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Romanò S, Nele V, Campani V, De Rosa G, Cinti S. A comprehensive guide to extract information from extracellular vesicles: a tutorial review towards novel analytical developments. Anal Chim Acta 2024; 1302:342473. [PMID: 38580402 DOI: 10.1016/j.aca.2024.342473] [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: 01/03/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
In the medical field, extracellular vesicles (EVs) are gaining importance as they act as cells mediators. These are phospholipid bilayer vesicles and contain crucial biochemical information about their mother cells being carrier of different biomolecules such as small molecules, proteins, lipids, and nucleic acids. After release into the extracellular matrix, they enter the systemic circulation and can be found in all human biofluids. Since EVs reflect the state of the cell of origin, there is exponential attention as potential source of new circulating biomarkers for liquid biopsy. The use of EVs in clinical practice faces several challenges that need to be addressed: these include the standardization of lysis protocols, the availability of low-cost reagents and the development of analytical tools capable of detecting biomarkers. The process of lysis is a crucial step that can impact all subsequent analyses, towards the development of novel analytical strategies. To aid researchers to support the evolution of measurement science technology, this tutorial review evaluates and discuss the most commonly protocols used to characterize the contents of EVs, including their advantages and disadvantages in terms of experimental procedures, time and equipment. The purpose of this tutorial review is to offer practical guide to researchers which are intended to develop novel analytical approaches. Some of the most significant applications are considered, highlighting their main characteristics divided per mechanism of action. Finally, comprehensive tables which provide an overview at a glance are provided to readers.
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Affiliation(s)
- Sabrina Romanò
- Department of Pharmacy, University of Naples Federico II, Italy.
| | - Valeria Nele
- Department of Pharmacy, University of Naples Federico II, Italy
| | | | | | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, Italy.
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2
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Huo Q, Wang J, Xie N. High HSPB1 expression predicts poor clinical outcomes and correlates with breast cancer metastasis. BMC Cancer 2023; 23:501. [PMID: 37268925 DOI: 10.1186/s12885-023-10983-3] [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: 08/22/2022] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Heat shock protein beta-1 (HSPB1) is a crucial biomarker for pathological processes in various cancers. However, the clinical value and function of HSPB1 in breast cancer has not been extensively explored. Therefore, we adopted a systematic and comprehensive approach to investigate the correlation between HSPB1 expression and clinicopathological features of breast cancer, as well as determine its prognostic value. We also examined the effects of HSPB1 on cell proliferation, invasion, apoptosis, and metastasis. METHODS We investigated the expression of HSPB1 in patients with breast cancer using The Cancer Genome Atlas and immunohistochemistry. Chi-squared test and Wilcoxon signed-rank test were used to examine the relationship between HSPB1 expression and clinicopathological characteristics. RESULTS We observed that HSPB1 expression was significantly correlated with the stage N, pathologic stages, as well as estrogen and progesterone receptors. Furthermore, high HSPB1 expression resulted in a poor prognosis for overall survival, relapse-free survival, and distant metastasis-free survival. Multivariable analysis showed that patients with poor survival outcomes had higher tumor, node, metastasis, and pathologic stages. Pathway analysis of HSPB1 and the altered neighboring genes suggested that HSPB1 is involved in the epithelial-to-mesenchymal transition. Functional analysis revealed showed that transient knockdown of HSPB1 inhibited the cell migration/invasion ability and promoted apoptosis. CONCLUSIONS HSPB1 may be involved in breast cancer metastasis. Collectively, our study demonstrated that HSPB1 has prognostic value for clinical outcomes and may serve as a therapeutic biomarker for breast cancer.
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Affiliation(s)
- Qin Huo
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, 518035, Shenzhen, China
| | - Juan Wang
- Department of General Practice, Army Medical Center of PLA, Chongqing, 400042, China
| | - Ni Xie
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, 518035, Shenzhen, China.
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3
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Biskup E, Schejbel L, de Oliveira DNP, Høgdall E. Test of the FlashFREEZE unit in tissue samples freezing for biobanking purposes. Cell Tissue Bank 2023; 24:435-447. [PMID: 36309911 PMCID: PMC10209260 DOI: 10.1007/s10561-022-10045-1] [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: 06/29/2022] [Accepted: 10/12/2022] [Indexed: 11/28/2022]
Abstract
Availability of molecularly intact biospecimens is essential in genetic diagnostics to obtain credible results. Integrity of nucleic acids (particularly RNA) may be compromised at various steps of tissue handling, and affected by factors such as time to freeze, freezing technique and storing temperature. At the same time, freezing and storing of the biological material should be feasible and safe for the operator. Here, we compared quality of DNA and RNA from biospecimens derived from different organs (breast, colon, adrenal glands, testes, rectum and uterus) frozen either using dry ice-cooled isopentane or with FlashFREEZE unit, in order to verify if the latter is suitable for routine use in biobanking. Implementing FlashFREEZE device would enable us to limit the use of isopentane, which is potentially toxic and environmentally harmful, whilst facilitate standardization of sample freezing time. We considered factors such RNA and DNA yield and purity. Furthermore, RNA integrity and RNA/DNA performance in routine analyses, such as qPCR, next generation sequencing or microarray, were also assessed. Our results indicate that freezing of tissue samples either with FlashFREEZE unit or isopentane ensures biological material with comparable expression profiles and DNA mutation status, indicating that RNA and DNA of similar quality can be extracted from both. Therefore, our findings support the use of the FlashFREEZE device in routine use for biobanking purposes.
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Affiliation(s)
- Edyta Biskup
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
| | - Lone Schejbel
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
| | | | - Estrid Høgdall
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
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4
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Ranjan R, Biswal JK, Sahoo PK, Tripathy JP, Singh RP. Diagnostic application of formalin fixed archived tissues for detection of foot-and-mouth disease. J Virol Methods 2023:114754. [PMID: 37230193 DOI: 10.1016/j.jviromet.2023.114754] [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: 03/03/2023] [Revised: 05/01/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
Early and definitive disease diagnosis is critical for effective disease control. 50% buffered glycerine is commonly used viral transport medium, which is not always available and required cold chain. Tissues samples archived in 10% neutral buffered formalin (NBF) can preserve nucleic acid that can be used in molecular studies and disease diagnosis. The present study's goal was to detect the foot-and-mouth disease (FMD) viral genome in formalin-fixed archived tissue which may avoid cold chain during transportation. This study used FMD suspected samples preserved in 10% neutral buffered formalin from 0 to 730 days post fixation (DPF). All archived tissues were positive for FMD viral genome by multiplex RT-PCR and RT-qPCR up to 30 DPF, whereas archived epithelium tissues and thigh muscle were positive for FMD vial genome up to 120 DPF. FMD viral genome was detected in cardiac muscle up to 60 DPF and 120 DPF, respectively. The findings suggest that 10% neutral buffered formalin could be used for sample preservation and transportation for timely and accurate FMD diagnosis. More samples need to be tested before implementing the use of 10% neutral buffered formalin as a preservative and transportation medium. The technique may add value in ensuring biosafety measures for creation during disease free zone as well.
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Affiliation(s)
- Rajeev Ranjan
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India.
| | - Jitendra Kumar Biswal
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India
| | - Prabin Kumar Sahoo
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India
| | - Jagannath Prasad Tripathy
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India
| | - Rabindra Prasad Singh
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India
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5
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Kato K, Okami J, Nakamura H, Honma K, Sato Y, Nakamura S, Kukita Y, Nakatsuka SI, Higashiyama M. Analytical Performance of a Highly Sensitive System to Detect Gene Variants Using Next-Generation Sequencing for Lung Cancer Companion Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13081476. [PMID: 37189577 DOI: 10.3390/diagnostics13081476] [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: 02/22/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
The recent increase in the number of molecular targeted agents for lung cancer has led to the demand for the simultaneous testing of multiple genes. Although gene panels using next-generation sequencing (NGS) are ideal, conventional panels require a high tumor content, and biopsy samples often do not meet this requirement. We developed a new NGS panel, called compact panel, characterized by high sensitivity, with detection limits for mutations of 0.14%, 0.20%, 0.48%, 0.24%, and 0.20% for EGFR exon 19 deletion, L858R, T790M, BRAF V600E, and KRAS G12C, respectively. Mutation detection also had a high quantitative ability, with correlation coefficients ranging from 0.966 to 0.992. The threshold for fusion detection was 1%. The panel exhibited good concordance with the approved tests. The identity rates were as follows: EGFR positive, 100% (95% confidence interval, 95.5-100); EGFR negative, 90.9 (82.2-96.3); BRAF positive, 100 (59.0-100); BRAF negative, 100 (94.9-100); KRAS G12C positive, 100 (92.7-100); KRAS G12C negative, 100 (93.0-100); ALK positive, 96.7 (83.8-99.9); ALK negative, 98.4 (97.2-99.2); ROS1 positive, 100 (66.4-100); ROS1 negative, 99.0 (94.6-100); MET positive, 98.0 (89.0-99.9); MET negative 100 (92.8-100); RET positive, 93.8 (69.8-100); RET negative, 100 (94.9-100). The analytical performance showed that the panel could handle various types of biopsy samples obtained by routine clinical practice without requiring strict pathological monitoring, as in the case of conventional NGS panels.
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Affiliation(s)
- Kikuya Kato
- Laboratory of Medical Genomics, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Jiro Okami
- Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | - Harumi Nakamura
- Laboratory of Genomic Pathology, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | - Keiichiro Honma
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | | | - Seiji Nakamura
- Laboratory of Medical Genomics, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Yoji Kukita
- Laboratory of Medical Genomics, Nara Institute of Science and Technology, Nara 630-0192, Japan
- Laboratory of Genomic Pathology, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | - Shin-Ichi Nakatsuka
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka 540-0008, Japan
| | - Masahiko Higashiyama
- Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka 540-0008, Japan
- Department of Thoracic Surgery, Higashiosaka City Medical Center, Osaka 578-8588, Japan
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Giannella E, Notarangelo V, Motta C, Sancesario G. Biobanking for Neurodegenerative Diseases: Challenge for Translational Research and Data Privacy. Neuroscientist 2023; 29:190-201. [PMID: 34353130 DOI: 10.1177/10738584211036693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Biobanking has emerged as a strategic challenge to promote knowledge on neurological diseases, by the application of translational research. Due to the inaccessibility of the central nervous system, the advent of biobanks, as structure collecting biospecimens and associated data, are essential to turn experimental results into clinical practice. Findings from basic research, omics sciences, and in silico studies, definitely require validation in clinically well-defined cohorts of patients, even more valuable when longitudinal, or including preclinical and asymptomatic individuals. Finally, collecting biological samples requires a great effort to guarantee respect for transparency and protection of sensitive data of patients and donors. Since the European General Data Protection Regulation 2016/679 has been approved, concerns about the use of data in biomedical research have emerged. In this narrative review, we focus on the essential role of biobanking for translational research on neurodegenerative diseases. Moreover, we address considerations for biological samples and data collection, the importance of standardization in the preanalytical phase, data protection (ethical and legal) and the role of donors in improving research in this field.
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Affiliation(s)
- Emilia Giannella
- Biobank, IRCCS Santa Lucia Foundation, Rome, Italy.,Experimental Neuroscience, European Center for Brain Research, Rome, Italy
| | | | - Caterina Motta
- Dept Clinical and Behavioural Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Giulia Sancesario
- Biobank, IRCCS Santa Lucia Foundation, Rome, Italy.,Experimental Neuroscience, European Center for Brain Research, Rome, Italy
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7
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Acharayothin O, Thiengtrong B, Juengwiwattanakitti P, Anekwiang P, Riansuwan W, Chinswangwatanakul V, Tanjak P. Impact of Washing Processes on RNA Quantity and Quality in Patient-Derived Colorectal Cancer Tissues. Biopreserv Biobank 2023; 21:31-37. [PMID: 35230139 DOI: 10.1089/bio.2021.0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Colorectal cancer (CRC) is a common and lethal cancer worldwide. Extraction of high-quality RNA from CRC samples plays a key role in scientific research and translational medicine. Specimen collection and washing methods that do not compromise RNA quality or quantity are needed to ensure high quality specimens for gene expression analysis and other RNA-based downstream applications. We investigated the effect of tissue specimen collection and different preparation processes on the quality and quantity of RNA extracted from surgical CRC tissues. Materials and Methods: After surgical resection, tissues were harvested and prepared with various washing processes in a room adjacent to the operating room. One hundred fourteen tissues from 36 CRC patients were separately washed in either cold phosphate-buffered saline reagent (n = 34) or Dulbecco's modified Eagle's medium (DMEM; n = 34) for 2-3 minutes until the stool was removed, and unwashed specimens served as controls (n = 34). Six tissue specimens were washed and immersed in DMEM for up to 1 hour at 4°C. Before RNA extraction, all specimens were kept in the stabilizing reagent for 3 months at -80°C. RNA was extracted, and the concentration per milligram of tissue was measured. RNA quality was assessed using the RNA integrity number (RIN) value. Results: Different washing processes did not result in significant differences in RNA quantity or RIN values. In the six tissues that were washed and immersed in DMEM for 1 hour, RIN values significantly decreased. The quality of the extracted RNA from most specimens was excellent with the average RIN greater than 7. Conclusions: RNA is stable in specimens washed in different processes for short periods, but RIN values may decrease with prolonged wash times.
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Affiliation(s)
- Onchira Acharayothin
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Benjarat Thiengtrong
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panudeth Juengwiwattanakitti
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panatna Anekwiang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Woramin Riansuwan
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Vitoon Chinswangwatanakul
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pariyada Tanjak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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8
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Smith S, Hoelzl F, Zahn S, Criscuolo F. Telomerase activity in ecological studies: What are its consequences for individual physiology and is there evidence for effects and trade-offs in wild populations. Mol Ecol 2022; 31:6239-6251. [PMID: 34664335 PMCID: PMC9788021 DOI: 10.1111/mec.16233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/10/2021] [Accepted: 09/24/2021] [Indexed: 02/02/2023]
Abstract
Increasing evidence at the cellular level is helping to provide proximate explanations for the balance between investment in growth, reproduction and somatic maintenance in wild populations. Studies of telomere dynamics have informed researchers about the loss and gain of telomere length both on a seasonal scale and across the lifespan of individuals. In addition, telomere length and telomere rate of loss seems to have evolved differently among taxonomic groups, and relate differently to organismal diversity of lifespan. So far, the mechanisms behind telomere maintenance remain elusive, although many studies have inferred a role for telomerase, an enzyme/RNA complex known to induce telomere elongation from laboratory studies. Exciting further work is also emerging that suggests telomerase (and/or its individual component parts) has a role in fitness that goes beyond the maintenance of telomere length. Here, we review the literature on telomerase biology and examine the evidence from ecological studies for the timing and extent of telomerase activation in relation to life history events associated with telomere maintenance. We suggest that the underlying mechanism is more complicated than originally anticipated, possibly involves several complimentary pathways, and is probably associated with high energetic costs. Potential pathways for future research are numerous and we outline what we see as the most promising prospects to expand our understanding of individual differences in immunity or reproduction efficiency.
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Affiliation(s)
- Steve Smith
- Konrad Lorenz Institute of EthologyUniversity of Veterinary Medicine, ViennaViennaAustria
| | - Franz Hoelzl
- Konrad Lorenz Institute of EthologyUniversity of Veterinary Medicine, ViennaViennaAustria
| | - Sandrine Zahn
- Department of Physiology, Evolution and BehaviourInstitut Pluridisciplinaire Hubert CurienCNRSUniversity of StrasbourgStrasbourgFrance
| | - François Criscuolo
- Department of Physiology, Evolution and BehaviourInstitut Pluridisciplinaire Hubert CurienCNRSUniversity of StrasbourgStrasbourgFrance
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9
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An Innovative Approach to Tissue Processing and Cell Sorting of Fixed Cells for Subsequent Single-Cell RNA Sequencing. Int J Mol Sci 2022; 23:ijms231810233. [PMID: 36142141 PMCID: PMC9499188 DOI: 10.3390/ijms231810233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/24/2022] Open
Abstract
Although single-cell RNA sequencing (scRNA-seq) is currently the gold standard for the analysis of cell-specific expression profiles, the options for processing, staining, and preserving fresh cells remain very limited. Immediate and correct tissue processing is a critical determinant of scRNA-seq success. One major limitation is the restricted compatibility of fixation approaches, which must not destabilize or alter antibody labeling or RNA content or interfere with cell integrity. An additional limitation is the availability of expensive, high-demand cell-sorting equipment to exclude debris and dead or unwanted cells before proceeding with sample sequencing. The goal of this study was to develop a method that allows cells to be fixed and stored prior to FACS sorting for scRNA-seq without compromising the quality of the results. Finally, the challenge of preserving as many living cells as possible during tissue processing is another crucial issue addressed in this study. Our study focused on pancreatic ductal adenocarcinoma samples, where the number of live cells is rather limited, as in many other tumor tissues. Harsh tissue dissociation methods and sample preparation for analysis can negatively affect cell viability. Using the murine pancreatic cancer model Pan02, we evaluated the semi-automated mechanical/enzymatic digestion of solid tumors by gentleMACS Dissociator and compared it with mechanical dissociation of the same tissue. Moreover, we investigated a type of cell fixation that is successful in preserving cell RNA integrity yet compatible with FACS and subsequent scRNA-sequencing. Our protocol allows tissue to be dissociated and stained in one day and proceeds to cell sorting and scRNA-seq later, which is a great advantage for processing clinical patient material.
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10
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Qian Y, Itzel T, Ebert M, Teufel A. Deep View of HCC Gene Expression Signatures and Their Comparison with Other Cancers. Cancers (Basel) 2022; 14:cancers14174322. [PMID: 36077860 PMCID: PMC9454845 DOI: 10.3390/cancers14174322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Gene expression signatures correlate genetic alterations with specific clinical features, providing the potential for clinical usage. A plethora of HCC-dependent gene signatures have been developed in the last two decades. However, none of them has made its way into clinical practice. Thus, we investigated the specificity of public gene signatures to HCC by establishing a comparative transcriptomic analysis, as this may be essential for clinical applications. METHODS We collected 10 public HCC gene signatures and evaluated them by utilizing four different (commercial and non-commercial) gene expression profile comparison tools: Oncomine Premium, SigCom LINCS, ProfileChaser (modified version), and GENEVA, which can assign similar pre-analyzed profiles of patients with tumors or cancer cell lines to our gene signatures of interests. Among the query results of each tool, different cancer entities were screened. In addition, seven breast and colorectal cancer gene signatures were included in order to further challenge tumor specificity of gene expression signatures. RESULTS Although the specificity of the evaluated HCC gene signatures varied considerably, none of the gene signatures showed strict specificity to HCC. All gene signatures exhibited potential significant specificity to other cancers, particularly for colorectal and breast cancer. Since signature specificity proved challenging, we furthermore investigated common core genes and overlapping enriched pathways among all gene signatures, which, however, showed no or only very little overlap, respectively. CONCLUSION Our study demonstrates that specificity, independent validation, and clinical use of HCC genetic signatures solely relying on gene expression remains challenging. Furthermore, our work made clear that standards in signature generation and statistical methods but potentially also in tissue preparation are urgently needed.
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Affiliation(s)
- Yuquan Qian
- Division of Hepatology, Division of Clinical Bioinformatics, Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Timo Itzel
- Division of Hepatology, Division of Clinical Bioinformatics, Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Matthias Ebert
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
- Clinical Cooperation Unit Healthy Metabolism, Center for Preventive Medicine and Digital Health Baden-Württemberg (CPDBW), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Andreas Teufel
- Division of Hepatology, Division of Clinical Bioinformatics, Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
- Clinical Cooperation Unit Healthy Metabolism, Center for Preventive Medicine and Digital Health Baden-Württemberg (CPDBW), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
- Correspondence: ; Tel.: +49-(0)621-383-4983; Fax: +49-(0)621-383-1467
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11
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Zhang X, Hu C, Huang C, Wei Y, Li X, Hu M, Li H, Wu J, Czajkowsky DM, Guo Y, Shao Z. Robust Acquisition of Spatial Transcriptional Programs in Tissues With Immunofluorescence-Guided Laser Capture Microdissection. Front Cell Dev Biol 2022; 10:853188. [PMID: 35399504 PMCID: PMC8990165 DOI: 10.3389/fcell.2022.853188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
The functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue, as local interactions precipitate intra-cellular events that often lead to changes in expression. However, our understanding of these processes in tissues, whether healthy or diseased, is limited at present owing to the difficulty in acquiring comprehensive transcriptional programs of spatially- and phenotypically-defined cells in situ. Here we present a robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to acquire finely resolved transcriptional programs with as few as tens of cells from snap-frozen or RNAlater-treated clinical tissues sufficient to resolve even isoforms. The protocol is optimized to protect the RNA with a small molecule inhibitor, the ribonucleoside vanadyl complex (RVC), which thereby enables the typical time-consuming immunostaining and laser capture steps of this procedure during which RNA is usually severely degraded in existing approaches. The efficacy of this approach is exemplified by the characterization of differentially expressed genes between the mouse small intestine lacteal cells at the tip versus the main capillary body, including those that function in sensing and responding to local environmental cues to stimulate intra-cellular signalling. With the extensive repertoire of specific antibodies that are presently available, our method provides an unprecedented capability for the analysis of transcriptional networks and signalling pathways during development, pathogenesis, and aging of specific cell types within native tissues.
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Affiliation(s)
- Xiaodan Zhang
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Wei
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Miaomiao Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Bio-X Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M. Czajkowsky
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Yan Guo
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Zhifeng Shao
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
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12
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Ferndale L, Moodley M, Chen WC, Wadee R, Wright CA, Parker MI, Willem P, Mathew CG. Processing and Analysis of Tissue Samples from Esophageal Cancer Patients in an African Setting. Biopreserv Biobank 2021; 20:185-194. [PMID: 34388042 DOI: 10.1089/bio.2021.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although infectious diseases continue to present a major health care problem in Africa, the incidence of cancer is increasing rapidly on the African continent and this merits an increased investment in cancer research in low to medium resource settings. Esophageal squamous cell carcinoma (ESCC) has a high incidence in Eastern and Southern Africa, with late clinical presentation and a very poor prognosis. There is limited research on the molecular pathology of this cancer in Africa, partly as a result of a lack of infrastructure for biobanking and sample processing in many African countries. The aim of this study was to establish a practical and robust workflow to collect, store, and process esophageal cancer samples such that both the tissue architecture and quality of the samples would be preserved and suitable for future genomic research. We developed a workflow that allows storage of fresh biopsy tissue in sterile Eppendorf tubes containing RNAlater, an efficient RNAse inhibitor. We collected 142 ESCC biopsy samples and showed that storage in RNAlater for up to 18 months did not alter tissue morphology, thus allowing histologic assessment by experienced pathologists and determination of tumor content in each biopsied sample. DNA and RNA extracted from tissue samples was assessed for purity, molecular size, and yield. The quantity and quality of nucleic acids obtained were suitable for genomic applications, and whole-exome sequencing of DNA from tumor tissues produced sequence data with a high proportion of both usable reads and correct base calling. We conclude that this workflow may be applicable to a wide range of malignancies for future genomic research in low-resource settings.
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Affiliation(s)
- Lucien Ferndale
- Department of Surgery, Grey's Hospital, Pietermaritzburg, South Africa.,Department of Surgery, College of Health Sciences, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Mishalan Moodley
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Service, Johannesburg, South Africa
| | - Wenlong C Chen
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa.,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Reubina Wadee
- Department of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Service, Johannesburg, South Africa
| | - Colleen A Wright
- Department of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Service, Johannesburg, South Africa.,Lancet Laboratories, Johannesburg, South Africa
| | - Mohamed Iqbal Parker
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Pascale Willem
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Service, Johannesburg, South Africa
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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13
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Sarro E, Sun P, Mauck K, Rodriguez-Arellano D, Yamanaka N, Woodard SH. An organizing feature of bumble bee life history: worker emergence promotes queen reproduction and survival in young nests. CONSERVATION PHYSIOLOGY 2021; 9:coab047. [PMID: 34221405 PMCID: PMC8242224 DOI: 10.1093/conphys/coab047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/13/2021] [Accepted: 06/10/2021] [Indexed: 05/14/2023]
Abstract
Bumble bee queens initiate nests solitarily and transition to living socially once they successfully rear their first cohort of offspring. Bumble bees are disproportionately important for early season pollination, and many populations are experiencing dramatic declines. In this system, the onset of the social stage is critical for nest survival, yet the mechanisms that facilitate this transition remain understudied. Further, the majority of conservation efforts target the social stage of the bumble bee life cycle and do not address the solitary founding stage. We experimentally manipulated the timing of worker emergence in young nests of bumble bee (Bombus impatiens) queens to determine whether and how queen fecundity and survival are impacted by the emergence of workers in the nest. We found that queens with workers added to the nest exhibit increased ovary activation, accelerated egg laying, elevated juvenile hormone (JH) titres and also lower mortality relative to solitary queens. We also show that JH is more strongly impacted by the social environment than associated with queen reproductive state, suggesting that this key regulator of insect reproduction has expanded its function in bumble bees to also influence social organization. We further demonstrate that these effects are independent of queen social history, suggesting that this underlying mechanism promoting queen fecundity is reversible and short lived. Synchronization between queen reproductive status and emergence of workers in the nest may ultimately increase the likelihood of early nesting success in social systems with solitary nest founding. Given that bumble bee workers regulate queen physiology as we have demonstrated, the timing of early worker emergence in the nest likely impacts queen fitness, colony developmental trajectories and ultimately nesting success. Collectively, our findings underline the importance of conservation interventions for bumble bees that support the early nesting period and facilitate the production and maintenance of workers in young nests.
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Affiliation(s)
- Erica Sarro
- Department of Entomology, The University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - Penglin Sun
- Department of Entomology, The University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - Kerry Mauck
- Department of Entomology, The University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - Damaris Rodriguez-Arellano
- Department of Entomology, The University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - Naoki Yamanaka
- Department of Entomology, The University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
| | - S Hollis Woodard
- Department of Entomology, The University of California Riverside, 900 University Ave., Riverside, CA 92521, USA
- Corresponding author: Department of Entomology, The University of California Riverside, 900 University Ave., Riverside, CA, USA. Tel: (951) 827-5761; Fax: (951) 827-3086.
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14
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Zhang D, Wan L, Yang F, Liu W, Liu L, He S, Xie N. VWCE Functions as a Tumor Suppressor in Breast Cancer Cells. Front Oncol 2020; 10:586342. [PMID: 33194737 PMCID: PMC7643001 DOI: 10.3389/fonc.2020.586342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/30/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer remains a leading cause of cancer-related death, for which the majority of deaths result from metastases. Von Willebrand factor C and EGF domain (VWCE) is a member of the Von Willebrand factor (VWF) gene family; however, its function, regulatory mechanism, and clinical value in breast cancer remain unclear. In the present study, we sought to elucidate the role of VWCE in breast cancer metastasis. We examined the expression of VWCE in breast cancer tissues and normal control tissues of 50 breast cancer patients. We found that VWCE expression was downregulated in breast cancer cells and tissues compared to normal breast epithelial cells or the adjacent normal tissues. To explore the role of VWCE in human breast cancer development, we introduced a VWCE-overexpressing or control lentiviral vector into the breast cancer MDA-MB-453 and MDA-MB-231 lines in vitro. The overexpression of VWCE inhibited the proliferation, migration, invasion, and chemoresistance of the breast cancer cell lines. More importantly, the forced expression of VWCE suppressed tumor formation and metastasis in nude mice. iTRAQ-based quantitative proteomic analysis revealed that VWCE overexpression induced a 10-fold decrease in the level of WD-repeat domain 1 (WDR1) protein expression. Rescue experiments further verified that WDR1 was a downstream molecule of VWCE, and WDR1 overexpression reversed the above effects of VWCE overexpression on tumor growth. Therefore, VWCE may represent a novel tumor suppressor, for which its deregulation promotes breast cancer progression via the upregulation of WDR1.
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Affiliation(s)
- Dan Zhang
- Health Science Center, Biobank Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lili Wan
- Health Science Center, Biobank Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Fan Yang
- Health Science Center, Biobank Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Wenlan Liu
- Health Science Center, Biobank Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Litao Liu
- Health Science Center, Biobank Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Shengnan He
- Health Science Center, Biobank Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ni Xie
- Health Science Center, Biobank Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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15
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Chakraborty N, Schmitt CW, Honnold CL, Moyler C, Butler S, Nachabe H, Gautam A, Hammamieh R. Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration. Front Mol Biosci 2020; 7:142. [PMID: 32793629 PMCID: PMC7387682 DOI: 10.3389/fmolb.2020.00142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023] Open
Abstract
At the heart of the phenome-to-genome approach is high throughput assays, which are liable to produce false results. This risk can be mitigated by minimizing the sample bias, specifically, recycling the same tissue specimen for both phenotypic and genotypic investigations. Therefore, our aim is to suggest a methodology of obtaining robust results from frozen specimens of compromised quality, particularly if the sample is produced in conditions with limited resources. For example, generating samples at the International Space Station (ISS) is challenging because the time and laboratory footprint allotted to a project can get expensive. In an effort to be economical with available resources, snap-frozen euthanized mice are the straightforward solution; however, this method increases the risk of temperature abuse during the thawing process at the beginning of the tissue collection. We found that prolonged immersion of snap frozen mouse carcass in 10% neutral buffered formalin at 4°C yielded minimal microscopic signs of ice crystallization and delivered tissues with histomorphology that is optimal for hematoxylin and eosin (H&E) staining and fixation on glass slides. We further optimized a method to sequester the tissue specimen from the H&E slides using an incubator shaker. Using this method, we were able to recover an optimal amount of RNA that could be used for downstream transcriptomics assays. Overall, we demonstrated a protocol that enables us to maximize scientific values from tissues collected in austere condition. Furthermore, our protocol can suggest an improvement in the spatial resolution of transcriptomic assays.
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Affiliation(s)
- Nabarun Chakraborty
- Geneva Foundation, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Connie W Schmitt
- Comparative Pathology, US Army Medical Research Institute of Chemical Defense, Gunpowder, MD, United States
| | - Cary L Honnold
- Comparative Pathology, US Army Medical Research Institute of Chemical Defense, Gunpowder, MD, United States
| | - Candace Moyler
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,ORISE, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Stephen Butler
- Geneva Foundation, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Hisham Nachabe
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,ORISE, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Aarti Gautam
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Walter Reed Army Institute of Research, Silver Spring, MD, United States
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16
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Reliable approaches to extract high-integrity RNA from skin and other pertinent tissues used in pain research. Pain Rep 2020; 5:e818. [PMID: 32440611 PMCID: PMC7209822 DOI: 10.1097/pr9.0000000000000818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
Introduction Comprehensive mRNA sequencing is a powerful tool for conducting unbiased, quantitative differential gene expression analysis. However, the reliability of these data is contingent on the extraction of high-quality RNA from samples. Preserving RNA integrity during extraction can be problematic, especially in tissues such as skin with dense, connective matrices and elevated ribonuclease expression. This is a major barrier to understanding the influences of altered gene expression in many preclinical pain models and clinical pain disorders where skin is the site of tissue injury. Objective This study developed and evaluated extraction protocols for skin and other tissues to maximize recovery of high-integrity RNA needed for quantitative mRNA sequencing. Methods Rodent and human tissue samples underwent one of the several different protocols that combined either RNA-stabilizing solution or snap-freezing with bead milling or cryosectioning. Indices of RNA integrity and purity were assessed for all samples. Results Extraction of high-integrity RNA is highly dependent on the methods used. Bead-milling skin collected in RNA-stabilizing solution resulted in extensive RNA degradation. Snap-freezing in liquid nitrogen was required for skin and highly preferable for other tissues. Skin also required cryosectioning to achieve effective penetration of RNA-stabilizing solution to preserve RNA integrity, whereas bead milling could be used instead with other tissues. Each method was reproducible across multiple experimenters. Electrophoretic anomalies that skewed RNA integrity value assignment required manual correction and often resulted in score reduction. Conclusion To achieve the potential of quantitative differential gene expression analysis requires verification of tissue-dependent extraction methods that yield high-integrity RNA.
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17
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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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18
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Hentze JL, Kringelbach TM, Novotny GW, Hamid BH, Ravn V, Christensen IJ, Høgdall C, Høgdall E. Optimized Biobanking Procedures for Preservation of RNA in Tissue: Comparison of Snap-Freezing and RNAlater-Fixation Methods. Biopreserv Biobank 2019; 17:562-569. [PMID: 31618057 DOI: 10.1089/bio.2019.0028] [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] [Indexed: 12/18/2022] Open
Abstract
Introduction: Personalized treatment, supported by biomarkers, would improve survival of ovarian cancer patients. RNA molecules are potentially important biomarkers. The Danish CancerBiobank provides an infrastructure for handling and storage of biological material, including RNA, from Danish cancer patients. The aim of this study was to investigate the effects of handling-time and fresh-freezing versus RNAlater® fixation on RNA degradation in solid tissue from pelvic mass samples. Materials and Methods: We evaluated RNA quality in surgical tissue from patients with a pelvic mass. Corresponding samples were either fresh-frozen or fixed in RNAlater, at eight different time points after the surgery. Integrity was measured using a bioanalyzer, and the amount and quality were further investigated by quantitative reverse transcription-polymerase chain reaction measuring the expression of housekeeping genes B2M and HPRT1. Results: Our results show that tissue RNA is stable up to at least 180 minutes after the surgery, as the quality was comparable to the quality of RNA handled immediately. Likewise, patient RNA was of acceptable quality after both fresh-frezing and RNAlater fixation, but RNAlater fixation was slightly more effective for RNA preservation. Discussion and Conclusion: Our data suggest that RNA in pelvic mass samples is relatively stable. Knowledge about RNA stability is an important prerequisite for research in RNA biomarkers, where the challenge is to balance the need for careful RNA handling and storage with the need for effective large-scale biobanking in a busy clinical setting where patient treatment is the main priority.
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Affiliation(s)
- Julie L Hentze
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Tina M Kringelbach
- Bio- and Genome Bank Denmark, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Guy W Novotny
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bushra H Hamid
- Department of Gynaecology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Vibeke Ravn
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Ib J Christensen
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus Høgdall
- Gynaecological Clinic, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Estrid Høgdall
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Bio- and Genome Bank Denmark, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
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19
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Suhovskih AV, Kazanskaya GM, Volkov AM, Tsidulko AY, Aidagulova SV, Grigorieva EV. Suitability of RNALater solution as a tissue-preserving reagent for immunohistochemical analysis. Histochem Cell Biol 2019; 152:239-247. [PMID: 31197457 DOI: 10.1007/s00418-019-01799-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2019] [Indexed: 11/26/2022]
Abstract
Histological and immunohistochemical studies require high-quality paraffin blocks, where proper fixation of tissue samples with formalin is a key point. However, in some cases, the possibility to preserve biological samples prior to the formalin fixation or to use deposited tissues from biobanks is important. RNA-stabilizing reagent RNALater represents a potential option, but its suitability for pathological and immunohistochemical studies remains underinvestigated. Here, comparative study of formalin-fixed tissues and those had undergone preservation with RNALater was performed for different SCID mice tissues (brain, liver, kidney, and lung) using histological staining (hematoxylin-eosin and Weigert-van Gieson) or immunostaining for b-actin, glial fibrillary acidic protein, and glycosaminoglycan chondroitin sulfate. It was shown that RNALater preservation for 7-14 days was suitable for histological characterisation of mouse lung tissue, whereas all other tissues demonstrated some changes. Immunoreactivity of all the studied tissues was affected to a different extent, and the observed changes were detected at the 7th day already and continued to get worse by the 14th day. Overall, RNALater preservation affects immunogenicity of normal mouse tissues (brain, liver, kidney, and lung) making them unsuitable for immunohistochemistry. Some tissues retain their morphology (lung tissue) or demonstrate moderate changes (brain, liver, kidney), suggesting a restricted suitability of the RNALater-preserved tissues for histological analysis.
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Affiliation(s)
- Anastasia V Suhovskih
- Institute of Molecular Biology and Biophysics FRC FTM, Timakova 2/12, Novosibirsk, 630117, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Galina M Kazanskaya
- Institute of Molecular Biology and Biophysics FRC FTM, Timakova 2/12, Novosibirsk, 630117, Russia
- E. N. Meshalkin, Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Alexander M Volkov
- E. N. Meshalkin, Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Alexandra Y Tsidulko
- Institute of Molecular Biology and Biophysics FRC FTM, Timakova 2/12, Novosibirsk, 630117, Russia
| | | | - Elvira V Grigorieva
- Institute of Molecular Biology and Biophysics FRC FTM, Timakova 2/12, Novosibirsk, 630117, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
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20
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Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation. Clin Proteomics 2019; 16:18. [PMID: 31049047 PMCID: PMC6482574 DOI: 10.1186/s12014-019-9239-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/17/2019] [Indexed: 01/06/2023] Open
Abstract
Certain tumors such as pancreatic ductal adenocarcinoma (PDAC) are known to contain a variety of hydrolytic enzymes including RNases and proteases that may lead to degradation of RNA and proteins during sample processing. For such tumor tissues with RNA instability, RNAlater containing a high concentration of quaternary ammonium sulfates that denature RNA-hydrolyzing enzymes is often used to protect RNAs from hydrolysis. Although a few studies have been carried out to determine the effect of RNAlater on DNA and RNA, whether RNAlater influences the proteome and phosphoproteome is largely unknown. In this study we carried out a systematic and comprehensive analysis of the effect of RNAlater on the proteome and phosphoproteome using high-resolution mass spectrometry. PDAC tissues from three patients were individually pulverized and the tissue powders of each patient were divided into two portions, one of which was incubated in RNAlater at 4 °C for 24 h (RNAlater tissue) while the other was kept at - 80 °C (frozen tissue). Comprehensive quantitative profiling experiments on the RNAlater tissues and the frozen tissues resulted in the identification of 99,136 distinct peptides of 8803 protein groups and 17,345 phosphopeptides of 16,436 phosphosites. The data exhibited no significant quantitative changes in both proteins and phosphorylation between the RNAlater tissues and the frozen tissue. In addition, the phosphoproteome data showed heterogeneously activated pathways among the three patients that were not altered by RNAlater. These results indicate that the tissue preservation method using RNAlater can be effectively used on PDAC tissues for proteogenomic studies where preservation of intact DNA, RNA and proteins is prerequisite. Data from this study are available via ProteomeXchange with the identifier PXD010710.
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21
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Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL. A comprehensive pipeline for translational top-down proteomics from a single blood draw. Nat Protoc 2019; 14:119-152. [PMID: 30518910 DOI: 10.1038/s41596-018-0085-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Top-down proteomics (TDP) by mass spectrometry (MS) is a technique by which intact proteins are analyzed. It has become increasingly popDesalting and concentrating GELFrEEular in translational research because of the value of characterizing distinct proteoforms of intact proteins. Compared to bottom-up proteomics (BUP) strategies, which measure digested peptide mixtures, TDP provides highly specific molecular information that avoids the bioinformatic challenge of protein inference. However, the technique has been difficult to implement widely because of inherent limitations of existing sample preparation methods and instrumentation. Recent improvements in proteoform pre-fractionation and the availability of high-resolution benchtop mass spectrometers have made it possible to use high-throughput TDP for the analysis of complex clinical samples. Here, we provide a comprehensive protocol for analysis of a common sample type in translational research: human peripheral blood mononuclear cells (PBMCs). The pipeline comprises multiple workflows that can be treated as modular by the reader and used for various applications. First, sample collection and cell preservation are described for two clinical biorepository storage schemes. Cell lysis and proteoform pre-fractionation by gel-eluted liquid fractionation entrapment electrophoresis are then described. Importantly, instrument setup and liquid chromatography-tandem MS are described for TDP analyses, which rely on high-resolution Fourier-transform MS. Finally, data processing and analysis are described using two different, application-dependent software tools: ProSight Lite for targeted analyses of one or a few proteoforms and TDPortal for high-throughput TDP in discovery mode. For a single sample, the minimum completion time of the entire experiment is 72 h.
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Affiliation(s)
- Timothy K Toby
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Kristina Srzentić
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Josh Levitsky
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - John Friedewald
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L Kelleher
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA.
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22
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Passow CN, Kono TJY, Stahl BA, Jaggard JB, Keene AC, McGaugh SE. Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods. Mol Ecol Resour 2018; 19:456-464. [PMID: 30447171 DOI: 10.1111/1755-0998.12965] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/19/2018] [Accepted: 11/08/2018] [Indexed: 01/30/2023]
Abstract
RNA sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer-term storage as it rapidly permeates tissue to protect cellular RNA. In this study, we assessed genome-wide expression patterns in 30-day-old fry collected from the same brood at the same time point that were flash-frozen in liquid nitrogen and stored at -80°C or submerged and stored in RNAlater at room temperature, simulating conditions of fieldwork. We show that sample storage is a significant factor influencing observed differential gene expression. In particular, genes with elevated GC content exhibit higher observed expression levels in liquid nitrogen flash-freezing relative to RNAlater storage. Further, genes with higher expression in RNAlater relative to liquid nitrogen experience disproportionate enrichment for functional categories, many of which are involved in RNA processing. This suggests that RNAlater may elicit a physiological response that has the potential to bias biological interpretations of expression studies. The biases introduced to observed gene expression arising from mimicking many field-based studies are substantial and should not be ignored.
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Affiliation(s)
- Courtney N Passow
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Bethany A Stahl
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - James B Jaggard
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota
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23
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DeLeo DM, Pérez-Moreno JL, Vázquez-Miranda H, Bracken-Grissom HD. RNA profile diversity across arthropoda: guidelines, methodological artifacts, and expected outcomes. Biol Methods Protoc 2018; 3:bpy012. [PMID: 32161805 PMCID: PMC6994094 DOI: 10.1093/biomethods/bpy012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 12/19/2022] Open
Abstract
High-quality RNA is an important precursor for high-throughput RNA sequencing (RNAseq) and subsequent analyses. However, the primary metric used to assess RNA quality, the RNA Integrity Number (RIN), was developed based on model bacterial and vertebrate organisms. Though the phenomenon is not widely recognized, invertebrate 28S ribosomal RNA (rRNA) is highly prone to a form of denaturation known as gap deletion, in which the subunit collapses into two smaller fragments. In many nonmodel invertebrates, this collapse of the 28S subunit appears as a single band similar in size to the 18S rRNA subunit. This phenomenon is hypothesized to be commonplace among arthropods and is often misinterpreted as a "degraded" rRNA profile. The limited characterization of gap deletion in arthropods, a highly diverse group, as well as other nonmodel invertebrates, often biases RNA quality assessments. To test whether the collapse of 28S is a general pattern or a methodological artifact, we sampled more than half of the major lineages within Arthropoda. We found that the 28S collapse is present in ∼90% of the species sampled. Nevertheless, RNA profiles exhibit considerable diversity with a range of banding patterns. High-throughput RNAseq and subsequent assembly of high-quality transcriptomes from select arthropod species exhibiting collapsed 28S subunits further illustrates the limitations of current RIN proxies in accurately characterizing RNA quality in nonmodel organisms. Furthermore, we show that this form of 28S denaturation, which is often mistaken for true "degradation," can occur at relatively low temperatures.
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Affiliation(s)
- Danielle M DeLeo
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA
| | - Jorge L Pérez-Moreno
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA
| | - Hernán Vázquez-Miranda
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA
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24
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Wang M, Ji X, Wang B, Li Q, Zhou J. Simultaneous Evaluation of the Preservative Effect of RNAlater on Different Tissues by Biomolecular and Histological Analysis. Biopreserv Biobank 2018; 16:426-433. [PMID: 30484701 DOI: 10.1089/bio.2018.0055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A major concern in biomedical research is the quality of biological samples. RNAlater is a stabilizer, which was originally developed for RNA preservation in fresh tissues and is important for collection and transportation. However, this reagent lacks a comprehensive and systematic evaluation of its preservative effect on different mammalian tissues under consistent experimental conditions. In this study, we collected liver, kidney, testis, brain, and colon tissues from mice and divided the samples into the following respective groups: fresh, RNAlater preserved, and liquid nitrogen snap frozen. Biomolecules (RNA, DNA, and protein) were extracted from each tissue in each group, and samples were formalin fixed and paraffin embedded for quality assessment. Our results revealed that high-quality (yield, purity, and integrity) nucleic acids could be extracted from all samples. Gene expression determined by quantitative real-time polymerase chain reaction exhibited no major difference among the three groups. Notably, we observed significant protein degradation in brain tissue preserved by RNAlater compared with fresh and snap-frozen tissue. Protein expression of the other four tissues was similar among the three groups. Hematoxylin and eosin staining of all tissue types indicated no apparent difference among the three groups. We concluded that high-quality nucleic acids can be obtained and tissue morphology conserved when tissues are preserved with RNAlater. However, there are tissue-specific differences in protein preservation when using RNAlater, which should be evaluated before extensive storage.
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Affiliation(s)
- Min Wang
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Ji
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bingjie Wang
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Li
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Junmei Zhou
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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25
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Hutson HN, Kujawa C, Eliceiri K, Campagnola P, Masters KS. Impact of tissue preservation on collagen fiber architecture. Biotech Histochem 2018; 94:134-144. [PMID: 30354688 DOI: 10.1080/10520295.2018.1530373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Microarchitectural features of collagen-rich extracellular matrices provide the mechanical foundation for tissue function and exhibit topographical cues that influence cellular behavior including proliferation, migration and protein expression. Preservation of tissue microarchitecture is required for accurate evaluation of tissue characteristics and pathology. It is unclear whether common tissue preservation methods possess equal ability to preserve microarchitecture. We investigated collagen microarchitecture in samples that had been flash frozen, fixed in formalin or preserved in RNAlater®, and which contained both collagen-rich and collagen-sparse regions. Fibrillar collagen organization was characterized using picrosirius red staining and second harmonic generation (SHG) microscopy. Maintenance of collagen fiber characteristics compared to the gold standard of flash freezing depended on both the method of preservation and the local collagen content of the tissue. Both formalin fixation and RNAlater® preserved collagen fiber characteristics similar to flash freezing in collagen-rich areas of the tissue, but not in collagen-sparse regions. Analysis using picrosirius red staining indicated preservation-dependent changes in overall tissue architecture and suprafibrillar organization. Together with considerations of cost, ease of use, storage conditions and ability to use the preserved tissue for RNA or protein analysis, our quantitative characterization of the effects of preservation method on collagen microarchitecture may help investigators select the most appropriate preservation approach for their needs.
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Affiliation(s)
- H N Hutson
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - C Kujawa
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - K Eliceiri
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA.,b Laboratory for Optical and Computational Instrumentation, Laboratory of Cell and Molecular Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - P Campagnola
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - K S Masters
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
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26
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Paskal W, Paskal AM, Dębski T, Gryziak M, Jaworowski J. Aspects of Modern Biobank Activity - Comprehensive Review. Pathol Oncol Res 2018; 24:771-785. [PMID: 29728978 PMCID: PMC6132819 DOI: 10.1007/s12253-018-0418-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 04/27/2018] [Indexed: 12/13/2022]
Abstract
Biobanks play an increasing role in contemporary research projects. These units meet all requirements to regard them as a one of the most innovative and up-to-date in the field of biomedical research. They enable conducting wide-scale research by the professional collection of biological specimens and correlated clinical data. Pathology units may be perceived roots of biobanking. The review aims at describing the concept of biobanks, their model of function and scientific potential. It comprises the division of biobanks, sample preservation methods and IT solutions as well as guidelines and recommendations for management of a vast number of biological samples and clinical data. Therefore, appropriate standard operating procedures and protocols are outlined. Constant individualization of diagnostic process and treatment procedures creates the niche for translational units. Thus, the role of biobanks in personalized medicine was also specified. The exceptionality of biobanks poses some new ethical-legal issues which have various solutions, in each legal system, amongst the world. Finally, distribution and activity of European biobanks are mentioned.
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Affiliation(s)
- Wiktor Paskal
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, ul. Banacha 1B, 02-097, Warsaw, Poland.
- Plastic Surgery Department, Centre of Postgraduate Medical Education, Warsaw, Poland.
- The Department of Applied Pharmacy, Medical University of Warsaw, Warsaw, Poland.
| | - Adriana M Paskal
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, ul. Banacha 1B, 02-097, Warsaw, Poland
| | - Tomasz Dębski
- Plastic Surgery Department, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Maciej Gryziak
- The Department of Applied Pharmacy, Medical University of Warsaw, Warsaw, Poland
- Maria Sklodowska-Curie Institute of Oncology, Warsaw, Poland
| | - Janusz Jaworowski
- The Department of Applied Pharmacy, Medical University of Warsaw, Warsaw, Poland
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27
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Ozgyin L, Horvath A, Balint BL. Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing. Oncotarget 2018; 9:31312-31329. [PMID: 30140372 PMCID: PMC6101130 DOI: 10.18632/oncotarget.25764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 06/22/2018] [Indexed: 11/25/2022] Open
Abstract
Biobanks operating at ambient temperatures would dramatically reduce the costs associated with standard cryogenic storage. In the present study, we used lyophilization to stabilize unfractionated human cells in a dried state at room temperature and tested the yield and integrity of the isolated RNA by microfluidic electrophoresis, RT-qPCR and RNA sequencing. RNA yields and integrity measures were not reduced for lyophilized cells (unstored, stored for two weeks or stored for two months) compared to their paired controls. The abundance of the selected mRNAs with various expression levels, as well as enhancer-associated RNAs and cancer biomarker long non-coding RNAs (MALAT1, GAS5 and TUG1), were not significantly different between the two groups as assessed by RT-qPCR. RNA sequencing data of three lyophilized samples stored for two weeks at room temperature revealed a high degree of similarity with their paired controls in terms of the RNA biotype distribution, cumulative gene diversity, gene body read coverage and per base mismatch rate. Among the 28 differentially expressed genes transcriptional regulators, as well as certain transcript properties suggestive of a residual active decay mechanism were enriched. Our study suggests that freeze-drying of human cells is a suitable alternative for the long-term stabilization of total RNA in whole human cells for routine diagnostics and high-throughput biomedical research.
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Affiliation(s)
- Lilla Ozgyin
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen H-4012, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen H-4012, Hungary.,Department of Biochemistry and Molecular Biology, Nuclear Hormone Receptor Research Laboratory, University of Debrecen, Debrecen H-4012, Hungary
| | - Balint Laszlo Balint
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen H-4012, Hungary
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28
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Susman S, Berindan-Neagoe I, Petrushev B, Pirlog R, Florian IS, Mihu CM, Berce C, Craciun L, Grewal R, Tomuleasa C. The role of the pathology department in the preanalytical phase of molecular analyses. Cancer Manag Res 2018; 10:745-753. [PMID: 29695931 PMCID: PMC5903845 DOI: 10.2147/cmar.s150851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
After introducing the new molecules for the treatment of patients with tumoral pathology, the therapeutical decision will be taken depending on the molecular profile performed upon the harvested tissues. This major modification makes the molecular and morphological analysis an essential part in the clinical management of patients and the pathologist plays an important role in this process. The quality and reproducibility of the results are imperative today and they depend on both the reliability of the molecular techniques and the quality of the tissue we use in the process. Also, the genomics and proteomics techniques, used increasingly often, require high-quality tissues, and pathology laboratories play a very significant role in the management of all phases of this process. In this paper the parameters which must be followed in order to obtain optimal results within the techniques which analyze nucleic acids and proteins were reviewed.
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Affiliation(s)
- Sergiu Susman
- Department of Pathology, Imogen Research Center.,Department of Morphological Sciences
| | | | - Bobe Petrushev
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ioan-Stefan Florian
- Department of Neurosurgery, Iuliu Hatieganu University of Medicine and Pharmacy
| | | | - Cristian Berce
- Research Center for Functional Genomics and Translational Medicine
| | | | - Ravnit Grewal
- Department of Hematology, Ion Chiricuta Oncology Institute
| | - Ciprian Tomuleasa
- Research Center for Functional Genomics and Translational Medicine.,Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Haematopathology, Tygerberg Academic Hospital, Tygerberg, South Africa
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29
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Reviewing the Utility of EUS FNA to Advance Precision Medicine in Pancreatic Cancer. Cancers (Basel) 2018; 10:cancers10020035. [PMID: 29382047 PMCID: PMC5836067 DOI: 10.3390/cancers10020035] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/24/2018] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Advanced pancreatic cancer (PC) is an aggressive malignancy with few effective therapeutic options. While the evolution of precision medicine in recent decades has changed the treatment landscape in many cancers, at present no targeted therapies are used in the routine management of PC. Only a minority of patients with PC present with surgically resectable disease, and in the remainder obtaining high quality biopsy material for both diagnosis and molecular testing can prove challenging. Endoscopic ultrasound-guided fine needle aspiration (EUS FNA) is a widely used diagnostic procedure in PC, and allows tumour sampling in patients with both early and late stage disease. This review will provide an update on the role of EUS FNA as a diagnostic tool, as well as a source of genetic material which can be used both for molecular analysis and for the creation of valuable preclinical disease models. We will also consider relevant clinical applications of EUS FNA in the management of PC, and the path towards bringing precision medicine closer to the clinic in this challenging disease.
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30
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Impact of Preanalytical Handling and Timing for Peripheral Blood Mononuclear Cells Isolation and RNA Studies: The Experience of the Interinstitutional Multidisciplinary BioBank (BioBIM). Int J Biol Markers 2018; 27:e90-8. [DOI: 10.5301/jbm.2012.9235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2012] [Indexed: 02/04/2023]
Abstract
Multicenter studies and biobanking projects require blood transportation from the participating center to a central collection or diagnostic laboratory. The impact of time delays between venous blood collection and peripheral blood mononuclear cells (PBMC) isolation prior to RNA extraction may affect the quality and quantity of isolated nucleic acids for genomic applications. Thus, standard operating procedure (SOP) optimization for the treatment of biological samples before RNA extraction is crucial in a biological repository. In order to define SOPs for whole blood preservation prior to RNA extraction, we sought to determine whether different blood storage times (0, 3, 6, 10, 24, and 30 hours) prior to PBMCs isolation and storage at –80°C, could affect the quality and quantity of extracted RNA. After spectrophotometric quantification, the quality and integrity of RNA were assessed by agarose gel electrophoresis, RNA integrity number and real time-PCR (RT-PCR). Across the different time points we did not observe significant differences within the first 24 hours of blood storage at room temperature, while a significant loss in RNA yield and integrity was detected between 24 and 30 hours. We conclude that time delays before PBMCs isolation prior to RNA extraction may have a significant impact on downstream molecular biological applications.
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31
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Vital ex vivo tissue labeling and pathology-guided micropunching to characterize cellular heterogeneity in the tissue microenvironment. Biotechniques 2018; 64:13-19. [PMID: 29384072 DOI: 10.2144/000114626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022] Open
Abstract
Cellular heterogeneity within the tissue microenvironment may underlie chemotherapeutic resistance and response, enabling tumor evolution; however, this heterogeneity it is difficult to characterize. Here, we present a new approach-pathology-guided micropunching (PGM)-that enables identification and characterization of heterogeneous foci identified in viable human and animal model tissue slices. This technique consists of live-cell tissue labeling using fluorescent antibodies/small molecules to identify heterogeneous foci (e.g., immune infiltrates or cells with high levels of reactive oxygen species) in viable tissues, coupled with a micropunch step to isolate cells from these heterogeneous foci for downstream molecular or vital functional analysis. Micropunches obtained from epithelial or stromal fibroblast foci in human prostate tissue show 6- to 12-fold enrichment in transcripts specific for EpCam/cytokeratin 8 and vimentin/a-smooth muscle actin/integrin 1-α, respectively. Transcriptional enrichment efficiency agrees with epithelial and stromal laser capture microdissection samples isolated from human prostate. Micropunched foci show a loss of cellular viability in the periphery, but centrally localized cells retained viability before and after dissociation and grew out in culture.
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32
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Toby TK, Abecassis M, Kim K, Thomas PM, Fellers RT, LeDuc RD, Kelleher NL, Demetris J, Levitsky J. Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients. Am J Transplant 2017; 17:2458-2467. [PMID: 28510335 PMCID: PMC5612406 DOI: 10.1111/ajt.14359] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/20/2017] [Accepted: 05/06/2017] [Indexed: 01/25/2023]
Abstract
Biomarker profiles of acute rejection in liver transplant recipients could enhance the diagnosis and management of recipients. Our aim was to identify diagnostic proteoform signatures of acute rejection in circulating immune cells, using an emergent "top-down" proteomics methodology. We prepared differentially processed and cryopreserved cell lysates from 26 nonviral liver transplant recipients by molecular weight-based fractionation and analyzed them by mass spectrometry of whole proteins in three steps: (i) Nanocapillary liquid chromatography coupled with high-resolution tandem mass spectrometry; (ii) database searching to identify and characterize intact proteoforms; (iii) data processing through a hierarchical linear model matching the study design to quantify proteoform fold changes in patients with rejection versus normal liver function versus acute dysfunction without rejection. Differentially expressed proteoforms were seen in patients with rejection versus normal and nonspecific controls, most evidently in the cell preparations stored in traditional serum-rich media. Mapping analysis of these proteins back to genes through gene ontology and pathway analysis tools revealed multiple signaling pathways, including inflammation mediated by cytokines and chemokines. Larger studies are needed to validate these novel rejection signatures and test their predictive value for use in clinical management.
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Affiliation(s)
- T. K. Toby
- Department of Molecular Biosciences and Chemistry, Northwestern University, Chicago, IL
| | - M. Abecassis
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - K. Kim
- Department of Molecular Biosciences and Chemistry, Northwestern University, Chicago, IL
| | - P. M. Thomas
- Department of Molecular Biosciences and Chemistry, Northwestern University, Chicago, IL,National Resource for Translational & Developmental Proteomics, Northwestern University, Chicago, IL
| | - R. T. Fellers
- National Resource for Translational & Developmental Proteomics, Northwestern University, Chicago, IL
| | - R. D. LeDuc
- National Resource for Translational & Developmental Proteomics, Northwestern University, Chicago, IL
| | - N. L. Kelleher
- Department of Molecular Biosciences and Chemistry, Northwestern University, Chicago, IL,National Resource for Translational & Developmental Proteomics, Northwestern University, Chicago, IL
| | - J. Demetris
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - J. Levitsky
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL,Division of Gastroenterology and Hepatology, Northwestern University Feinberg School of Medicine, Chicago, IL,Corresponding author: Josh Levitsky,
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33
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Raddatz BB, Spitzbarth I, Matheis KA, Kalkuhl A, Deschl U, Baumgärtner W, Ulrich R. Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review. Vet Pathol 2017. [PMID: 28641485 DOI: 10.1177/0300985817709887] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms. The scientific literature concerning high-throughput data-mining techniques usually addresses mathematicians or computer scientists as the target audience. In contrast, the present review provides the reader with a clear and systematic basis from a veterinary pathologist's perspective. Therefore, the aims are (1) to introduce the reader to the necessary methodological background; (2) to introduce the sequential steps commonly performed in a microarray analysis including quality control, annotation, normalization, selection of differentially expressed genes, clustering, gene ontology and pathway analysis, analysis of manually selected genes, and biomarker discovery; and (3) to provide references to publically available and user-friendly software suites. In summary, the data analysis methods presented within this review will enable veterinary pathologists to analyze high-throughput transcriptome data obtained from their own experiments, supplemental data that accompany scientific publications, or public repositories in order to obtain a more in-depth insight into underlying disease mechanisms.
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Affiliation(s)
- Barbara B Raddatz
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Ingo Spitzbarth
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Katja A Matheis
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Arno Kalkuhl
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Ulrich Deschl
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Wolfgang Baumgärtner
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Reiner Ulrich
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany.,4 Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institute, Greifswald, Germany
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34
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Somers GR, Vargas SO, Coffin CM. Society for Pediatric Pathology Comment on Proposed Changes to Regulations on Research with Human Tissues (Docket ID#: HHS-OPHS-2015-0008). Pediatr Dev Pathol 2017; 19:428-430. [PMID: 26926166 DOI: 10.2350/16-03-1784-let.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Gino R Somers
- Division of Pathology Hospital for Sick Children & University of Toronto, Toronto, Canada
| | - Sara O Vargas
- Department of Pathology Boston Children's Hospital & Harvard Medical School, Boston, MA, USA
| | - Cheryl M Coffin
- Department of Pathology Vanderbilt Medical Center, Nashville, TN, USA
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35
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Eroh GD, Clayton FC, Florell SR, Cassidy PB, Chirife A, Marón CF, Valenzuela LO, Campbell MS, Seger J, Rowntree VJ, Leachman SA. Cellular and ultrastructural characterization of the grey-morph phenotype in southern right whales (Eubalaena australis). PLoS One 2017; 12:e0171449. [PMID: 28170433 PMCID: PMC5295704 DOI: 10.1371/journal.pone.0171449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/20/2017] [Indexed: 11/18/2022] Open
Abstract
Southern right whales (SRWs, Eubalena australis) are polymorphic for an X-linked pigmentation pattern known as grey morphism. Most SRWs have completely black skin with white patches on their bellies and occasionally on their backs; these patches remain white as the whale ages. Grey morphs (previously referred to as partial albinos) appear mostly white at birth, with a splattering of rounded black marks; but as the whales age, the white skin gradually changes to a brownish grey color. The cellular and developmental bases of grey morphism are not understood. Here we describe cellular and ultrastructural features of grey-morph skin in relation to that of normal, wild-type skin. Melanocytes were identified histologically and counted, and melanosomes were measured using transmission electron microscopy. Grey-morph skin had fewer melanocytes when compared to wild-type skin, suggesting reduced melanocyte survival, migration, or proliferation in these whales. Grey-morph melanocytes had smaller melanosomes relative to wild-type skin, normal transport of melanosomes to surrounding keratinocytes, and normal localization of melanin granules above the keratinocyte nuclei. These findings indicate that SRW grey-morph pigmentation patterns are caused by reduced numbers of melanocytes in the skin, as well as by reduced amounts of melanin production and/or reduced sizes of mature melanosomes. Grey morphism is distinct from piebaldism and albinism found in other species, which are genetic pigmentation conditions resulting from the local absence of melanocytes, or the inability to synthesize melanin, respectively.
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Affiliation(s)
- Guy D. Eroh
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- University of Georgia, Athens, Georgia, United States of America
| | - Fred C. Clayton
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Scott R. Florell
- Department of Dermatology, University of Utah, Salt Lake City, Utah, United States of America
| | - Pamela B. Cassidy
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Andrea Chirife
- Programa de Monitoreo Sanitario Ballena Franca Austral, Puerto Madryn, Chubut, Argentina
| | - Carina F. Marón
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Instituto de Conservación de Ballenas, Buenos Aires, Argentina
| | - Luciano O. Valenzuela
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Buenos Aires, Argentina
| | - Michael S. Campbell
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jon Seger
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Victoria J. Rowntree
- Programa de Monitoreo Sanitario Ballena Franca Austral, Puerto Madryn, Chubut, Argentina
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Instituto de Conservación de Ballenas, Buenos Aires, Argentina
- Ocean Alliance/Whale Conservation Institute, Gloucester, Massachusetts, United States of America
| | - Sancy A. Leachman
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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Choi S, Ray HE, Lai SH, Alwood JS, Globus RK. Preservation of Multiple Mammalian Tissues to Maximize Science Return from Ground Based and Spaceflight Experiments. PLoS One 2016; 11:e0167391. [PMID: 27907194 PMCID: PMC5132293 DOI: 10.1371/journal.pone.0167391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 11/10/2016] [Indexed: 12/27/2022] Open
Abstract
Background Even with recent scientific advancements, challenges posed by limited resources and capabilities at the time of sample dissection continue to limit the collection of high quality tissues from experiments that can be conducted only infrequently and at high cost, such as in space. The resources and time it takes to harvest tissues post-euthanasia, and the methods and duration of long duration storage, potentially have negative impacts on sample quantity and quality, thereby limiting the scientific outcome that can be achieved. Objectives The goals of this study were to optimize methods for both sample recovery and science return from rodent experiments, with possible relevance to both ground based and spaceflight studies. The first objective was to determine the impacts of tissue harvest time post-euthanasia, preservation methods, and storage duration, focusing on RNA quality and enzyme activities in liver and spleen as indices of sample quality. The second objective was to develop methods that will maximize science return by dissecting multiple tissues after long duration storage in situ at -80°C. Methods Tissues of C57Bl/6J mice were dissected and preserved at various time points post-euthanasia and stored at -80°C for up to 11 months. In some experiments, tissues were recovered from frozen carcasses which had been stored at -80°C up to 7 months. RNA quantity and quality was assessed by measuring RNA Integrity Number (RIN) values using an Agilent Bioanalyzer. Additionally, the quality of tissues was assessed by measuring activities of hepatic enzymes (catalase, glutathione reductase and GAPDH). Results Fresh tissues were collected up to one hour post-euthanasia, and stored up to 11 months at -80°C, with minimal adverse effects on the RNA quality of either livers or RNAlater-preserved spleens. Liver enzyme activities were similar to those of positive controls, with no significant effect observed at any time point. Tissues dissected from frozen carcasses that had been stored for up to 7 months at -80°C had variable results, depending on the specific tissue analyzed. RNA quality of liver, heart, and kidneys were minimally affected after 6–7 months of storage at -80°C, whereas RNA degradation was evident in tissues such as small intestine, bone, and bone marrow when they were collected from the carcasses frozen for 2.5 months. Conclusion These results demonstrate that 1) the protocols developed for spaceflight experiments with on-orbit dissections support the retrieval of high quality samples for RNA expression and some protein analyses, despite delayed preservation post-euthanasia or prolonged storage, and 2) many additional tissues for gene expression analysis can be obtained by dissection even following prolonged storage of the tissue in situ at -80°C. These findings have relevance both to high value, ground-based experiments when sample collection capability is severely constrained, and to spaceflight experiments that entail on-orbit sample recovery by astronauts.
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Affiliation(s)
- Sungshin Choi
- KBRwyle, Moffett Field, California, United States of America
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
| | - Hami E. Ray
- ASRC Federal Space and Defense, Inc., Moffett Field, California, United States of America
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
| | - San-Huei Lai
- KBRwyle, Moffett Field, California, United States of America
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
| | - Joshua S. Alwood
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
| | - Ruth K. Globus
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
- * E-mail:
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Seiler C, Sharpe A, Barrett JC, Harrington EA, Jones EV, Marshall GB. Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality? BMC Clin Pathol 2016. [PMID: 28649177 PMCID: PMC5477763 DOI: 10.1186/s12907-016-0039-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Advanced genomic techniques such as Next-Generation-Sequencing (NGS) and gene expression profiling, including NanoString, are vital for the development of personalised medicines, as they enable molecular disease classification. This has become increasingly important in the treatment of cancer, aiding patient selection. However, it requires efficient nucleic acid extraction often from formalin-fixed paraffin-embedded tissue (FFPE). METHODS Here we provide a comparison of several commercially available manual and automated methods for DNA and/or RNA extraction from FFPE cancer cell line samples from Qiagen, life Technologies and Promega. Differing extraction geometric mean yields were evaluated across each of the kits tested, assessing dual DNA/RNA extraction vs. specialised single extraction, manual silica column based extraction techniques vs. automated magnetic bead based methods along with a comparison of subsequent nucleic acid purity methods, providing a full evaluation of nucleic acids isolated. RESULTS Out of the four RNA extraction kits evaluated the RNeasy FFPE kit, from Qiagen, gave superior geometric mean yields, whilst the Maxwell 16 automated method, from Promega, yielded the highest quality RNA by quantitative real time RT-PCR. Of the DNA extraction kits evaluated the PicoPure DNA kit, from Life Technologies, isolated 2-14× more DNA. A miniaturised qPCR assay was developed for DNA quantification and quality assessment. CONCLUSIONS Careful consideration of an extraction kit is necessary dependent on quality or quantity of material required. Here we provide a flow diagram on the factors to consider when choosing an extraction kit as well as how to accurately quantify and QC the extracted material.
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Affiliation(s)
- Caroline Seiler
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, UK.,Leeds University-AZ Sandwich Placement, Leeds, UK
| | - Alan Sharpe
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, UK
| | | | | | | | - Gayle B Marshall
- AstraZeneca Oncology Innovative Medicines, Alderley Park, Macclesfield, UK.,AstraZeneca, 8AF6, Mereside, Alderley Park, Alderley Edge, Cheshire SK10 4TG UK
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Zhang X, Lu W, Zheng Y, Wang W, Bai L, Chen L, Feng Y, Zhang Z, Yuan Z. In situ analysis of intrahepatic virological events in chronic hepatitis B virus infection. J Clin Invest 2016; 126:1079-92. [PMID: 26901811 DOI: 10.1172/jci83339] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/23/2015] [Indexed: 12/11/2022] Open
Abstract
Persistent hepatitis B virus (HBV) infection is established by the formation of an intranuclear pool of covalently closed circular DNA (cccDNA) in the liver. Very little is known about the intrahepatic distribution of HBV cccDNA in infected patients, particularly at the single-cell level. Here, we established a highly sensitive and specific ISH assay for the detection of HBV RNA, DNA, and cccDNA. The specificity of our cccDNA probe set was confirmed by its strict intranuclear signal and by a series of Southern blot analyses. Use of our in situ assay in conjunction with IHC or immunofluorescence uncovered a surprisingly mosaic distribution of viral antigens and nucleic acids. Most strikingly, a mutually exclusive pattern was found between HBV surface antigen-positive (HBsA-positive) and HBV DNA- and cccDNA-positive cells. A longitudinal observation of patients over a 1-year period of adeforvir therapy confirmed the persistence of a nuclear reservoir of viral DNA, although cytoplasmic DNA was effectively depleted in these individuals. In conclusion, our method for detecting viral nucleic acids, including cccDNA, with single-cell resolution provides a means for monitoring intrahepatic virological events in chronic HBV infection. More important, our observations unravel the complexity of the HBV life cycle in vivo.
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White R, Crossman DJ, Isaacson M, Gibbs H, Ruygrok PN. Confocal Scanning Microscopy in Assessment of Cardiac Allograft Rejection--A Pilot Study. Transplant Proc 2015; 47:2513-6. [PMID: 26518961 DOI: 10.1016/j.transproceed.2015.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/03/2015] [Indexed: 11/17/2022]
Abstract
Cardiac allograft rejection is typically diagnosed on the basis of hematoxylin and eosin (H&E) histology of endomyocardial biopsies. This diagnosis is made based on the degree of immune cell infiltrate and associated myocyte damage. However, considerable variability in rejection grading between pathologists can occur. Confocal microscopy provides high contrast and high resolution imaging that has the potential to provide detailed views of pathological features of allograft rejection. In this pilot study we sought to determine if confocal microscopy could be used to detect features of cardiac rejection. This was achieved by collection of additional sample at 30 biopsy procedures from 15 heart transplant patients. Routine pathological grading of H&E histology identified 5 gradings of 0R, 21 gradings of 1R, and 3 gradings of 2R. From these gradings, 3 samples for 0R, 9 samples for 1R, and 3 samples for 2R were imaged by confocal microscopy. This was achieved by fluorescently labeling sections with DAPI, wheat germ agglutinin, and phalloidin, to visualize the cell nuclei, cell border and extracellular matrix, and muscle cell actin, respectively. Labeling with these fluorescent markers was of high contrast. However, we did note variability in DAPI and phalloidin labeling of tissue sections. Confocal imaging of these labels revealed the following features at high resolution: perivascular and/or interstitial infiltrate, myocyte damage, and Quilty lesions. In particular increased detail of damaged myocytes reveals distortion in myofilament organization that could be exploited to distinguish between 1R and 2R grades. In conclusion, confocal microscopy provided high contrast and resolution imaging of cardiac biopsies that could be explored further to aid assessment of cardiac allograft rejection.
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Affiliation(s)
- R White
- Cardiology, Auckland District Health Board, Auckland City Hospital, Park Road, Grafton, Private Bag 92024, Auckland 1030, New Zealand
| | - D J Crossman
- Department of Physiology, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | - M Isaacson
- Department of Physiology, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - H Gibbs
- Cardiology, Auckland District Health Board, Auckland City Hospital, Park Road, Grafton, Private Bag 92024, Auckland 1030, New Zealand
| | - P N Ruygrok
- Cardiology, Auckland District Health Board, Auckland City Hospital, Park Road, Grafton, Private Bag 92024, Auckland 1030, New Zealand
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Toward Rare Blood Cell Preservation for RNA Sequencing. J Mol Diagn 2015; 17:352-9. [PMID: 25989392 DOI: 10.1016/j.jmoldx.2015.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 03/03/2015] [Accepted: 03/24/2015] [Indexed: 02/04/2023] Open
Abstract
Cancer is driven by various events leading to cell differentiation and disease progression. Molecular tools are powerful approaches for describing how and why these events occur. With the growing field of next-generation DNA sequencing, there is an increasing need for high-quality nucleic acids derived from human cells and tissues-a prerequisite for successful cell profiling. Although advances in RNA preservation have been made, some of the largest biobanks still do not employ RNA blood preservation as standard because of limitations in low blood-input volume and RNA stability over the whole gene body. Therefore, we have developed a robust protocol for blood preservation and long-term storage while maintaining RNA integrity. Furthermore, we explored the possibility of using the protocol for preserving rare cell samples, such as circulating tumor cells. The results of our study confirmed that gene expression was not impacted by the preservation procedure (r(2) > 0.88) or by long-term storage (r(2) = 0.95), with RNA integrity number values averaging over 8. Similarly, cell surface antigens were still available for antibody selection (r(2) = 0.95). Lastly, data mining for fusion events showed that it was possible to detect rare tumor cells among a background of other cells present in blood irrespective of fixation. Thus, the developed protocol would be suitable for rare blood cell preservation followed by RNA sequencing analysis.
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A tissue retrieval and postharvest processing regimen for rodent reproductive tissues compatible with long-term storage on the international space station and postflight biospecimen sharing program. BIOMED RESEARCH INTERNATIONAL 2015; 2015:475935. [PMID: 25654107 PMCID: PMC4309301 DOI: 10.1155/2015/475935] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/18/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022]
Abstract
Collection and processing of tissues to preserve space flight effects from animals after return to Earth is challenging. Specimens must be harvested with minimal time after landing to minimize postflight readaptation alterations in protein expression/translation, posttranslational modifications, and expression, as well as changes in gene expression and tissue histological degradation after euthanasia. We report the development of a widely applicable strategy for determining the window of optimal species-specific and tissue-specific posteuthanasia harvest that can be utilized to integrate into multi-investigator Biospecimen Sharing Programs. We also determined methods for ISS-compatible long-term tissue storage (10 months at −80°C) that yield recovery of high quality mRNA and protein for western analysis after sample return. Our focus was reproductive tissues. The time following euthanasia where tissues could be collected and histological integrity was maintained varied with tissue and species ranging between 1 and 3 hours. RNA quality was preserved in key reproductive tissues fixed in RNAlater up to 40 min after euthanasia. Postfixation processing was also standardized for safe shipment back to our laboratory. Our strategy can be adapted for other tissues under NASA's Biospecimen Sharing Program or similar multi-investigator tissue sharing opportunities.
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Evaluation of DNA/RNAshells for Room Temperature Nucleic Acids Storage. Biopreserv Biobank 2015; 13:49-55. [DOI: 10.1089/bio.2014.0060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Olivieri EHR, Franco LDA, Pereira RG, Mota LDC, Campos AHJFM, Carraro DM. Biobanking practice: RNA storage at low concentration affects integrity. Biopreserv Biobank 2014; 12:46-52. [PMID: 24620769 DOI: 10.1089/bio.2013.0056] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A critical issue in defining protocols for biobanking practices is the preservation of total RNA for assessing the whole transcriptome and ensuring that it can be utilized in clinically oriented studies. Storage conditions, such as temperature and the length of time that tissues and purified RNA stay frozen, may directly impact RNA preservation. In this study, we evaluated a) the quality of RNA (as measured by RNA Integrity Number) purified from head and neck tumor tissues stored at -140°C for distinct time intervals of up to 7 years, and b) the quality of their respective RNAs stored for 4 years at -80°C when diluted at either 250 ng/μL or 25 ng/μL, with repeated freezing and thawing. Additionally, we generated a profile of the RNA collection of human tumors from different body sites stored at the AC Camargo Biobank. Our results showed no significant change in RIN values according to length of storage at -140°C. With respect to RNA aliquots stored at -80°C, RNA integrity at 250 ng/μL was preserved, while statistically significant degradation was observed at 25 ng/μL after only 8 months of storage. The RNA collection from most of the human tumors stored at the AC Camargo Biobank exhibited high quality, with average RIN around seven. However, ovary and stomach samples had the greatest RNA degradation. Taken together, the results show that both the temperature of preservation and the concentration of RNA should be strictly controlled by the biobank staff involved in macromolecule purification. Moreover, the RNAs from our biobank can be useful for the most demanding methods of gene expression analysis by virtue of adherence to optimal standard operating procedures for both tissue and macromolecule laboratories.
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Stanta G, Bonin S, Machado I, Llombart-Bosch A. Models of biobanking and tissue preservation: RNA quality in archival samples in pathology laboratories and "in vivo biobanking" by tumor xenografts in nude mice-two models of quality assurance in pathology. Biopreserv Biobank 2014; 9:149-55. [PMID: 24846260 DOI: 10.1089/bio.2011.0010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Tissue banks represent essential resources and platforms for biomedical research serving basic, translational, and clinical research projects. In this article, we describe 2 models of biobanking and tissue preservation with different approaches and aims. Archive tissue biobanking is described here as a resource of residual pathology tissues for translational research, which represents the huge clinical heterogeneity. In this context, managing of tissues and RNA quality in archive tissue are discussed. The other model of tissue biobanking is referred to as xenograft tissue banking, which represents an alternative method for obtaining large amounts of tissue, over an indefinite period, in so far as the tumor can be transferred in vivo over generations, maintaining the histological and genetic particularities. A description of the method and examples of the application are given with particular emphasis on sarcomas (Ewing's sarcoma/primitive neuroectodermal sarcoma, synovial sarcomas, and rhabdomyosarcomas) and early stages of tumor angiogenesis in sarcomas.
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Affiliation(s)
- Giorgio Stanta
- 1 Department of Medical, Surgical and Health Sciences, University of Trieste , Cattinara Hospital, Trieste, Italy
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McKinnon B, Bertschi D, Wotzkow C, Bersinger NA, Evers J, Mueller MD. Glucose transporter expression in eutopic endometrial tissue and ectopic endometriotic lesions. J Mol Endocrinol 2014; 52:169-79. [PMID: 24412827 DOI: 10.1530/jme-13-0194] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Endometriosis is an extremely prevalent disorder characterized by the growth of endometrial tissue at ectopic locations. Glycolysis is an energy-producing mechanism that occurs in almost all cells and requires an adequate uptake of glucose mediated by glucose transporter (GLUT) proteins. At present, however, very little is known about their expression in either the endometrium or the endometriotic lesions. The objective of this study was to examine the expression of SLC2A genes in the endometrium of women with and without endometriosis and in the matching ectopic tissue, and to confirm the presence of the GLUT proteins in ectopic lesions. There was a significantly higher expression of SLC2A3 and a significantly lower expression of SLC2A4 in women with endometriosis compared with those without. In women with endometriosis, the ectopic expression of SLC2A3, SLC2A4 and SLC2A5 was significantly higher than that observed in the matching eutopic tissue. GLUT1 protein expression was present in both epithelial and stromal cells and GLUT3 was confined to CD45-positive leukocytes. GLUT4 expression was strong in both ectopic epithelial and stromal cells and localized to the cellular membrane in epithelial cells. These results show that GLUT expression is altered between eutopic and ectopic tissue and between women with and without endometriosis, and that GLUT4 may represent a significant entry route for glucose into the endometriotic epithelial cells. The inducible nature of GLUT4 and its limited cellular expression may make GLUT4 an attractive target for non-hormone-based treatments of endometriosis.
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Affiliation(s)
- Brett McKinnon
- Department of Obstetrics and Gynecology, Inselspital, Berne University Hospital, Effingerstrasse 102, Berne CH-3010, Switzerland Department of Clinical Research, University of Bern, Murtenstrasse 35, Bern CH-3010, Switzerland
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Molecular fixative enables expression microarray analysis of microdissected clinical cervical specimens. Exp Mol Pathol 2014; 96:168-77. [PMID: 24412268 DOI: 10.1016/j.yexmp.2013.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/06/2013] [Indexed: 11/21/2022]
Abstract
Formalin-fixed tissue has been a mainstay of clinical pathology laboratories, but formalin alters many biomolecules, including nucleic acids and proteins. Meanwhile, frozen tissues contain better-preserved biomolecules, but tissue morphology is affected, limiting their diagnostic utility. Molecular fixatives promise to bridge this gap by simultaneously preserving morphology and biomolecules, enabling clinical diagnosis and molecular analyses on the same specimen. While previous reports have broadly evaluated the use of molecular fixative in various human tissues, we present here the first detailed assessment of the applicability of molecular fixative to both routine histopathological diagnosis and molecular analysis of cervical tissues. Ten specimens excised via the loop electrosurgical excision procedure, which removes conical tissue samples from the cervix, were cut into alternating pieces preserved in either formalin or molecular fixative. Cervical specimens preserved in molecular fixative were easily interpretable, despite featuring more eosinophilic cytoplasm and more recognizable chromatin texture than formalin-fixed specimens. Immunohistochemical staining patterns of p16 and Ki-67 were similar between fixatives, although Ki-67 staining was stronger in the molecular fixative specimens. The RNA of molecular fixative specimens from seven cases representing various dysplasia grades was assessed for utility in expression microarray analysis. Cluster analysis and scatter plots of duplicate samples suggest that data of sufficient quality can be obtained from as little as 50ng of RNA from molecular fixative samples. Taken together, our results show that molecular fixative may be a more versatile substitute for formalin, simultaneously preserving tissue morphology for clinical diagnosis and biomolecules for immunohistochemistry and gene expression analysis.
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Abstract
Powerful technologies critical to personalized medicine and targeted therapeutics require the analysis of carefully validated, procured, stored, and managed biospecimens. Reflecting advancements in biospecimen science, the National Cancer Institute and the International Society for Biological and Environmental Repositories are periodically publishing best practices that can guide the biobanker. The modern biobank will operate more like a clinical laboratory with formal accreditation, standard operating procedures, and quality assurance protocols. This chapter highlights practical issues of consent, procurement, storage, quality assurance, disbursement, funding, and space. Common topics of concern are discussed including the differences between clinical and research biospecimens, stabilization of biospecimens during procurement, optimal storage temperatures, and technical validation of biospecimen content and quality. With quickly expanding biospecimen needs and limited healthcare budgets, biobanks may need to be selective as to what is stored. Furthermore, a shift to room-temperature storage modalities where possible can reduce long-term space and fiscal requirements.
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Affiliation(s)
- William H Yong
- Translational Pathology Core Laboratory, Brain Tumor Translational Resource, Department of Pathology and Laboratory Medicine, Center for Health Sciences, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, 18-161 CHS, Los Angeles, CA, 90095, USA,
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Collection and preparation of rodent embryonic samples for transcriptome study. Methods Mol Biol 2013. [PMID: 24318829 DOI: 10.1007/978-1-60327-292-6_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The need for large-scale collection of rodent embryos and individual embryonic tissues for genomic and proteomic studies requires modification of traditional practices of embryo necropsy. The sample intended for transcriptome study should be rapidly dissected and stabilized to preserve its molecular integrity. The retrieval of high-quality RNA, DNA, and proteins from the target tissue is crucial for informative molecular analysis (e.g., gene profiling on microarray platform). We present a reliable method of collection and preparation of rodent embryos for genomic studies supported by detailed protocols and RNA extraction results for different stages of mouse embryonic development.
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Cadoret K, Bridle AR, Leef MJ, Nowak BF. Evaluation of fixation methods for demonstration of Neoparamoeba perurans infection in Atlantic salmon, Salmo salar L., gills. JOURNAL OF FISH DISEASES 2013; 36:831-839. [PMID: 23384040 DOI: 10.1111/jfd.12078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/19/2012] [Accepted: 11/26/2012] [Indexed: 06/01/2023]
Abstract
Formaldehyde-based fixatives are generally employed in histopathology despite some significant disadvantages associated with their usage. Formaldehyde fixes tissue by covalently cross-linking proteins, a process known to mask epitopes which in turn can reduce the intensity of immunohistochemical stains widely used in disease diagnostics. Additionally, formaldehyde fixation greatly limits the ability to recover DNA and mRNA from fixed specimens to the detriment of further downstream molecular analyses. Amoebic gill disease (AGD) has been reliably diagnosed from histological examination of gills although complementary methods such as in situ hybridization (ISH) and polymerase chain reaction (PCR) are required to confirm the presence of Neoparamoeba perurans, the causative agent of AGD. As molecular techniques are becoming more prevalent for pathogen identification, there is a need to adapt specimen collection and preservation so that both histology and molecular biology can be used to diagnose the same sample. This study used a general approach to evaluate five different fixatives for Atlantic salmon, Salmo salar L., gills. Neutral-buffered formalin and seawater Davidson's, formaldehyde-based fixatives commonly used in fish histopathology, were compared to formalin-free commercial fixatives PAXgene®, HistoChoice™MB* and RNAlater™. Each fixative was assessed by a suite of analyses used to demonstrate AGD including routine histochemical stains, immunohistochemical stains, ISH and DNA extraction followed by PCR. All five fixatives were suitable for histological examination of Atlantic salmon gills, with seawater Davidson's providing the best quality histopathology results. Of the fixatives evaluated seawater Davidson's and PAXgene® were shown to be the most compatible with molecular biology techniques. They both provided good DNA recovery, quantity and integrity, from fixed and embedded specimens. The capacity to preserve tissue and cellular morphology in addition to allowing molecular analyses of the same specimens makes seawater Davidson's and PAXgene® appear to be the best fixation methods for diagnosis and research on AGD in Atlantic salmon gills.
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Affiliation(s)
- K Cadoret
- National Centre for Marine Conservation and Resource Sustainability, Australian Maritime College, University of Tasmania, Launceston, Tasmania, Australia
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Kashofer K, Viertler C, Pichler M, Zatloukal K. Quality control of RNA preservation and extraction from paraffin-embedded tissue: implications for RT-PCR and microarray analysis. PLoS One 2013; 8:e70714. [PMID: 23936242 PMCID: PMC3729557 DOI: 10.1371/journal.pone.0070714] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 06/28/2013] [Indexed: 12/20/2022] Open
Abstract
Analysis of RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathological diagnostics. We have performed a comprehensive and systematic investigation of the impact of factors in the pre-analytical workflow, such as different fixatives, fixation time, RNA extraction method and storage of tissues in paraffin blocks, on several downstream reactions including complementary DNA (cDNA) synthesis, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and microarray hybridization. We compared the effects of routine formalin fixation with the non-crosslinking, alcohol-based Tissue Tek Xpress Molecular Fixative (TTXMF, Sakura Finetek), and cryopreservation as gold standard for molecular analyses. Formalin fixation introduced major changes into microarray gene expression data and led to marked gene-to-gene variations in delta-ct values of qRT-PCR. We found that qRT-PCR efficiency and gene-to-gene variations were mainly attributed to differences in the efficiency of cDNA synthesis as the most sensitive step. These differences could not be reliably detected by quality assessment of total RNA isolated from formalin-fixed tissues by electrophoresis or spectrophotometry. Although RNA from TTXMF fixed samples was as fragmented as RNA from formalin fixed samples, much higher cDNA yield and lower ct-values were obtained in qRT-PCR underlining the negative impact of crosslinking by formalin. In order to better estimate the impact of pre-analytical procedures such as fixation on the reliability of downstream analysis, we applied a qRT-PCR-based assay using amplicons of different length and an assay measuring the efficiency of cDNA generation. Together these two assays allowed better quality assessment of RNA extracted from fixed and paraffin-embedded tissues and should be used to supplement quality scores derived from automated electrophoresis. A better standardization of the pre-analytical workflow, application of additional quality controls and detailed sample information would markedly improve the comparability and reliability of molecular studies based on formalin-fixed and paraffin-embedded tissue samples.
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Affiliation(s)
- Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | - Martin Pichler
- Division of Oncology, Medical University of Graz, Graz, Austria
| | - Kurt Zatloukal
- Institute of Pathology, Medical University of Graz, Graz, Austria
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