1
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Bhamidimarri PM, Salameh L, Mahdami A, Abdullah HW, Mahboub B, Hamoudi R. LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue. Heliyon 2024; 10:e32896. [PMID: 38988576 PMCID: PMC11234047 DOI: 10.1016/j.heliyon.2024.e32896] [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: 02/23/2024] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p < 0.0001) improving the mean read lengths (p < 0.05) in WTA. Overall, increased mean read length positively correlated with on-target reads (Pearson's r = 0.71, p < 0.0001) in both amplified and unamplified RNA-seq analysis. Gene expression analysis compared between unamplified and amplified group displayed substantial overlap of the differentially expressed genes (DEGs) (log2 fold change cut-off < -2 and >2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.
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Affiliation(s)
- Poorna Manasa Bhamidimarri
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Laila Salameh
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
| | - Amena Mahdami
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Hanan Wael Abdullah
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Sciences, University College London, London, United Kingdom
- BIMAI-Lab, Biomedically Informed Artificial Inelligence Laboratory, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Centre of Excelence for Precision Medicine, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
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2
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Ji B, Chen J, Gong H, Li X. Streamlined Full-Length Total RNA Sequencing of Paraformaldehyde-Fixed Brain Tissues. Int J Mol Sci 2024; 25:6504. [PMID: 38928210 PMCID: PMC11204141 DOI: 10.3390/ijms25126504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Paraformaldehyde (PFA) fixation is the preferred method for preserving tissue architecture for anatomical and pathological observations. Meanwhile, PFA reacts with the amine groups of biomolecules to form chemical cross-linking, which preserves RNA within the tissue. This has great prospects for RNA sequencing to characterize the molecular underpinnings after anatomical and pathological observations. However, RNA is inaccessible due to cross-linked adducts forming between RNA and other biomolecules in prolonged PFA-fixed tissue. It is also difficult to perform reverse transcription and PCR, resulting in low sequencing sensitivity and reduced reproducibility. Here, we developed a method to perform RNA sequencing in PFA-fixed tissue, which is easy to use, cost-effective, and allows efficient sample multiplexing. We employ cross-link reversal to recover RNA and library construction using random primers without artificial fragmentation. The yield and quality of recovered RNA significantly increased through our method, and sequencing quality metrics and detected genes did not show any major differences compared with matched fresh samples. Moreover, we applied our method for gene expression analysis in different regions of the mouse brain and identified unique gene expression profiles with varied functional implications. We also find significant dysregulation of genes involved in Alzheimer's disease (AD) pathogenesis within the medial septum (MS)/vertical diagonal band of Broca (VDB) of the 5×FAD mouse brain. Our method can thus increase the performance of high-throughput RNA sequencing with PFA-fixed samples and allows longitudinal studies of small tissue regions isolated by their in situ context.
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Affiliation(s)
- Bingqing Ji
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jiale Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (B.J.); (J.C.); (H.G.)
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215125, China
| | - Xiangning Li
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, HUST-Suzhou Institute for Brainsmatics, JITRI, Chinese Academy of Medical Sciences, Suzhou 215125, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou 570228, China
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3
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Madill-Thomsen K, Halloran P. Precision diagnostics in transplanted organs using microarray-assessed gene expression: concepts and technical methods of the Molecular Microscope® Diagnostic System (MMDx). Clin Sci (Lond) 2024; 138:663-685. [PMID: 38819301 PMCID: PMC11147747 DOI: 10.1042/cs20220530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
There is a major unmet need for improved accuracy and precision in the assessment of transplant rejection and tissue injury. Diagnoses relying on histologic and visual assessments demonstrate significant variation between expert observers (as represented by low kappa values) and have limited ability to assess many biological processes that produce little histologic changes, for example, acute injury. Consensus rules and guidelines for histologic diagnosis are useful but may have errors. Risks of over- or under-treatment can be serious: many therapies for transplant rejection or primary diseases are expensive and carry risk for significant adverse effects. Improved diagnostic methods could alleviate healthcare costs by reducing treatment errors, increase treatment efficacy, and serve as useful endpoints for clinical trials of new agents that can improve outcomes. Molecular diagnostic assessments using microarrays combined with machine learning algorithms for interpretation have shown promise for increasing diagnostic precision via probabilistic assessments, recalibrating standard of care diagnostic methods, clarifying ambiguous cases, and identifying potentially missed cases of rejection. This review describes the development and application of the Molecular Microscope® Diagnostic System (MMDx), and discusses the history and reasoning behind many common methods, statistical practices, and computational decisions employed to ensure that MMDx scores are as accurate and precise as possible. MMDx provides insights on disease processes and highly reproducible results from a comparatively small amount of tissue and constitutes a general approach that is useful in many areas of medicine, including kidney, heart, lung, and liver transplants, with the possibility of extrapolating lessons for understanding native organ disease states.
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Affiliation(s)
- Katelynn S. Madill-Thomsen
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
| | - Philip F. Halloran
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
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4
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Ura H, Niida Y. Comparison of RNA-Sequencing Methods for Degraded RNA. Int J Mol Sci 2024; 25:6143. [PMID: 38892331 PMCID: PMC11172666 DOI: 10.3390/ijms25116143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
RNA sequencing (RNA-Seq) is a powerful technique and is increasingly being used in clinical research and drug development. Currently, several RNA-Seq methods have been developed. However, the relative advantage of each method for degraded RNA and low-input RNA, such as RNA samples collected in the field of clinical setting, has remained unknown. The Standard method of RNA-Seq captures mRNA by poly(A) capturing using Oligo dT beads, which is not suitable for degraded RNA. Here, we used three commercially available RNA-Seq library preparation kits (SMART-Seq, xGen Broad-range, and RamDA-Seq) using random primer instead of Oligo dT beads. To evaluate the performance of these methods, we compared the correlation, the number of detected expressing genes, and the expression levels with the Standard RNA-Seq method. Although the performance of RamDA-Seq was similar to that of Standard RNA-Seq, the performance for low-input RNA and degraded RNA has decreased. The performance of SMART-Seq was better than xGen and RamDA-Seq in low-input RNA and degraded RNA. Furthermore, the depletion of ribosomal RNA (rRNA) improved the performance of SMART-Seq and xGen due to increased expression levels. SMART-Seq with rRNA depletion has relative advantages for RNA-Seq using low-input and degraded RNA.
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Affiliation(s)
- Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku 920-0923, Japan;
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku 920-0923, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku 920-0923, Japan;
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku 920-0923, Japan
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5
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Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [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: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
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Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
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6
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Thompson SD, Pichika R, Lieber RL, Lavasani M. Extracting high-quality RNA from formaldehyde-fixed naturally aged neuromusculoskeletal tissues. Biotechniques 2024; 76:153-160. [PMID: 38334498 PMCID: PMC10988388 DOI: 10.2144/btn-2023-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/22/2023] [Indexed: 02/10/2024] Open
Abstract
Modern approaches to discovering molecular mechanisms and validating treatments for age-related neuromusculoskeletal dysfunction typically rely on high-throughput transcriptome analysis. Previously harvested and fixed tissues offer an incredible reservoir of untapped molecular information. However, obtaining RNA from such formaldehyde-fixed neuromusculoskeletal tissues, especially fibrotic aged tissues, is technically challenging and often results in RNA degradation, chemical modification and yield reduction, prohibiting further analysis. Therefore, we developed a protocol to extract high-quality RNA from formaldehyde-fixed brain, cartilage, muscle and peripheral nerve isolated from naturally aged mice. Isolated RNA produced reliable gene expression data comparable to fresh and flash-frozen tissues and was sensitive enough to detect age-related changes, making our protocol valuable to researchers in the field of aging.
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Affiliation(s)
- Seth D Thompson
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Graduate Program, Northwestern University, Chicago, IL 60611, USA
| | - Rajeswari Pichika
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr VA Medical Center, Maywood, IL 60153, USA
| | - Richard L Lieber
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr VA Medical Center, Maywood, IL 60153, USA
| | - Mitra Lavasani
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Graduate Program, Northwestern University, Chicago, IL 60611, USA
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7
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Gonçalves-Reis M, Proença D, Frazão LP, Neto JL, Silva S, Pinto-Marques H, Pereira-Leal JB, Cardoso J. Analytical validation and algorithm improvement of HepatoPredict kit to assess hepatocellular carcinoma prognosis before a liver transplantation. Pract Lab Med 2024; 39:e00365. [PMID: 38371895 PMCID: PMC10869278 DOI: 10.1016/j.plabm.2024.e00365] [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: 08/01/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
Objectives To verify the analytical performance of the HepatoPredict kit, a novel tool developed to stratify Hepatocellular Carcinoma (HCC) patients according to their risk of relapse after a Liver Transplantation (LT). Methods The HepatoPredict tool combines clinical variables and a gene expression signature in an ensemble of machine-learning algorithms to forecast the benefit of a LT in HCC patients. To ensure the accuracy and reliability of this method, extensive analytical validation was conducted to verify its specificity and robustness. The experiments were designed following the guidelines for multi-target genomic assays such as ISO201395-2019, MIQE, CLSI-MM16, CLSI-MM17, and CLSI-EP17-A. The validation process included reproducibility between operators and between RNA extractions and RT-qPCR runs, and interference of input RNA levels or varying reagent levels. A recently retrained version of the HepatoPredict algorithms was also tested. Results The validation process demonstrated that the HepatoPredict kit met the required standards for robustness (p > 0.05), analytical specificity (inclusivity of 95 %), and sensitivity (LoB, LoD, linear range, and amplification efficiency between 90 and 110 %). The operator, equipment, input RNA, and reagents used had no significant effect on the HepatoPredict results. Additionally, the testing of a recently retrained version of the HepatoPredict algorithm, showed that this new version further improved the accuracy of the kit and performed better than existing clinical criteria in accurately identifying HCC patients who are more likely to benefit LT. Conclusions Even with the introduced variations in molecular and clinical variables, the HepatoPredict kit's prognostic information remains consistent. It can accurately identify HCC patients who are more likely to benefit from a LT. Its robust performance also confirms that it can be easily integrated into standard diagnostic laboratories.
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Affiliation(s)
| | | | | | - João L. Neto
- Ophiomics – Precision Medicine, Lisbon, Portugal
| | - Sílvia Silva
- Hepato-Biliary-Pancreatic and Transplantation Centre, Curry Cabral Hospital, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Hugo Pinto-Marques
- Hepato-Biliary-Pancreatic and Transplantation Centre, Curry Cabral Hospital, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
- Chronic Diseases Research Center (CEDOC), NOVA Medical School, Universidade NOVA de Lisboa (NMS/UNL), Lisbon, Portugal
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8
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Barth J, Yang Y, Xiao G, Wang X. MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data. Bioinformatics 2024; 40:btae024. [PMID: 38237909 PMCID: PMC10826904 DOI: 10.1093/bioinformatics/btae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/28/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
MOTIVATION Non-informative or diffuse prior distributions are widely employed in Bayesian data analysis to maintain objectivity. However, when meaningful prior information exists and can be identified, using an informative prior distribution to accurately reflect current knowledge may lead to superior outcomes and great efficiency. RESULTS We propose MetaNorm, a Bayesian algorithm for normalizing NanoString nCounter gene expression data. MetaNorm is based on RCRnorm, a powerful method designed under an integrated series of hierarchical models that allow various sources of error to be explained by different types of probes in the nCounter system. However, a lack of accurate prior information, weak computational efficiency, and instability of estimates that sometimes occur weakens the approach despite its impressive performance. MetaNorm employs priors carefully constructed from a rigorous meta-analysis to leverage information from large public data. Combined with additional algorithmic enhancements, MetaNorm improves RCRnorm by yielding more stable estimation of normalized values, better convergence diagnostics and superior computational efficiency. AVAILABILITY AND IMPLEMENTATION R Code for replicating the meta-analysis and the normalization function can be found at github.com/jbarth216/MetaNorm.
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Affiliation(s)
- Jackson Barth
- Department of Statistics and Data Science, Southern Methodist University, Dallas, TX 75275, United States
- Department of Statistical Science, Baylor University, Waco, TX 76798, United States
| | - Yuqiu Yang
- Department of Statistics and Data Science, Southern Methodist University, Dallas, TX 75275, United States
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
| | - Xinlei Wang
- Department of Statistics and Data Science, Southern Methodist University, Dallas, TX 75275, United States
- Department of Mathematics, University of Texas at Arlington, Arlington, TX 76019 United States
- Division of Data Science, College of Science, University of Texas at Arlington, Arlington, TX 76019, United States
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9
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Amemiya K, Hirotsu Y, Nagakubo Y, Mochizuki H, Oyama T, Omata M. Influence of formalin fixation duration on RNA quality and quantity from formalin-fixed paraffin-embedded hepatocellular carcinoma tissues. Pathol Int 2023; 73:593-600. [PMID: 37933792 DOI: 10.1111/pin.13385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023]
Abstract
Analyzing RNA samples from formalin-fixed paraffin-embedded (FFPE) tissues is essential for precision medicine. We investigated RNA quantity and quality from FFPE tumor tissues fixed in formalin for various times and compared sequencing metrics from next-generation sequencing (NGS). Hepatocellular carcinoma (HCC) tissues were fixed in 10% neutral buffered formalin (1-240 h) and FFPE blocks were prepared. Total RNA was extracted, and the quantity and quality were assessed using the NanoDrop, Qubit and Bioanalyzer. After preparing sequencing libraries, NGS was performed on the Oncomine Dx Multi-CDx system. Total RNA yields of all samples met the threshold required for NGS, but longer fixation times resulted in decreased total RNA and long RNA fragment (>200 nt) yields. NGS analysis showed fewer sequencing reads of internal control genes from RNA with longer fixation times. RNA extracted from FFPE blocks stored for 500 days had reduced RNA yield and quality compared with RNA obtained from FFPE blocks prepared immediately. In conclusion, short and over-fixation should be avoided because of their negative impact on sequencing quality. Fixation process should be finished promptly within recommended guidelines (6-72 h) for cancer patients.
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Affiliation(s)
- Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuki Nagakubo
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshio Oyama
- Pathology Division, Laboratory Department, Yamanashi Prefectural Central Hospital, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
- The University of Tokyo, Tokyo, Japan
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10
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Song K, Elboudwarej E, Zhao X, Zhuo L, Pan D, Liu J, Brachmann C, Patterson SD, Yoon OK, Zavodovskaya M. RNA-seq RNAaccess identified as the preferred method for gene expression analysis of low quality FFPE samples. PLoS One 2023; 18:e0293400. [PMID: 37883360 PMCID: PMC10602291 DOI: 10.1371/journal.pone.0293400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Clinical tumor tissues that are preserved as formalin-fixed paraffin-embedded (FFPE) samples result in extensive cross-linking, fragmentation, and chemical modification of RNA, posing significant challenges for RNA-seq-based gene expression profiling. This study sought to define an optimal RNA-seq protocol for FFPE samples. We employed a common RNA extraction method and then compared RNA-seq library preparation protocols including RNAaccess, RiboZero and PolyA in terms of sequencing quality and concordance of gene expression using FFPE and case-matched fresh-frozen (FF) triple-negative breast cancer (TNBC) tissues. We found that RNAaccess, a method based on exome capture, produced the most concordant results. Applying RNAaccess to FFPE gastric cancer tissues, we established a minimum RNA DV200 requirement of 10% and a RNA input amount of 10ng that generated highly reproducible gene expression data. Lastly, we demonstrated that RNAaccess and NanoString platforms produced highly concordant expression profiles from FFPE samples for shared genes; however, RNA-seq may be preferred for clinical biomarker discovery work because of the broader coverage of the transcriptome. Taken together, these results support the selection of RNA-seq RNAaccess method for gene expression profiling of FFPE samples. The minimum requirements for RNA quality and input established here may allow for inclusion of clinical FFPE samples of sub-optimal quality in gene expression analyses and ultimately increasing the statistical power of such analyses.
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Affiliation(s)
- Kai Song
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Emon Elboudwarej
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Xi Zhao
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Luting Zhuo
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - David Pan
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Jinfeng Liu
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Carrie Brachmann
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Scott D. Patterson
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Oh Kyu Yoon
- Gilead Sciences, Inc., Foster City, California, United States of America
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11
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Sounart H, Lázár E, Masarapu Y, Wu J, Várkonyi T, Glasz T, Kiss A, Borgström E, Hill A, Rezene S, Gupta S, Jurek A, Niesnerová A, Druid H, Bergmann O, Giacomello S. Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections. Genome Biol 2023; 24:237. [PMID: 37858234 PMCID: PMC10588020 DOI: 10.1186/s13059-023-03080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
Technologies to study localized host-pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host-pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.
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Affiliation(s)
- Hailey Sounart
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Enikő Lázár
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Yuvarani Masarapu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Jian Wu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Tibor Várkonyi
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Tibor Glasz
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - András Kiss
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | | | | | - Sefanit Rezene
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Soham Gupta
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Olaf Bergmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany
- Universitätsmedizin Göttingen, Institute of Pharmacology and Toxicology, Göttingen, Germany
| | - Stefania Giacomello
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.
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12
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Guo Y, Wang W, Ye K, He L, Ge Q, Huang Y, Zhao X. Single-Nucleus RNA-Seq: Open the Era of Great Navigation for FFPE Tissue. Int J Mol Sci 2023; 24:13744. [PMID: 37762049 PMCID: PMC10530744 DOI: 10.3390/ijms241813744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Single-cell sequencing (scRNA-seq) has revolutionized our ability to explore heterogeneity and genetic variations at the single-cell level, opening up new avenues for understanding disease mechanisms and cell-cell interactions. Single-nucleus RNA-sequencing (snRNA-seq) is emerging as a promising solution to scRNA-seq due to its reduced ionized transcription bias and compatibility with richer samples. This approach will provide an exciting opportunity for in-depth exploration of billions of formalin-fixed paraffin-embedded (FFPE) tissues. Recent advancements in single-cell/nucleus gene expression workflows tailored for FFPE tissues have demonstrated their feasibility and provided crucial guidance for future studies utilizing FFPE specimens. In this review, we provide a broad overview of the nuclear preparation strategies, the latest technologies of snRNA-seq applicable to FFPE samples. Finally, the limitations and potential technical developments of snRNA-seq in FFPE samples are summarized. The development of snRNA-seq technologies for FFPE samples will lay a foundation for transcriptomic studies of valuable samples in clinical medicine and human sample banks.
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Affiliation(s)
| | | | | | | | | | | | - Xiangwei Zhao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.G.); (W.W.); (K.Y.); (L.H.); (Q.G.); (Y.H.)
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13
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Gitto L, Middleton FA, Reynolds ES, Thangamani S, Jaeger DA, Mihaila DM. Quantification and persistence of COVID-19 virus in recently deceased individuals before and after embalming. ANATOMICAL SCIENCES EDUCATION 2023; 16:802-813. [PMID: 37332120 DOI: 10.1002/ase.2300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 04/07/2023] [Accepted: 05/05/2023] [Indexed: 06/20/2023]
Abstract
The COVID-19 pandemic severely affected the medical education worldwide. The infection risk for medical students and healthcare personnel who work with COVID-19 positive cadavers or tissues remains unclear. Moreover, COVID-19 positive cadavers have been rejected by medical schools, adversely impacting the continuum of medical education. Herein, the viral genome abundance in tissues from four COVID-19 positive donors before and after embalming were compared. Tissue samples were collected from the lungs, liver, spleen, and brain both pre- and postembalming. The possible presence of infectious COVID-19 was determined by inoculating human tissue homogenates onto a monolayer of human A549-hACE2 cells and observing for cytopathic effects up to 72 h postinoculation. A real- time quantitative reverse transcription polymerase chain reaction was performed to quantify COVID-19 present in culture supernatants. Fully intact viral genome sequence was possible to obtain in samples with higher levels of virus, even several days postmortem. The embalming procedure described above substantially reduces the abundance of viable COVID-19 genomes in all tissues, sometimes even to undetectable levels. However, in some cases, COVID-19 RNA can still be detected, and a cytopathic effect can be seen both pre- and postembalmed tissues. This study suggests that embalmed COVID-19 positive cadavers might be used safely with appropriate precautions followed in gross anatomy laboratories and in clinical and scientific research. Deep lung tissue is the best specimen to test for the virus. If the tests on the lung tissues are negative, there is a very low likelihood that other tissues will show positive results.
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Affiliation(s)
- Lorenzo Gitto
- Department of Pathology, Cook County Medical Examiner's Office, Chicago, Illinois, USA
| | - Frank A Middleton
- Department of Neuroscience and Physiology, Norton College of Medicine, The State University of New York Upstate Medical University, Syracuse, New York, USA
- Department of Psychiatry and Behavioral Sciences, Norton College of Medicine, The State University of New York Upstate Medical University, Syracuse, New York, USA
- Department of Biochemistry and Molecular Biology, Norton College of Medicine, The State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Erin S Reynolds
- Department of Microbiology and Immunology, Norton College of Medicine, The State University of New York Upstate Medical University, Syracuse, New York, USA
- State University of New York Center for Vector-Borne Diseases, The State University of New York Upstate Medical University, Syracuse, New York, USA
- Vector Biocontainment Laboratories, The State University of New York Upstate Medical University, Syracuse, New York, USA
- Institute for Global Health and Translational Sciences, The State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Saravanan Thangamani
- Department of Microbiology and Immunology, Norton College of Medicine, The State University of New York Upstate Medical University, Syracuse, New York, USA
- State University of New York Center for Vector-Borne Diseases, The State University of New York Upstate Medical University, Syracuse, New York, USA
- Vector Biocontainment Laboratories, The State University of New York Upstate Medical University, Syracuse, New York, USA
- Institute for Global Health and Translational Sciences, The State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Daniel A Jaeger
- Department of Cell and Developmental Biology, Norton College of Medicine, The State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Dana M Mihaila
- Department of Cell and Developmental Biology, Norton College of Medicine, The State University of New York Upstate Medical University, Syracuse, New York, USA
- Department of Neurology, Norton College of Medicine, The State University of New York Upstate Medical University, Syracuse, New York, USA
- Department of Physical Therapy, College of Health Professions, The State University of New York Upstate Medical University, Syracuse, New York, USA
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14
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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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15
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Nakamura Y, Tsuji K, Shiraishi T, Sako S, Ogura R, Taga H, Inoue Y, Ohashi M, Ueda S, Yamada T, Ueda T, Fujihara A, Hongo F, Ukimura O. Novel device for dividing core needle biopsy specimens to provide paired mirror image-like tissues for genetic and pathological tests. Sci Rep 2023; 13:6610. [PMID: 37095303 PMCID: PMC10126131 DOI: 10.1038/s41598-023-33776-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 04/18/2023] [Indexed: 04/26/2023] Open
Abstract
In a world that seeks precision medicine, genetic testing is gaining importance in clinical decision making. We previously reported the utility of a novel tool for longitudinally dividing core needle biopsy (CNB) tissues into two filamentous tissues that can provide paired mirror image-like tissues (mirror-tissues) that spatially match each other. In this study, we investigated its application in gene panel testing in patients who underwent prostate CNB. Four hundred and forty-three biopsy cores were obtained from 40 patients. Of them, 361 biopsy cores (81.5%) were judged by a physician to be appropriate for dividing into two pieces using the new device, of which a histopathological diagnosis was successfully reached in 358 biopsy cores (99.2%). Among them, the quality and quantity of nucleic acid in 16 appropriately divided cores were assessed and found to be sufficient for gene panel testing, and histopathological diagnosis was successfully obtained from the remaining divided cores. The novel device for longitudinally-dividing CNB tissue provided mirror image-like paired-tissues for gene panel and pathology testing. The device might be a promising tool for obtaining genetic and molecular biological information, in addition to histopathological diagnosis, helping to advance personalized medicine.
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Affiliation(s)
- Yuichi Nakamura
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Keisuke Tsuji
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Takumi Shiraishi
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan.
| | - Satoshi Sako
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Ryota Ogura
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Hideto Taga
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Yuta Inoue
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Munehiro Ohashi
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Saya Ueda
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Takeshi Yamada
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Takashi Ueda
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Atsuko Fujihara
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Fumiya Hongo
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
| | - Osamu Ukimura
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-Ku, Kyoto, 602-8566, Japan
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16
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Le Coz C, Oldridge DA, Herati RS, De Luna N, Garifallou J, Cruz Cabrera E, Belman JP, Pueschl D, Silva LV, Knox AVC, Reid W, Yoon S, Zur KB, Handler SD, Hakonarson H, Wherry EJ, Gonzalez M, Romberg N. Human T follicular helper clones seed the germinal center-resident regulatory pool. Sci Immunol 2023; 8:eade8162. [PMID: 37027481 PMCID: PMC10329285 DOI: 10.1126/sciimmunol.ade8162] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023]
Abstract
The mechanisms by which FOXP3+ T follicular regulatory (Tfr) cells simultaneously steer antibody formation toward microbe or vaccine recognition and away from self-reactivity remain incompletely understood. To explore underappreciated heterogeneity in human Tfr cell development, function, and localization, we used paired TCRVA/TCRVB sequencing to distinguish tonsillar Tfr cells that are clonally related to natural regulatory T cells (nTfr) from those likely induced from T follicular helper (Tfh) cells (iTfr). The proteins iTfr and nTfr cells differentially expressed were used to pinpoint their in situ locations via multiplex microscopy and establish their divergent functional roles. In silico analyses and in vitro tonsil organoid tracking models corroborated the existence of separate Treg-to-nTfr and Tfh-to-iTfr developmental trajectories. Our results identify human iTfr cells as a distinct CD38+, germinal center-resident, Tfh-descended subset that gains suppressive function while retaining the capacity to help B cells, whereas CD38- nTfr cells are elite suppressors primarily localized in follicular mantles. Interventions differentially targeting specific Tfr cell subsets may provide therapeutic opportunities to boost immunity or more precisely treat autoimmune diseases.
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Affiliation(s)
- Carole Le Coz
- Division of Immunology and Allergy, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Derek A. Oldridge
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA
| | - Ramin S. Herati
- Department of Medicine, NYU Grossman School of Medicine, New York, NY
| | - Nina De Luna
- Division of Immunology and Allergy, Children’s Hospital of Philadelphia, Philadelphia, PA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - James Garifallou
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Emylette Cruz Cabrera
- Division of Immunology and Allergy, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Jonathan P Belman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Dana Pueschl
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Luisa V. Silva
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ainsley V. C. Knox
- Division of Immunology and Allergy, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Whitney Reid
- Division of Immunology and Allergy, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Samuel Yoon
- Division of Immunology and Allergy, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Karen B. Zur
- Pediatric Otolaryngology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Otolaryngology: Head and Neck Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Steven D. Handler
- Pediatric Otolaryngology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Otolaryngology: Head and Neck Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - E. John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael Gonzalez
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Center for Cytokine Storm Treatment & Laboratory, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Neil Romberg
- Division of Immunology and Allergy, Children’s Hospital of Philadelphia, Philadelphia, PA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
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17
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Angerilli V, Fornaro L, Pepe F, Rossi SM, Perrone G, Malapelle U, Fassan M. FGFR2 testing in cholangiocarcinoma: translating molecular studies into clinical practice. Pathologica 2023; 115:71-82. [PMID: 37017301 PMCID: PMC10462997 DOI: 10.32074/1591-951x-859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a heterogeneous group of neoplasms burdened by a dismal prognosis. Several studies have investigated the genomic profile of CCA and identified numerous druggable genetic alterations, including FGFR2 fusions/rearrangements. Approximately 5-7% of CCAs and 10-20% of intrahepatic iCCAs harbor FGFR2 fusions. With the recent advent of FGFR-targeting therapies into clinical practice, a standardization of molecular testing for FGFR2 alterations in CCA will be necessary. In this review, we describe the technical aspects and challenges related to FGFR2 testing in routine practice, focusing on the comparison between Next-Generation Sequencing (NGS) and FISH assays, the best timing to perform the test, and on the role of liquid biopsy.
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Affiliation(s)
- Valentina Angerilli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua (PD), Italy
| | - Lorenzo Fornaro
- Medical Oncology, Azienda Ospedaliero-Universitaria Pisana, Pisa (PI), Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples (NA), Italy
| | - Silvia Maria Rossi
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico di Roma, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy
| | - Giuseppe Perrone
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico di Roma, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples (NA), Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua (PD), Italy
- Veneto Institute of Oncology, IOV - IRCCS, Padua (PD), Italy
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18
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Chung JY, Kim K, Ylaya K, Walker-Bawa KE, Perry C, Star RA, Hewitt SM. The Application of Guanidinium to Improve Biomolecule Quality in Fixed, Paraffin-embedded Tissue. J Histochem Cytochem 2023; 71:87-101. [PMID: 36869703 PMCID: PMC10088100 DOI: 10.1369/00221554231159451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/31/2023] [Indexed: 03/05/2023] Open
Abstract
Neutral buffered formalin (NBF) is the most common fixative in clinical applications. However, NBF damages proteins and nucleic acids, limiting the quality of proteomic and nucleic acid-based assays. Prior studies have demonstrated that BE70, a fixative of buffered 70% ethanol, has many benefits over NBF but the degradation of proteins and nucleic acids in archival paraffin blocks remain a challenge. Thus, we evaluated the addition of guanidinium salts to BE70 with the hypothesis that this may protect RNA and protein. Guanidinium salt supplemented BE70 (BE70G)-fixed tissue is comparable with that of BE70 via histology and immunohistochemistry. Western blot analysis also revealed that HSP70, AKT, and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) expression signals in BE70G-fixed tissue were higher than those in BE70-fixed tissue. The quality of nucleic acids extracted from BE70G-fixed, paraffin-embedded tissue was also superior, and BE70G provides improved protein and RNA quality at shorter fixation times than its predecessors. The degradation of proteins, AKT and GAPDH, in archival tissue blocks is also decreased with the addition of guanidinium salt to BE70. In conclusion, BE70G fixative improves the quality of molecular analysis with more rapid fixation of tissue and enhanced long-term storage of paraffin blocks at room temperature for evaluation of protein epitopes.
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Affiliation(s)
- Joon-Yong Chung
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Kyungeun Kim
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
- Department of Pathology, School of Medicine,
Kangbuk Samsung Hospital, Sungkyunkwan University, Seoul, Republic of
Korea
| | - Kris Ylaya
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Katharine E. Walker-Bawa
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Candice Perry
- Antibody Characterization Laboratory, Advanced
Technology Program, Leidos Biomedical Research, Inc., Frederick,
Maryland
| | - Robert A. Star
- Renal Diagnostics and Therapeutics Unit,
National Institutes of Diabetes and Digestive and Kidney Disease, National
Institutes of Health, Bethesda, Maryland
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
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19
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Horie T, Takagi W, Aburatani N, Yamazaki M, Inokuchi M, Tachizawa M, Okubo K, Ohtani-Kaneko R, Tokunaga K, Wong MKS, Hyodo S. Segment-Dependent Gene Expression Profiling of the Cartilaginous Fish Nephron Using Laser Microdissection for Functional Characterization of Nephron at Segment Levels. Zoolog Sci 2023; 40:91-104. [PMID: 37042689 DOI: 10.2108/zs220092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/21/2022] [Indexed: 01/18/2023]
Abstract
For adaptation to a high salinity marine environment, cartilaginous fishes have evolved a ureosmotic strategy. They have a highly elaborate "four-loop nephron" in the kidney, which is considered to be important for reabsorption of urea from the glomerular filtrate to maintain a high concentration of urea in the body. However, the function and regulation, generally, of the "four-loop nephron" are still largely unknown due to the complicated configuration of the nephron and its many subdivided segments. Laser microdissection (LMD) followed by RNA-sequencing (RNA-seq) analysis is a powerful technique to obtain segment-dependent gene expression profiles. In the present study, using the kidney of cloudy catshark, Scyliorhinus torazame, we tested several formaldehyde-free and formaldehyde-based fixatives to optimize the fixation methods. Fixation by 1% neutral buffered formalin for 15 min resulted in sufficient RNA and structural integrities, which allowed LMD clipping of specific nephron segments and subsequent RNA-seq analysis. RNA-seq from the LMD samples of the second-loop, the fourth-loop, and the five tubular segments in the bundle zone revealed a number of specific membrane transporter genes that can characterize each segment. Among them, we examined expressions of the Na + -coupled cotransporters abundantly expressed in the second loop samples. Although the proximal II segment of the second loop is known for the elimination of excess solutes, the present results imply that the PII segment is also crucial for reabsorption of valuable solutes. Looking ahead to future studies, the segment-dependent gene expression profiling will be a powerful technique for unraveling the renal mechanisms and regulation in euryhaline elasmobranchs.
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Affiliation(s)
- Takashi Horie
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Wataru Takagi
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Naotaka Aburatani
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Manabu Yamazaki
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Mayu Inokuchi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Masaya Tachizawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Kataaki Okubo
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | | | - Kotaro Tokunaga
- Ibaraki Prefectural Oarai Aquarium, Oarai, Ibaraki 311-1301, Japan
| | - Marty Kwok-Sing Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan
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20
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Repeat-associated non-AUG translation induces cytoplasmic aggregation of CAG repeat-containing RNAs. Proc Natl Acad Sci U S A 2023; 120:e2215071120. [PMID: 36623192 PMCID: PMC9934169 DOI: 10.1073/pnas.2215071120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
CAG trinucleotide repeat expansions cause several neurodegenerative diseases, including Huntington's disease and spinocerebellar ataxia. RNAs with expanded CAG repeats contribute to disease in two unusual ways. First, these repeat-containing RNAs may agglomerate in the nucleus as foci that sequester several RNA-binding proteins. Second, these RNAs may undergo aberrant repeat-associated non-AUG (RAN) translation in multiple frames and produce aggregation-prone proteins. The relationship between RAN translation and RNA foci, and their relative contributions to cellular dysfunction, are unclear. Here, we show that CAG repeat-containing RNAs that undergo RAN translation first accumulate at nuclear foci and, over time, are exported to the cytoplasm. In the cytoplasm, these RNAs are initially dispersed but, upon RAN translation, aggregate with the RAN translation products. These RNA-RAN protein agglomerates sequester various RNA-binding proteins and are associated with the disruption of nucleocytoplasmic transport and cell death. In contrast, RNA accumulation at nuclear foci alone does not produce discernable defects in nucleocytoplasmic transport or cell viability. Inhibition of RAN translation prevents cytoplasmic RNA aggregation and alleviates cell toxicity. Our findings demonstrate that RAN translation-induced RNA-protein aggregation correlates with the key pathological hallmarks observed in disease and suggest that cytoplasmic RNA aggregation may be an underappreciated phenomenon in CAG trinucleotide repeat expansion disorders.
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21
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An automated system for nucleic acid extraction from formalin-fixed paraffin-embedded samples using high intensity focused ultrasound technology. Anal Bioanal Chem 2022; 414:8201-8213. [PMID: 36260128 DOI: 10.1007/s00216-022-04360-5] [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: 08/11/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/01/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples are routinely used in prospective and retrospective studies. It is crucial to obtain high-quality nucleic acid (NA) from FFPE samples for downstream molecular analysis, such as quantitative polymerase chain reaction (PCR), Sanger sequencing, next-generation sequencing, and microarray, in both clinical diagnosis and basic research. The current NA extraction methods from FFPE samples using chemical solvent are tedious, environmentally unfriendly, and unamenable to automation or field deployment. We present a tool for NA extraction from FFPE samples using a high-intensity focused ultrasound (HIFU) technology. A cartridge strip containing reagents for FFPE sample deparaffinization and NA extraction and purification is operated by an automation tool consisting of a HIFU module, a liquid handling robot unit, and accessories including a thermal block and magnets. The HIFU module is a single concaved piezoelectric ceramic plate driven by a current-mode class-D power amplifier. Based on the ultrasonic cavitation effects, the HIFU module provides highly concentrated energy introducing paraffin emulsification and disintegration. The high quantity and quality of NA extracted using the reported system are evaluated by PCR and compared with the quantity and quality of NA extracted using the current standard methods.
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Köhler SA, Brandl L, Strissel PL, Gloßner L, Ekici AB, Angeloni M, Ferrazzi F, Bahlinger V, Hartmann A, Beckmann MW, Eckstein M, Strick R. Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping. Int J Mol Sci 2022; 23:ijms231810267. [PMID: 36142180 PMCID: PMC9499321 DOI: 10.3390/ijms231810267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known if MB influences RNA used for gene expression studies. Therefore, we analyzed MIBC using five different RNA isolation methods comparing patient matched FFPE and fresh frozen (FF) tissues pre-stained with or without MB. We demonstrate a positive impact of MB on RNA integrity with FF tissues using real time PCR with no interference of its chemical properties. FFPE tissues showed no improvement of RNA integrity, which we propose is due to formalin induced nucleotide crosslinks. Using direct multiplex RNA hybridization the best genes for normalization of MIBC and control tissues were identified from 34 reference genes. In addition, 5SrRNA and 5.8SrRNA were distinctive reference genes detecting <200 bp fragments important for mRNA analyses. Using these normalized RNAs from MB stained MIBC and applying multiplex RNA hybridization and mRNA sequencing, a minimal gene expression panel precisely identified luminal and basal MIBC tumor subtypes, important for diagnosis, prognosis and chemotherapy response.
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Affiliation(s)
- Stefanie A. Köhler
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Lisa Brandl
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Pamela L. Strissel
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Laura Gloßner
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Miriam Angeloni
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Fulvia Ferrazzi
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Veronika Bahlinger
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Matthias W. Beckmann
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Markus Eckstein
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Reiner Strick
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Correspondence: ; Tel.: +49-91318536671
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Al-Maawi S, Valenzuela P, Dohle E, Heselich A, Sader R, Ghanaati S. Comparison of Different Fixation Methods for Combined Histological and Biomolecular Analysis of Fixed and Decalcified Bone Samples. Methods Protoc 2022; 5:mps5040064. [PMID: 35893590 PMCID: PMC9326524 DOI: 10.3390/mps5040064] [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: 05/12/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 11/25/2022] Open
Abstract
The combination of histological and biomolecular analyses provides deep understanding of different biological processes and is of high interest for basic and applied research. However, the available analytical methods are still limited, especially when considering bone samples. This study compared different fixation media to identify a sufficient analytical method for the combination of histological, immuno-histological and biomolecular analyses of the same fixed, processed and paraffin embedded bone sample. Bone core biopsies of rats’ femurs were fixed in different media (RNAlater + formaldehyde (R + FFPE), methacarn (MFPE) or formaldehyde (FFPE)) for 1 week prior to decalcification by EDTA and further histological processing and paraffin embedding. Snap freezing (unfixed frozen tissue, UFT) and incubation in RNAlater were used as additional controls. After gaining the paraffin sections for histological and immunohistological analysis, the samples were deparaffined and RNA was isolated by a modified TRIZOL protocol. Subsequently, gene expression was evaluated using RT-qPCR. Comparable histo-morphological and immuno-histological results were evident in all paraffin embedded samples of MFPE, FFPE and R + FFPE. The isolated RNA in the group of MFPE showed a high concentration and high purity, which was comparable to the UFT and RNAlater groups. However, in the groups of FFPE and R + FFPE, the RNA quality and quantity were statistically significantly lower when compared to MFPE, UFT and RNAlater. RT-qPCR results showed a comparable outcome in the group of MFPE and UFT, whereas the groups of FFPE and R + FFPE did not result in a correctly amplified gene product. Sample fixation by means of methacarn is of high interest for clinical samples to allow a combination of histological, immunohistological and biomolecular analysis. The implementation of such evaluation method in clinical research may allow a deeper understanding of the processes of bone formation and regeneration.
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Kim SY, Kim TE, Park CK, Yoon HK, Sa YJ, Kim HR, Woo IS, Kim TJ. Comprehensive Comparison of 22C3 and SP263 PD-L1 Expression in Non-Small-Cell Lung Cancer Using Routine Clinical and Conditioned Archives. Cancers (Basel) 2022; 14:cancers14133138. [PMID: 35804910 PMCID: PMC9265108 DOI: 10.3390/cancers14133138] [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: 06/05/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 12/10/2022] Open
Abstract
PD-L1 harmonization studies revealed a strong correlation between the 22C3 and SP263 assays in non-small-cell lung cancer (NSCLC). However, the assays’ characteristics have yet to be validated in a variety of clinical and analytical settings. The results of 431 NSCLC samples tested concurrently in routine clinical practice with the PD-L1 22C3 and SP263 assays were reviewed, and both assays were performed on 314 archives of surgically resected NSCLCs to assess PD-L1 expression in relation to variables such as FFPE block age and FFPE section storage condition. In routine clinical samples, 22C3 showed the highest concordance rate with 94.5% of SP263 tumor proportion score (TPS) ≥50% and 92.3% of SP263 TPS ≥1%, while SP263 showed a concordance rate with 79.6% of 22C3 TPS ≥50% and 89.9% of 22C3 TPS ≥1%. In the archival analysis, the high TPS of 22C3 and SP263 (versus TPS 1%) were significantly associated with a more recent block (<3 years versus ≥3 years) (p = 0.007 and p = 0.009, respectively). Only the TPS of 22C3 was reduced when FFPE sections were stored at room temperature compared to SP263. However, when stored at 4 °C, the storage duration had no effect on expression in either assay. For 22C3 TPS 1−49 percent and ≥50 percent (OR = 1.73, p = 0.006 and OR = 1.98, p = 0.002, respectively). There was a considerably larger chance of preserved 22C3 expression in recent room-temperature paraffin section storage, although SP263 demonstrated preserved expression in prolonged room-temperature section storage. Despite the good association between PD-L1 22C3 and SP263 in routine clinical samples, FFPE blocks older than 3 years and sections held at room temperature for more than 1 week may result in an underestimation of PD-L1 status, particularly for the 22C3 test. However, the SP263 assay was more sensitive under these conditions.
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Affiliation(s)
- Sue Youn Kim
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Tae-Eun Kim
- Department of Hospital Pathology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea;
| | - Chan Kwon Park
- Division of Pulmonology, Department of Internal Medicine, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea; (C.K.P.); (H.-K.Y.)
| | - Hyoung-Kyu Yoon
- Division of Pulmonology, Department of Internal Medicine, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea; (C.K.P.); (H.-K.Y.)
| | - Young Jo Sa
- Department of Thoracic Surgery, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea;
| | - Hyo Rim Kim
- Department of Radiology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea;
| | - In Sook Woo
- Department of Medical Oncology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea;
| | - Tae-Jung Kim
- Department of Hospital Pathology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul 07345, Korea;
- Correspondence: ; Tel.: +82-2-3779-2157
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Balasubramaniam SD, Balakrishnan V, Oon CE, Kaur G. Gene expression profiling of HPV-associated cervical carcinogenesis in formalin-fixed paraffin-embedded (FFPE) tissues using the NanoString nCounter TM platform. Gene X 2022; 825:146385. [PMID: 35288200 DOI: 10.1016/j.gene.2022.146385] [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: 09/06/2021] [Revised: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 11/25/2022] Open
Abstract
Infection by high-risk human papillomavirus (HPV) causes genetic alterations in host cervical cells with consequent changes in gene expression affecting downstream molecular pathways, leading to the development of cervical cancer. In this exploratory study, we aimed to identify the perturbed cellular pathways during the various stages of cervical carcinogenesis. Total RNA was extracted from three formalin-fixed paraffin-embedded (FFPE) samples each of normal cervix, HPV-infected low-grade squamous intraepithelial lesion (LSIL), high-grade SIL (HSIL) and squamous cell carcinoma (SCC). Gene expression profiling was performed using the 770-gene panel from NanoString nCounter® PanCancer Pathways Panel to identify differentially expressed genes (DEGs) and significantly associated pathways in each stage of cervical cancer development. We identified 121 DEGs involved in cervical carcinogenesis. In the transformation from normal cells to LSIL, the MAPK, transcriptional misregulation and JAK-STAT pathways are implicated, while IL1B may promote inflammation and indirectly activates MMP9, resulting in collagen breakdown and cell migration. The cell cycle - apoptosis pathway with upregulation of E2F1 and MCM2, and DNA repair genes BRCA2-BRIP1 and FANCA are crucial during the progression from LSIL to HSIL. In the final stage of progression to SCC, the cell cycle and signaling pathways, as well as upregulation of c-MYC appear essential. In conclusion, archived FFPE-derived tissue samples are a valuable resource for gene expression profiling. The postulated dysregulated pathways and genes provide a guide of the molecular mechanisms that may be involved in the development of HPV-associated cervical cancer, for further investigation and validation studies.
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Affiliation(s)
- Shandra Devi Balasubramaniam
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia; Unit of Microbiology, Faculty of Medicine, AIMST University, Semeling, Bedong 8100, Malaysia
| | - Venugopal Balakrishnan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Chern Ein Oon
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Gurjeet Kaur
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia.
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Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action. Toxicol Rep 2022; 9:883-894. [DOI: 10.1016/j.toxrep.2022.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/19/2022] Open
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Li M, Lu S, Huang P, Xia T, Yu Z, Jiang W, Mao Y, Yang C, Yu S, Wu W, Zhang Y. High-quality, large-scale, semi-thin, & ultra-thin sections of the optic nerve in large animals: An optimized procedure. Exp Eye Res 2022; 219:108956. [PMID: 35367250 DOI: 10.1016/j.exer.2022.108956] [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: 10/26/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 11/25/2022]
Abstract
Large animal model of optic nerve (ON) injury is an essential tool for translational medicine. Perfusion fixation with paraformaldehyde is mainly used for preparing the semi-thin (1-2 μm thick) and ultra-thin (<0.5 μm thick) sections of the ON tissues. However, this conventional fixation technique in large animals needs a large volume of fixatives, which increases the risk of toxic exposure and is environmentally unfriendly. Additionally, fixed residual ON cannot be used for other tests that require fresh tissue samples. Although conventional immersion fixation is feasible for preparing a semi-thin section of the ON in small animals (0.2-0.6 mm in diameter), it faces technical challenges when fixing the ON of large animals (3 mm in diameters), as increased diameter limits the permeability of the fixatives into deeper tissue. Therefore, we optimized the immersion-fixation method to obtain high-quality, large-scale, semi-thin, and ultra-thin sections for the ON of goat and rhesus macaques. Using this optimized technique, the ON microstructure was well preserved throughout the entire area of 1.5*1.5 square millimeters, allowing confident quantification of axon density/diameter on semi-thin section and identification of specific organelles and glial cells on ultra-thin sections. Furthermore, the optimized technique is a quick, simple, and environmentally friendly fixation method. Notably, the ON regions of large animals with or without an intact neurovascular system can be prepared for light and electron microscopy. In contrast, the residual unfixed ON from the same animal can be further utilized for experiments such as tissue culture and biomolecular tests.
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Affiliation(s)
- Mengyun Li
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Shenjian Lu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - PingPing Huang
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Tian Xia
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhonghao Yu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wenhao Jiang
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yiyang Mao
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Chen Yang
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Shuaishuai Yu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wencan Wu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Yikui Zhang
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.
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Raevskiy M, Sorokin M, Zakharova G, Tkachev V, Borisov N, Kuzmin D, Kremenchutckaya K, Gudkov A, Kamashev D, Buzdin A. Better Agreement of Human Transcriptomic and Proteomic Cancer Expression Data at the Molecular Pathway Activation Level. Int J Mol Sci 2022; 23:ijms23052611. [PMID: 35269755 PMCID: PMC8910457 DOI: 10.3390/ijms23052611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
Previously, we have shown that the aggregation of RNA-level gene expression profiles into quantitative molecular pathway activation metrics results in lesser batch effects and better agreement between different experimental platforms. Here, we investigate whether pathway level of data analysis provides any advantage when comparing transcriptomic and proteomic data. We compare the paired proteomic and transcriptomic gene expression and pathway activation profiles obtained for the same human cancer biosamples in The Cancer Genome Atlas (TCGA) and the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) projects, for a total of 755 samples of glioblastoma, breast, liver, lung, ovarian, pancreatic, and uterine cancers. In a CPTAC assay, expression levels of 15,112 protein-coding genes were profiled using the Thermo QE series of mass spectrometers. In TCGA, RNA expression levels of the same genes were obtained using the Illumina HiSeq 4000 engine for the same biosamples. At the gene level, absolute gene expression values are compared, whereas pathway-grade comparisons are made between the pathway activation levels (PALs) calculated using average sample-normalized transcriptomic and proteomic profiles. We observed remarkably different average correlations between the primary RNA- and protein expression data for different cancer types: Spearman Rho between 0.017 (p = 1.7 × 10−13) and 0.27 (p < 2.2 × 10−16). However, at the pathway level we detected overall statistically significantly higher correlations: averaged Rho between 0.022 (p < 2.2 × 10−16) and 0.56 (p < 2.2 × 10−16). Thus, we conclude that data analysis at the PAL-level yields results of a greater similarity when comparing high-throughput RNA and protein expression profiles.
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Affiliation(s)
- Mikhail Raevskiy
- I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- OmicsWay Corp., Walnut, CA 91789, USA; (M.S.); (G.Z.); (A.G.); (D.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Maxim Sorokin
- OmicsWay Corp., Walnut, CA 91789, USA; (M.S.); (G.Z.); (A.G.); (D.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Galina Zakharova
- OmicsWay Corp., Walnut, CA 91789, USA; (M.S.); (G.Z.); (A.G.); (D.K.)
| | | | - Nicolas Borisov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (N.B.); (D.K.); (K.K.)
| | - Denis Kuzmin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (N.B.); (D.K.); (K.K.)
| | | | - Alexander Gudkov
- OmicsWay Corp., Walnut, CA 91789, USA; (M.S.); (G.Z.); (A.G.); (D.K.)
| | - Dmitry Kamashev
- OmicsWay Corp., Walnut, CA 91789, USA; (M.S.); (G.Z.); (A.G.); (D.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Anton Buzdin
- OmicsWay Corp., Walnut, CA 91789, USA; (M.S.); (G.Z.); (A.G.); (D.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (N.B.); (D.K.); (K.K.)
- Correspondence: ; Tel./Fax: +1-626-7657785
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Matsubara A, Miyashita T, Nakashima K, Mori N, Song SY, Hoshikawa H. Low-salt diet increases mRNA expression of aldosterone-regulated transporters in the intermediate portion of the endolymphatic sac. Pflugers Arch 2022; 474:505-515. [PMID: 35112133 DOI: 10.1007/s00424-021-02661-9] [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: 07/09/2021] [Revised: 12/08/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022]
Abstract
The endolymphatic sac is a small sac-shaped organ at the end of the membranous labyrinth of the inner ear. The endolymphatic sac absorbs the endolymph, in which the ion balance is crucial for inner ear homeostasis. Of the three sections of the endolymphatic sac, the intermediate portion is the center of endolymph absorption, particularly sodium transport, and is thought to be regulated by aldosterone. Disorders of the endolymphatic sac may cause an excess of endolymph (endolymphatic hydrops), a histological observation in Meniere's disease. A low-salt diet is an effective treatment for Meniere's disease, and is based on the assumption that the absorption of endolymph in the endolymphatic sac abates endolymphatic hydrops through a physiological increase in aldosterone level. However, the molecular basis of endolymph absorption in each portion of the endolymphatic sac is largely unknown because of difficulties in gene expression analysis, resulting from its small size and intricate structure. The present study combined reverse transcription-quantitative polymerase chain reaction and laser capture microdissection techniques to analyze the difference of gene expression of the aldosterone-controlled epithelial Na+ channel, thiazide-sensitive Na+-Cl- cotransporter, and Na+, K+-ATPase genes in the three individual portions of the endolymphatic sac in a rat model. A low-salt diet increased the expression of aldosterone-controlled ion transporters, particularly in the intermediate portion of the endolymphatic sac. Our findings will contribute to the understanding of the physiological function of the endolymphatic sac and the pathophysiology of Meniere's disease.
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Affiliation(s)
- Ai Matsubara
- Department of Otolaryngology, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
| | - Takenori Miyashita
- Department of Otolaryngology, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Kentaro Nakashima
- Institute of Neuroscience, Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Sanuki, Kagawa, Japan
| | - Nozomu Mori
- Department of Otolaryngology, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Si-Young Song
- Institute of Neuroscience, Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Sanuki, Kagawa, Japan
| | - Hiroshi Hoshikawa
- Department of Otolaryngology, Faculty of Medicine, Kagawa University, Ikenobe 1750-1, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
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Beaufrère A, Caruso S, Calderaro J, Poté N, Bijot JC, Couchy G, Cauchy F, Vilgrain V, Zucman-Rossi J, Paradis V. Gene expression signature as a surrogate marker of microvascular invasion on routine hepatocellular carcinoma biopsies. J Hepatol 2022; 76:343-352. [PMID: 34624411 DOI: 10.1016/j.jhep.2021.09.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Microvascular invasion (MVI), a major risk factor for tumor recurrence after surgery in hepatocellular carcinoma (HCC), is only detectable by microscopic examination of the surgical specimen. We aimed to define a transcriptomic signature associated with MVI in HCC than can be applied to formalin-fixed paraffin-embedded (FFPE) biopsies for use in clinical practice. METHODS To identify a gene expression signature related to MVI by using NanoString technology, we selected a set of 200 genes according to the literature and RNA-sequencing data obtained from a cohort of 150 frozen HCC samples previously published. We used 178 FFPE-archived HCC samples, including 109 surgical samples for the training set and 69 paired pre-operative biopsies for the validation set. In 14 cases of the training set, a paired biopsy was available and was also analyzed. RESULTS We identified a 6-gene signature (ROS1, UGT2B7, FAS, ANGPTL7, GMNN, MKI67) strongly associated with MVI in the training set of FFPE surgical HCC samples, with 82% accuracy (sensitivity 82%, specificity 81%, AUC 0.82). The NanoString gene expression was highly correlated in 14 paired surgical/biopsy HCC samples (mean R: 0.97). In the validation set of 69 FFPE HCC biopsies, the 6-gene NanoString signature predicted MVI with 74% accuracy (sensitivity 73%, specificity 76%, AUC 0.74). Moreover, on multivariate analysis, the MVI signature was associated with overall survival in both sets (hazard ratio 2.29; 95% CI 1.03-5.07; p = 0.041). CONCLUSION We defined a 6-gene signature that can accurately predict MVI in FFPE HCC biopsy samples, which is also associated with overall survival, although its survival impact must be confirmed by extensive study with further clinical data. LAY SUMMARY Microvascular invasion, a major risk factor for tumor recurrence after surgery in hepatocellular carcinoma, is only detectable by microscopic examination of a surgical specimen. In this study, we defined a relevant surrogate signature of microvascular invasion in hepatocellular carcinoma that may be applied in clinical practice with routine tumor biopsy and integrated into the therapeutic strategy.
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Affiliation(s)
- Aurélie Beaufrère
- Université de Paris, Paris, France; APHP, Department of Pathology, Hôpital Beaujon, 100 boulevard du Général Leclerc, Clichy, 92110, France; INSERM UMR 1149, Centre de Recherche sur l'Inflammation, 16 rue Henri Huchard, Paris, 75018, France
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, INSERM, Functional Genomics of Solid Tumors laboratory, F-75006 Paris, France
| | - Julien Calderaro
- Department of Pathology, Hôpital Henri Mondor, AP-HP, 51 Avenue du Maréchal de Lattre de Tassigny, Créteil, 94010, France
| | - Nicolas Poté
- Université de Paris, Paris, France; Department of Pathology, Hôpital Bichat, AP-HP.Nord, 46 Rue Henri Huchard, Paris, 75018, France
| | - Jean-Charles Bijot
- Université de Paris, Paris, France; Department of Radiology, Hôpital Beaujon, AP-HP, 100 boulevard du Général Leclerc, Clichy, 92110, France
| | - Gabielle Couchy
- Université de Paris, Paris, France; Centre de Recherche des Cordeliers, INSERM, Functional Genomics of Solid Tumors laboratory, F-75006 Paris, France
| | - François Cauchy
- Université de Paris, Paris, France; INSERM UMR 1149, Centre de Recherche sur l'Inflammation, 16 rue Henri Huchard, Paris, 75018, France; Department of HPB and Pancreatic surgery, Beaujon AP-HP, Clichy, 92110, France
| | - Valérie Vilgrain
- Université de Paris, Paris, France; INSERM UMR 1149, Centre de Recherche sur l'Inflammation, 16 rue Henri Huchard, Paris, 75018, France; Department of Radiology, Hôpital Beaujon, AP-HP, 100 boulevard du Général Leclerc, Clichy, 92110, France
| | - Jessica Zucman-Rossi
- Université de Paris, Paris, France; Centre de Recherche des Cordeliers, INSERM, Functional Genomics of Solid Tumors laboratory, F-75006 Paris, France; Department of Oncology, Hopital Européen Georges Pompidou, AP-HP, F-75015, Paris, France
| | - Valérie Paradis
- Université de Paris, Paris, France; APHP, Department of Pathology, Hôpital Beaujon, 100 boulevard du Général Leclerc, Clichy, 92110, France; INSERM UMR 1149, Centre de Recherche sur l'Inflammation, 16 rue Henri Huchard, Paris, 75018, France.
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The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues. Int J Mol Sci 2022; 23:ijms23031103. [PMID: 35163027 PMCID: PMC8834906 DOI: 10.3390/ijms23031103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Cancer cells accumulate epigenomic aberrations that contribute to cancer initiation and progression by altering both the genomic stability and the expression of genes. The awareness of such alterations could improve our understanding of cancer dynamics and the identification of new therapeutic strategies and biomarkers to refine tumor classification and treatment. Formalin fixation and paraffin embedding (FFPE) is the gold standard to preserve both tissue integrity and organization, and, in the last decades, a huge number of biological samples have been archived all over the world following this procedure. Recently, new chromatin immunoprecipitation (ChIP) techniques have been developed to allow the analysis of histone post-translational modifications (PTMs) and transcription factor (TF) distribution in FFPE tissues. The application of ChIP to genome-wide chromatin studies using real archival samples represents an unprecedented opportunity to conduct retrospective clinical studies thanks to the possibility of accessing large cohorts of samples and their associated diagnostic records. However, although recent attempts to standardize have been made, fixation and storage conditions of clinical specimens are still extremely variable and can affect the success of chromatin studies. The procedures introduced in the last few years dealt with this problem proponing successful strategies to obtain high-resolution ChIP profiles from FFPE archival samples. In this review, we compare the different FFPE-ChIP techniques, highlighting their strengths, limitations, common features, and peculiarities, as well as pitfalls and caveats related to ChIP studies in FFPE samples, in order to facilitate their application.
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Custódio N, Savisaar R, Carvalho C, Bak-Gordon P, Ribeiro MI, Tavares J, Nunes PB, Peixoto A, Pinto C, Escudeiro C, Teixeira MR, Carmo-Fonseca M. Expression Profiling in Ovarian Cancer Reveals Coordinated Regulation of BRCA1/2 and Homologous Recombination Genes. Biomedicines 2022; 10:biomedicines10020199. [PMID: 35203410 PMCID: PMC8868827 DOI: 10.3390/biomedicines10020199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Predictive biomarkers are crucial in clarifying the best strategy to use poly(ADP-ribose) polymerase inhibitors (PARPi) for the greatest benefit to ovarian cancer patients. PARPi are specifically lethal to cancer cells that cannot repair DNA damage by homologous recombination (HR), and HR deficiency is frequently associated with BRCA1/2 mutations. Genetic tests for BRCA1/2 mutations are currently used in the clinic, but results can be inconclusive due to the high prevalence of rare DNA sequence variants of unknown significance. Most tests also fail to detect epigenetic modifications and mutations located deep within introns that may alter the mRNA. The aim of this study was to investigate whether quantitation of BRCA1/2 mRNAs in ovarian cancer can provide information beyond the DNA tests. Using the nCounter assay from NanoString Technologies, we analyzed RNA isolated from 38 ovarian cancer specimens and 11 normal fallopian tube samples. We found that BRCA1/2 expression was highly variable among tumors. We further observed that tumors with lower levels of BRCA1/2 mRNA showed downregulated expression of 12 additional HR genes. Analysis of 299 ovarian cancer samples from The Cancer Genome Atlas (TCGA) confirmed the coordinated expression of BRCA1/2 and HR genes. To facilitate the routine analysis of BRCA1/2 mRNA in the clinical setting, we developed a targeted droplet digital PCR approach that can be used with FFPE samples. In conclusion, this study underscores the potential clinical benefit of measuring mRNA levels in tumors when BRCA1/2 DNA tests are negative or inconclusive.
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Affiliation(s)
- Noélia Custódio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
- Correspondence: ; Tel.: +35-121-799-9411
| | - Rosina Savisaar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Célia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Maria I. Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Joana Tavares
- Serviço de Anatomia Patológica, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-028 Lisboa, Portugal;
| | - Paula B. Nunes
- Hospital CUF Descobertas, 1998-018 Lisboa, Portugal;
- Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Peixoto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Pinto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Escudeiro
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Manuel R. Teixeira
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
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Begum S, Prabhu V, Mohanty V, Upadhyaya KK, Abdulla R. Unveiling the arcanum of formalin-fixed paraffin-embedded archival tissue blocks: A valuable resource for genomic DNA extraction. J Oral Maxillofac Pathol 2022; 26:289. [PMID: 35968182 PMCID: PMC9364647 DOI: 10.4103/jomfp.jomfp_424_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/04/2021] [Accepted: 12/25/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Formalin-fixed paraffin-embedded (FFPE) tissue blocks are routinely preserved after pathological diagnosis and possess tremendous potential for biomarker discovery. These archival samples are prone to degradation on prolonged storage due to the formalin cross-linking. AIMS This study aimed to evaluate whether the storage period of the formalin-fixed paraffin-embedded tumor blocks had a significant impact on the yield and purity of the isolated DNA archived for 11 years. SETTINGS AND DESIGN A retrospective study was carried out in the Department of Oral Pathology and Microbiology in accordance with the Institutional Ethics Committee. MATERIALS AND METHODS Genomic DNA extraction was performed using TaKaRa DEXPAT Easy DNA kit from 40 FFPE tissue blocks of oral squamous cell carcinoma archived for 11 years (2006-2017). NanoDrop spectrophotometer was used to determine the DNA yield (A260) and purity (A260/A280 ratio). The quality of DNA fragments was validated using agarose gel electrophoresis. STATISTICAL ANALYSIS USED Statistical analysis was obtained by SPSS 22, MS Excel and analyzed using the analysis of variance (ANOVA) test. P < 0.05 was set for statistical significance. RESULTS There was no statistically significant difference observed both in terms of DNA yield (P = 0.996) and purity (P = 0.997) of FFPE tumor blocks archived for 11 years among the study groups. CONCLUSIONS It was concluded that, irrespective of years of storage of the FFPE, it is possible to extract genomic DNA and use it for molecular studies.
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Affiliation(s)
- Sameera Begum
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangaluru, Karnataka, India
| | - Vishnudas Prabhu
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangaluru, Karnataka, India
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangaluru, Karnataka, India
| | - K. Krishnaraj Upadhyaya
- Department of General Pathology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangaluru, Karnataka, India
| | - Riaz Abdulla
- Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangaluru, Karnataka, India,Address for correspondence: Dr. Riaz Abdulla, Department of Oral Pathology, Yenepoya Dental College, Yenepoya (Deemed to be University), Mangaluru- 575 018, Karnataka, India. E-mail:
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34
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Manjunath HS, Al Khulaifi M, Sidahmed H, Ammar A, Vadakekolathu J, Rutella S, Al-Mohannadi MJ, Elawad M, Mifsud W, Charles A, Maccalli C, Tomei S. Gene Expression Profiling of FFPE Samples: A Titration Test. Technol Cancer Res Treat 2022; 21:15330338221129710. [PMID: 36415121 PMCID: PMC9706083 DOI: 10.1177/15330338221129710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/23/2022] [Indexed: 12/23/2023] Open
Abstract
The gene expression analysis of formalin-fixed paraffin-embedded (FFPE) tissues is often hampered by poor RNA quality, which results from the oxidation, cross-linking and other chemical modifications induced by the inclusion in paraffin. Yet, FFPE samples are a valuable source for molecular studies and can provide great insights into disease progression and prognosis. With the advancement of genomic technologies, new methods have been established that offer reliable and accurate gene expression workflows on samples of poor quality. NanoString is a probe-based technology that allows the direct counting of the mRNA transcripts and can be applied to degraded samples. Here, we have tested 2 RNA extraction methods for FFPE samples, and we have performed a titration experiment to evaluate the impact of RNA degradation and RNA input on the gene expression profiles assessed using the NanoString IO360 panel. We have selected FFPE samples of different DV200 values and assessed them on the nCounter platform with 2 different amounts of input RNA. This study concludes that the nCounter is a robust and reliable platform to assess the gene expression of RNA samples with DV200 > 30%; its robustness and ease of use could be of particular benefit to clinical settings.
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Affiliation(s)
| | - Moza Al Khulaifi
- Laboratory of Immune and Biological Therapy, Research Department,
Sidra
Medicine, Doha, Qatar
| | - Heba Sidahmed
- Laboratory of Immune and Biological Therapy, Research Department,
Sidra
Medicine, Doha, Qatar
| | - Adham Ammar
- Department of Pathology, Hamad Medical
Corporation, Doha, Qatar
| | - Jayakumar Vadakekolathu
- John van Geest Cancer Research Centre, School of Science and
Technology, Nottingham
Trent University, Nottingham, UK
| | - Sergio Rutella
- John van Geest Cancer Research Centre, School of Science and
Technology, Nottingham
Trent University, Nottingham, UK
| | | | - Mamoun Elawad
- Department of Gastroenterology, Sidra Medicine,
Doha, Qatar
| | - William Mifsud
- Department of Anatomical Pathology,
Sidra
Medicine, Doha, Qatar
| | - Adrian Charles
- Department of Anatomical Pathology,
Sidra
Medicine, Doha, Qatar
| | - Cristina Maccalli
- Laboratory of Immune and Biological Therapy, Research Department,
Sidra
Medicine, Doha, Qatar
| | - Sara Tomei
- Omics Core, Integrated Genomics Services, Research Department,
Sidra
Medicine, Doha, Qatar
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35
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MacCuaig WM, Thomas A, Carlos-Sorto JC, Gomez-Gutierrez JG, Alexander AC, Wellberg EA, Grizzle WE, McNally LR. Differential expression of microRNA between triple negative breast cancer patients of African American and European American descent. Biotech Histochem 2022; 97:1-10. [PMID: 34979848 PMCID: PMC9047185 DOI: 10.1080/10520295.2021.2005147] [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: 01/07/2023] Open
Abstract
There are racial disparities in the outcome of triple negative breast cancer (TNBC) patients between women of African ancestry and women of European ancestry, even after accounting for lifestyle, socioeconomic and clinical factors. MicroRNA (miRNA) are non-coding molecules whose level of expression is associated with cancer suppression, proliferation and drug resistance; therefore, these have potential for biomarker applications in cancers including TNBC. Historically, miRNAs up-regulated in African American (AA) patients have received less attention than for patients of European ancestry. Using laser capture microdissection (LCM) to acquire ultrapure tumor cell samples, miRNA expression was evaluated in 15 AA and 15 European American (EA) TNBC patients. Tumor sections were evaluated using RNA extraction followed by miRNA analysis and profiling. Results were compared based on ethnicity and method of tissue fixation. miRNAs that showed high differential expression in AA TNBC patients compared to EA included: miR-19a, miR-192, miR-302a, miR-302b, miR-302c, miR-335, miR-520b, miR-520f and miR-645. LCM is a useful technique for isolation of tumor cells. We found a greater abundance of RNA in frozen samples compared to formalin fixed, paraffin embedded samples. miRNA appears to be a useful biomarker for TNBC to improve diagnosis and treatment.
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Affiliation(s)
- William M. MacCuaig
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma
| | - Alexandra Thomas
- Department of Hematology Oncology, Wake Forest Baptist Health, Winston-Salem, North Carolina
| | - Juan C. Carlos-Sorto
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Surgery, University of Oklahoma, Oklahoma City, Oklahoma
| | | | - Adam C. Alexander
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Family and Preventive Medicine, University of Oklahoma, Oklahoma City, Oklahoma
| | - Elizabeth A. Wellberg
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Pathology, University of Oklahoma, Oklahoma City, Oklahoma
| | - William E. Grizzle
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lacey R. McNally
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Surgery, University of Oklahoma, Oklahoma City, Oklahoma
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Sebestyén E, Nagy Á, Marosvári D, Rajnai H, Kajtár B, Deák B, Matolcsy A, Brandner S, Storhoff J, Chen N, Bagó AG, Bödör C, Reiniger L. Distinct miRNA Expression Signatures of Primary and Secondary Central Nervous System Lymphomas. J Mol Diagn 2021; 24:224-240. [DOI: 10.1016/j.jmoldx.2021.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 01/07/2023] Open
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37
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Parker DM, Winkenbach LP, Parker A, Boyson S, Nishimura EO. Improved Methods for Single-Molecule Fluorescence In Situ Hybridization and Immunofluorescence in Caenorhabditis elegans Embryos. Curr Protoc 2021; 1:e299. [PMID: 34826343 PMCID: PMC9020185 DOI: 10.1002/cpz1.299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Visualization of gene products in Caenorhabditis elegans has provided insights into the molecular and biological functions of many novel genes in their native contexts. Single-molecule fluorescence in situ hybridization (smFISH) and immunofluorescence (IF) enable the visualization of the abundance and localization of mRNAs and proteins, respectively, allowing researchers to ultimately elucidate the localization, dynamics, and functions of the corresponding genes. Whereas both smFISH and immunofluorescence have been foundational techniques in molecular biology, each protocol poses challenges for use in the C. elegans embryo. smFISH protocols suffer from high initial costs and can photobleach rapidly, and immunofluorescence requires technically challenging permeabilization steps and slide preparation. Most importantly, published smFISH and IF protocols have predominantly been mutually exclusive, preventing the exploration of relationships between an mRNA and a relevant protein in the same sample. Here, we describe protocols to perform immunofluorescence and smFISH in C. elegans embryos either in sequence or simultaneously. We also outline the steps to perform smFISH or immunofluorescence alone, including several improvements and optimizations to existing approaches. These protocols feature improved fixation and permeabilization steps to preserve cellular morphology while maintaining probe and antibody accessibility in the embryo, a streamlined, in-tube approach for antibody staining that negates freeze-cracking, a validated method to perform the cost-reducing single molecule inexpensive FISH (smiFISH) adaptation, slide preparation using empirically determined optimal antifade products, and straightforward quantification and data analysis methods. Finally, we discuss tricks and tips to help the reader optimize and troubleshoot individual steps in each protocol. Together, these protocols simplify existing workflows for single-molecule RNA and protein detection. Moreover, simultaneous, high-resolution imaging of proteins and RNAs of interest will permit analysis, quantification, and comparison of protein and RNA distributions, furthering our understanding of the relationship between RNAs and their protein products or cellular markers in early development. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Sequential immunofluorescence and single-molecule fluorescence in situ hybridization Alternate Protocol: Abbreviated protocol for simultaneous immunofluorescence and single-molecule fluorescence in situ hybridization Basic Protocol 2: Simplified immunofluorescence in C. elegans embryos Basic Protocol 3: Single-molecule fluorescence in situ hybridization or single-molecule inexpensive fluorescence in situ hybridization.
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Affiliation(s)
- Dylan M Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Lindsay P Winkenbach
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Annemarie Parker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Sam Boyson
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
| | - Erin Osborne Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado
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Mena J, Ariyama N, Navarro C, Quezada M, Brevis C, Rojas D, Medina RA, Brito B, Ruiz Á, Neira V. Ubiquitous influenza A virus in Chilean swine before the H1N1pdm09 introduction. Transbound Emerg Dis 2021; 68:3174-3179. [PMID: 34288514 PMCID: PMC8684045 DOI: 10.1111/tbed.14243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/16/2021] [Indexed: 12/16/2022]
Abstract
Influenza A virus (IAV) was a neglected swine pathogen in South America before the 2009 H1N1 pandemic (A(H1N1)pdm2009). The A(H1N1)pdm2009 strain has widely spread among the Chilean swine population and co-circulates with endemic H1N2 and H3N2 viruses. The presence of IAV as a swine pathogen in Chilean swine before the 2009 pandemic is unknown. To understand the IAV in swine prior to 2009, aY retrospective study of samples from pigs affected with respiratory diseases was conducted. Ninety formalin-fixed and paraffin-embedded lung tissues belonging to 21 intensive pig production companies located in five different administrative regions of Chile, collected between 2005 and 2008, were evaluated. The tissues were tested by immunohistochemistry (IHC), identifying that 9 out of 21 farms (42.8%) and 31 out of 90 (34.4%) samples were IAV positive. Only three out of the 31 IHC-positive samples were positive upon RNA extraction and rtRT-PCR analysis. Partial nucleotide sequences were obtained from one sample and characterized as an H3N2 subtype closely related to a human seasonal H3N2 IAVs that circulated globally in the mid-90s. These results indicate that IAV was circulating in swine before 2009 and highlight the value of conducting retrospective studies through genomic strategies to analyse historical samples.
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Affiliation(s)
- Juan Mena
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile, Santiago, Chile
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Animales y Ambientes (ICA3), Instituto de Ciencias Agroalimentarias, Universidad de O'Higgins, San Fernando, Chile
| | - Naomi Ariyama
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Camila Navarro
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Manuel Quezada
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Cristina Brevis
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Daniela Rojas
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Rafael A Medina
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Barbara Brito
- The ithree institute - University of Technology Sydney, Sydney, New South Wales, Australia
| | - Álvaro Ruiz
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Victor Neira
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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Halloran PF, Madill-Thomsen KS, Böhmig GA, Myslak M, Gupta G, Kumar D, Viklicky O, Perkowska-Ptasinska A, Famulski KS. A 2-fold Approach to Polyoma Virus (BK) Nephropathy in Kidney Transplants: Distinguishing Direct Virus Effects From Cognate T Cell-mediated Inflammation. Transplantation 2021; 105:2374-2384. [PMID: 34310102 DOI: 10.1097/tp.0000000000003884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND BK nephropathy (BKN) in kidney transplants diagnosed by histology is challenging because it involves damage from both virus activity and cognate T cell-mediated inflammation, directed against alloantigens (rejection) or viral antigens. The present study of indication biopsies from the Integrated Diagnostic System in the International Collaborative Microarray Study Extension study measured major capsid viral protein 2 (VP2) mRNA to assess virus activity and a T cell-mediated rejection (TCMR) classifier to assess cognate T cell-mediated inflammation. METHODS Biopsies were assessed by local standard-of-care histology and by genome-wide microarrays and Molecular Microscope Diagnostic System (MMDx) algorithms to detect rejection and injury. In a subset of 102 biopsies (50 BKN and 52 BKN-negative biopsies with various abnormalities), we measured VP2 transcripts by real-time polymerase chain reaction. RESULTS BKN was diagnosed in 55 of 1679 biopsies; 30 had cognate T cell-mediated activity assessed by by MMDx and TCMR lesions, but only 3 of 30 were histologically diagnosed as TCMR. We developed a BKN probability classifier that predicted histologic BKN (area under the curve = 0.82). Virus activity (VP2 expression) was highly selective for BKN (area under the curve = 0.94) and correlated with acute injury, atrophy-fibrosis, macrophage activation, and the BKN classifier, but not with the TCMR classifier. BKN with molecular TCMR had more tubulitis and inflammation than BKN without molecular TCMR. In 5 BKN cases with second biopsies, VP2 mRNA decreased in second biopsies, whereas in 4 of 5 TCMR classifiers, scores increased. Genes and pathways associated with BKN and VP2 mRNA were similar, reflecting injury, inflammation, and macrophage activation but none was selective for BKN. CONCLUSIONS Risk-benefit decisions in BKN may be assisted by quantitative assessment of the 2 major pathologic processes, virus activity and cognate T cell-mediated inflammation.
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, AB, Canada
| | | | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Marek Myslak
- Department of Nephrology and Kidney Transplantation, SPWSZ Hospital in Szczecin, Pomeranian Medical University, Szczecin, Poland
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Dhiren Kumar
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Ondrej Viklicky
- Department of Nephrology and Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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Caveolin-1 in Kidney Chronic Antibody-Mediated Rejection: An Integrated Immunohistochemical and Transcriptomic Analysis Based on the Banff Human Organ Transplant (B-HOT) Gene Panel. Biomedicines 2021; 9:biomedicines9101318. [PMID: 34680435 PMCID: PMC8533527 DOI: 10.3390/biomedicines9101318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 02/07/2023] Open
Abstract
Caveolin-1 overexpression has previously been reported as a marker of endothelial injury in kidney chronic antibody-mediated rejection (c-ABMR), but conclusive evidence supporting its use for daily diagnostic practice is missing. This study aims to evaluate if Caveolin-1 can be considered an immunohistochemical surrogate marker of c-ABMR. Caveolin-1 expression was analyzed in a selected series of 22 c-ABMR samples and 11 controls. Caveolin-1 immunohistochemistry proved positive in peritubular and glomerular capillaries of c-ABMR specimens, irrespective of C4d status whereas all controls were negative. Multiplex gene expression profiling in c-ABMR cases confirmed Caveolin-1 overexpression and identified additional genes (n = 220) and pathways, including MHC Class II antigen presentation and Type II interferon signaling. No differences in terms of gene expression (including Caveolin-1 gene) were observed according to C4d status. Conversely, immune cell signatures showed a NK-cell prevalence in C4d-negative samples compared with a B-cell predominance in C4d-positive cases, a finding confirmed by immunohistochemical assessment. Finally, differentially expressed genes were observed between c-ABMR and controls in pathways associated with Caveolin-1 functions (angiogenesis, cell metabolism and cell–ECM interaction). Based on our findings, Caveolin-1 resulted as a key player in c-ABMR, supporting its role as a marker of this condition irrespective of C4d status.
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Burgess HJ, Lockerbie BP, Ayalew LE, Dibernardo A, Hrazdilová K, Modry D, Bollinger TK. Species-specific PCR assay for the detection of Babesia odocoilei. J Vet Diagn Invest 2021; 33:1188-1192. [PMID: 34550025 PMCID: PMC8546463 DOI: 10.1177/10406387211032927] [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] [Indexed: 11/26/2022] Open
Abstract
We developed a PCR assay for the detection of Babesia odocoilei based on the 18S rRNA gene. Multiple specimens of B. odocoilei were examined, and the assay consistently produced a small specific PCR product of 306 bp. The PCR assay was also challenged with DNA from 13 other Babesia species and 2 Theileria species, originating from 10 different host species; however, nonspecific DNA amplification and multiple banding patterns were observed, and the amplicon banding patterns varied between different isolates of the same species. Sensitivity was determined to be 6.4 pg of DNA, and an estimated 0.0001% parasitism. This assay can be utilized for species-specific differential detection of B. odocoilei.
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Affiliation(s)
- Hilary J Burgess
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Betty P Lockerbie
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lisanework E Ayalew
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Antonia Dibernardo
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kristýna Hrazdilová
- CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - David Modry
- CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Trent K Bollinger
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Canadian Wildlife Health Cooperative, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Saraji A, Offermann A, Stegmann-Frehse J, Hempel K, Kang D, Krupar R, Watermann C, Jonigk D, Kühnel MP, Kirfel J, Perner S, Sailer V. Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffin-embedded bone tissue. PLoS One 2021; 16:e0257416. [PMID: 34529723 PMCID: PMC8445430 DOI: 10.1371/journal.pone.0257416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/31/2021] [Indexed: 11/18/2022] Open
Abstract
With the advance of precision medicine, the availability of tumor tissue for molecular analysis has become a limiting factor. This is particularly the case for bone metastases which are frequently occurring in cancer types such as prostate cancer. Due to the necessary decalcification process it was long thought that transcriptome analysis will not be feasible from decalcified formalin-fixed, paraffin-embedded (DFFPE) in a large manner. Here we demonstrate that mRNA extraction from DFFPE is feasible, quick, robust and reproducible and that decalcification does not hamper subsequent gene expression analysis. This might assist in implementing transcriptome analysis from DFFPE into every day practice.
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Affiliation(s)
- Alireza Saraji
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Anne Offermann
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Janine Stegmann-Frehse
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Katharina Hempel
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Duan Kang
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | | | - Christian Watermann
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| | - Mark Philipp Kühnel
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| | - Jutta Kirfel
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sven Perner
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Verena Sailer
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- * E-mail:
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Haley L, Parimi V, Jiang L, Pallavajjala A, Hardy M, Yonescu R, Morsberger L, Stinnett V, Long P, Zou YS, Gocke CD. Diagnostic Utility of Gene Fusion Panel to Detect Gene Fusions in Fresh and Formalin-Fixed, Paraffin-Embedded Cancer Specimens. J Mol Diagn 2021; 23:1343-1358. [PMID: 34358677 DOI: 10.1016/j.jmoldx.2021.07.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/04/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022] Open
Abstract
Somatic gene fusions are common in leukemias/lymphomas and solid tumors. The detection of gene fusions is crucial for diagnosis. NanoString fusion technology is a multiplexed hybridization method that interrogates hundreds of gene fusions in a single reaction. This study's objective was to determine the performance characteristics and diagnostic utility of NanoString fusion assay in a clinical diagnostics laboratory. Validation using 100 positive specimens and 15 negative specimens by a combined reference standard of fluorescence in situ hybridization (FISH)/RT-PCR/next-generation sequencing (NGS) assays achieved 100% sensitivity in leukemias/lymphomas and 95.0% sensitivity and 100% specificity in solid tumors. Subsequently, 214 consecutive clinical cases, including 73 leukemia/lymphoma specimens and 141 formalin-fixed, paraffin-embedded solid tumor specimens, were analyzed by gene fusion panels across 638 unique gene fusion transcripts. A variety of comparator tests, including FISH panels, conventional karyotyping, a DNA-based targeted NGS assay, and custom RT-PCR testing, were performed in parallel. The gene fusion assay detected 31 gene fusions, including 16 in leukemia/lymphoma specimens and 15 in solid tumor specimens. The overall sensitivity, specificity, and accuracy of gene fusions detected by the gene fusion panel in all 329 specimens (validation and consecutive clinical specimens) tested in this study were 94.8%, 100%, and 97.9%, respectively, compared with FISH/RT-PCR/NGS assays. The gene fusion panel is a reliable approach that maximizes molecular detection of fusions among both fresh and formalin-fixed, paraffin-embedded cancer specimens.
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Affiliation(s)
- Lisa Haley
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vamsi Parimi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Liqun Jiang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aparna Pallavajjala
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Melanie Hardy
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Raluca Yonescu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Laura Morsberger
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Victoria Stinnett
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Patty Long
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Ying S Zou
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland.
| | - Christopher D Gocke
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Lahiri P, Mukherjee S, Ghosh B, Das D, Lahiri B, Varshney SK, Pal M, Paul RR, Chatterjee J. Comprehensive Evaluation of PAXgene Fixation on Oral Cancer Tissues Using Routine Histology, Immunohistochemistry, and FTIR Microspectroscopy. Biomolecules 2021; 11:biom11060889. [PMID: 34203873 PMCID: PMC8232633 DOI: 10.3390/biom11060889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 11/25/2022] Open
Abstract
The choice of tissue fixation is critical for preserving the morphology and biochemical information of tissues. Fragile oral tissues with lower tensile strength are challenging to process for histological applications as they are prone to processing damage, such as tissue tear, wrinkling, and tissue fall-off from slides. This leads to loss of morphological information and unnecessary delay in experimentation. In this study, we have characterized the new PAXgene tissue fixation system on oral buccal mucosal tissue of cancerous and normal pathology for routine histological and immunohistochemical applications. We aimed to minimize the processing damage of tissues and improve the quality of histological experiments. We also examined the preservation of biomolecules by PAXgene fixation using FTIR microspectroscopy. Our results demonstrate that the PAXgene-fixed tissues showed significantly less tissue fall-off from slides. Hematoxylin and Eosin staining showed comparable morphology between formalin-fixed and PAXgene-fixed tissues. Good quality and slightly superior immunostaining for cancer-associated proteins p53 and CK5/6 were observed in PAXgene-fixed tissues without antigen retrieval than formalin-fixed tissues. Further, FTIR measurements revealed superior preservation of glycogen, fatty acids, and amide III protein secondary structures in PAXgene-fixed tissues. Overall, we present the first comprehensive evaluation of the PAXgene tissue fixation system in oral tissues. This study concludes that the PAXgene tissue fixation system can be applied to oral tissues to perform diagnostic molecular pathology experiments without compromising the quality of the morphology or biochemistry of biomolecules.
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Affiliation(s)
- Pooja Lahiri
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
- Correspondence:
| | - Suranjana Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Biswajoy Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Debnath Das
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Basudev Lahiri
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (B.L.); (S.K.V.)
| | - Shailendra Kumar Varshney
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (B.L.); (S.K.V.)
| | - Mousumi Pal
- Guru Nanak Institute of Dental Sciences and Research (GNIDSR), Kolkata 700114, India;
| | - Ranjan Rashmi Paul
- Department of Oral & Dental Sciences, JIS University, Kolkata 700109, India;
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
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Amplification-free gene expression analysis of formalin-fixed paraffin-embedded samples using scanning single-molecule counting. Anal Biochem 2021; 625:114220. [PMID: 33915118 DOI: 10.1016/j.ab.2021.114220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/21/2022]
Abstract
In this paper, we present the applications of our newly developed, highly sensitive fluorescent detection method referred to as scanning single-molecule counting (SSMC). We found that the target RNA added to the total RNA was detected with high sensitivity at 384 aM by combining a magnetic bead-based assay and SSMC (MB-BA + SSMC). Gene expression analysis without reverse transcription or amplification confirmed that the pattern of gene expression was identical to that of real-time polymerase chain reaction (PCR). MB-BA + SSMC was also applied to formalin-fixed paraffin-embedded (FFPE) samples. RNA fragmentation and crosslinking owing to FFPE processing slightly affected gene expression. Conversely, FFPE samples showed an increase in gene Ct values and a decrease in the number of detectable genes when analyzed using real-time PCR. Overall, our results suggested that SSMC is a powerful tool for target RNA detection and amplification-free gene expression analysis.
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Nicolás-Párraga S, Torres M, Alemany L, Félix A, Cruz E, de Sanjosé S, Bosch FX, Bravo IG. Human DNA decays faster with time than viral dsDNA: an analysis on HPV16 using pathology archive samples spanning 85 years. Virol J 2021; 18:65. [PMID: 33781303 PMCID: PMC8008572 DOI: 10.1186/s12985-021-01529-9] [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: 12/03/2020] [Accepted: 03/05/2021] [Indexed: 12/01/2022] Open
Abstract
Background Quality of the nucleic acids extracted from Formalin Fixed Paraffin Embedded (FFPE) samples largely depends on pre-analytic, fixation and storage conditions. We assessed the differential sensitivity of viral and human double stranded DNA (dsDNA) to degradation with storage time. Methods We randomly selected forty-four HPV16-positive invasive cervical cancer (ICC) FFPE samples collected between 1930 and 1935 and between 2000 and 2004. We evaluated through qPCR the amplification within the same sample of two targets of the HPV16 L1 gene (69 bp, 134 bp) compared with two targets of the human tubulin-β gene (65 bp, 149 bp). Results Both viral and human, short and long targets were amplified from all samples stored for 15 years. In samples archived for 85 years, we observed a significant decrease in the ability to amplify longer targets and this difference was larger in human than in viral DNA: longer fragments were nine times (CI 95% 2.6–35.2) less likely to be recovered from human DNA compared with 1.6 times (CI 95% 1.1–2.2) for viral DNA. Conclusions We conclude that human and viral DNA show a differential decay kinetics in FFPE samples. The faster degradation of human DNA should be considered when assessing viral DNA prevalence in long stored samples, as HPV DNA detection remains a key biomarker of viral-associated transformation. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01529-9.
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Affiliation(s)
- Sara Nicolás-Párraga
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.
| | - Montserrat Torres
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.
| | - Laia Alemany
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ana Félix
- Pathology Unit, Portuguese Institute of Oncology Francisco Gentil (IPO Lisbon), Lisbon, Portugal
| | - Eugenia Cruz
- Pathology Unit, Portuguese Institute of Oncology Francisco Gentil (IPO Coimbra), Coimbra, Portugal
| | - Silvia de Sanjosé
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Sexual and Reproductive Health, PATH, Seattle, USA.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Francesc Xavier Bosch
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Biomedical Research Networking Centre On Cancer (CIBERONC), Madrid, Spain.,Universitat Oberta de Catalunya, Barcelona, Spain
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.,Laboratory MIVEGEC (CNRS IRD Univ Montpellier), French National Center for Scientific Research (CNRS), Montpellier, France.,Center for Research On the Ecology and Evolution of Diseases (CREES), Montpellier, France
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A novel approach for microRNA in situ hybridization using locked nucleic acid probes. Sci Rep 2021; 11:4504. [PMID: 33627751 PMCID: PMC7904755 DOI: 10.1038/s41598-021-83888-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/05/2021] [Indexed: 11/12/2022] Open
Abstract
Identification of target tissue microRNAs (miR) using in situ hybridization (ISH), with digoxigenin-labeled locked nucleic acid (LNA) probes, is influenced by preanalytic parameters. To determine the best retrieval method for common microRNAs, a multiblock composed of paraffin-embedded tonsil, cervix, placenta, and hyperplastic prostate tissue were included. Tissue were fixed in 10% formalin in a range of 5–144 hours (h). Cut sections (5 μm) from the multiblock were subjected to combinations of pretreatment procedures: variable periods of proteinase K (PK) digestion or Heat-induced microRNA Retrieval (HmiRR) using target retrieval solution (TRS) pH 6.1 or 9, with or without enzymatic treatment (pepsin). Results for the overall categories: TRS pH 9 versus PK; p = 2.9e−23, TRS pH 9 versus TRS pH 6.1; p = 1.1e−14, TRS pH 6.1 versus PK; p = 2.9e−03. A long fixation time, resulted in the best microRNA preservation and staining intensity (long vs. short: p = 3.5e−47, long vs. moderate: p = 1.6e−44, moderate vs. short: p = 4.3e−16), was enhanced using HmiRR TRS pH 9 with or without pepsin providing high sensitivity and specificity. These observations conflict with other ISH techniques (e.g., messenger ribonucleic acid), which typically require shorter fixation periods, and therefore, further studies are warranted.
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Laprovitera N, Riefolo M, Ambrosini E, Klec C, Pichler M, Ferracin M. Cancer of Unknown Primary: Challenges and Progress in Clinical Management. Cancers (Basel) 2021; 13:cancers13030451. [PMID: 33504059 PMCID: PMC7866161 DOI: 10.3390/cancers13030451] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Patients with cancer of unknown primary site suffer the burden of an uncertain disease, which is characterized by the impossibility to identify the tissue where the tumor has originated. The identification of the primary site of a tumor is of great importance for the patient to have access to site-specific treatments and be enrolled in clinical trials. Therefore, patients with cancer of unknown primary have reduced therapeutic opportunities and poor prognosis. Advancements have been made in the molecular characterization of this tumor, which could be used to infer the tumor site-of-origin and thus broaden the diagnostic outcome. Moreover, we describe here the novel therapeutic opportunities that are based on the genetic and immunophenotypic characterization of the tumor, and thus independent from the tumor type, which could provide most benefit to patients with cancer of unknown primary. Abstract Distant metastases are the main cause of cancer-related deaths in patients with advanced tumors. A standard diagnostic workup usually contains the identification of the tissue-of-origin of metastatic tumors, although under certain circumstances, it remains elusive. This disease setting is defined as cancer of unknown primary (CUP). Accounting for approximately 3–5% of all cancer diagnoses, CUPs are characterized by an aggressive clinical behavior and represent a real therapeutic challenge. The lack of determination of a tissue of origin precludes CUP patients from specific evidence-based therapeutic options or access to clinical trial, which significantly impacts their life expectancy. In the era of precision medicine, it is essential to characterize CUP molecular features, including the expression profile of non-coding RNAs, to improve our understanding of CUP biology and identify novel therapeutic strategies. This review article sheds light on this enigmatic disease by summarizing the current knowledge on CUPs focusing on recent discoveries and emerging diagnostic strategies.
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Affiliation(s)
- Noemi Laprovitera
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy; (N.L.); (M.R.); (E.A.)
- Department of Life Sciences and Biotechnologies, University of Ferrara, 44121 Ferrara, Italy
| | - Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy; (N.L.); (M.R.); (E.A.)
| | - Elisa Ambrosini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy; (N.L.); (M.R.); (E.A.)
| | - Christiane Klec
- Division of Oncology, Medical University of Graz, 8036 Graz, Austria; (C.K.); (M.P.)
| | - Martin Pichler
- Division of Oncology, Medical University of Graz, 8036 Graz, Austria; (C.K.); (M.P.)
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy; (N.L.); (M.R.); (E.A.)
- Correspondence: ; Tel.: +39-051-209-4714
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Channathodiyil P, Houseley J. Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry. PLoS One 2021; 16:e0240769. [PMID: 33481798 PMCID: PMC7822327 DOI: 10.1371/journal.pone.0240769] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/04/2021] [Indexed: 01/07/2023] Open
Abstract
A simple method for extraction of high quality RNA from cells that have been fixed, stained and sorted by flow cytometry would allow routine transcriptome analysis of highly purified cell populations and single cells. However, formaldehyde fixation impairs RNA extraction and inhibits RNA amplification. Here we show that good quality RNA can be readily extracted from stained and sorted mammalian cells if formaldehyde is replaced by glyoxal—a well-characterised fixative that is widely compatible with immunofluorescent staining methods. Although both formaldehyde and glyoxal efficiently form protein-protein crosslinks, glyoxal does not crosslink RNA to proteins nor form stable RNA adducts, ensuring that RNA remains accessible and amenable to enzymatic manipulation after glyoxal fixation. We find that RNA integrity is maintained through glyoxal fixation, permeabilisation with methanol or saponin, indirect immunofluorescent staining and flow sorting. RNA can then be extracted by standard methods and processed into RNA-seq libraries using commercial kits; mRNA abundances measured by poly(A)+ RNA-seq correlate well between freshly harvested cells and fixed, stained and sorted cells. We validate the applicability of this approach to flow cytometry by staining MCF-7 cells for the intracellular G2/M-specific antigen cyclin B1 (CCNB1), and show strong enrichment for G2/M-phase cells based on transcriptomic data. Switching to glyoxal fixation with RNA-compatible staining methods requires only minor adjustments of most existing staining and sorting protocols, and should facilitate routine transcriptomic analysis of sorted cells.
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Affiliation(s)
| | - Jonathan Houseley
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- * E-mail:
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Kano T, Morita T, Sumida K, Yumoto H, Baba O. Expression of fibroblast growth factor receptor1, -2c, and -3c transcripts in mouse molars after tooth eruption. Anat Sci Int 2021; 96:301-309. [PMID: 33433858 DOI: 10.1007/s12565-020-00594-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/15/2020] [Indexed: 11/30/2022]
Abstract
A previous study suggested that fibroblast growth factor (FGF) signaling plays an important role in dentin formation during tooth development. In this study, to examine dentin formation after tooth eruption involving secondary and tertiary dentin, we analyzed the expression patterns and expressing cells of Fgfr1, -2c, and -3c in mouse maxillary first molars (M1). Since it is difficult to recover the mRNAs from mineralized tissues, we tested methods for extraction after fixation and decalcification of teeth. We successfully obtained consistent results with quantitative real-time PCR (qPCR) using β-actin transcripts for validation. qPCR for Dentin sialo phosphoprotein (Dspp), Fgfr1, -2c, and -3c transcripts was performed on mice at ages of 2-20 weeks. The results showed that the highest expression levels of Dspp and Fgfr2c occurred at 2 weeks old followed by lower expression levels after 4 weeks old. However, the expression levels of Fgfr1 and Fgfr3c were constant throughout the experimental period. By in situ hybridization, Dspp, Fgfr1, and Fgfr3c transcripts were detected in odontoblasts at ages of 2 and 4 weeks. In addition, Dspp and Fgfr1 transcripts were detected in odontoblasts facing reactionary dentin at 8 weeks old. These results suggest that FGF-FGFR signaling might be involved in the regulation of odontoblasts even after tooth eruption, including secondary and tertiary dentin formation. Moreover, our modified method for extracting mRNA from mineralized tissues after fixation and decalcification successfully produced consistent results.
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Affiliation(s)
- Tsuyoshi Kano
- Department of Oral and Maxillofacial Anatomy, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15, Kuramoto-cho, Tokushima-shi, Tokushima, 770-8504, Japan
| | - Tsuyoshi Morita
- Department of Oral and Maxillofacial Anatomy, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15, Kuramoto-cho, Tokushima-shi, Tokushima, 770-8504, Japan.
| | - Kaori Sumida
- Department of Oral and Maxillofacial Anatomy, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15, Kuramoto-cho, Tokushima-shi, Tokushima, 770-8504, Japan
| | - Hiromichi Yumoto
- Department of Periodontology and Endodontology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Otto Baba
- Department of Oral and Maxillofacial Anatomy, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15, Kuramoto-cho, Tokushima-shi, Tokushima, 770-8504, Japan
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