1
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Mairaville C, Broyon M, Maurel M, Chentouf M, Chiavarina B, Turtoi A, Pirot N, Martineau P. Identification of monoclonal antibodies from naive antibody phage-display libraries for protein detection in formalin-fixed paraffin-embedded tissues. J Immunol Methods 2024; 532:113730. [PMID: 39059744 DOI: 10.1016/j.jim.2024.113730] [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: 04/08/2024] [Revised: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Most antibodies used in immunohistochemistry (IHC) have been developed by animal immunization. We wanted to explore naive antibody repertoires displayed on filamentous phages as a source of full-length antibodies for IHC on Formalin-Fixed and Paraffin-Embedded (FFPE) tissues. We used two isogenic mouse fibroblast cell lines that express or not human HER2 to generate positive and negative FFPE pseudo-tissue respectively. Using these pseudo-tissues and previously described approaches based on differential panning, we isolated very efficient antibody clones, but not against HER2. To optimize HER2 targeting and tissue specificity, we first performed 3-4 rounds of in vitro panning using recombinant HER2 extracellular domain (ECD) to enrich the phage library in HER2 binders, followed by one panning round using the two FFPE pseudo-tissues to retain binders for IHC conditions. We then analyzed the bound phages using next-generation sequencing to identify antibody sequences specifically associated with the HER2-positive pseudo-tissue. Using this approach, the top-ranked clone identified by sequencing was specific to the HER2-positive pseudo-tissue and showed a staining pattern similar to that of the antibody used for the clinical diagnosis of HER2-positive breast cancer. However, we could not optimize staining on other tissues, showing that specificity was restricted to the tissue used for selection and screening. Therefore, future optimized protocols must consider tissue diversity early during the selection by panning using a wide collection of tissue types.
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Affiliation(s)
| | - Morgane Broyon
- BCM, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Margaux Maurel
- IRCM, Univ. Montpellier, ICM, INSERM, Montpellier, France
| | | | | | - Andrei Turtoi
- IRCM, Univ. Montpellier, ICM, INSERM, Montpellier, France
| | - Nelly Pirot
- IRCM, Univ. Montpellier, ICM, INSERM, Montpellier, France; BCM, Univ. Montpellier, CNRS, INSERM, Montpellier, France
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2
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Song Z, Bian W, Lin J, Guo Y, Shi W, Meng H, Chen Y, Zhang M, Liu Z, Lin Z, Ma K, Li L. Heart proteomic profiling discovers MYH6 and COX5B as biomarkers for sudden unexplained death. Forensic Sci Int 2024; 361:112121. [PMID: 38971138 DOI: 10.1016/j.forsciint.2024.112121] [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: 12/04/2023] [Revised: 04/03/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Sudden unexplained death (SUD) is not uncommon in forensic pathology. Yet, diagnosis of SUD remains challenging due to lack of specific biomarkers. This study aimed to screen differentially expressed proteins (DEPs) and validate their usefulness as diagnostic biomarkers for SUD cases. We designed a three-phase investigation, where in the discovery phase, formalin-fixed paraffin-embedded (FFPE) heart specimens were screened through label-free proteomic analysis of cases dying from SUD, mechanical injury and carbon monoxide (CO) intoxication. A total of 26 proteins were identified to be DEPs for the SUD cases after rigorous criterion. Bioinformatics and Adaboost-recursive feature elimination (RFE) analysis further revealed that three of the 26 proteins (MYH6, COX5B and TNNT2) were potential discriminative biomarkers. In the training phase, MYH6 and COX5B were verified to be true DEPs in cardiac tissues from 29 independent SUD cases as compared with a serial of control cases (n = 42). Receiver operating characteristic (ROC) analysis illustrated that combination of MYH6 and COX5B achieved optimal diagnostic sensitivity (89.7 %) and specificity (84.4 %), with area under the curve (AUC) being 0.91. A diagnostic software based on the logistic regression formula derived from the training phase was then constructed. In the validation phase, the diagnostic software was applied to eight authentic SUD cases, seven (87.5 %) of which were accurately recognized. Our study provides a valid strategy towards practical diagnosis of SUD by integrating cardiac MYH6 and COX5B as dual diagnostic biomarkers.
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Affiliation(s)
- Ziyan Song
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Wensi Bian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Junyi Lin
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Yadong Guo
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, Hunan 410013, PR China.
| | - Weibo Shi
- Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, Hebei 050017, PR China.
| | - Hang Meng
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
| | - Yuanyuan Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, Jiangxi 341000, PR China.
| | - Molin Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Zheng Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Zijie Lin
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China.
| | - Kaijun Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
| | - Liliang Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China; Hebei Key Laboratory of Forensic Medicine, Shijiazhuang, Hebei 050017, PR China; Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Public Security, Bureau, Shanghai 200083, PR China.
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3
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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [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] [Indexed: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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Tan YC, Mustangin M, Rosli N, Wan Ahmad Kammal WSE, Md Isa N, Low TY, Lee PY, Chellappan DK, Jarmin R, Zuhdi Z, Azman A, Ian C, Yusof NM, Lim LC. EtOH-LN cryoembedding workflow to minimize freezing artifact in frozen tissues: A pilot study in preparing tissues compatible with mass spectrometry-based spatial proteomics application. Cryobiology 2024; 114:104843. [PMID: 38158171 DOI: 10.1016/j.cryobiol.2023.104843] [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: 07/06/2023] [Revised: 11/27/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Coolant-assisted liquid nitrogen (LN) flash freezing of frozen tissues has been widely adopted to preserve tissue morphology for histopathological annotations in mass spectrometry-based spatial proteomics techniques. However, existing coolants pose health risks upon inhalation and are expensive. To overcome this challenge, we present our pilot study by introducing the EtOH-LN workflow, which demonstrates the feasibility of using 95 % ethanol as a safer and easily accessible alternative to existing coolants for LN-based cryoembedding of frozen tissues. Our study reveals that both the EtOH-LN and LN-only cryoembedding workflows exhibit significantly reduced freezing artifacts compared to cryoembedding in cryostat (p < 0.005), while EtOH-LN (SD = 0.56) generates more consistent results compared to LN-only (SD = 1.29). We have modified a previously reported morphology restoration method to incorporate the EtOH-LN workflow, which successfully restored the tissue architecture from freezing artifacts (p < 0.05). Additional studies are required to validate the impact of the EtOH-LN workflow on the molecular profiles of tissues.
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Affiliation(s)
- Yong Chiang Tan
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia.
| | - Muaatamarulain Mustangin
- Department of Pathology, UKM Medical Centre (UKMMC), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Nurwahyuna Rosli
- Department of Pathology, UKM Medical Centre (UKMMC), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | | | - Nurismah Md Isa
- Department of Pathology, UKM Medical Centre (UKMMC), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia.
| | - Razman Jarmin
- Department of Surgery, UKM Medical Centre (UKMMC), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Zamri Zuhdi
- Department of Surgery, UKM Medical Centre (UKMMC), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Azlanudin Azman
- Department of Surgery, UKM Medical Centre (UKMMC), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Chik Ian
- Department of Surgery, UKM Medical Centre (UKMMC), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Nursuhadah Mohamed Yusof
- Department of Surgery, UKM Medical Centre (UKMMC), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Lay Cheng Lim
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia.
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5
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G Jagadeeshaprasad M, Zeng J, Zheng N. LC-MS bioanalysis of protein biomarkers and protein therapeutics in formalin-fixed paraffin-embedded tissue specimens. Bioanalysis 2024; 16:245-258. [PMID: 38226835 DOI: 10.4155/bio-2023-0210] [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] [Indexed: 01/17/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) is a form of preservation and preparation for biopsy specimens. FFPE tissue specimens are readily available as part of oncology studies because they are often collected for disease diagnosis or confirmation. FFPE tissue specimens could be extremely useful for retrospective studies on protein biomarkers because the samples preserved in FFPE blocks could be stable for decades. However, LC-MS bioanalysis of FFPE tissues poses significant challenges. In this Perspective, we review the benefits and recent developments in LC-MS approach for targeted protein biomarker and protein therapeutic analysis using FFPE tissues and their clinical and translational applications. We believe that LC-MS bioanalysis of protein biomarkers in FFPE tissue specimens represents a great potential for its clinical applications.
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Affiliation(s)
| | - Jianing Zeng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
| | - Naiyu Zheng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
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6
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McMahon JN, Gaffney EF, Aliaga-Kelly WJ, Stephens JF, Jalali A, Curran B. P53 loss of heterozygosity (LOH) in formalin-fixed paraffin-embedded leiomyosarcoma (LMS): a novel report. Ir J Med Sci 2024; 193:65-71. [PMID: 37468695 DOI: 10.1007/s11845-023-03370-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/05/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND The occurrence of p53 loss of heterozygosity (LOH) is a common genetic event in malignancy. LOH occurs when a heterozygous locus loses one of its two parental alleles, becoming homozygous at that locus, by either copy number loss (CNL-LOH) or by becoming copy number neutral (CNN-LOH). A role for CNL-LOH (cnLOH) has been postulated in cancer aetiology. Loss of heterozygosity (LOH) results in irreversible genetic loss. AIMS LOH was determined in DNA extracted from formalin-fixed paraffin-embedded (FFPE) leiomyosarcoma (LMS) specimens in a retrospective study from 30 patients, to assess the prognostic significance of LOH. The findings were analysed and their validity assessed. LOH was an adverse prognostic factor in LMS. Prospective uniform standardisation of formalin-fixation techniques is required. METHODS DNA was extracted from 169 formalin-fixed paraffin blocks of 30 patients with LMS, following extensive tissue microdissection. Genomic DNA was amplified using the polymerase chain reaction (PCR) technique. Fluorescence-based microsatellite PCR was used to detect and quantitate heterozygosity loss. RESULTS LOH was detected at gene locus 17p13 in 16 LMS (Four grade 2 and 12 grade 3 LMS). LOH was not detected in 14 LMS cases (one grade 1, five grade 2 and eight grade 3 LMS). LOH was associated with shorter patient survival. CONCLUSIONS The results reported herein endorse the value of utilizing FFPE DNA in identifying LOH as a prognostic factor in LMS. The results have implications for tumour biobanking and precision medicine in patients with sarcomas.
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Affiliation(s)
- John N McMahon
- Research Laboratory, St Vincent's University Hospital, University College Dublin, PathologyDublin, Ireland.
| | - Eoin F Gaffney
- Department of Histopathology, St James's Hospital and Trinity College Dublin, Dublin, Ireland
| | | | - John F Stephens
- Research Laboratory, St Vincent's University Hospital, University College Dublin, PathologyDublin, Ireland
| | | | - Bernadette Curran
- Department of Biochemistry, Royal College of Surgeons in Ireland, Dublin, Ireland
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7
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Darville LNF, Lockhart JH, Putty Reddy S, Fang B, Izumi V, Boyle TA, Haura EB, Flores ER, Koomen JM. A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues. Methods Mol Biol 2024; 2823:193-223. [PMID: 39052222 DOI: 10.1007/978-1-0716-3922-1_13] [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] [Indexed: 07/27/2024]
Abstract
Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the cross-linking and pre-analytical variables, these samples have utility for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients' medical histories. Proteomics of formalin-fixed paraffin-embedded (FFPE) tissues also integrates with histological evaluation and molecular pathology strategies, so that additional collection of research biopsies or resected tumor aliquots is not needed. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the protein extraction and proteomics sample preparation from FFPE samples can be onerous, particularly for small (i.e., limited or precious) samples. Therefore, we provide a protocol for a recently introduced kit-based EasyPep method with benchmarking against a modified version of the well-established filter-aided sample preparation strategy using laser-capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables while also supporting the development of methods for spatial proteomics to examine intratumoral heterogeneity. Data are posted in ProteomeXchange (PXD045879).
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Affiliation(s)
| | | | | | - Bin Fang
- H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | | | - John M Koomen
- H. Lee Moffitt Cancer Center, Tampa, FL, USA.
- Molecular Oncology/Pathology, Moffitt Cancer Center, Tampa, FL, USA.
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8
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Grignani P, Visonà SD, Fronda MV, Borrelli P, Monti MC, Bertoglio B, Conti A, Fattorini P, Previderè C. The role of single nucleotide polymorphisms related to iron homeostasis in mesothelioma susceptibility after asbestos exposure: a genetic study on autoptic samples. Front Public Health 2023; 11:1236558. [PMID: 37942251 PMCID: PMC10628177 DOI: 10.3389/fpubh.2023.1236558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
Asbestos-related diseases still represent a major public health problem all over the world. Among them, malignant mesothelioma (MM) is a poor-prognosis cancer, arising from the serosal lining of the pleura, pericardium and peritoneum, triggered by asbestos exposure. Literature data suggest the key role of iron metabolism in the coating process leading to the formation of asbestos bodies, considered to be both protective and harmful. Two sample sets of individuals were taken into consideration, both residing in Broni or neighboring cities (Northwestern Italy) where an asbestos cement factory was active between 1932 and 1993. The present study aims to compare the frequency of six SNPs involved in iron trafficking, previously found to be related to protection/predisposition to MM after asbestos exposure, between 48 male subjects with documented asbestos exposure who died of MM and 48 male subjects who were exposed to asbestos but did not develop MM or other neoplastic respiratory diseases (Non-Mesothelioma Asbestos Exposed - NMAE). The same analysis was performed on 76 healthy male controls. The allelic and genotypic frequencies of a sub-group of 107 healthy Italian individuals contained in the 1000 genomes database were considered for comparison. PCR-multiplex amplification followed by SNaPshot mini-sequencing reaction was used. The findings presented in this study show that the allelic and genotypic frequencies for six SNP markers involved in iron metabolism/homeostasis and the modulation of tumor microenvironment are not significantly different between the two sample sets of MM and NMAE. Therefore, the SNPs here considered do not seem to be useful markers for individual susceptibility to mesothelioma. This finding is not in agreement with previous literature.
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Affiliation(s)
- Pierangela Grignani
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Silvia Damiana Visonà
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Maria Vittoria Fronda
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Paola Borrelli
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
- Laboratory of Biostatistics, Department of Medical, Oral and Biotechnological Sciences, G. d’Annunzio, University of Chieti, Chieti, Italy
| | - Maria Cristina Monti
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Barbara Bertoglio
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Adelaide Conti
- Department of Medical and Surgical Specialities, Radiological Sciences and Public Health, Forensic Medicine Unit, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Ospedale di Cattinara, Trieste, Italy
| | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
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9
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Eccher A, Dei Tos AP, Scarpa A, L'Imperio V, Munari E, Troncone G, Naccarato AG, Seminati D, Pagni F. Cost analysis of archives in the pathology laboratories: from safety to management. J Clin Pathol 2023; 76:659-663. [PMID: 37532289 PMCID: PMC10511949 DOI: 10.1136/jcp-2023-209035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023]
Abstract
CONTEXT Despite the reluctance to invest and the challenging estimation of necessary supporting costs, optimising the archives seems to be one of the hottest topics in the future management of the pathology laboratories. Historically, archives were only partially designed to securely store and organise tissue specimens, and tracking systems were often flawed, posing significant risks to patients' health and legal ramifications for pathologists. OBJECTIVE The current review explores the available data from the literature on archives' management in pathology, including comprehensive business plans, structure setup, outfit, inventories, ongoing conservation and functional charges. DATA SOURCES Electronic searches in PubMed-MEDLINE and Embase were made to extract pertinent articles from the literature. Works about the archiving process and storage were included and analysed to extract information. Prepublication servers were ignored. Italian Institutional Regional databases for public competitive bidding processes were queried too. CONCLUSIONS A new emergent feeling in the pathology laboratory is growing for archives management; the digital pathology era is a great opportunity to apply innovation to tracking systems and samples preservation. The main aim is a critical evaluation of the return of investment in developing automatic and tracked archiving processes for improving not only quality, efficacy and efficiency of the labs but also patients' healthcare.
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Affiliation(s)
- Albino Eccher
- Department of Diagnostics and Public Health, Università degli Studi di Verona, Verona, Italy
| | | | - Aldo Scarpa
- Department of Diagnostics and Public Health, Università degli Studi di Verona, Verona, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
| | - Enrico Munari
- Department of Pathology, University of Brescia, Brescia, Italy
| | - Giancarlo Troncone
- Public Health, University of Naples Federico II School of Medicine and Surgery, Napoli, Italy
| | | | - Davide Seminati
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
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10
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Zhang S, He S, Zhu X, Wang Y, Xie Q, Song X, Xu C, Wang W, Xing L, Xia C, Wang Q, Li W, Zhang X, Yu J, Ma S, Shi J, Gu H. DNA methylation profiling to determine the primary sites of metastatic cancers using formalin-fixed paraffin-embedded tissues. Nat Commun 2023; 14:5686. [PMID: 37709764 PMCID: PMC10502058 DOI: 10.1038/s41467-023-41015-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Identifying the primary site of metastatic cancer is critical to guiding the subsequent treatment. Approximately 3-9% of metastatic patients are diagnosed with cancer of unknown primary sites (CUP) even after a comprehensive diagnostic workup. However, a widely accepted molecular test is still not available. Here, we report a method that applies formalin-fixed, paraffin-embedded tissues to construct reduced representation bisulfite sequencing libraries (FFPE-RRBS). We then generate and systematically evaluate 28 molecular classifiers, built on four DNA methylation scoring methods and seven machine learning approaches, using the RRBS library dataset of 498 fresh-frozen tumor tissues from primary cancer patients. Among these classifiers, the beta value-based linear support vector (BELIVE) performs the best, achieving overall accuracies of 81-93% for identifying the primary sites in 215 metastatic patients using top-k predictions (k = 1, 2, 3). Coincidentally, BELIVE also successfully predicts the tissue of origin in 81-93% of CUP patients (n = 68).
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Affiliation(s)
- Shirong Zhang
- Translational Medicine Research Center, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China
| | - Shutao He
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, 100089, Beijing, China
| | - Xin Zhu
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, 310022, Hangzhou, Zhejiang Province, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Qionghuan Xie
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Xianrang Song
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Chunwei Xu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangshu Province, China
| | - Wenxian Wang
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, 310022, Hangzhou, Zhejiang Province, China
| | - Ligang Xing
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Chengqing Xia
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Qian Wang
- Department of Respiratory Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, 210029, Nanjing, Jiangshu Province, China
| | - Wenfeng Li
- Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang Province, China
| | - Xiaochen Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 310006, Hangzhou, Zhejiang Province, China
| | - Jinming Yu
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Shenglin Ma
- Translational Medicine Research Center, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China.
- Department of Oncology, Hangzhou Cancer Hospital, 310006, Hangzhou, Zhejiang Province, China.
| | - Jiantao Shi
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, Anhui Province, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, 230031, Hefei, Anhui Province, China.
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11
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Schatz S, Willnow L, Winkels M, Rosengarten JF, Theek B, Johnston ICD, Stitz J. Generation of Antibodies Selectively Recognizing Epitopes in a Formaldehyde-Fixed Cell-Surface Antigen Using Virus-like Particle Display and Hybridoma Technology. Antibodies (Basel) 2023; 12:57. [PMID: 37753971 PMCID: PMC10525569 DOI: 10.3390/antib12030057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023] Open
Abstract
Efficient induction of target-specific antibodies can be elicited upon immunization with highly immunogenic virus-like particles (VLPs) decorated with desired membrane-anchored target antigens (Ags). However, for example, for diagnostic purposes, monoclonal antibodies (mAbs) are required to enable the histological examination of formaldehyde-fixed paraffin-embedded (FFPE) biopsy tissue samples. Aiming at the generation of FFPE-antigen-specific mAbs and as a proof of concept (POC), we first established a simplified protocol using only formaldehyde and 90 °C heat fixation (FF90) of cells expressing the target Ag nerve growth factor receptor (NGFR). The FF90 procedure was validated using flow cytometric analysis and two mAbs recognizing either the native and FFPE-Ag or exclusively the native Ag. C-terminally truncated NGFR (trNGFR)-displaying native and FF90-treated VLPs derived from HIV-1 did not reveal distinctive changes in particle morphology using transmission electron microscopy (TEM) and dynamic light scattering (DLS) analysis. Mice were subsequently repetitively immunized with trNGFR-decorated FF90-VLPs and hybridoma technology was used to establish mAb-producing cell clones. In multiple screening rounds, nine cell clones were identified producing mAbs distinctively recognizing epitopes in FF90- and FFPE-NGFR. This POC of a new methodology should foster the future generation of mAbs selectively targeting FFPE-fixed cell-surface Ags.
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Affiliation(s)
- Stefanie Schatz
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, University of Applied Sciences Cologne, Campusplatz 1, 51379 Leverkusen, Germany
- Institute of Technical Chemistry, Gottfried Wilhelm Leibniz University Hannover, Calinstrasse 3-9, 30167 Hannover, Germany
| | - Lena Willnow
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Strasse 68, 51429 Bergisch Gladbach, Germany
| | - Monika Winkels
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Strasse 68, 51429 Bergisch Gladbach, Germany
| | - Jamila Franca Rosengarten
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, University of Applied Sciences Cologne, Campusplatz 1, 51379 Leverkusen, Germany
- Institute of Technical Chemistry, Gottfried Wilhelm Leibniz University Hannover, Calinstrasse 3-9, 30167 Hannover, Germany
| | - Benjamin Theek
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Strasse 68, 51429 Bergisch Gladbach, Germany
| | - Ian C. D. Johnston
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Strasse 68, 51429 Bergisch Gladbach, Germany
| | - Jörn Stitz
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, University of Applied Sciences Cologne, Campusplatz 1, 51379 Leverkusen, Germany
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12
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O’Sullivan B, Seoighe C. Comprehensive and realistic simulation of tumour genomic sequencing data. NAR Cancer 2023; 5:zcad051. [PMID: 37746635 PMCID: PMC10516706 DOI: 10.1093/narcan/zcad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Accurate identification of somatic mutations and allele frequencies in cancer has critical research and clinical applications. Several computational tools have been developed for this purpose but, in the absence of comprehensive 'ground truth' data, assessing the accuracy of these methods is challenging. We created a computational framework to simulate tumour and matched normal sequencing data for which the source of all loci that contain non-reference bases is known, based on a phased, personalized genome. Unlike existing methods, we account for sampling errors inherent in the sequencing process. Using this framework, we assess accuracy and biases in inferred mutations and their frequencies in an established somatic mutation calling pipeline. We demonstrate bias in existing methods of mutant allele frequency estimation and show, for the first time, the observed mutation frequency spectrum corresponding to a theoretical model of tumour evolution. We highlight the impact of quality filters on detection sensitivity of clinically actionable variants and provide definitive assessment of false positive and false negative mutation calls. Our simulation framework provides an improved means to assess the accuracy of somatic mutation calling pipelines and a detailed picture of the effects of technical parameters and experimental factors on somatic mutation calling in cancer samples.
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Affiliation(s)
- Brian O’Sullivan
- School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
| | - Cathal Seoighe
- School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
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13
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Vitošević K, Todorović D, Slović Ž, Varljen T, Radaković I, Radojević D, Čanović V, Todorović M. The quality of DNA isolated from autopsy formalin-fixed and formalin-fixed paraffin-embedded tissues: study of 1662 samples. Mol Biol Rep 2023; 50:6323-6336. [PMID: 37310548 DOI: 10.1007/s11033-023-08491-5] [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: 01/05/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND There are enormous formalin-fixed paraffin-embedded tissue archives and a constantly growing number of methods for molecular analyses but, the isolation of DNA from this tissue is still challenging due to the damaging effect of formalin on DNA. To determine the extent to which DNA purity, yield and integrity depend on the process of fixation in formalin, and to what extent on the process of tissue paraffin embedding, we compared the quality of DNA isolated from fixed tissues and DNA isolated from tissues embedded in paraffin blocks after fixation. METHODS AND RESULTS Heart, liver and brain tissues obtained from healthy people who suddenly died a violent death were fixed in 10% buffered formalin as well as in 4% unbuffered formalin for 6 h, 1-7 days (every 24 h), 10, 14, 28 days and 2 months. Additionally, the same tissues were fixed in 4% unbuffered formalin embedded in a paraffin block and stored from a few months to 30 years. The yield and purity of the DNA samples isolated from these tissues were measured using spectrophotometry. PCR amplification of the hTERT gene was performed to evaluate the degree of DNA fragmentation. Although the purity of the DNA isolated from almost all tissue samples was satisfactory, the DNA yields changed significantly. There was a decrease in successful PCR amplification of the hTERT gene in DNA samples isolated from tissue fixed in buffered and unbuffered formalin for up to 2 months from 100% to 8.3%. Archiving the tissue in paraffin blocks for up to 30 years also impacts the integrity of DNA, so there was a decrease in PCR amplification of the hTERT gene from 91% success to 3%. CONCLUSION The largest decrease in DNA yield was observed after tissue formalin fixation after 14 days of fixation in buffered and unbuffered formalin. DNA integrity depends on the time of tissue formalin fixation, especially after 6 days for tissue fixed in unbuffered formalin, while for tissue fixed in buffered formalin the time is prolonged up to 28 days. The age of paraffin blocks also impacted DNA integrity, after 1 year and 16 years of archiving the paraffin blocks of tissues, there was a decrease in the success of PCR amplification.
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Affiliation(s)
- Katarina Vitošević
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia.
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia.
| | - Danijela Todorović
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Živana Slović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
| | - Tatjana Varljen
- Institute of Legal Medicine, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Radaković
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Dušan Radojević
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Vanja Čanović
- Faculty of Medical Sciences, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Miloš Todorović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
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Powell CL, Saddoughi SA, Wigle DA. Progress in genome-inspired treatment decisions for multifocal lung adenocarcinoma. Expert Rev Respir Med 2023; 17:1009-1021. [PMID: 37982734 DOI: 10.1080/17476348.2023.2286277] [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: 07/05/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023]
Abstract
INTRODUCTION Multifocal lung adenocarcinoma (MFLA) is becoming increasingly recognized as a distinct subset of lung cancer, with unique biology, disease course, and treatment outcomes. While definitions remain controversial, MFLA is characterized by the development and concurrent presence of multiple independent (non-metastatic) lesions on the lung adenocarcinoma spectrum. Disease progression typically follows an indolent course measured in years, with a lower propensity for nodal and distant metastases than other more common forms of non-small cell lung cancer. AREAS COVERED Traditional imaging and histopathological analyses of tumor biopsies are frequently unable to fully characterize the disease, prompting interest in molecular diagnosis. We highlight some of the key questions in the field, including accurate definitions to identify and stage MLFA, molecular tests to stratify patients and treatment decisions, and the lack of clinical trial data to delineate best management for this poorly understood subset of lung cancer patients. We review the existing literature and progress toward a genomic diagnosis for this unique disease entity. EXPERT OPINION Multifocal lung adenocarcinoma behaves differently than other forms of non-small cell lung cancer. Progress in molecular diagnosis may enhance potential for accurate definition, diagnosis, and optimizing treatment approach.
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Affiliation(s)
- Chelsea L Powell
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Sahar A Saddoughi
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Dennis A Wigle
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
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15
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Civil YA, Oei AL, Duvivier KM, Bijker N, Meijnen P, Donkers L, Verheijen S, van Kesteren Z, Palacios MA, Schijf LJ, Barbé E, Konings IRHM, -van der Houven van Oordt CWM, Westhoff PG, Meijer HJM, Diepenhorst GMP, Thijssen V, Mouliere F, Slotman BJ, van der Velde S, van den Bongard HJGD. Prediction of pathologic complete response after single-dose MR-guided partial breast irradiation in low-risk breast cancer patients: the ABLATIVE-2 trial-a study protocol. BMC Cancer 2023; 23:419. [PMID: 37161377 PMCID: PMC10169374 DOI: 10.1186/s12885-023-10910-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Partial breast irradiation (PBI) is standard of care in low-risk breast cancer patients after breast-conserving surgery (BCS). Pre-operative PBI can result in tumor downstaging and more precise target definition possibly resulting in less treatment-related toxicity. This study aims to assess the pathologic complete response (pCR) rate one year after MR-guided single-dose pre-operative PBI in low-risk breast cancer patients. METHODS The ABLATIVE-2 trial is a multicenter prospective single-arm trial using single-dose ablative PBI in low-risk breast cancer patients. Patients ≥ 50 years with non-lobular invasive breast cancer ≤ 2 cm, grade 1 or 2, estrogen receptor-positive, HER2-negative, and tumor-negative sentinel node procedure are eligible. A total of 100 patients will be enrolled. PBI treatment planning will be performed using a radiotherapy planning CT and -MRI in treatment position. The treatment delivery will take place on a conventional or MR-guided linear accelerator. The prescribed radiotherapy dose is a single dose of 20 Gy to the tumor, and 15 Gy to the 2 cm of breast tissue surrounding the tumor. Follow-up MRIs, scheduled at baseline, 2 weeks, 3, 6, 9, and 12 months after PBI, are combined with liquid biopsies to identify biomarkers for pCR prediction. BCS will be performed 12 months after radiotherapy or after 6 months, if MRI does not show a radiologic complete response. The primary endpoint is the pCR rate after PBI. Secondary endpoints are radiologic response, toxicity, quality of life, cosmetic outcome, patient distress, oncological outcomes, and the evaluation of biomarkers in liquid biopsies and tumor tissue. Patients will be followed up to 10 years after radiation therapy. DISCUSSION This trial will investigate the pathological tumor response after pre-operative single-dose PBI after 12 months in patients with low-risk breast cancer. In comparison with previous trial outcomes, a longer interval between PBI and BCS of 12 months is expected to increase the pCR rate of 42% after 6-8 months. In addition, response monitoring using MRI and biomarkers will help to predict pCR. Accurate pCR prediction will allow omission of surgery in future patients. TRIAL REGISTRATION The trial was registered prospectively on April 28th 2022 at clinicaltrials.gov (NCT05350722).
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Affiliation(s)
- Yasmin A. Civil
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
| | - Arlene L. Oei
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Department of Radiation Oncology, Amsterdam UMC Location Universiteit van Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Katya M. Duvivier
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Department of Radiology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - Nina Bijker
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
| | - Philip Meijnen
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
| | - Lorraine Donkers
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - Sonja Verheijen
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - Zdenko van Kesteren
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
| | - Miguel A. Palacios
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
| | - Laura J. Schijf
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Department of Radiology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - Ellis Barbé
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - Inge R. H. M. Konings
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - C. Willemien Menke -van der Houven van Oordt
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - Paulien G. Westhoff
- Department of Radiation Oncology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
| | - Hanneke J. M. Meijer
- Department of Radiation Oncology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
| | - Gwen M. P. Diepenhorst
- Department of Surgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - Victor Thijssen
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Florent Mouliere
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - Berend J. Slotman
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
| | - Susanne van der Velde
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Department of Surgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
| | - H. J. G. Desirée van den Bongard
- Department of Radiation Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
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16
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Eccher A, Scarpa A, Dei Tos AP. Impact of a centralized archive for pathology laboratories on the health system. Pathol Res Pract 2023; 245:154488. [PMID: 37116365 DOI: 10.1016/j.prp.2023.154488] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 04/30/2023]
Abstract
The pathology archive of any hospital is likely to contain tens of thousands of slides and formalin-fixed and paraffin-embedded (FFPE) blocks, with their number constantly increasing. As a result, serious space and management issues are created. There has always been a favorable location for the pathology laboratory to rapidly and efficiently collect specimens and to meet the different service requirements of clinicians and patients. However, archiving may be one of the most neglected issues in the planning of spaces and activities, so much so that many laboratories are currently in trouble and looking for space inside and outside their hospitals. Another crucial issue is related to the environmental conditions of the identified preservation place, which, based on their characteristics, probably provide suboptimal habitats in most cases. For FFPE blocks, controlled temperature (<27 °C) and humidity (>30% and <70%) are recommended, with control systems for parasite infestation. For glass slides, systems suitable for guaranteeing their safety, traceability and conservation suitable for possible revision are recommended. The aim of this position paper is to outline the issues that currently exist in archives and to suggest a rational health policy solution to overcome the problems raised.
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Affiliation(s)
- Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy.
| | - Aldo Scarpa
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Angelo Paolo Dei Tos
- Surgical Pathology & Cytopathology Unit, Department of Medicine - DIMED, University of Padua, Padua, Italy
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17
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Nguyen TT, Hamdan D, Angeli E, Feugeas JP, Le QV, Pamoukdjian F, Bousquet G. Genomics of Breast Cancer Brain Metastases: A Meta-Analysis and Therapeutic Implications. Cancers (Basel) 2023; 15:cancers15061728. [PMID: 36980614 PMCID: PMC10046845 DOI: 10.3390/cancers15061728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/05/2023] [Accepted: 03/05/2023] [Indexed: 03/14/2023] Open
Abstract
Breast cancer brain metastases are a challenging daily practice, and the biological link between gene mutations and metastatic spread to the brain remains to be determined. Here, we performed a meta-analysis on genomic data obtained from primary tumors, extracerebral metastases and brain metastases, to identify gene alterations associated with metastatic processes in the brain. Articles with relevant findings were selected using Medline via PubMed, from January 1999 up to February 2022. A critical review was conducted according to the Preferred Reporting Items for Systematic Review and Meta-analysis statement (PRISMA). Fifty-seven publications were selected for this meta-analysis, including 37,218 patients in all, 11,906 primary tumor samples, 5541 extracerebral metastasis samples, and 1485 brain metastasis samples. We report the overall and sub-group prevalence of gene mutations, including comparisons between primary tumors, extracerebral metastases and brain metastases. In particular, we identified six genes with a higher mutation prevalence in brain metastases than in extracerebral metastases, with a potential role in metastatic processes in the brain: ESR1, ERBB2, EGFR, PTEN, BRCA2 and NOTCH1. We discuss here the therapeutic implications. Our results underline the added value of obtaining biopsies from brain metastases to fully explore their biology, in order to develop personalized treatments.
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Affiliation(s)
- Thuy Thi Nguyen
- National Cancer Hospital, Ha Noi 100000, Vietnam
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Department of Pediatrics, Hanoi Medical University, Ha Noi 100000, Vietnam
- Institut Galilée, Université Sorbonne Paris Nord, 93439 Villetaneuse, France
| | - Diaddin Hamdan
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Hôpital La Porte Verte, 78000 Versailles, France
| | - Eurydice Angeli
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Institut Galilée, Université Sorbonne Paris Nord, 93439 Villetaneuse, France
- Service d’Oncologie Médicale, Hôpital Avicenne, Assistance Publique Hôpitaux de Paris, 93000 Bobigny, France
| | - Jean-Paul Feugeas
- INSERM U1098, 25030 Besançon, France
- Laboratoire de Biochimie Hôpital Jean Minjoz, Université de Franche-Comté, 25000 Besançon, France
- Correspondence: (J.-P.F.); (G.B.)
| | - Quang Van Le
- National Cancer Hospital, Ha Noi 100000, Vietnam
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
| | - Frédéric Pamoukdjian
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Institut Galilée, Université Sorbonne Paris Nord, 93439 Villetaneuse, France
- Service de Médecine Gériatrique, Hôpital Avicenne, Assistance Publique Hôpitaux de Paris, 93000 Bobigny, France
| | - Guilhem Bousquet
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Université Paris Cité, UMR_S942 MASCOT, 75006 Paris, France (F.P.)
- Institut Galilée, Université Sorbonne Paris Nord, 93439 Villetaneuse, France
- Service d’Oncologie Médicale, Hôpital Avicenne, Assistance Publique Hôpitaux de Paris, 93000 Bobigny, France
- Correspondence: (J.-P.F.); (G.B.)
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18
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Thorsen ASF, Riber LPS, Rasmussen LM, Overgaard M. A targeted multiplex mass spectrometry method for quantitation of abundant matrix and cellular proteins in formalin-fixed paraffin embedded arterial tissue. J Proteomics 2023; 272:104775. [PMID: 36414230 DOI: 10.1016/j.jprot.2022.104775] [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: 04/29/2022] [Revised: 08/30/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022]
Abstract
Assessment of proteins in formalin-fixed paraffin-embedded (FFPE) tissue traditionally hinges on immunohistochemistry and immunoblotting. These methods are far from optimal for quantitative studies and not suitable for large-scale testing of multiple protein panels. In this study, we developed and optimised a novel targeted isotope dilution mass spectrometry (MS)-based method for FFPE samples, designed to quantitate 17 matrix and cytosolic proteins abundantly present in arterial tissue. Our new method was developed on FFPE human tissue samples of the internal thoracic artery obtained from coronary artery bypass graft (CABG) operations. The workflow has a limit of 60 samples per day. Assay precision improved by normalisation to both beta-actin and smooth muscle actin with inter-assay coefficients of variation (CV) ranging from 5.3% to 31.9%. To demonstrate clinical utility of the assay we analysed 40 FFPE artery specimens from two groups of patients with or without type 2 diabetes. We observed increased levels of collagen type IV α1 and α2 in patients with diabetes. The assay is scalable for larger cohorts and advantageous for pathophysiological studies in diabetes and the method is easily convertible to analysis of other proteins in FFPE artery samples. SIGNIFICANCE: This article presents a novel robust and precise targeted mass spectrometry assay for relative quantitation of a panel of abundant matrix and cellular arterial proteins in archived formalin-fixed paraffin-embedded arterial samples. We demonstrate its utility in pathophysiological studies of cardiovascular disease in diabetes.
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Affiliation(s)
- Anne-Sofie Faarvang Thorsen
- Department of Clinical Biochemistry and Center for Individualised Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Steno Diabetes Center Odense (SDCO), Odense, Denmark
| | - Lars Peter Schødt Riber
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Department of Cardiac, Thoracic and Vascular Surgery, Odense University Hospital, Odense, Denmark
| | - Lars Melholt Rasmussen
- Department of Clinical Biochemistry and Center for Individualised Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin Overgaard
- Department of Clinical Biochemistry and Center for Individualised Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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19
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Hamdan D, Marisa L, Tlemsani C, Angeli E, Soussan M, Derive N, Laurent-Puig P, Bousquet G. Olaparib in the Setting of Radiotherapy-Associated Sarcoma: What Can Precision Medicine Offer For Rare Cancers? JCO Precis Oncol 2023; 7:e2200582. [PMID: 36848605 DOI: 10.1200/po.22.00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Affiliation(s)
- Diaddin Hamdan
- Université Paris Cité, INSERM, UMR_S942 MASCOT, Paris, France.,Medical Oncology Department, Hôpital La Porte Verte, Versailles, France
| | | | - Camille Tlemsani
- Multi-site Medical Biology Laboratory SeqOIA, Paris, France.,Medical Oncology Department, Hôpital Cochin, AP-HP, Paris, France.,Université Paris Cité, Paris, France
| | - Eurydice Angeli
- Université Paris Cité, INSERM, UMR_S942 MASCOT, Paris, France.,Université Sorbonne Paris Nord, Villetaneuse, France.,Medical Oncology Department, AP-HP-Hôpital Avicenne, Bobigny, France
| | - Michael Soussan
- Université Sorbonne Paris Nord, Villetaneuse, France.,Nuclear Medicine Departments, AP-HP-Hôpital Avicenne, Bobigny, France
| | - Nicolas Derive
- Multi-site Medical Biology Laboratory SeqOIA, Paris, France
| | - Pierre Laurent-Puig
- Multi-site Medical Biology Laboratory SeqOIA, Paris, France.,Institut of Cancer Paris CARPEM, AP-HP-Hôpital Européen Georges Pompidou, Paris, France.,Centre de Recherche des Cordeliers, INSERM, CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, Paris, France
| | - Guilhem Bousquet
- Université Paris Cité, INSERM, UMR_S942 MASCOT, Paris, France.,Université Sorbonne Paris Nord, Villetaneuse, France.,Medical Oncology Department, AP-HP-Hôpital Avicenne, Bobigny, France
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20
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Obi EN, Tellock DA, Thomas GJ, Veenstra TD. Biomarker Analysis of Formalin-Fixed Paraffin-Embedded Clinical Tissues Using Proteomics. Biomolecules 2023; 13:biom13010096. [PMID: 36671481 PMCID: PMC9855471 DOI: 10.3390/biom13010096] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
The relatively recent developments in mass spectrometry (MS) have provided novel opportunities for this technology to impact modern medicine. One of those opportunities is in biomarker discovery and diagnostics. Key developments in sample preparation have enabled a greater range of clinical samples to be characterized at a deeper level using MS. While most of these developments have focused on blood, tissues have also been an important resource. Fresh tissues, however, are difficult to obtain for research purposes and require significant resources for long-term storage. There are millions of archived formalin-fixed paraffin-embedded (FFPE) tissues within pathology departments worldwide representing every possible tissue type including tumors that are rare or very small. Owing to the chemical technique used to preserve FFPE tissues, they were considered intractable to many newer proteomics techniques and primarily only useful for immunohistochemistry. In the past couple of decades, however, researchers have been able to develop methods to extract proteins from FFPE tissues in a form making them analyzable using state-of-the-art technologies such as MS and protein arrays. This review will discuss the history of these developments and provide examples of how they are currently being used to identify biomarkers and diagnose diseases such as cancer.
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21
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Verheggen K, Bhattacharya N, Verhaert M, Goossens B, Sciot R, Verhaert P. HistoSnap: A Novel Software Tool to Extract m/z-Specific Images from Large MSHC Datasets. Methods Mol Biol 2023; 2688:15-26. [PMID: 37410280 DOI: 10.1007/978-1-0716-3319-9_2] [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] [Indexed: 07/07/2023]
Abstract
We describe an informatics tool for comfortable browsing through highly complex, multi-gigabyte mass spectrometry histochemistry (MSHC) datasets, via clever ion-specific image extraction.The package is developed particularly for the untargeted localization/discovery of biomolecules such as endogenous (neuro)secretory peptides on histological sections of biobanked formaldehyde-fixed paraffin-embedded (FFPE) samples straight from tissue banks.Atmospheric pressure-MALDI-Orbitrap MSHC data of sections through human pituitary adenomas in which two well-known human neuropeptides are detected are used as an example to demonstrate the key features of the novel software, named HistoSnap.
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Affiliation(s)
| | | | - Marthe Verhaert
- ProteoFormiX, Beerse, Belgium
- Department of Medical Oncology at Institute Jules Bordet, Brussels, Belgium
| | | | - Raf Sciot
- ProteoFormiX, Beerse, Belgium
- Translational Tissue and Cell Research Unit, Department of Imaging and Pathology, University Hospital, Leuven, Belgium
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22
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Decruyenaere P, Verniers K, Poma-Soto F, Van Dorpe J, Offner F, Vandesompele J. RNA Extraction Method Impacts Quality Metrics and Sequencing Results in Formalin-Fixed, Paraffin-Embedded Tissue Samples. J Transl Med 2023; 103:100027. [PMID: 37039153 DOI: 10.1016/j.labinv.2022.100027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/19/2022] [Accepted: 11/03/2022] [Indexed: 01/11/2023] Open
Abstract
Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are being increasingly used in molecular cancer research. Compared with fresh-frozen tissue, the nucleic acid analysis of FFPE tissue is technically more challenging. This study aimed to compare the impact of 3 different RNA extraction methods on yield, quality, and sequencing-based gene expression results in FFPE samples. RNA extraction was performed in 16 FFPE tumor specimens from patients with diffuse large B-cell lymphoma and in reference FFPE material from microsatellite-stable and microsatellite-instable cell lines (3 replicates each) using 2 silica-based procedures (A, miRNeasy FFPE; C, iCatcher FFPE Tissue RNA) and 1 isotachophoresis-based procedure (B, Ionic FFPE to Pure RNA). The RNA yield; RNA integrity, as reflected by the distribution value 200; and RNA purity, as reflected by the 260/280 and the 260/230 nm absorbance ratios, were determined. The RNA was sequenced on the NovaSeq 6000 instrument using the TruSeq RNA Exome and SMARTer Stranded Total RNA-Seq Pico v3 library preparations kits. Our results highlight the impact of RNA extraction methodology on both preanalytical and sequencing-based gene expression results. Overall, methods B and C outperformed method A because these showed significantly higher fractions of uniquely mapped reads, an increased number of detectable genes, a lower fraction of duplicated reads, and better representation of the B-cell receptor repertoire. Differences among the extraction methods were generally more explicit for the total RNA sequencing method than for the exome-capture sequencing method. Importantly, the predicative value of quality metrics varies among extraction kits, and caution should be applied when comparing and interpreting results obtained using different methods.
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23
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Miki Y, Iwabuchi E, Suzuki T. In Situ Proximity Ligation Assay to Visualize Protein-Protein Interactions in Tumor Specimens. Methods Mol Biol 2023; 2660:123-135. [PMID: 37191794 DOI: 10.1007/978-1-0716-3163-8_9] [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] [Indexed: 05/17/2023]
Abstract
Protein-protein interactions (PPI) are the basis of various biological phenomena, such as intracellular signal transduction, gene transcription, and metabolism. PPI are also considered to be involved in the pathogenesis and development of various diseases, including cancer. PPI phenomenon and their functions have been elucidated by gene transfection and molecular detection technologies. On the other hand, in histopathological analysis, although immunohistochemical analyses provide information pertaining to protein expression and their localization in pathophysiological tissues, it has been difficult to visualize the PPI of these proteins. An in situ proximity ligation assay (PLA) was developed as a microscopic visualization technique for PPI in formalin-fixed, paraffin-embedded (FFPE) tissues as well as in cultured cells and frozen tissues. PLA using histopathological specimens enables cohort studies of PPI, which can clarify the significance of PPI in pathology. We have previously shown the dimerization pattern of estrogen receptors and significance of HER2-binding proteins using breast cancer FFPE tissues. In this chapter, we describe a methodology for the visualization of PPI using PLA in pathological specimens.
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Affiliation(s)
- Yasuhiro Miki
- Department of Nursing, Faculty of Medical Science and Welfare, Tohoku Bunka Gakuen University, Sendai, Japan.
| | - Erina Iwabuchi
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
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24
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Orlow I, Sadeghi KD, Edmiston SN, Kenney JM, Lezcano C, Wilmott JS, Cust AE, Scolyer RA, Mann GJ, Lee TK, Burke H, Jakrot V, Shang P, Ferguson PM, Boyce TW, Ko JS, Ngo P, Funchain P, Rees JR, O'Connell K, Hao H, Parrish E, Conway K, Googe PB, Ollila DW, Moschos SJ, Hernando E, Hanniford D, Argibay D, Amos CI, Lee JE, Osman I, Luo L, Kuan PF, Aurora A, Gould Rothberg BE, Bosenberg MW, Gerstenblith MR, Thompson C, Bogner PN, Gorlov IP, Holmen SL, Brunsgaard EK, Saenger YM, Shen R, Seshan V, Nagore E, Ernstoff MS, Busam KJ, Begg CB, Thomas NE, Berwick M. InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. PLoS One 2023; 18:e0269324. [PMID: 37011054 PMCID: PMC10069769 DOI: 10.1371/journal.pone.0269324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
INTRODUCTION We are conducting a multicenter study to identify classifiers predictive of disease-specific survival in patients with primary melanomas. Here we delineate the unique aspects, challenges, and best practices for optimizing a study of generally small-sized pigmented tumor samples including primary melanomas of at least 1.05mm from AJTCC TNM stage IIA-IIID patients. We also evaluated tissue-derived predictors of extracted nucleic acids' quality and success in downstream testing. This ongoing study will target 1,000 melanomas within the international InterMEL consortium. METHODS Following a pre-established protocol, participating centers ship formalin-fixed paraffin embedded (FFPE) tissue sections to Memorial Sloan Kettering Cancer Center for the centralized handling, dermatopathology review and histology-guided coextraction of RNA and DNA. Samples are distributed for evaluation of somatic mutations using next gen sequencing (NGS) with the MSK-IMPACTTM assay, methylation-profiling (Infinium MethylationEPIC arrays), and miRNA expression (Nanostring nCounter Human v3 miRNA Expression Assay). RESULTS Sufficient material was obtained for screening of miRNA expression in 683/685 (99%) eligible melanomas, methylation in 467 (68%), and somatic mutations in 560 (82%). In 446/685 (65%) cases, aliquots of RNA/DNA were sufficient for testing with all three platforms. Among samples evaluated by the time of this analysis, the mean NGS coverage was 249x, 59 (18.6%) samples had coverage below 100x, and 41/414 (10%) failed methylation QC due to low intensity probes or insufficient Meta-Mixed Interquartile (BMIQ)- and single sample (ss)- Noob normalizations. Six of 683 RNAs (1%) failed Nanostring QC due to the low proportion of probes above the minimum threshold. Age of the FFPE tissue blocks (p<0.001) and time elapsed from sectioning to co-extraction (p = 0.002) were associated with methylation screening failures. Melanin reduced the ability to amplify fragments of 200bp or greater (absent/lightly pigmented vs heavily pigmented, p<0.003). Conversely, heavily pigmented tumors rendered greater amounts of RNA (p<0.001), and of RNA above 200 nucleotides (p<0.001). CONCLUSION Our experience with many archival tissues demonstrates that with careful management of tissue processing and quality control it is possible to conduct multi-omic studies in a complex multi-institutional setting for investigations involving minute quantities of FFPE tumors, as in studies of early-stage melanoma. The study describes, for the first time, the optimal strategy for obtaining archival and limited tumor tissue, the characteristics of the nucleic acids co-extracted from a unique cell lysate, and success rate in downstream applications. In addition, our findings provide an estimate of the anticipated attrition that will guide other large multicenter research and consortia.
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Affiliation(s)
- Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Keimya D Sadeghi
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Sharon N Edmiston
- Department of Dermatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jessica M Kenney
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Cecilia Lezcano
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Anne E Cust
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- The Daffodil Centre, University of Sydney, a joint venture with Cancer Council New South Wales, Australia
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Tim K Lee
- British Columbia Cancer Research Center, Vancouver, British Columbia, Canada
| | - Hazel Burke
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Valerie Jakrot
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Ping Shang
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Tawny W Boyce
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, United States of America
| | - Jennifer S Ko
- Department of Pathology, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Peter Ngo
- Department of Hospital Medicine, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Pauline Funchain
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Judy R Rees
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Kelli O'Connell
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Honglin Hao
- Department of Dermatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Eloise Parrish
- Department of Dermatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kathleen Conway
- Department of Dermatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paul B Googe
- Department of Dermatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David W Ollila
- Department of Surgery, Division of Surgical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stergios J Moschos
- Department of Medicine, Division of Medical Oncology, The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, United States of America
| | - Eva Hernando
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Douglas Hanniford
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Diana Argibay
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jeffrey E Lee
- Department of Surgical Oncology, University of Texas, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Iman Osman
- Department of Urology, New York University Grossman School of Medicine, New York, NY, United States of America
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America
- Department of Dermatology, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Li Luo
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, United States of America
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
| | - Arshi Aurora
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Bonnie E Gould Rothberg
- Smilow Cancer Hospital, Yale-New Haven Health System, New Haven, Connecticut, United States of America
| | - Marcus W Bosenberg
- Department of Internal Medicine, Section of Medical Oncology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Meg R Gerstenblith
- Department of Dermatology, University Hospitals Cleveland Medical Center/Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Cheryl Thompson
- Department of Nutrition, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Public Health Sciences, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Paul N Bogner
- Department of Dermatology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Ivan P Gorlov
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sheri L Holmen
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
- Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
| | - Elise K Brunsgaard
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, Utah, United States of America
| | - Yvonne M Saenger
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, New York, United States of America
- Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Marc S Ernstoff
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, ImmunoOncology Branch, Developmental Therapeutics Program, Rockville, Maryland, United States of America
| | - Klaus J Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Nancy E Thomas
- Department of Dermatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Marianne Berwick
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, United States of America
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Benini S, Gamberi G, Cocchi S, Magagnoli G, Fortunato AR, Sciulli E, Righi A, Gambarotti M. The Efficacy of Molecular Analysis in the Diagnosis of Bone and Soft Tissue Sarcoma: A 15-Year Mono-Institutional Study. Int J Mol Sci 2022; 24:ijms24010632. [PMID: 36614077 PMCID: PMC9820733 DOI: 10.3390/ijms24010632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
The histological diagnosis of sarcoma can be difficult as it sometimes requires the combination of morphological and immunophenotypic analyses with molecular tests. A total of 2705 tissue samples of sarcoma consecutively collected from 2006 until 2020 that had undergone molecular analysis were assessed to evaluate their diagnostic utility compared with histological assessments. A total of 3051 molecular analyses were performed, including 1484 gene fusions tested by c/qRT-PCR, 992 gene rearrangements analysed by FISH, 433 analyses of the gene status of MDM2, 126 mutational analyses and 16 NGS analysis. Of the samples analysed, 68% were from formalin-fixed, paraffin-embedded tissue and 32% were from frozen tissue. C/qRT-PCR and FISH analyses were conclusive on formalin-fixed, paraffin-embedded tissue in 74% and 76% of samples, respectively, but the combination of the two methods gave us conclusive results in 96% and 89% of frozen and formalin-fixed, paraffin-embedded tissues, respectively. We demonstrate the utility of c/qRT-PCR and FISH for sarcoma diagnosis and that each has advantages in specific contexts. We conclude that it is possible to accurately predict the sarcoma subtype using a panel of different subtype-specific FISH probes and c/qRT-PCR assays, thereby greatly facilitating the differential diagnosis of these tumours.
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Affiliation(s)
- Stefania Benini
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Gabriella Gamberi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy
| | - Stefania Cocchi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Giovanna Magagnoli
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | | | - Enrica Sciulli
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Alberto Righi
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
- Correspondence: ; Tel.: +39-051-636-6665
| | - Marco Gambarotti
- Department of Pathology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
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26
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Bradbury M, Borràs E, Vilar M, Castellví J, Sánchez-Iglesias JL, Pérez-Benavente A, Gil-Moreno A, Santamaria A, Sabidó E. A combination of molecular and clinical parameters provides a new strategy for high-grade serous ovarian cancer patient management. J Transl Med 2022; 20:611. [PMID: 36544142 PMCID: PMC9773449 DOI: 10.1186/s12967-022-03816-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND High-grade serous carcinoma (HGSC) is the most common and deadly subtype of ovarian cancer. Although most patients will initially respond to first-line treatment with a combination of surgery and platinum-based chemotherapy, up to a quarter will be resistant to treatment. We aimed to identify a new strategy to improve HGSC patient management at the time of cancer diagnosis (HGSC-1LTR). METHODS A total of 109 ready-available formalin-fixed paraffin-embedded HGSC tissues obtained at the time of HGSC diagnosis were selected for proteomic analysis. Clinical data, treatment approach and outcomes were collected for all patients. An initial discovery cohort (n = 21) were divided into chemoresistant and chemosensitive groups and evaluated using discovery mass-spectrometry (MS)-based proteomics. Proteins showing differential abundance between groups were verified in a verification cohort (n = 88) using targeted MS-based proteomics. A logistic regression model was used to select those proteins able to correctly classify patients into chemoresistant and chemosensitive. The classification performance of the protein and clinical data combinations were assessed through the generation of receiver operating characteristic (ROC) curves. RESULTS Using the HGSC-1LTR strategy we have identified a molecular signature (TKT, LAMC1 and FUCO) that combined with ready available clinical data (patients' age, menopausal status, serum CA125 levels, and treatment approach) is able to predict patient response to first-line treatment with an AUC: 0.82 (95% CI 0.72-0.92). CONCLUSIONS We have established a new strategy that combines molecular and clinical parameters to predict the response to first-line treatment in HGSC patients (HGSC-1LTR). This strategy can allow the identification of chemoresistance at the time of diagnosis providing the optimization of therapeutic decision making and the evaluation of alternative treatment strategies. Thus, advancing towards the improvement of patient outcome and the individualization of HGSC patients' care.
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Affiliation(s)
- Melissa Bradbury
- grid.473715.30000 0004 6475 7299Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain ,grid.7080.f0000 0001 2296 0625Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Vall, d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Gynecology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Eva Borràs
- grid.473715.30000 0004 6475 7299Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Marta Vilar
- grid.473715.30000 0004 6475 7299Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain ,grid.7080.f0000 0001 2296 0625Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Vall, d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Josep Castellví
- grid.411083.f0000 0001 0675 8654Department of Pathology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - José Luis Sánchez-Iglesias
- grid.7080.f0000 0001 2296 0625Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Vall, d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Gynecology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Assumpció Pérez-Benavente
- grid.7080.f0000 0001 2296 0625Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Vall, d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Gynecology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Antonio Gil-Moreno
- grid.7080.f0000 0001 2296 0625Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Vall, d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Gynecology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain ,grid.413448.e0000 0000 9314 1427Centro de Investigación Biomédica en Red (CIBERONC), Instituto de Salud Carlos III, Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Anna Santamaria
- grid.7080.f0000 0001 2296 0625Biomedical Research Group in Gynecology, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Vall, d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain ,grid.7080.f0000 0001 2296 0625Cell Cycle and Cancer Laboratory, Biomedical Research Group in Urology, Vall Hebron Institut de Recerca, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Eduard Sabidó
- grid.473715.30000 0004 6475 7299Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
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Qin R, Zhao H, He Q, Li F, Li Y, Zhao H. Advances in single-cell sequencing technology in the field of hepatocellular carcinoma. Front Genet 2022; 13:996890. [PMID: 36303541 PMCID: PMC9592975 DOI: 10.3389/fgene.2022.996890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Tumors are a class of diseases characterized by altered genetic information and uncontrolled growth. Sequencing technology provide researchers with a better way to explore specific tumor pathogenesis. In recent years, single-cell sequencing technology has shone in tumor research, especially in the study of liver cancer, revealing phenomena that were unexplored by previous studies. Single-cell sequencing (SCS) is a technique for sequencing the cellular genome, transcriptome, epigenome, proteomics, or metabolomics after dissociation of tissues into single cells. Compared with traditional bulk sequencing, single-cell sequencing can dissect human tumors at single-cell resolution, finely delineate different cell types, and reveal the heterogeneity of tumor cells. In view of the diverse pathological types and complex pathogenesis of hepatocellular carcinoma (HCC), the study of the heterogeneity among tumor cells can help improve its clinical diagnosis, treatment and prognostic judgment. On this basis, SCS has revolutionized our understanding of tumor heterogeneity, tumor immune microenvironment, and clonal evolution of tumor cells. This review summarizes the basic process and development of single-cell sequencing technology and its increasing role in the field of hepatocellular carcinoma.
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Affiliation(s)
- Rongyi Qin
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Haichao Zhao
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Qizu He
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Feng Li
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Yanjun Li
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Yanjun Li, ; Haoliang Zhao,
| | - Haoliang Zhao
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Yanjun Li, ; Haoliang Zhao,
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Bapat PR, Epari S, Joshi PV, Dhanavade DS, Rumde RH, Gurav MY, Shetty OA, Desai SB. Comparative Assessment of DNA Extraction Techniques From Formalin-Fixed, Paraffin-Embedded Tumor Specimens and Their Impact on Downstream Analysis. Am J Clin Pathol 2022; 158:739-749. [PMID: 36197908 DOI: 10.1093/ajcp/aqac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Good-quality nucleic acid extraction from formalin-fixed, paraffin-embedded (FFPE) specimens remains a challenge in molecular-oncopathology practice. This study evaluates the efficacy of an in-house developed FFPE extraction buffer compared with other commercially available kits. METHODS Eighty FFPE specimens processed in different surgical pathology laboratories formed the study sample. DNA extraction was performed using three commercial kits and the in-house developed FFPE extraction buffer. DNA yield was quantified by a NanoDrop spectrophotometer and Qubit Fluorometer, and its purity was measured by the 260/280-nm ratio. A fragment analyzer system was used for accurate sizing of DNA fragments of FFPE DNA. The downstream effects of all extraction methods were evaluated by polymerase chain reaction (PCR) and Sanger sequencing. RESULTS In comparison with the commercial kits, the in-house buffer yielded higher DNA quantity and quality number (P < .0001). In addition, DNA integrity and fragment size were preserved in a significantly greater number of samples isolated with the in-house buffer (P < .05). The target PCR amplification rate with the in-house buffer extracted samples was also significantly higher, with 98% of the samples showing interpretable sequencing results. CONCLUSIONS The in-house developed FFPE extraction buffer performed superior to other methods in terms of suitability for downstream applications, time, cost-efficiency, and ease of performance.
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Affiliation(s)
- Prachi R Bapat
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sridhar Epari
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Pradnya V Joshi
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Dipika S Dhanavade
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Rachna H Rumde
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Mamta Y Gurav
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Omshree A Shetty
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sangeeta B Desai
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
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Yadav RP, Polavarapu VK, Xing P, Chen X. FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded Samples. Curr Protoc 2022; 2:e535. [PMID: 35994571 DOI: 10.1002/cpz1.535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In basic and translational cancer research, the majority of biopsies are stored in formalin-fixed paraffin-embedded (FFPE) samples. Chromatin accessibility reflects the degree to which nuclear macromolecules can physically interact with chromatinized DNA and plays a key role in gene regulation in different physiological conditions. As such, the profiling of chromatin accessibility in archived FFPE tissue can be critical to understanding gene regulation in health and disease. Due to the high degree of DNA damage in FFPE samples, accurate mapping of chromatin accessibility in these specimens is extremely difficult. To address this issue, we recently established FFPE-ATAC, a highly sensitive method based on T7-Tn5-mediated transposition followed by in vitro transcription (IVT), to generate high-quality chromatin accessibility profiles with 500-50,000 nuclei from a single FFPE tissue section. In FFPE-ATAC, which we describe here, the T7-Tn5 adaptors are inserted into the genome after FFPE sample preparation and are unlikely to sustain the DNA breakage that occurs during reverse cross-linking of these samples. It should, therefore, remain at the ends of broken accessible chromatin sites after reverse cross-linking. IVT is then used to convert the two ends of the broken DNA fragments to RNA molecules before making sequencing libraries from the IVT RNAs and further decoding Tn5 adaptor insertion sites in the genome. Through this strategy, users can decode the flanking sequences of the accessible chromatin even if there are breaks between adjacent pairs of T7-T5 adaptor insertion sites. This method is applicable to dissecting chromatin profiles of a small section of the tissue sample, characterizing stage and region-specific gene regulation and disease-associated chromatin regulation in FFPE tissues. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Nuclei isolation from FFPE tissue samples Basic Protocol 2: T7-Tn5 transposase tagmentation, reverse-crosslinking, and in vitro transcription Basic Protocol 3: Preparation of libraries for high-throughput sequencing.
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Affiliation(s)
- Ram Prakash Yadav
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Li J, Zhang J, Xu M, Yang Z, Yue S, Zhou W, Gui C, Zhang H, Li S, Wang PG, Yang S. Advances in glycopeptide enrichment methods for the analysis of protein glycosylation over the past decade. J Sep Sci 2022; 45:3169-3186. [PMID: 35816156 DOI: 10.1002/jssc.202200292] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/16/2022] [Accepted: 07/01/2022] [Indexed: 11/12/2022]
Abstract
Advances in bioanalytical technology have accelerated the analysis of complex protein glycosylation, which is beneficial to understanding glycosylation in drug discovery and disease diagnosis. Due to its biological uniqueness in the course of disease occurrence and development, disease-specific glycosylation requires quantitative characterization of protein glycosylation. We provide a comprehensive review of recent advances in glycosylation analysis, including workflows for glycoprotein digestion, glycopeptide separation and enrichment, and mass-spectrometry sequencing. We specifically focus on different strategies for glycopeptide enrichment through physical interaction, chemical oxidation, or metabolic labeling of intact glycopeptides. The recent advances and challenges of O-glycosylation analysis are presented, and the development of improved enrichment methods combining different proteases to analyze O-glycosylation is also proposed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jiajia Li
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Jie Zhang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Mingming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Zeren Yang
- AstraZeneca, Medimmune Ct, Frederick, MD, 21703, USA
| | - Shuang Yue
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Wanlong Zhou
- U.S. Food and Drug Administration, Forensic Chemistry Center, Cincinnati, OH, 45237, USA
| | - Chunshan Gui
- Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Haiyang Zhang
- Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Shuwei Li
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu, 210033, China
| | - Perry G Wang
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740, USA
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China.,Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
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Bledsoe MJ, Grizzle WE. The Use of Human Tissues for Research: What Investigators Need to Know. Altern Lab Anim 2022; 50:265-274. [PMID: 35801971 DOI: 10.1177/02611929221107933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
While laboratory animals are necessary for some aspects of the development of scientific and biomedical advances, including those of precision medicine, the use of human tissues is necessary in order to explore the findings and ensure that they are relevant to human systems. Many sources of human tissues exist, but researchers - particularly those making the transition from animal to human systems - may not be aware of how best to find quality sources of human tissues or how best to use them in their research. In this article, we discuss the advantages of using human tissues in research. In addition, we highlight some of the major advances made possible through the use of human tissue, and describe how human tissue is collected for research. We discuss the various types of bioresources that make human tissue available, and advise on how investigators can find and use appropriate bioresources to support their research - with the hope that this information will help facilitate the transition from research on animals to research using human tissues, as rapidly as is practicable.
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Affiliation(s)
| | - William E Grizzle
- Department of Pathology; 9968University of Alabama at Birmingham, Birmingham, AL, USA
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32
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van Deventer BS, du Toit-Prinsloo L, van Niekerk C. Practical tips to using formalin-fixed paraffin-embedded tissue archives for molecular diagnostics in a South African setting. Afr J Lab Med 2022; 11:1587. [PMID: 35811747 PMCID: PMC9257738 DOI: 10.4102/ajlm.v11i1.1587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 03/21/2022] [Indexed: 11/05/2022] Open
Abstract
Background Formalin-fixed paraffin-embedded (FFPE) tissue archives in hospitals, biobanks, and others offer a vast collection of extensive, readily available specimens for molecular testing. Unfortunately, the use of tissue samples for molecular diagnostic applications is challenging; thus, the forensic pathology FFPE tissue archives in Africa have been a largely unexploited genetic resource, with the usability of DNA obtainable from these samples being unknown. Intervention The study, conducted from January 2015 to August 2016, determined the usefulness of FFPE tissue as a reliable source of genetic material for successful post-mortem molecular applications and diagnostics. Formalin-fixed paraffin-embedded tissue samples were collected and archived from autopsies conducted over 13 years in the forensic medicine department of the University of Pretoria (Pretoria, South Africa). Deoxyribonucleic acid from FFPE tissue samples and control blood samples was amplified by high-resolution melt real-time polymerase chain reaction before sequencing. The procurement parameters and fixation times were compared with the quantity and quality of the extracted DNA and the efficiency of its subsequent molecular applications. Lessons learnt This study has shown that FFPE samples are still usable in molecular forensics, despite inadequate sample preparation, and offer immense value to forensic molecular diagnostics. Recommendations FFPE samples fixed in formalin for more than 24 h should still be used in molecular diagnostics or research, as long as the primer design targets amplicons not exceeding 300 base pairs.
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Affiliation(s)
- Barbara S van Deventer
- Department of Forensic Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Lorraine du Toit-Prinsloo
- Department of Forensic Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Chantal van Niekerk
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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33
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Jagomast T, Idel C, Klapper L, Kuppler P, Proppe L, Beume S, Falougy M, Steller D, Hakim SG, Offermann A, Roesch MC, Bruchhage KL, Perner S, Ribbat-Idel J. Comparison of manual and automated digital image analysis systems for quantification of cellular protein expression. Histol Histopathol 2022; 37:527-541. [PMID: 35146728 DOI: 10.14670/hh-18-434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Quantifying protein expression in immunohistochemically stained histological slides is an important tool for oncologic research. The use of computer-aided evaluation of IHC-stained slides significantly contributes to objectify measurements. Manual digital image analysis (mDIA) requires a user-dependent annotation of the region of interest (ROI). Others have built-in machine learning algorithms with automated digital image analysis (aDIA) and can detect the ROIs automatically. We aimed to investigate the agreement between the results obtained by aDIA and those derived from mDIA systems. METHODS We quantified chromogenic intensity (CI) and calculated the positive index (PI) in cohorts of tissue microarrays (TMA) using mDIA and aDIA. To consider the different distributions of staining within cellular sub-compartments and different tumor architecture our study encompassed nuclear and cytoplasmatic stainings in adenocarcinomas and squamous cell carcinomas. RESULTS Within all cohorts, we were able to show a high correlation between mDIA and aDIA for the CI (p<0.001) along with high agreement for the PI. Moreover, we were able to show that the cell detections of the programs were comparable as well and both proved to be reliable when compared to manual counting. CONCLUSION mDIA and aDIA show a high correlation in acquired IHC data. Both proved to be suitable to stratify patients for evaluation with clinical data. As both produce the same level of information, aDIA might be preferable as it is time-saving, can easily be reproduced, and enables regular and efficient output in large studies in a reasonable time period.
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Affiliation(s)
- T Jagomast
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.
| | - C Idel
- Department of Otorhinolaryngology, University of Luebeck, Luebeck, Germany.
| | - L Klapper
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - P Kuppler
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - L Proppe
- Department of Gynecology and Obstetrics, University of Luebeck, Luebeck, Germany
| | - S Beume
- Department of Gynecology and Obstetrics, University of Luebeck, Luebeck, Germany
| | - M Falougy
- Department of Oral and Maxillofacial Surgery, University of Luebeck, Luebeck, Germany
| | - D Steller
- Department of Oral and Maxillofacial Surgery, University of Luebeck, Luebeck, Germany
| | - S G Hakim
- Department of Oral and Maxillofacial Surgery, University of Luebeck, Luebeck, Germany
| | - A Offermann
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - M C Roesch
- Department of Urology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - K L Bruchhage
- Department of Otorhinolaryngology, University of Luebeck, Luebeck, Germany
| | - S Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - J Ribbat-Idel
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
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34
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Isberg OG, Giunchiglia V, McKenzie JS, Takats Z, Jonasson JG, Bodvarsdottir SK, Thorsteinsdottir M, Xiang Y. Automated Cancer Diagnostics via Analysis of Optical and Chemical Images by Deep and Shallow Learning. Metabolites 2022; 12:455. [PMID: 35629959 PMCID: PMC9143055 DOI: 10.3390/metabo12050455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has long been the gold standard to analyse tissue samples for the diagnostics of various diseases, such as cancer. The current diagnostic workflow is time-consuming and labour-intensive, and manual annotation by a qualified pathologist is needed. With the ever-increasing number of tissue blocks and the complexity of molecular diagnostics, new approaches have been developed as complimentary or alternative solutions for the current workflow, such as digital pathology and mass spectrometry imaging (MSI). This study compares the performance of a digital pathology workflow using deep learning for tissue recognition and an MSI approach utilising shallow learning to annotate formalin-fixed and paraffin-embedded (FFPE) breast cancer tissue microarrays (TMAs). Results show that both deep learning algorithms based on conventional optical images and MSI-based shallow learning can provide automated diagnostics with F1-scores higher than 90%, with the latter intrinsically built on biochemical information that can be used for further analysis.
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Affiliation(s)
- Olof Gerdur Isberg
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, 107 Reykjavik, Iceland
- Biomedical Center, School of Health Sciences, University of Iceland, 101 Reykjavik, Iceland;
| | - Valentina Giunchiglia
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
| | - James S. McKenzie
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
| | - Jon Gunnlaugur Jonasson
- Department of Pathology, Landspitali the National University Hospital, Hringbraut, 101 Reykjavik, Iceland;
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | | | - Margret Thorsteinsdottir
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, 107 Reykjavik, Iceland
- Biomedical Center, School of Health Sciences, University of Iceland, 101 Reykjavik, Iceland;
| | - Yuchen Xiang
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
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35
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Tarling TE, Byrne JA, Watson PH. The Availability of Human Biospecimens to Support Biomarker Research. Biomark Insights 2022; 17:11772719221091750. [PMID: 35464611 PMCID: PMC9021506 DOI: 10.1177/11772719221091750] [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: 02/02/2021] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Preserved biospecimens held in biobank inventories and clinical archives are important resources for biomarker research. Recent advances in technologies have led to an increase in use of clinical archives in particular, in order to study retrospective cohorts and to generate data relevant to tissue biomarkers. This raises the question of whether the current sizes of biobank inventories are appropriate to meet the demands of biomarker research. This commentary discusses this question by considering data concerning overall biobank and biospecimen numbers to estimate current biospecimen supply and use. The data suggests that biospecimen supply exceeds current demand. Therefore, it may be important for individual biobanks to reassess the targets for their inventories, consider culling unused portions of these inventories, and shift resources towards providing prospective custom biobanking services.
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Affiliation(s)
- Tamsin E Tarling
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, BC, Canada.,Canadian Tissue Repository Network, Vancouver, Canada
| | - Jennifer A Byrne
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Peter H Watson
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, BC, Canada.,Canadian Tissue Repository Network, Vancouver, Canada
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36
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A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens. Int J Mol Sci 2022; 23:ijms23084443. [PMID: 35457260 PMCID: PMC9031572 DOI: 10.3390/ijms23084443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 12/22/2022] Open
Abstract
Most human tumor tissues that are obtained for pathology and diagnostic purposes are formalin-fixed and paraffin-embedded (FFPE). To perform quantitative proteomics of FFPE samples, paraffin has to be removed and formalin-induced crosslinks have to be reversed prior to proteolytic digestion. A central component of almost all deparaffinization protocols is xylene, a toxic and highly flammable solvent that has been reported to negatively affect protein extraction and quantitative proteome analysis. Here, we present a 'green' xylene-free protocol for accelerated sample preparation of FFPE tissues based on paraffin-removal with hot water. Combined with tissue homogenization using disposable micropestles and a modified protein aggregation capture (PAC) digestion protocol, our workflow enables streamlined and reproducible quantitative proteomic profiling of FFPE tissue. Label-free quantitation of FFPE cores from human ductal breast carcinoma in situ (DCIS) xenografts with a volume of only 0.79 mm3 showed a high correlation between replicates (r2 = 0.992) with a median %CV of 16.9%. Importantly, this small volume is already compatible with tissue micro array (TMA) cores and core needle biopsies, while our results and its ease-of-use indicate that further downsizing is feasible. Finally, our FFPE workflow does not require costly equipment and can be established in every standard clinical laboratory.
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37
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Mitiushkina NV, Romanko AA, Preobrazhenskaya EV, Tiurin VI, Ermachenkova TI, Martianov AS, Mulkidjan RS, Sokolova TN, Kholmatov MM, Bizin IV, Ivantsov AO, Yatsuk OS, Zaitseva OA, Iyevleva AG, Kuligina ES, Imyanitov EN. Comprehensive evaluation of the test for 5'-/3'-end mRNA unbalanced expression as a screening tool for ALK and ROS1 fusions in lung cancer. Cancer Med 2022; 11:3226-3237. [PMID: 35322575 PMCID: PMC9468436 DOI: 10.1002/cam4.4686] [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: 10/20/2021] [Revised: 02/02/2022] [Accepted: 03/04/2022] [Indexed: 11/19/2022] Open
Abstract
Background Despite the progress in the development of next‐generation sequencing (NGS), diagnostic PCR assays remain to be utilized in clinical routine due to their simplicity and low cost. Tests for 5′‐/3′‐end mRNA unbalanced expression can be used for variant‐independent detection of translocations, however, many technical aspects of this methodology require additional investigations. Methods Known ALK/ROS1 fusions and 5′‐/3′‐end unbalanced expression were analyzed in 2009 EGFR mutation‐negative non‐small cell lung cancer (NSCLC) samples with RT‐PCR tests, which were optimized for the use with FFPE‐derived RNA. Results Variant‐specific PCR tests for 4 common ALK and 15 common ROS1 translocations detected 115 (5.7%) and 44 (2.2%) rearrangements, respectively. Virtually all samples with common ALK fusions demonstrated some level of 5′/3′ mRNA ends unbalanced expression, and 8 additional NSCLCs with rare ALK fusions were further identified by PCR or NGS among 48 cases selected based on ALK expression measurements. Interestingly, NSCLCs with unbalanced 5′‐/3′‐end ALK expression but without identified ALK translocations had elevated frequency of RAS mutations (21/40, 53%) suggesting the role of RAS activation in the alternative splicing of ALK gene. In contrast to ALK, only a minority of ROS1 translocation‐positive cases demonstrated unbalanced gene expression, with both 5′‐ and 3′‐end mRNA expression being elevated in most of the samples with translocations. Surprisingly, high ROS1 expression level was also found to be characteristic for NSCLCs with activating mutations in other tyrosine kinases such as EGFR, ALK, or MET. Conclusions Comprehensive ALK analysis can be performed by the test for 5′‐/3′‐end unbalanced expression with minimal risk of missing an ALK rearrangement. In contrast, the use of the test for 5′‐/3′‐end unbalanced expression for the detection of ROS1 fusions is complicated; hence, the utilization of variant‐specific PCR assays for ROS1 testing is preferable.
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Affiliation(s)
- Natalia V Mitiushkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Alexandr A Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Elena V Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia
| | - Vladislav I Tiurin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Tatiana I Ermachenkova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Alexandr S Martianov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia
| | - Rimma S Mulkidjan
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Tatiana N Sokolova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Maksim M Kholmatov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Ilya V Bizin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Alexandr O Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia
| | - Olga S Yatsuk
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Olga A Zaitseva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia
| | - Ekatherina Sh Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, Russia.,Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg, Russia.,Department of Oncology, I.P. Pavlov St.-Petersburg State Medical University, St.-Petersburg, Russia
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Monibi FA, Pannellini T, Otero M, Warren RF, Rodeo SA. Histologic and molecular features in pathologic human menisci from knees with and without osteoarthritis. J Orthop Res 2022; 40:504-512. [PMID: 33792974 PMCID: PMC8484374 DOI: 10.1002/jor.25047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/12/2021] [Accepted: 03/28/2021] [Indexed: 02/04/2023]
Abstract
The objective of this study was to evaluate histologic and molecular features of meniscus degeneration in cohorts of patients with and without osteoarthritis (OA) of the knee. Menisci were obtained from patients undergoing total knee arthroplasty for OA (TKA) or arthroscopic partial meniscectomy (APM) for a torn knee meniscus. Degenerative meniscal tears were among the most common tear type in the APM group based on the pattern. Using an integrative workflow for molecular evaluation of formalin-fixed and paraffin-embedded tissues, human menisci underwent blinded histologic evaluation and NanoString gene expression analyses. Histology revealed increased proteoglycan content in TKA menisci compared to APM menisci, but otherwise no significant differences in the total pathology score or sub-scores between patients based on age or cohort. NanoString analyses revealed differential expression of genes primarily associated with the PI3K-AKT signaling pathway, cell cycle, and apoptosis. These data provide new insights into histological and molecular features of meniscus degeneration in patients with and without knee OA. Histologic assessment of menisci showed similar severity of overall degeneration between cohorts, but there were differences at the molecular level. The dysregulated pathways identified in this study could contribute to early-onset meniscus degeneration, or to a predisposition to meniscus tears and subsequent knee OA. Further studies that validate genes and pathways uncovered in this study will allow us to evaluate novel approaches to assess and treat meniscal degeneration.
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Affiliation(s)
- Farrah A. Monibi
- Orthopaedic Soft Tissue Research Program, Hospital for Special Surgery, New York, New York, USA
| | - Tania Pannellini
- Hospital for Special Surgery, Pathology and Laboratory Medicine, New York, New York, USA
| | - Miguel Otero
- Hospital for Special Surgery, Tissue Engineering, Regeneration and Repair Program, New York, New York, USA
| | - Russell F. Warren
- Hospital for Special Surgery, Sports Medicine and Shoulder Service, New York, New York, USA
| | - Scott A. Rodeo
- Hospital for Special Surgery, Lab. for Soft Tissue Research, New York, New York, USA
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Genomics of Clear-cell Renal Cell Carcinoma: A Systematic Review and Meta-analysis. Eur Urol 2022; 81:349-361. [PMID: 34991918 DOI: 10.1016/j.eururo.2021.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 11/21/2022]
Abstract
CONTEXT Although antiangiogenic treatments and immunotherapies have significantly improved the prognosis of metastatic renal cell carcinoma (RCC), many patients will develop resistance, leading to treatment failure. Genetic tumor heterogeneity is a major cause of this resistance. OBJECTIVE To perform a meta-analysis of genomic data for clear-cell RCC obtained from primary tumors and metastases to assess the prevalence of gene mutations and copy number alterations (CNAs). EVIDENCE ACQUISITION Articles were selected from Medline and Embase libraries using the search algorithm ("Kidney Neoplasms"[Mesh] OR "Renal Cell Carcinoma") AND ("Genomics"[Mesh] OR "Mutation") from January 1999 to February 2021. A critical review was conducted according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement. Ninety-three publications were selected for inclusion in this meta-analysis. EVIDENCE SYNTHESIS Our meta-analysis included a total 14 696 patients, 14 299 primary tumor samples, and 969 metastatic samples. We evaluated the overall and subgroup prevalence of gene mutations and CNAs, including comparisons between primary tumors and metastases. In particular, for metastases we observed that the mutation prevalence was significantly more marked for ten genes compared to primary tumors, with no or little heterogeneity across studies. The VHL mutation prevalence increased significantly from 64% in primary tumors to 75% in metastases (p < 0.001). There was a significant increase in CNA prevalence from primary tumors to metastases for chromosomes 1p36.11, 9p21.3, and 18 in terms of losses, and for chromosomes 1q21.3, 7q36.3, 8q, and 20q11.21 in terms of gains. CDKN2A, also called p16 and involved in cell-cycle progression, is located at the 9p21.3 locus and was lost in 76% of metastatic samples. ASXL1, located on 20p11.21 and amplified in 50% of metastatic RCCs compared to 21% of primary tumors (p < 0.001), is closely linked to BAP1 function. CONCLUSIONS Our results underline the added value of preferential biopsies on RCC metastases to fully explore the biology of metastatic disease for therapeutic purposes. PATIENT SUMMARY We reviewed the literature on genetic mutations in primary tumors and metastatic lesions in kidney cancer. Our pooled results for all the relevant studies show a higher level of mutations in metastases than in primary tumors. This highlights the importance of taking biopsies of metastases to analyze genetic mutations and potentially guide selection of the most suitable treatment strategy.
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40
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A Versatile Terahertz Chemical Microscope and Its Application for the Detection of Histamine. PHOTONICS 2022. [DOI: 10.3390/photonics9010026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Terahertz waves have gained increasingly more attention because of their unique characteristics and great potential in a variety of fields. In this study, we introduced the recent progress of our versatile terahertz chemical microscope (TCM) in the detection of small biomolecules, ions, cancer cells, and antibody–antigen immunoassaying. We highlight the advantages of our TCM for chemical sensing and biosensing, such as label-free, high-sensitivity, rapid response, non-pretreatment, and minute amount sample consumption, compared with conventional methods. Furthermore, we demonstrated its new application in detection of allergic-related histamine at low concentration in buffer solutions.
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Hickey SM, Ung B, Bader C, Brooks R, Lazniewska J, Johnson IRD, Sorvina A, Logan J, Martini C, Moore CR, Karageorgos L, Sweetman MJ, Brooks DA. Fluorescence Microscopy-An Outline of Hardware, Biological Handling, and Fluorophore Considerations. Cells 2021; 11:35. [PMID: 35011596 PMCID: PMC8750338 DOI: 10.3390/cells11010035] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
Fluorescence microscopy has become a critical tool for researchers to understand biological processes at the cellular level. Micrographs from fixed and live-cell imaging procedures feature in a plethora of scientific articles for the field of cell biology, but the complexities of fluorescence microscopy as an imaging tool can sometimes be overlooked or misunderstood. This review seeks to cover the three fundamental considerations when designing fluorescence microscopy experiments: (1) hardware availability; (2) amenability of biological models to fluorescence microscopy; and (3) suitability of imaging agents for intended applications. This review will help equip the reader to make judicious decisions when designing fluorescence microscopy experiments that deliver high-resolution and informative images for cell biology.
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Affiliation(s)
- Shane M. Hickey
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
| | - Ben Ung
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
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Zhao L, Xing P, Polavarapu VK, Zhao M, Valero-Martínez B, Dang Y, Maturi N, Mathot L, Neves I, Yildirim I, Swartling FJ, Sjöblom T, Uhrbom L, Chen X. FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers. Nucleic Acids Res 2021; 49:e125. [PMID: 34534335 PMCID: PMC8643707 DOI: 10.1093/nar/gkab813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/16/2021] [Accepted: 09/06/2021] [Indexed: 01/05/2023] Open
Abstract
The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10-20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7-pA-Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing ∼4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease.
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Affiliation(s)
- Linxuan Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | | | - Miao Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Blanca Valero-Martínez
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Yonglong Dang
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Nagaprathyusha Maturi
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Rudbeck Laboratory, SE-75185 Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Inês Neves
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Rudbeck Laboratory, SE-75185 Uppsala, Sweden
| | - Irem Yildirim
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Rudbeck Laboratory, SE-75185 Uppsala, Sweden
| | | | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Rudbeck Laboratory, SE-75185 Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden
- Beijer Laboratories, Uppsala University, Uppsala, Sweden
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Marcel SS, Quimby AL, Noel MP, Jaimes OC, Mehrab-Mohseni M, Ashur SA, Velasco B, Tsuruta JK, Kasoji SK, Santos CM, Dayton PA, Parker JS, Davis IJ, Pattenden SG. Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors. Genome Res 2021; 31:2327-2339. [PMID: 34815311 PMCID: PMC8647830 DOI: 10.1101/gr.275219.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/22/2021] [Indexed: 01/01/2023]
Abstract
Chromatin accessibility states that influence gene expression and other nuclear processes can be altered in disease. The constellation of transcription factors and chromatin regulatory complexes in cells results in characteristic patterns of chromatin accessibility. The study of these patterns in tissues has been limited because existing chromatin accessibility assays are ineffective for archival formalin-fixed, paraffin-embedded (FFPE) tissues. We have developed a method to efficiently extract intact chromatin from archival tissue via enhanced cavitation with a nanodroplet reagent consisting of a lipid shell with a liquid perfluorocarbon core. Inclusion of nanodroplets during the extraction of chromatin from FFPE tissues enhances the recovery of intact accessible and nucleosome-bound chromatin. We show that the addition of nanodroplets to the chromatin accessibility assay formaldehyde-assisted isolation of regulatory elements (FAIRE), does not affect the accessible chromatin signal. Applying the technique to FFPE human tumor xenografts, we identified tumor-relevant regions of accessible chromatin shared with those identified in primary tumors. Further, we deconvoluted non-tumor signal to identify cellular components of the tumor microenvironment. Incorporation of this method of enhanced cavitation into FAIRE offers the potential for extending chromatin accessibility to clinical diagnosis and personalized medicine, while also enabling the exploration of gene regulatory mechanisms in archival samples.
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Affiliation(s)
- Shelsa S Marcel
- Curriculum in Bioinformatics and Computational Biology, Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Austin L Quimby
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Melodie P Noel
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Oscar C Jaimes
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Marjan Mehrab-Mohseni
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina 27599, USA
| | - Suud A Ashur
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brian Velasco
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina 27599, USA
| | - James K Tsuruta
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina 27599, USA
| | - Sandeep K Kasoji
- Triangle Biotechnology, Incorporated, Chapel Hill, North Carolina 27517, USA
| | - Charlene M Santos
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Paul A Dayton
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Joint Department of Biomedical Engineering, The University of North Carolina and North Carolina State University, Chapel Hill, North Carolina 27599, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Samantha G Pattenden
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Jarosch S, Köhlen J, Sarker RS, Steiger K, Janssen KP, Christians A, Hennig C, Holler E, D'Ippolito E, Busch DH. Multiplexed imaging and automated signal quantification in formalin-fixed paraffin-embedded tissues by ChipCytometry. CELL REPORTS METHODS 2021; 1:100104. [PMID: 35475000 PMCID: PMC9017205 DOI: 10.1016/j.crmeth.2021.100104] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/30/2021] [Accepted: 10/06/2021] [Indexed: 12/17/2022]
Abstract
Deciphering the spatial composition of cells in tissues is essential for detailed understanding of biological processes in health and disease. Recent technological advances enabled the assessment of the enormous complexity of tissue-derived parameters by highly multiplexed tissue imaging (HMTI), but elaborate machinery and data analyses are required. This severely limits broad applicability of HMTI. Here we demonstrate for the first time the application of ChipCytometry technology, which has unique features for widespread use, on formalin-fixed paraffin-embedded samples, the most commonly used storage technique of clinically relevant patient specimens worldwide. The excellent staining quality permits workflows for automated quantification of signal intensities, which we further optimized to compensate signal spillover from neighboring cells. In combination with the high number of validated markers, the reported platform can be used from unbiased analyses of tissue composition to detection of phenotypically complex rare cells, and can be easily implemented in both routine research and clinical pathology.
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Affiliation(s)
- Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Jan Köhlen
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Rim S.J. Sarker
- Comparative Experimental Pathology, Institute for Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Katja Steiger
- Comparative Experimental Pathology, Institute for Pathology, Technical University of Munich, 81675 Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | | | | | - Ernst Holler
- Department of Hematology/Oncology, University Medical Center, 93053 Regensburg, Germany
| | - Elvira D'Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), 81675 Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, 81675 Munich, Germany
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Yoshida Y, Ding X, Iwatsuki K, Taniizumi K, Inoue H, Wang J, Sakai K, Kiwa T. Detection of Lung Cancer Cells in Solutions Using a Terahertz Chemical Microscope. SENSORS 2021; 21:s21227631. [PMID: 34833707 PMCID: PMC8622933 DOI: 10.3390/s21227631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/13/2021] [Accepted: 11/14/2021] [Indexed: 12/04/2022]
Abstract
Cancer genome analysis has recently attracted attention for personalized cancer treatment. In this treatment, evaluation of the ratio of cancer cells in a specimen tissue is essential for the precise analysis of the genome. Conventionally, the evaluation takes at least two days and depends on the skill of the pathologist. In our group, a terahertz chemical microscope (TCM) was developed to easily and quickly measure the number of cancer cells in a solution. In this study, an antibody was immobilized on a sensing plate using an avidin-biotin reaction to immobilize it for high density and to improve antibody alignment. In addition, as the detected terahertz signals vary depending on the sensitivity of the sensing plate, the sensitivity was evaluated using pH measurement. The result of the cancer cell detection was corrected using the result of pH measurement. These results indicate that a TCM is expected to be an excellent candidate for liquid biopsies in cancer diagnosis.
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Affiliation(s)
- Yuichi Yoshida
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (Y.Y.); (X.D.); (K.I.); (K.T.); (J.W.); (K.S.)
| | - Xue Ding
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (Y.Y.); (X.D.); (K.I.); (K.T.); (J.W.); (K.S.)
| | - Kohei Iwatsuki
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (Y.Y.); (X.D.); (K.I.); (K.T.); (J.W.); (K.S.)
| | - Katsuya Taniizumi
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (Y.Y.); (X.D.); (K.I.); (K.T.); (J.W.); (K.S.)
| | - Hirofumi Inoue
- Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan;
| | - Jin Wang
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (Y.Y.); (X.D.); (K.I.); (K.T.); (J.W.); (K.S.)
| | - Kenji Sakai
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (Y.Y.); (X.D.); (K.I.); (K.T.); (J.W.); (K.S.)
| | - Toshihiko Kiwa
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan; (Y.Y.); (X.D.); (K.I.); (K.T.); (J.W.); (K.S.)
- Correspondence: ; Tel.: +81-86-251-8130
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Bando Y, Kobayashi T, Miyakami Y, Sumida S, Kakimoto T, Saijo Y, Uehara H. Triple-negative breast cancer and basal-like subtype : Pathology and targeted therapy. THE JOURNAL OF MEDICAL INVESTIGATION 2021; 68:213-219. [PMID: 34759133 DOI: 10.2152/jmi.68.213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Triple-negative breast cancer (TNBC) is a heterogenous disease. For personalized medicine, it is essential to identify and classify tumor subtypes to develop effective therapeutic strategies. Although gene expression profiling has identified several TNBC subtypes, classification of these tumors remains complex. Most TNBCs exhibit an aggressive phenotype, but some rare types have a favorable clinical course. In this review, we summarize the classification and characteristics related to the various TNBC subtypes, including the rare types. Therapeutic methods that are suitable for each subtype are also discussed. Of the intrinsic breast cancer subtypes identified by gene expression analysis, the basal-like subtype specifically displayed decreased expression of an estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) cluster. We also present results that characterize the TNBC and basal-like phenotypes. TNBC may be categorized into four major classes : basal-like, immune-enriched, mesenchymal, and luminal androgen receptor. Therapeutic strategies for each subtype have been proposed along with newly approved targeted therapies for TNBC, such as immune checkpoint inhibitors. Understanding the classification of TNBC based on gene expression profiling in association with clinicopathological factors will facilitate accurate pathological diagnosis and effective treatment selection. J. Med. Invest. 68 : 213-219, August, 2021.
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Affiliation(s)
- Yoshimi Bando
- Division of Pathology, Tokushima University Hospital, Tokushima, Japan
| | - Tomoko Kobayashi
- Division of Pathology, Tokushima University Hospital, Tokushima, Japan
| | - Yuko Miyakami
- Division of Pathology, Tokushima University Hospital, Tokushima, Japan
| | - Satoshi Sumida
- Division of Pathology, Tokushima University Hospital, Tokushima, Japan
| | - Takumi Kakimoto
- Division of Pathology, Tokushima University Hospital, Tokushima, Japan
| | - Yasuyo Saijo
- Department of Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hisanor Uehara
- Division of Pathology, Tokushima University Hospital, Tokushima, Japan
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Polavarapu VK, Xing P, Zhang H, Zhao M, Mathot L, Zhao L, Rosen G, Swartling FJ, Sjöblom T, Chen X. Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples. Genome Res 2021; 32:150-161. [PMID: 34261731 PMCID: PMC8744681 DOI: 10.1101/gr.275269.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/08/2021] [Indexed: 11/25/2022]
Abstract
Archived formalin-fixed paraffin-embedded (FFPE) samples are the global standard format for preservation of the majority of biopsies in both basic research and translational cancer studies, and profiling chromatin accessibility in the archived FFPE tissues is fundamental to understanding gene regulation. Accurate mapping of chromatin accessibility from FFPE specimens is challenging because of the high degree of DNA damage. Here, we first showed that standard ATAC-seq can be applied to purified FFPE nuclei but yields lower library complexity and a smaller proportion of long DNA fragments. We then present FFPE-ATAC, the first highly sensitive method for decoding chromatin accessibility in FFPE tissues that combines Tn5-mediated transposition and T7 in vitro transcription. The FFPE-ATAC generates high-quality chromatin accessibility profiles with 500 nuclei from a single FFPE tissue section, enables the dissection of chromatin profiles from the regions of interest with the aid of hematoxylin and eosin (H&E) staining, and reveals disease-associated chromatin regulation from the human colorectal cancer FFPE tissue archived for more than 10 years. In summary, the approach allows decoding of the chromatin states that regulate gene expression in archival FFPE tissues, thereby permitting investigators, to better understand epigenetic regulation in cancer and precision medicine.
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Frasquilho SG, Sanchez I, Yoo C, Antunes L, Bellora C, Mathieson W. Do Tissues Fixed in a Non-crosslinking Fixative Require a Dedicated Formalin-free Processor? J Histochem Cytochem 2021; 69:389-405. [PMID: 34010071 DOI: 10.1369/00221554211017859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative were cut into three pieces then processed in a flushed tissue processor previously used for formalin-fixed, paraffin-embedded (FFPE) blocks (neutral buffered formalin [NBF]+ve), a formalin-free system (NBF-ve), or left unprocessed. Histomorphology and immunohistochemistry were compared using hematoxylin/eosin staining and antibodies for MLH-1, Ki-67, and CK-7. Nucleic acid was extracted using the PAXgene Tissue RNA/DNA kits and an FFPE RNA extraction kit. RNA integrity was assessed using RNA integrity number (RIN), reverse transcription polymerase chain reaction (RT-PCR) (four amplicons), and quantitative RT-PCR (three genes). For DNA, multiplex PCR, quantitative PCR, DNA integrity number, and gel electrophoresis were used. Compared with NBF-ve, RNA from NBF+ve blocks had 88% lower yield and poorer purity; average RIN reduced from 5.0 to 3.8, amplicon length was 408 base pairs shorter, and Cq numbers were 1.9-2.4 higher. Using the FFPE extraction kit rescued yield and purity, but RIN further declined by 1.1 units. Differences between NBF+ve and NBF-ve in respect of DNA, histomorphology, and immunohistochemistry were either non-existent or small in magnitude. Formalin contamination of a tissue processor and its reagents therefore critically reduce RNA yield and integrity. We discuss the available options users can adopt to ameliorate this problem.
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Affiliation(s)
| | | | - Changyoung Yoo
- The Catholic University of Korea, St. Vincent's Hospital, Seoul, Korea
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Äyräväinen A, Pasanen A, Ahvenainen T, Heikkinen T, Pakarinen P, Härkki P, Vahteristo P. Systematic molecular and clinical analysis of uterine leiomyomas from fertile-aged women undergoing myomectomy. Hum Reprod 2021; 35:2237-2244. [PMID: 32829387 DOI: 10.1093/humrep/deaa187] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
STUDY QUESTION What are the distributions and associated clinical characteristics of mediator complex subunit 12 (MED12), high mobility group AT-hook 2 (HMGA2) and fumarate hydratase (FH) aberrations in uterine leiomyomas from fertile-aged myomectomy patients? SUMMARY ANSWER These driver mutations account for the majority (83%) of tumours in fertile-aged patients. WHAT IS KNOWN ALREADY Alterations affecting MED12, HMGA2 and FH account for 80-90% of uterine leiomyomas from middle-aged hysterectomy patients, while the molecular background of tumours from young myomectomy patients has not been systematically studied. STUDY DESIGN, SIZE, DURATION A retrospective series of 361 archival uterine leiomyoma samples from 234 women aged ≤45 years undergoing myomectomy in 2009-2014 was examined. Associations between the molecular data and detailed clinical information of the patients and tumours were analysed. PARTICIPANTS/MATERIALS, SETTING, METHODS DNA was extracted from formalin-fixed paraffin-embedded samples and MED12 exons 1 and 2 were sequenced to identify mutations. Level of HMGA2 expression was evaluated by immunohistochemistry. Biallelic FH inactivation was analysed with 2-succinylcysteine staining, which is an indirect method of assessing FH deficiency. All patients' medical histories were reviewed, and clinical information of patients and tumours was combined with molecular data. MAIN RESULTS AND THE ROLE OF CHANCE The median age at operation was 34 years. The majority (58%) of patients were operated on for a single leiomyoma. Known driver mutations were identified in 83% of tumours (71% MED12; 9% HMGA2; 3% FH). In solitary leiomyomas, the MED12 mutation frequency was only 43%, and 29% were wild-type for all driver alterations. MED12 mutations were associated with multiple tumours, smaller tumour size and subserosal location. LIMITATIONS, REASONS FOR CAUTION Although comprehensive, the study is retrospective in nature and all samples have been collected for routine diagnostic purposes. The use of paraffin-embedded samples and immunohistochemistry may have led to an underestimation of mutations. Due to the limited sample size and rarity of especially FH-deficient leiomyomas, the data are partly descriptive. WIDER IMPLICATIONS OF THE FINDINGS The contribution of driver mutations in leiomyomas from young myomectomy patients is comparable to tumours obtained from hysterectomies of mostly middle-aged women. Our results support the earlier findings that MED12 mutations are associated with multiple tumours, smaller tumour size and subserosal location. The study emphasizes the distinct molecular background of solitary leiomyomas, and more research is needed to clarify the underlying causes of the notable proportion of wild-type leiomyomas. STUDY FUNDING/COMPETING INTEREST(S) The study was supported by the Academy of Finland (307773), the Sigrid Jusélius Foundation, the Cancer Foundation Finland and the iCAN Digital Precision Cancer Medicine Flagship. The authors declare no conflicts of interest. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- A Äyräväinen
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - A Pasanen
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - T Ahvenainen
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - T Heikkinen
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - P Pakarinen
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - P Härkki
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - P Vahteristo
- Applied Tumor Genomics Research Program and Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy. Biomolecules 2021; 11:biom11050621. [PMID: 33922016 PMCID: PMC8143498 DOI: 10.3390/biom11050621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023] Open
Abstract
The use of gene expression profiling (GEP) in cancer management is rising, as GEP can be used for disease classification and diagnosis, tailoring treatment to underlying genetic determinants of pharmacological response, monitoring of therapy response, and prognosis. However, the reliability of GEP heavily depends on the input of RNA in sufficient quantity and quality. This highlights the need for standard procedures to ensure best practices for RNA extraction from often small tumor biopsies with variable tissue handling. We optimized an RNA extraction protocol from fresh-frozen (FF) core needle biopsies (CNB) from breast cancer patients and from formalin-fixed paraffin-embedded (FFPE) tissue when FF CNB did not yield sufficient RNA. Methods to avoid ribonucleases andto homogenize or to deparaffinize tissues and the impact of tissue composition on RNA extraction were studied. Additionally, RNA’s compatibility with the nanoString nCounter® technology was studied. This technology platform enables GEP using small RNA fragments. After optimization of the protocol, RNA of high quality and sufficient quantity was obtained from FF CNB in 92% of samples. For the remaining 8% of cases, FFPE material prepared by the pathology department was used for RNA extraction. Both resulting RNA end products are compatible with the nanoString nCounter® technology.
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