in response to ischemia revealed minor variations in both normal and tumor tissue; however, significant changes were identified in the phosphorylation of individual isoforms. In normal tissue post-operative ischemia, phosphorylation was increased in two AKT isoforms, two ERK1/2 isoforms, and one MEK1/2 isoform and decreased in one MEK1/2 isoform and one c-MET isoform. Following ischemia in tumor tissue, one AKT isoform showed decreased phosphorylation and there was an overall increase in unphosphorylated ERK1/2, whereas an increase in the phosphorylation of two MEK1/2 isoforms was observed. There were no changes in c-MET phosphorylation in tumor tissue. CONCLUSION This study provides insight into the influence of post-operative ischemia on tissue sample biology, which may inform the future development of markers of tissue quality and assist in the development of diagnostic tests.
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Affiliation(s)
| | - Nicole Lange
- Indivumed GmbH, Falkenried 88, 20251, Hamburg, Germany.
| | - Jana Krüger
- Indivumed GmbH, Falkenried 88, 20251, Hamburg, Germany.
| | | | - Helen Moore
- Biorepositories and Biospecimen Research Branch,National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lokesh Agrawal
- Biorepositories and Biospecimen Research Branch,National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Hartmut Juhl
- Indivumed GmbH, Falkenried 88, 20251, Hamburg, Germany.
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18
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Caixeiro NJ, Lai K, Lee CS. Quality assessment and preservation of RNA from biobank tissue specimens: a systematic review. J Clin Pathol 2015; 69:260-5. [DOI: 10.1136/jclinpath-2015-203384] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/27/2015] [Indexed: 11/04/2022]
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19
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Argon A, Şener A, Zekioğlu O, Kapkaç M, Özdemir N. The effect of freezing on the immunoprofile of breast carcinoma cells. Balkan Med J 2015; 31:335-9. [PMID: 25667788 DOI: 10.5152/balkanmedj.2014.14389] [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: 06/02/2014] [Accepted: 08/31/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Intraoperative frozen section procedure may be required in some operations performed for breast masses. AIMS We investigated the effect of frozen section procedure on the immunoprofile of breast carcinoma cells. STUDY DESIGN Cross-sectional study. METHODS A total of 53 breast carcinoma cases evaluated with intraoperative frozen sections were included in this study. Immunohistochemically, oestrogen (ER), progesterone (PR) and HER2 primary antibodies were evaluated in both frozen and non-frozen sections of each tumour sample. RESULTS No difference was found between the frozen and non-frozen sections in 33 cases in terms of staining rate and intensity of ER, PR and HER2. A decrease was found in the ER, PR and HER2 staining rate (in 10 cases, 9 cases and 6 cases, respectively). Likewise, a decrease was detected in ER, PR and HER2 staining intensity in 6 patients for each. Although there was no staining in frozen sections, immunopositivity was observed in 3 non-frozen sections for ER, in 2 for PR and in 5 for HER2. Statistically, a significant difference was found between the frozen and non-frozen sections in terms of staining rate and intensity for each of the three markers. CONCLUSION In this study, the frozen section procedure in breast carcinoma had a negative effect on the immunoprofile. However, considering the importance of hormone receptor status in the treatment, these results should be supported with larger series.
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Affiliation(s)
- Asuman Argon
- Department of Pathology, İzmir Bozyaka Training and Research Hospital, İzmir, Turkey
| | - Alper Şener
- Department of Pathology, Ege University Faculty of Medicine, İzmir, Turkey
| | - Osman Zekioğlu
- Department of Pathology, Ege University Faculty of Medicine, İzmir, Turkey
| | - Murat Kapkaç
- Department of General Surgery, Ege University Faculty of Medicine, İzmir, Turkey
| | - Necmettin Özdemir
- Department of Pathology, Ege University Faculty of Medicine, İzmir, Turkey
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