1
|
De Martino E, Medeot C, D'Amico L, Stanta G, Bonin S. Impact of standardization in tissue processing: the performance of different fixatives. N Biotechnol 2022; 71:30-36. [PMID: 35878783 DOI: 10.1016/j.nbt.2022.07.001] [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: 03/15/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 10/31/2022]
Abstract
Most tissues in clinical practice are formalin-fixed and paraffin-embedded for histological as well as molecular analyses. The reproducibility and uniformity of molecular analyses is strictly dependent on the quality of the biomolecules, which is highly influenced by pre-analytical processes. In this study, the effect of different fixatives was compared, including formalin, Bouin's solution, RCL2® and TAG-1™ fixatives, by stringent application of ISO standards in mouse liver tissue processing, including formalin-free transport of tissues and tissue grossing in a refrigerated environment. The effect of fixatives was studied in terms of nucleic acid quality at the time of tissue processing and after one year of tissue storage at room temperature in the dark. Furthermore, a microcomputed tomography (CT) scan analysis was applied to investigate the paraffin embedding. The results show that the application of ISO standards in tissue processing allows analysis of 400 bases amplicons from RNA and 1000 bases from DNA, even in extracts from formalin-fixed and paraffin-embedded tissues. However, after one year storage at room temperature in the dark, a degradation of the nucleic acids was observed. Nevertheless, extracts can still be analyzed, but for metachronous tests it is highly recommended to repeat the quantitation of housekeeping genes in order to standardize the extent of nucleic acid degradation.
Collapse
Affiliation(s)
| | - Caterina Medeot
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Lorenzo D'Amico
- Department of Physics, University of Trieste, Trieste, Italy; Elettra-Sincrotrone Trieste S.C.p.A., Area Science Park, Trieste, Italy
| | - Giorgio Stanta
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Serena Bonin
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
| |
Collapse
|
2
|
Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing. BMC Genomics 2021; 22:69. [PMID: 33478392 PMCID: PMC7818915 DOI: 10.1186/s12864-021-07381-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to freeze-thaw and RNA degradation, e.g. the RNA Integrity Score, makes such assessments challenging. Results Here we quantify the impact of repeated freeze-thaw cycles on the reliability of RNA-Seq by examining poly(A)-enriched and ribosomal RNA depleted RNA-seq from frozen leukocytes drawn from a toddler Autism cohort. To do so, we estimate the relative noise, or percentage of random counts, separating technical replicates. Using this approach we measured noise associated with RIN and freeze-thaw cycles. As expected, RIN does not fully capture sample degradation due to freeze-thaw. We further examined differential expression results and found that three freeze-thaws should extinguish the differential expression reproducibility of similar experiments. Freeze-thaw also resulted in a 3′ shift in the read coverage distribution along the gene body of poly(A)-enriched samples compared to ribosomal RNA depleted samples, suggesting that library preparation may exacerbate freeze-thaw-induced sample degradation. Conclusion The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07381-z.
Collapse
Affiliation(s)
- Benjamin P Kellman
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Hratch M Baghdassarian
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Tiziano Pramparo
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Isaac Shamie
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Vahid Gazestani
- Department of Pediatrics, University of California, San Diego, USA.,Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Arjana Begzati
- Department of Medicine, University of California San Diego, San Diego, USA
| | - Shangzhong Li
- Department of Pediatrics, University of California, San Diego, USA.,Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Srinivasa Nalabolu
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Sarah Murray
- Department of Pathology, University of California San Diego, San Diego, USA
| | - Linda Lopez
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, USA. .,Department of Bioengineering, University of California San Diego, San Diego, USA. .,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, USA.
| |
Collapse
|
3
|
Annaratone L, Marchiò C, Sapino A. Tissues under-vacuum to overcome suboptimal preservation. N Biotechnol 2019; 52:104-109. [PMID: 31150841 DOI: 10.1016/j.nbt.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/23/2019] [Accepted: 05/26/2019] [Indexed: 12/11/2022]
Abstract
The accuracy of histopathological diagnosis is strictly reliant on adequate tissue preservation, which is completely dependent on pre-analytical variables. Among these variables, the time interval between the end of surgical excision to the onset of fixation (the cold ischemia time) may adversely affect preservation of tissue morphology, influencing the interpretation and reproducibility of diagnosis. During this time interval, the activation of enzymes may produce autolysis and degradation of antigens and nucleic acids, thus potentially affecting immunocytochemical and molecular results. Several studies have described under-vacuum at 4 °C storage of fresh surgical specimens as a safe and reliable method to control cold ischemia and preserve fresh tissues, as well as to standardize fixation times and implement tissue-banking. This review article gives a systematic overview of the advantages and drawbacks of the use of under-vacuum tissue preservation and cooling in surgical pathology, highlighting the impact this procedure may have on diagnostic and experimental pathology. It also documents our experience acquired within daily practice and national and international projects.
Collapse
Affiliation(s)
- Laura Annaratone
- Department of Medical Sciences, University of Turin, Corso Dogliotti 14, 10126, Turin, Italy.
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Corso Dogliotti 14, 10126, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Provinciale 142 km 3.95, 10060, Candiolo (Turin), Italy.
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Corso Dogliotti 14, 10126, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Str. Provinciale 142 km 3.95, 10060, Candiolo (Turin), Italy.
| |
Collapse
|
4
|
Zhang X, Han QY, Zhao ZS, Zhang JG, Zhou WJ, Lin A. Biobanking of Fresh-Frozen Gastric Cancer Tissues: Impact of Long-Term Storage and Clinicopathological Variables on RNA Quality. Biopreserv Biobank 2019; 17:58-63. [PMID: 30457887 DOI: 10.1089/bio.2018.0038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Xia Zhang
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Qiu-Yue Han
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Zhang-Sheng Zhao
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Jian-Gang Zhang
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Wen-Jun Zhou
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Aifen Lin
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| |
Collapse
|
5
|
Abstract
Compared to DNA, analysis of RNA is one step closer on the central dogma of biology to assessing cellular function. This makes it an extremely valuable target for research and clinical testing in nearly all areas of molecular biology. Most RNA molecules are ephemeral by nature. They exist as temporary intermediates, ostensibly enabling data transfer between the genome and the organism. Their ribose backbone renders them sensitive to simple degradation over time and they are the target molecule for numerous and abundant ribonucleases which have evolved to chop them to pieces with extreme efficiency. At the biochemical level, this means that they degrade rapidly in most physiological and laboratory conditions and are thus challenging to study. When considering specimen banking, it is critical to keep this reality in mind, as some commonly used banking modalities will not adequately preserve the relevant RNA molecules in a measureable state.In this chapter, we explore the broad range of RNA testing methodologies in current use, with particular focus on how specimen preparation impacts analysis. Following an overview in the introduction, Subheading 2 covers the major specimen types amenable to RNA analysis in the context of biobanking. Subheading 3 discusses the applications of various RNA analysis modalities to research and clinical testing.
Collapse
|
6
|
Zheng XH, Zhang SD, Zhang PF, Li XZ, Hu YZ, Tian T, Zhu L, Wang RZ, Jia WH. Tumor Cell Content and RNA Integrity of Surgical Tissues from Different Types of Tumors and Its Correlation with Ex Vivo and In Vivo Ischemia. Ann Surg Oncol 2018; 25:3764-3770. [PMID: 30225832 DOI: 10.1245/s10434-018-6697-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Tissues from tumor patients are important resources for promoting cancer research, and therefore many biobanks have been established to collect tumor tissues; however, the quality of tumor tissues after surgical resection has not been well documented. METHODS A total of 896 cases of tissues from 12 types of tumors were chosen for this study. First, histopathological examination was conducted to evaluate the tumor cell content; second, microchip electrophoresis was used to determine the RNA integrity number (RIN) in 466 cases of tissues with a tumor cell content ≥ 75%; and, finally, a correlation test was used to analyze the effect of ischemia on RNA integrity in 384 cases of tissues with a recorded ischemia time. RESULTS Tumor tissues from 12 different organs had different tumor cell contents and RNA integrity. The liver had the highest percentage (69.7%) of tissue samples with a tumor cell content ≥ 75%, and the highest percentage (96%) of samples with an RIN ≥ 7. RNA integrity was not correlated with limited ex vivo ischemia time (5-60 min) in any of the 12 types of tumors. In contrast, a significant correlation with in vivo ischemia time was observed in several types of tumors. CONCLUSIONS Not every sample of excised tumor tissue has a sufficient amount of tumor cells and enough RNA integrity. In vivo ischemia has a more significant influence on RNA integrity, and tumor tissues have different tolerances to pre-analytical variables. Those conducting translational research should pay attention to pre-analytical variables when collecting and utilizing tumor tissues.
Collapse
Affiliation(s)
- Xiao-Hui Zheng
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China.,Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China
| | - Shao-Dan Zhang
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Pei-Fen Zhang
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Xi-Zhao Li
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Ye-Zhu Hu
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Tian Tian
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Lin Zhu
- Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China
| | - Ruo-Zheng Wang
- Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
| | - Wei-Hua Jia
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China. .,Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
| |
Collapse
|
7
|
Abstract
OBJECTIVES Attaining high-quality RNA from the tissues or organs of deceased donors used for research can be challenging due to physiological and logistical considerations. In this investigation, METHODS: RNA Integrity Number (RIN) was determined in pancreatic samples from 236 organ donors and used to define high (≥6.5) and low (≤4.5) quality RNAs. Logistic regression was used to evaluate the potential effects of novel or established organ and donor factors on RIN. RESULTS Univariate analysis revealed donor cause of death (odds ratio [OR], 0.35; 95% confidence interval [CI], 0.15-0.77; P = 0.01), prolonged tissue storage before RNA extraction (OR, 0.65; 95% CI, 0.52-0.79; P < 0.01), pancreas region sampled (multiple comparisons, P < 0.01), and sample type (OR, 0.32; 95% CI, 0.15-0.67; P < 0.01) negatively influenced outcome. Conversely, duration of final hospitalization (OR, 3.95; 95% CI, 1.59-10.37; P < 0.01) and sample collection protocol (OR, 8.48; 95% CI, 3.96-19.30; P < 0.01) positively impacted outcome. Islet RNA obtained via laser capture microdissection improved RIN when compared with total pancreatic RNA from the same donor (ΔRIN = 1.3; 95% CI, 0.6-2.0; P < 0.01). CONCLUSIONS A multivariable model demonstrates that autopsy-free and biopsy-free human pancreata received, processed, and preserved at a single center, using optimized procedures, from organ donors dying of anoxia with normal lipase levels increase the odds of obtaining high-quality RNA.
Collapse
|
8
|
Galissier T, Schneider C, Nasri S, Kanagaratnam L, Fichel C, Coquelet C, Diebold MD, Kianmanesh R, Bellon G, Dedieu S, Marchal Bressenot A, Boulagnon-Rombi C. Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality? PLoS One 2016; 11:e0154326. [PMID: 27124490 PMCID: PMC4849710 DOI: 10.1371/journal.pone.0154326] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/12/2016] [Indexed: 12/01/2022] Open
Abstract
Medical research projects become increasingly dependent on biobanked tissue of high quality because the reliability of gene expression is affected by the quality of extracted RNA. Hence, the present study aimed to determine if clinical, surgical, histological, and molecular parameters influence RNA quality of normal and tumoral frozen colonic tissues. RNA Quality Index (RQI) was evaluated on 241 adenocarcinomas and 115 matched normal frozen colon tissues collected between October 2006 and December 2012. RQI results were compared to patients’ age and sex, tumor site, kind of surgery, anastomosis failure, adenocarcinoma type and grade, tumor cell percentage, necrosis extent, HIF-1α and cleaved caspase-3 immunohistochemistry, and BRAF, KRAS and microsatellites status. The RQI was significantly higher in colon cancer tissue than in matched normal tissue. RQI from left-sided colonic cancers was significantly higher than RQI from right-sided cancers. The RNA quality was not affected by ischemia and storage duration. According to histological control, 7.9% of the samples were unsatisfactory because of inadequate sampling. Biobanked tumoral tissues with RQI ≥5 had lower malignant cells to stromal cells ratio than samples with RQI <5 (p <0.05). Cellularity, necrosis extent and mucinous component did not influence RQI results. Cleaved caspase-3 and HIF-1α immunolabelling were not correlated to RQI. BRAF, KRAS and microsatellites molecular status did not influence RNA quality. Multivariate analysis revealed that the tumor location, the surgical approach (laparoscopy versus open colectomy) and the occurrence of anastomotic leakage were the only parameters influencing significantly RQI results of tumor samples. We failed to identify parameter influencing RQI of normal colon samples. These data suggest that RNA quality of colonic adenocarcinoma biospecimens is determined by clinical and surgical parameters. More attention should be paid during the biobanking procedure of right-sided colon cancer or laparoscopic colectomy specimen. Histological quality control remains essential to control sampling accuracy.
Collapse
Affiliation(s)
- Thibaut Galissier
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
| | - Christophe Schneider
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Saviz Nasri
- Tumorothèque de Champagne Ardenne, Reims, France
| | - Lukshe Kanagaratnam
- Unité d’Aide Méthodologique, Centre Hospitalier Universitaire, Reims, France
| | - Caroline Fichel
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | | | - Marie-Danièle Diebold
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Tumorothèque de Champagne Ardenne, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Reza Kianmanesh
- Service de Chirurgie Digestive, Centre Hospitalier Universitaire, Reims, France
| | - Georges Bellon
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire de Biochimie, Centre Hospitalier Universitaire, Reims, France
| | - Stéphane Dedieu
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Aude Marchal Bressenot
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Camille Boulagnon-Rombi
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
- * E-mail:
| |
Collapse
|