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Smail C, Montgomery SB. RNA Sequencing in Disease Diagnosis. Annu Rev Genomics Hum Genet 2024; 25:353-367. [PMID: 38360541 DOI: 10.1146/annurev-genom-021623-121812] [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: 02/17/2024]
Abstract
RNA sequencing (RNA-seq) enables the accurate measurement of multiple transcriptomic phenotypes for modeling the impacts of disease variants. Advances in technologies, experimental protocols, and analysis strategies are rapidly expanding the application of RNA-seq to identify disease biomarkers, tissue- and cell-type-specific impacts, and the spatial localization of disease-associated mechanisms. Ongoing international efforts to construct biobank-scale transcriptomic repositories with matched genomic data across diverse population groups are further increasing the utility of RNA-seq approaches by providing large-scale normative reference resources. The availability of these resources, combined with improved computational analysis pipelines, has enabled the detection of aberrant transcriptomic phenotypes underlying rare diseases. Further expansion of these resources, across both somatic and developmental tissues, is expected to soon provide unprecedented insights to resolve disease origin, mechanism of action, and causal gene contributions, suggesting the continued high utility of RNA-seq in disease diagnosis.
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Affiliation(s)
- Craig Smail
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, Missouri, USA;
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Department of Genetics, and Department of Pathology, Stanford University School of Medicine, Stanford, California, USA;
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2
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Bhamidimarri PM, Salameh L, Mahdami A, Abdullah HW, Mahboub B, Hamoudi R. LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue. Heliyon 2024; 10:e32896. [PMID: 38988576 PMCID: PMC11234047 DOI: 10.1016/j.heliyon.2024.e32896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p < 0.0001) improving the mean read lengths (p < 0.05) in WTA. Overall, increased mean read length positively correlated with on-target reads (Pearson's r = 0.71, p < 0.0001) in both amplified and unamplified RNA-seq analysis. Gene expression analysis compared between unamplified and amplified group displayed substantial overlap of the differentially expressed genes (DEGs) (log2 fold change cut-off < -2 and >2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.
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Affiliation(s)
- Poorna Manasa Bhamidimarri
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Laila Salameh
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
| | - Amena Mahdami
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Hanan Wael Abdullah
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Sciences, University College London, London, United Kingdom
- BIMAI-Lab, Biomedically Informed Artificial Inelligence Laboratory, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Centre of Excelence for Precision Medicine, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
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3
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Mikami H, Noguchi S, Akatsuka J, Hasegawa H, Obayashi K, Takeda H, Endo Y, Toyama Y, Takei H, Kimura G, Kondo Y, Takizawa T. snRNAs from Radical Prostatectomy Specimens Have the Potential to Serve as Prognostic Factors for Clinical Recurrence after Biochemical Recurrence in Patients with High-Risk Prostate Cancer. Cancers (Basel) 2024; 16:1757. [PMID: 38730709 PMCID: PMC11083327 DOI: 10.3390/cancers16091757] [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: 04/10/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
In patients with high-risk prostate cancer (HRPC) after radical prostatectomy (RP), biochemical recurrence (BCR) increases the risk of distant metastasis. Accordingly, additional prognostic biomarkers are required to identify the subpopulation of patients with HRPC who develop clinical recurrence (CR) after BCR. The objective of this study was to identify biomarkers in formalin-fixed paraffin-embedded (FFPE) RP samples that are prognostic for CR in patients with HRPC who experience BCR after RP (post-RP BCR). First, we performed a preliminary RNA sequencing analysis to comprehensively profile RNA expression in FFPE RP samples obtained from patients with HRPC who developed CR after post-RP BCR and found that many snRNAs were very abundant in preserved FFPE samples. Subsequently, we used quantitative polymerase chain reaction (qPCR) to compare the expression levels of highly abundant snRNAs in FFPE RP samples from patients with HRPC with and without CR after post-RP BCR (21 CR patients and 46 non-CR patients who had more than 5 years of follow-up after BCR). The qPCR analysis revealed that the expression levels of snRNA RNU1-1/1-2 and RNU4-1 were significantly higher in patients with CR than in patients without CR. These snRNAs were significantly correlated with clinical recurrence-free survival (RFS) in patients with HRPC who experienced post-RP BCR. Furthermore, snRNA RNU1-1/1-2 could serve as an independent prognostic factor for clinical RFS in post-RP BCR of HRPC cases where known prognostic factors (e.g., Gleason score) cannot distinguish between CR and non-CR patients. Our findings provide new insights into the involvement of snRNAs in prostate cancer progression.
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Affiliation(s)
- Hikaru Mikami
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Syunya Noguchi
- Department of Molecular Medicine and Anatomy, Nippon Medical School, Tokyo 113-8602, Japan;
| | - Jun Akatsuka
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Hiroya Hasegawa
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Kotaro Obayashi
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Hayato Takeda
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Yuki Endo
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Yuka Toyama
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Hiroyuki Takei
- Department of Breast Surgical Oncology, Nippon Medical School, Tokyo 113-8602, Japan;
| | - Go Kimura
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Yukihiro Kondo
- Department of Urology, Nippon Medical School Hospital, Tokyo 113-8603, Japan; (H.M.); (J.A.); (H.H.); (K.O.); (H.T.); (Y.E.); (Y.T.); (G.K.); (Y.K.)
| | - Toshihiro Takizawa
- Department of Molecular Medicine and Anatomy, Nippon Medical School, Tokyo 113-8602, Japan;
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4
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Kotlov N, Shaposhnikov K, Tazearslan C, Chasse M, Baisangurov A, Podsvirova S, Fernandez D, Abdou M, Kaneunyenye L, Morgan K, Cheremushkin I, Zemskiy P, Chelushkin M, Sorokina M, Belova E, Khorkova S, Lozinsky Y, Nuzhdina K, Vasileva E, Kravchenko D, Suryamohan K, Nomie K, Curran J, Fowler N, Bagaev A. Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data. Commun Biol 2024; 7:392. [PMID: 38555407 PMCID: PMC10981711 DOI: 10.1038/s42003-024-06020-z] [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: 03/24/2023] [Accepted: 03/06/2024] [Indexed: 04/02/2024] Open
Abstract
With the increased use of gene expression profiling for personalized oncology, optimized RNA sequencing (RNA-seq) protocols and algorithms are necessary to provide comparable expression measurements between exome capture (EC)-based and poly-A RNA-seq. Here, we developed and optimized an EC-based protocol for processing formalin-fixed, paraffin-embedded samples and a machine-learning algorithm, Procrustes, to overcome batch effects across RNA-seq data obtained using different sample preparation protocols like EC-based or poly-A RNA-seq protocols. Applying Procrustes to samples processed using EC and poly-A RNA-seq protocols showed the expression of 61% of genes (N = 20,062) to correlate across both protocols (concordance correlation coefficient > 0.8, versus 26% before transformation by Procrustes), including 84% of cancer-specific and cancer microenvironment-related genes (versus 36% before applying Procrustes; N = 1,438). Benchmarking analyses also showed Procrustes to outperform other batch correction methods. Finally, we showed that Procrustes can project RNA-seq data for a single sample to a larger cohort of RNA-seq data. Future application of Procrustes will enable direct gene expression analysis for single tumor samples to support gene expression-based treatment decisions.
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Affiliation(s)
| | | | | | | | | | | | | | - Mary Abdou
- BostonGene, Corp., Waltham, MA, 02453, USA
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5
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Kehl A, Aupperle-Lellbach H, de Brot S, van der Weyden L. Review of Molecular Technologies for Investigating Canine Cancer. Animals (Basel) 2024; 14:769. [PMID: 38473154 DOI: 10.3390/ani14050769] [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: 12/21/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Genetic molecular testing is starting to gain traction as part of standard clinical practice for dogs with cancer due to its multi-faceted benefits, such as potentially being able to provide diagnostic, prognostic and/or therapeutic information. However, the benefits and ultimate success of genomic analysis in the clinical setting are reliant on the robustness of the tools used to generate the results, which continually expand as new technologies are developed. To this end, we review the different materials from which tumour cells, DNA, RNA and the relevant proteins can be isolated and what methods are available for interrogating their molecular profile, including analysis of the genetic alterations (both somatic and germline), transcriptional changes and epigenetic modifications (including DNA methylation/acetylation and microRNAs). We also look to the future and the tools that are currently being developed, such as using artificial intelligence (AI) to identify genetic mutations from histomorphological criteria. In summary, we find that the molecular genetic characterisation of canine neoplasms has made a promising start. As we understand more of the genetics underlying these tumours and more targeted therapies become available, it will no doubt become a mainstay in the delivery of precision veterinary care to dogs with cancer.
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Affiliation(s)
- Alexandra Kehl
- Laboklin GmbH & Co. KG, Steubenstr. 4, 97688 Bad Kissingen, Germany
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675 München, Germany
| | - Heike Aupperle-Lellbach
- Laboklin GmbH & Co. KG, Steubenstr. 4, 97688 Bad Kissingen, Germany
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675 München, Germany
| | - Simone de Brot
- Institute of Animal Pathology, COMPATH, University of Bern, 3012 Bern, Switzerland
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Andelic M, Marchi M, Marcuzzo S, Lombardi R, Faber CG, Lauria G, Salvi E. Archival skin biopsy specimens as a tool for miRNA-based diagnosis: Technical and post-analytical considerations. Mol Ther Methods Clin Dev 2023; 31:101116. [PMID: 37808256 PMCID: PMC10550798 DOI: 10.1016/j.omtm.2023.101116] [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: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023]
Abstract
Archived specimens, taken by standardized procedures in clinical practice, represent a valuable resource in translational medicine. Their use in retrospective molecular-based studies could provide disease and therapy predictors. Microfluidic array is a user-friendly and cost-effective method allowing profiling of hundreds of microRNAs (miRNAs) from a low amount of RNA. However, even though tissue miRNAs may include potentially robust biomarkers, non-uniformed post-analytical pipelines could hinder translation into clinics. In this study, epidermal RNA from archival skin biopsy specimens was isolated from patients with peripheral neuropathy and healthy individuals. Unbiased miRNA profiling was performed using RT-qPCR-based microfluidic array. We demonstrated that RNA obtained from archival tissue is appropriate for miRNA profiling, providing evidence that different practices in threshold selection could significantly influence the final results. We showed the utility of software-based quality control for amplification curves. We revealed that selection of the most stable reference and the calculation of geometric mean are suitable when utilizing microfluidic arrays without known references. By applying appropriate post-analytical settings, we obtained miRNA profile of human epidermis associated with biological processes and a list of suitable references. Our results, which outline technical and post-analytical considerations, support the broad use of archived specimens for miRNA analysis to unravel disease-specific molecular signatures.
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Affiliation(s)
- Mirna Andelic
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- School of Mental Health and Neuroscience, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ Maastricht, the Netherlands
| | - Margherita Marchi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Stefania Marcuzzo
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Raffaella Lombardi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Catharina G. Faber
- Department of Neurology and School for Mental Health and Neuroscience, Maastricht University Medical Centre+, P.O. Box 5800, 6202 AZ Maastricht, the Netherlands
| | - Giuseppe Lauria
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milan, Italy
| | - Erika Salvi
- Neuroalgology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Data Science Center, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
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7
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Van Loon K, Mmbaga EJ, Mushi BP, Selekwa M, Mwanga A, Akoko LO, Mwaiselage J, Mosha I, Ng DL, Wu W, Silverstein J, Mulima G, Kaimila B, Gopal S, Snell JM, Benz SC, Vaske C, Sanborn Z, Sedgewick AJ, Radenbaugh A, Newton Y, Collisson EA. A Genomic Analysis of Esophageal Squamous Cell Carcinoma in Eastern Africa. Cancer Epidemiol Biomarkers Prev 2023; 32:1411-1420. [PMID: 37505926 DOI: 10.1158/1055-9965.epi-22-0775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 04/19/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) comprises 90% of all esophageal cancer cases globally and is the most common histology in low-resource settings. Eastern Africa has a disproportionately high incidence of ESCC. METHODS We describe the genomic profiles of 61 ESCC cases from Tanzania and compare them to profiles from an existing cohort of ESCC cases from Malawi. We also provide a comparison to ESCC tumors in The Cancer Genome Atlas (TCGA). RESULTS We observed substantial transcriptional overlap with other squamous histologies via comparison with TCGA PanCan dataset. DNA analysis revealed known mutational patterns, both genome-wide as well as in genes known to be commonly mutated in ESCC. TP53 mutations were the most common somatic mutation in tumors from both Tanzania and Malawi but were detected at lower frequencies than previously reported in ESCC cases from other settings. In a combined analysis, two unique transcriptional clusters were identified: a proliferative/epithelial cluster and an invasive/migrative/mesenchymal cluster. Mutational signature analysis of the Tanzanian cohort revealed common signatures associated with aging and cytidine deaminase activity (APOBEC) and an absence of signature 29, which was previously reported in the Malawi cohort. CONCLUSIONS This study defines the molecular characteristics of ESCC in Tanzania, and enriches the Eastern African dataset, with findings of overall similarities but also some heterogeneity across two unique sites. IMPACT Despite a high burden of ESCC in Eastern Africa, investigations into the genomics in this region are nascent. This represents the largest comprehensive genomic analysis ESCC from sub-Saharan Africa to date.
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Affiliation(s)
- Katherine Van Loon
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Elia J Mmbaga
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Beatrice P Mushi
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Msiba Selekwa
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ally Mwanga
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Larry O Akoko
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | | | - Dianna L Ng
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Wei Wu
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Jordyn Silverstein
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | | | | | - Satish Gopal
- UNC Project-Malawi, Lilongwe, Malawi
- University of North Carolina, Chapel Hill, North Carolina
| | - Jeff M Snell
- University of North Carolina, Chapel Hill, North Carolina
| | | | | | - Zack Sanborn
- NantOmics/NantHealth, Inc., El Segundo, California
| | | | | | - Yulia Newton
- NantOmics/NantHealth, Inc., El Segundo, California
| | - Eric A Collisson
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
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Romanko AA, Mulkidjan RS, Tiurin VI, Saitova ES, Preobrazhenskaya EV, Krivosheyeva EA, Mitiushkina NV, Shestakova AD, Belogubova EV, Ivantsov AO, Iyevleva AG, Imyanitov EN. Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples. Int J Mol Sci 2023; 24:14203. [PMID: 37762506 PMCID: PMC10531831 DOI: 10.3390/ijms241814203] [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: 07/27/2023] [Revised: 08/26/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The majority of NTRK1, NTRK2, and NTRK3 rearrangements result in increased expression of the kinase portion of the involved gene due to its fusion to an actively transcribed gene partner. Consequently, the analysis of 5'/3'-end expression imbalances is potentially capable of detecting the entire spectrum of NTRK gene fusions. Archival tumor specimens obtained from 8075 patients were subjected to manual dissection of tumor cells, DNA/RNA isolation, and cDNA synthesis. The 5'/3'-end expression imbalances in NTRK genes were analyzed by real-time PCR. Further identification of gene rearrangements was performed by variant-specific PCR for 44 common NTRK fusions, and, whenever necessary, by RNA-based next-generation sequencing (NGS). cDNA of sufficient quality was obtained in 7424/8075 (91.9%) tumors. NTRK rearrangements were detected in 7/6436 (0.1%) lung carcinomas, 11/137 (8.0%) pediatric tumors, and 13/851 (1.5%) adult non-lung malignancies. The highest incidence of NTRK translocations was observed in pediatric sarcomas (7/39, 17.9%). Increased frequency of NTRK fusions was seen in microsatellite-unstable colorectal tumors (6/48, 12.5%), salivary gland carcinomas (5/93, 5.4%), and sarcomas (7/143, 4.9%). None of the 1293 lung carcinomas with driver alterations in EGFR/ALK/ROS1/RET/MET oncogenes had NTRK 5'/3'-end expression imbalances. Variant-specific PCR was performed for 744 tumors with a normal 5'/3'-end expression ratio: there were no rearrangements in 172 EGFR/ALK/ROS1/RET/MET-negative lung cancers and 125 pediatric tumors, while NTRK3 fusions were detected in 2/447 (0.5%) non-lung adult malignancies. In conclusion, this study describes a diagnostic pipeline that can be used as a cost-efficient alternative to conventional methods of NTRK1-3 analysis.
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Affiliation(s)
- Aleksandr A. Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Rimma S. Mulkidjan
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Vladislav I. Tiurin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Evgeniya S. Saitova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Elena V. Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Elena A. Krivosheyeva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Natalia V. Mitiushkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Anna D. Shestakova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Evgeniya V. Belogubova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Alexandr O. Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
| | - Aglaya G. Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia (V.I.T.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
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9
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Fasching PA, Szeto C, Denkert C, Benz S, Weber K, Spilman P, Budczies J, Schneeweiss A, Stickeler E, Schmatloch S, Jackisch C, Karn T, Sinn HP, Warm M, van Mackelenbergh M, Rabizadeh S, Schem C, Heinmöller E, Mueller V, Marmé F, Soon-Shiong P, Nekljudova V, Untch M, Loibl S. Inferred Immune-Cell Activity Is an Independent Predictor of HER2-Negative Breast Cancer Prognosis and Response to Paclitaxel-Based Therapy in the GeparSepto Trial. Clin Cancer Res 2023; 29:2456-2465. [PMID: 37014668 PMCID: PMC10320466 DOI: 10.1158/1078-0432.ccr-22-2213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/13/2022] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
PURPOSE Tumor microenvironment (TME) immune markers have been correlated with both response to neoadjuvant therapy and prognosis in patients with breast cancer. Here, immune-cell activity of breast cancer tumors was inferred by expression-based analysis to determine if it is prognostic and/or predictive of response to neoadjuvant paclitaxel-based therapy in the GeparSepto (G7) trial (NCT01583426). EXPERIMENTAL DESIGN Pre-study biopsies from 279 patients with HER2-negative breast cancer in the G7 trial underwent RNA-seq-based profiling of 104 immune-cell-specific genes to assess inferred Immune Cell Activity (iICA) of 23 immune-cell types. Hierarchical clustering was used to classify tumors as iICA "hot," "warm," or "cold" by comparison of iICA in the G7 cohort relative to that of 1,467 samples from a tumor database established by Nantomics LLC. Correlations between iICA cluster, pathology-assessed tumor-infiltrating lymphocytes (TIL), and hormone receptor (HR) status for pathologic complete response (pCR), disease-free survival (DFS), and overall survival (OS) were determined. RESULTS iICA cluster correlated with TIL levels. The highest pCR rates were observed in hot cluster tumors, and those with relatively higher TILs. Greater inferred activity of several T-cell types was significantly associated with pCR and survival. DFS and OS were prolonged in patients with hot or warm cluster tumors, the latter particularly for HR negative tumors, even if TILs were relatively low. CONCLUSIONS Overall, TIL level better predicted pCR, but iICA cluster better predicted survival. Differences in associations between TILs, cluster, pCR, and survival were observed for HR-positive tumors versus HR-negative tumors, suggesting expanded study of the implication of these findings is warranted.
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Affiliation(s)
- Peter A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-EMN, Erlangen, Germany
| | | | - Carsten Denkert
- Institute for Pathology, Philipps University of Marburg, Marburg, Germany
| | | | | | | | - Jan Budczies
- Institute for Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Heidelberg University Hospital, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elmar Stickeler
- Department of Gynecology and Obstetrics, University Hospital, RWTH Aachen, Germany
| | | | - Christian Jackisch
- Department of Gynecology and Obstetrics, Sana Hospital Offenbach, Offenbach, Germany
| | - Thomas Karn
- Department of Gynecology and Obstetrics, Goethe University Frankfurt, UCT-Frankfurt-Marburg, Frankfurt, Germany
| | - Hans Peter Sinn
- Division of Gynecopathology, Institute for Pathology, University Hospital Heidelberg, Germany
| | | | - Marion van Mackelenbergh
- University Hospital Schleswig-Holstein, Clinic for Gynecology and Obstetrics, Schleswig-Holstein, Germany
| | | | | | | | - Volkmar Mueller
- Department of Gynecology and Obstetrics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Frederik Marmé
- Department of Gynecology and Obstetrics, University Hospital Mannheim, Mannheim, Germany
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10
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Biskup E, Schejbel L, de Oliveira DNP, Høgdall E. Test of the FlashFREEZE unit in tissue samples freezing for biobanking purposes. Cell Tissue Bank 2023; 24:435-447. [PMID: 36309911 PMCID: PMC10209260 DOI: 10.1007/s10561-022-10045-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/12/2022] [Indexed: 11/28/2022]
Abstract
Availability of molecularly intact biospecimens is essential in genetic diagnostics to obtain credible results. Integrity of nucleic acids (particularly RNA) may be compromised at various steps of tissue handling, and affected by factors such as time to freeze, freezing technique and storing temperature. At the same time, freezing and storing of the biological material should be feasible and safe for the operator. Here, we compared quality of DNA and RNA from biospecimens derived from different organs (breast, colon, adrenal glands, testes, rectum and uterus) frozen either using dry ice-cooled isopentane or with FlashFREEZE unit, in order to verify if the latter is suitable for routine use in biobanking. Implementing FlashFREEZE device would enable us to limit the use of isopentane, which is potentially toxic and environmentally harmful, whilst facilitate standardization of sample freezing time. We considered factors such RNA and DNA yield and purity. Furthermore, RNA integrity and RNA/DNA performance in routine analyses, such as qPCR, next generation sequencing or microarray, were also assessed. Our results indicate that freezing of tissue samples either with FlashFREEZE unit or isopentane ensures biological material with comparable expression profiles and DNA mutation status, indicating that RNA and DNA of similar quality can be extracted from both. Therefore, our findings support the use of the FlashFREEZE device in routine use for biobanking purposes.
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Affiliation(s)
- Edyta Biskup
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
| | - Lone Schejbel
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
| | | | - Estrid Høgdall
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
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11
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Reproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis. Sci Rep 2022; 12:19511. [PMID: 36376423 PMCID: PMC9663554 DOI: 10.1038/s41598-022-23651-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/03/2022] [Indexed: 11/15/2022] Open
Abstract
Spatial transcriptome analysis of formalin-fixed paraffin-embedded (FFPE) tissues using RNA-sequencing (RNA-seq) provides interactive information on morphology and gene expression, which is useful for clinical applications. However, despite the advantages of long-term storage at room temperature, FFPE tissues may be severely damaged by methylene crosslinking and provide less gene information than fresh-frozen tissues. In this study, we proposed a sensitive FFPE micro-tissue RNA-seq method that combines the punching of tissue sections (diameter: 100 μm) and the direct construction of RNA-seq libraries. We evaluated a method using mouse liver tissues at two years after fixation and embedding and detected approximately 7000 genes in micro-punched tissue-spots (thickness: 10 μm), similar to that detected with purified total RNA (2.5 ng) equivalent to the several dozen cells in the spot. We applied this method to clinical FFPE specimens of lung cancer that had been fixed and embedded 6 years prior, and found that it was possible to determine characteristic gene expression in the microenvironment containing tumor and non-tumor cells of different morphologies. This result indicates that spatial gene expression analysis of the tumor microenvironment is feasible using FFPE tissue sections stored for extensive periods in medical facilities.
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12
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Maier AD. Malignant meningioma. APMIS 2022; 130 Suppl 145:1-58. [DOI: 10.1111/apm.13276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Andrea Daniela Maier
- Department of Neurosurgery, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
- Department of Pathology, Rigshospitalet Copenhagen University Hospital Copenhagen Denmark
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13
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Zaitsev A, Chelushkin M, Dyikanov D, Cheremushkin I, Shpak B, Nomie K, Zyrin V, Nuzhdina E, Lozinsky Y, Zotova A, Degryse S, Kotlov N, Baisangurov A, Shatsky V, Afenteva D, Kuznetsov A, Paul SR, Davies DL, Reeves PM, Lanuti M, Goldberg MF, Tazearslan C, Chasse M, Wang I, Abdou M, Aslanian SM, Andrewes S, Hsieh JJ, Ramachandran A, Lyu Y, Galkin I, Svekolkin V, Cerchietti L, Poznansky MC, Ataullakhanov R, Fowler N, Bagaev A. Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes. Cancer Cell 2022; 40:879-894.e16. [PMID: 35944503 DOI: 10.1016/j.ccell.2022.07.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/10/2022] [Accepted: 07/12/2022] [Indexed: 12/21/2022]
Abstract
Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. We present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of >9,400 tissue and blood sorted cell RNA profiles incorporated into millions of artificial transcriptomes to accurately reconstruct the tumor microenvironment (TME). Bioinformatics correction for technical and biological variability, aberrant cancer cell expression inclusion, and accurate quantification and normalization of transcript expression increased Kassandra stability and robustness. Performance was validated on 4,000 H&E slides and 1,000 tissues by comparison with cytometric, immunohistochemical, or single-cell RNA-seq measurements. Kassandra accurately deconvolved TME elements, showing the role of these populations in tumor pathogenesis and other biological processes. Digital TME reconstruction revealed that the presence of PD-1-positive CD8+ T cells strongly correlated with immunotherapy response and increased the predictive potential of established biomarkers, indicating that Kassandra could potentially be utilized in future clinical applications.
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Affiliation(s)
| | | | | | | | - Boris Shpak
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | - Krystle Nomie
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | - Vladimir Zyrin
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | | | | | | | - Nikita Kotlov
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | | | - Daria Afenteva
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | - Susan Raju Paul
- The Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Diane L Davies
- Division of Thoracic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick M Reeves
- The Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Lanuti
- Division of Thoracic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Madison Chasse
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | - Iris Wang
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | - Mary Abdou
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | | | - James J Hsieh
- Molecular Oncology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Akshaya Ramachandran
- Molecular Oncology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Yang Lyu
- Molecular Oncology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Ilia Galkin
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | - Leandro Cerchietti
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Mark C Poznansky
- The Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Nathan Fowler
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA; Department of Lymphoma and Myeloma, MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 429, Houston, TX 77030, USA.
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14
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Li X, Zhang P, Wang H, Yu Y. Genes expressed at low levels raise false discovery rates in RNA samples contaminated with genomic DNA. BMC Genomics 2022; 23:554. [PMID: 35922750 PMCID: PMC9351092 DOI: 10.1186/s12864-022-08785-1] [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: 02/19/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022] Open
Abstract
Background RNA preparations contaminated with genomic DNA (gDNA) are frequently disregarded by RNA-seq studies. Such contamination may generate false results; however, their effect on the outcomes of RNA-seq analyses is unknown. To address this gap in our knowledge, here we added different concentrations of gDNA to total RNA preparations and subjected them to RNA-seq analysis. Results We found that the contaminating gDNA altered the quantification of transcripts at relatively high concentrations. Differentially expressed genes (DEGs) resulting from gDNA contamination may therefore contribute to higher rates of false enrichment of pathways compared with analogous samples lacking numerous DEGs. A strategy was developed to correct gene expression levels in gDNA-contaminated RNA samples, which assessed the magnitude of contamination to improve the reliability of the results. Conclusions Our study indicates that caution must be exercised when interpreting results associated with low-abundance transcripts. The data provided here will likely serve as a valuable resource to evaluate the influence of gDNA contamination on RNA-seq analysis, particularly related to the detection of putative novel gene elements. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08785-1.
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Affiliation(s)
- Xiangnan Li
- Ministry of Education Key Laboratory of Contemporary Anthropology and Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Haijian Wang
- Shanghai Pudong Hospital, Ministry of Education Key Laboratory of Contemporary Anthropology and Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Ying Yu
- Human Phenome Institute, Fudan University, Shanghai, China.
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15
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Dickman J, Howell M, Hoopes R, Wang Y, Dickerson TJ, Bottomley M, Shamma HN, Rapp CM, Turner MJ, Rohan CA, Travers JB. Insights into Lichen Planus Pigmentosus Inversus using Minimally Invasive Dermal Patch and Whole Transcriptome Analysis. JOURNAL OF CLINICAL AND INVESTIGATIVE DERMATOLOGY 2022; 10:10.13188/2373-1044.1000077. [PMID: 36003415 PMCID: PMC9397586 DOI: 10.13188/2373-1044.1000077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lichen Planus Pigmentosus inversus (LPPi) is a rare interface and lichenoid dermatitis (ILD) and supposed variant of lichen planus (LP) that presents as well-demarcated brown to grey macules in flexural and intertriginous areas. LPPi is deemed 'inversus' because its anatomical distribution in skin folds is opposite that seen in lichen planus pigmentosus (LPP) whose pigmented lesions arise on sun-exposed skin. Biopsy is required for the clinical diagnosis of all ILDs. Though multiple clinically-oriented studies have reported differences between LPP, LPPi, and LP, few molecular studies have been performed. In this case study, 3 patients, 2 with LPPi and one with LP, provided samples using minimally invasive whole transcriptome analysis using a dermal biomarker patch. This study confirms the involvement of interferon signaling and T-cell activation in LPPi and suggests an expression profile distinct from LP. Specific genes significantly upregulated in LPPi vs LP include an intergenic splice variant of the primary pigmentation determining receptor in humans and dysregulation of genes essential for ceramide synthesis and construction of the cornified envelope. This work expands upon our knowledge of the pathogenesis of LPPi vs LP, and supports the potential use of this technology in the diagnostic clinical setting to mitigate the need for invasive procedures.
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Affiliation(s)
- Jacob Dickman
- Department of Pharmacology & Toxicology, Wright State University, Dayton Ohio
| | - Michael Howell
- Department of Pharmacology & Toxicology, Wright State University, Dayton Ohio
| | - Robert Hoopes
- Department of Pharmacology & Toxicology, Wright State University, Dayton Ohio
| | | | | | - Michael Bottomley
- Department of Mathematics and Statistics, Wright State University, Dayton Ohio
| | - H. Nicholas Shamma
- Department of Dermatology, Wright State University, Dayton Ohio
- American Dermatopathology, LLC, Centerville, Ohio
| | - Christine M. Rapp
- Department of Pharmacology & Toxicology, Wright State University, Dayton Ohio
| | - Matthew J. Turner
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana
- Roudebush Veterans Administration Medical Center, Indianapolis, Indiana
| | - Craig A. Rohan
- Department of Pharmacology & Toxicology, Wright State University, Dayton Ohio
- Department of Dermatology, Wright State University, Dayton Ohio
| | - Jeffrey B. Travers
- Department of Pharmacology & Toxicology, Wright State University, Dayton Ohio
- Department of Dermatology, Wright State University, Dayton Ohio
- Dayton Veterans Administration Medical Center, Dayton, Ohio
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16
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Weke K, Kote S, Faktor J, Al Shboul S, Uwugiaren N, Brennan PM, Goodlett DR, Hupp TR, Dapic I. DIA-MS proteome analysis of formalin-fixed paraffin-embedded glioblastoma tissues. Anal Chim Acta 2022; 1204:339695. [DOI: 10.1016/j.aca.2022.339695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/11/2022]
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17
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Macagno N, Pissaloux D, de la Fouchardière A, Karanian M, Lantuejoul S, Galateau Salle F, Meurgey A, Chassagne-Clement C, Treilleux I, Renard C, Roussel J, Gervasoni J, Cockenpot V, Crozes C, Baltres A, Houlier A, Paindavoine S, Alberti L, Duc A, Loarer FL, Dufresne A, Brahmi M, Corradini N, Blay JY, Tirode F. Wholistic approach - transcriptomic analysis and beyond using archival material for molecular diagnosis. Genes Chromosomes Cancer 2022; 61:382-393. [PMID: 35080790 DOI: 10.1002/gcc.23026] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/29/2021] [Indexed: 11/07/2022] Open
Abstract
Many neoplasms remain unclassified after histopathological examination, which requires further molecular analysis. To this regard, mesenchymal neoplasms are particularly challenging due to the combination of their rarity and the large number of subtypes, and many entities still lack robust diagnostic hallmarks. RNA transcriptomic profiles have proven to be a reliable basis for the classification of previously unclassified tumors and notably for mesenchymal neoplasms. Using exome-based RNA capture sequencing on more than 5000 samples of archival material (FFPE), the combination of expression profiles analyzes (including several clustering methods), fusion genes, and small nucleotide variations has been developed at the Centre Léon Bérard (CLB) in Lyon for the molecular diagnosis of challenging neoplasms and the discovery of new entities. The molecular basis of the technique, the protocol, and the bioinformatics algorithms used are described herein, as well as its advantages and limitations.
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Affiliation(s)
- Nicolas Macagno
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France.,Aix-Marseille University, Marmara institute, INSERM, U1251, MMG, DOD-CET, Marseille, France.,NETSARC+, French Sarcoma Group (GSF-GETO) network, France.,CARADERM, French network of rare skin cancers, France
| | - Daniel Pissaloux
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France.,INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Arnaud de la Fouchardière
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France.,INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Marie Karanian
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France.,NETSARC+, French Sarcoma Group (GSF-GETO) network, France.,INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France.,Department of Biopathology, UNICANCER, Bergonié Institute, Bordeaux, France
| | - Sylvie Lantuejoul
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France.,INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France.,Grenoble Alpes University, Grenoble, France.,MESOPATH, MESOBANK, French network of mesothelioma, France
| | - Françoise Galateau Salle
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France.,MESOPATH, MESOBANK, French network of mesothelioma, France
| | - Alexandra Meurgey
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France.,NETSARC+, French Sarcoma Group (GSF-GETO) network, France
| | | | | | - Caroline Renard
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Juliette Roussel
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Julie Gervasoni
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Vincent Cockenpot
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Carole Crozes
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Aline Baltres
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Aurélie Houlier
- Department of Biopathology, UNICANCER, Centre Léon Bérard, Lyon, France
| | | | - Laurent Alberti
- INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Adeline Duc
- INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Francois Le Loarer
- NETSARC+, French Sarcoma Group (GSF-GETO) network, France.,Department of Biopathology, UNICANCER, Bergonié Institute, Bordeaux, France
| | - Armelle Dufresne
- NETSARC+, French Sarcoma Group (GSF-GETO) network, France.,INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France.,Department of Oncology, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Mehdi Brahmi
- NETSARC+, French Sarcoma Group (GSF-GETO) network, France.,INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France.,Department of Oncology, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Nadège Corradini
- NETSARC+, French Sarcoma Group (GSF-GETO) network, France.,INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France.,Institute of pediatric oncology, IHOPe, UNICANCER, Centre Léon Bérard, Lyon, France
| | - Jean-Yves Blay
- NETSARC+, French Sarcoma Group (GSF-GETO) network, France.,Department of Oncology, UNICANCER, Centre Léon Bérard, Lyon, France.,Univ Lyon, Université Claude Bernard Lyon I, Lyon, France.,Headquarters, UNICANCER, Paris, France
| | - Franck Tirode
- INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon, France.,Department of Biopathology, UNICANCER, Bergonié Institute, Bordeaux, France.,Univ Lyon, Université Claude Bernard Lyon I, Lyon, France
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18
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Weckbach LT, Schweizer L, Kraechan A, Bieber S, Ishikawa-Ankerhold H, Hausleiter J, Massberg S, Straub T, Klingel K, Grabmaier U, Zwiebel M, Mann M, Schulz C. Association of Complement and MAPK Activation With SARS-CoV-2-Associated Myocardial Inflammation. JAMA Cardiol 2021; 7:286-297. [PMID: 34910083 PMCID: PMC8674808 DOI: 10.1001/jamacardio.2021.5133] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Question What is the cardiac phenotype of patients with SARS-CoV-2 infection compared with viral and immune-mediated myocarditis and noninflammatory cardiomyopathy? Findings In this case series of 19 patients undergoing endomyocardial biopsies, cardiac specimens of patients with SARS-CoV-2 infection had a higher abundance of complement-associated factors and serine/threonine protein kinases, with mitogen-activated protein kinase–associated pathways having the highest abundance. Similarities in the cardiac immune signature were found among those with SARS-CoV-2 infection and viral myocarditis. Meaning In this study, the exploratory data, which characterized myocardial inflammation by deep phenotyping, have implications for the development of treatment strategies to reduce SARS-CoV-2–mediated tissue injury; these findings require confirmation in a prospective and extended cohort of patients. Importance Myocardial injury is a common feature of patients with SARS-CoV-2 infection. However, the cardiac inflammatory processes associated with SARS-CoV-2 infection are not completely understood. Objective To investigate the inflammatory cardiac phenotype associated with SARS-CoV-2 infection compared with viral myocarditis, immune-mediated myocarditis, and noninflammatory cardiomyopathy by integrating histologic, transcriptomic, and proteomic profiling. Design, Setting, and Participants This case series was a cooperative study between the Ludwig Maximilian University Hospital Munich and the Cardiopathology Referral Center at the University of Tübingen in Germany. A cohort of 19 patients with suspected myocarditis was examined; of those, 5 patients were hospitalized with SARS-CoV-2 infection between March and May 2020. Cardiac tissue specimens from those 5 patients were compared with specimens from 5 patients with immune-mediated myocarditis, 4 patients with non–SARS-CoV-2 viral myocarditis, and 5 patients with noninflammatory cardiomyopathy, collected from January to August 2019. Exposures Endomyocardial biopsy. Main Outcomes and Measures The inflammatory cardiac phenotypes were measured by immunohistologic analysis, RNA exome capture sequencing, and mass spectrometry–based proteomic analysis of endomyocardial biopsy specimens. Results Among 19 participants, the median age was 58 years (range, 37-76 years), and 15 individuals (79%) were male. Data on race and ethnicity were not collected. The abundance of CD163+ macrophages was generally higher in the cardiac tissue of patients with myocarditis, whereas lymphocyte counts were lower in the tissue of patients with SARS-CoV-2 infection vs patients with non–SARS-CoV-2 virus-associated and immune-mediated myocarditis. Among those with SARS-CoV-2 infection, components of the complement cascade, including C1q subunits (transcriptomic analysis: 2.5-fold to 3.6-fold increase; proteomic analysis: 2.0-fold to 3.4-fold increase) and serine/cysteine proteinase inhibitor clade G member 1 (transcriptomic analysis: 1.7-fold increase; proteomic analysis: 2.6-fold increase), belonged to the most commonly upregulated transcripts and differentially abundant proteins. In cardiac macrophages, the abundance of C1q was highest in SARS-CoV-2 infection. Assessment of important signaling cascades identified an upregulation of the serine/threonine mitogen-activated protein kinase pathways. Conclusions and Relevance This case series found that the cardiac immune signature varied in inflammatory conditions with different etiologic characteristics. Future studies are needed to examine the role of these immune pathways in myocardial inflammation.
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Affiliation(s)
- Ludwig T Weckbach
- Medizinische Klinik und Poliklinik I, Ludwig Maximilian University Hospital Munich, Munich, Germany.,Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig Maximilian University Munich, Planegg-Martinsried, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
| | - Lisa Schweizer
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Planegg-Martinsried, Germany
| | - Angelina Kraechan
- Medizinische Klinik und Poliklinik I, Ludwig Maximilian University Hospital Munich, Munich, Germany.,Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig Maximilian University Munich, Planegg-Martinsried, Germany
| | - Stephanie Bieber
- Medizinische Klinik und Poliklinik I, Ludwig Maximilian University Hospital Munich, Munich, Germany
| | | | - Jörg Hausleiter
- Medizinische Klinik und Poliklinik I, Ludwig Maximilian University Hospital Munich, Munich, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
| | - Steffen Massberg
- Medizinische Klinik und Poliklinik I, Ludwig Maximilian University Hospital Munich, Munich, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
| | - Tobias Straub
- Core Facility Bioinformatics, Biomedical Center, Ludwig Maximilian University Munich, Planegg-Martinsried, Germany
| | - Karin Klingel
- Cardiopathology Department, Institute for Pathology and Neuropathology, Tübingen University Hospital, Tübingen, Germany
| | - Ulrich Grabmaier
- Medizinische Klinik und Poliklinik I, Ludwig Maximilian University Hospital Munich, Munich, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
| | - Maximilian Zwiebel
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Planegg-Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Planegg-Martinsried, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Schulz
- Medizinische Klinik und Poliklinik I, Ludwig Maximilian University Hospital Munich, Munich, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
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19
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Xie Q, Wang D, Luo X, Li Z, Hu A, Yang H, Tang J, Gao P, Sun T, Kong L. Proteome profiling of formalin-fixed, paraffin-embedded lung adenocarcinoma tissues using a tandem mass tag-based quantitative proteomics approach. Oncol Lett 2021; 22:706. [PMID: 34457061 PMCID: PMC8358594 DOI: 10.3892/ol.2021.12967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/22/2021] [Indexed: 12/18/2022] Open
Abstract
Over the past few decades, increasing efforts have been made to improve the understanding of, and treatment options for, lung adenocarcinoma (LUAD). However, considering the heterogeneity of LUAD, precise proteomics-based characterization at the molecular level is an urgent clinical requirement for effective treatment. Formalin-fixed, paraffin-embedded (FFPE) tissue is a good option as the working tool for proteomics studies. The present study aimed to obtain a global protein profile using LUAD FFPE tissue samples. Using a quantitative proteomics approach, the study revealed that 360 proteins were significantly more highly expressed in LUAD than in adjacent nontumor lung tissues. Also, 19 differentially expressed membrane proteins were found to be primarily responsible for immune processes. Epidermal growth factor (EGF)-like domain and laminin EGF domain showed markedly different expression levels between cancer tissues and tumor-adjacent normal tissues. Furthermore, Gene Ontology functional enrichment analysis showed that significantly upregulated proteins were associated with the endoplasmic reticulum lumen, protein disulfide isomerase activity, vitamin binding, cell cycle G1/S phase transition, to name but a few. Also, numerous kinases and post-translational modification enzymes were significantly upregulated across all eight LUAD samples compared with paracarcinoma tissues. Proteomics analysis revealed that AAA domain containing 3A (ATAD3a), a member of the ATPase family, was highly expressed in LUAD tissues, which was supported by immunohistochemical analysis. Furthermore, the study confirmed that ATAD3a enhanced the cisplatin sensitivity of LUAD cells. Collectively, the findings of the present study provide new potential candidate targets in patients with LUAD, and may aid auxiliary LUAD diagnosis and surveillance in a noninvasive manner.
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Affiliation(s)
- Qi Xie
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Dan Wang
- Department of Neorology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Xiao Luo
- International Medical Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Zhen Li
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Aixia Hu
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Hui Yang
- Department of Thoracic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Jinxing Tang
- Department of Thoracic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Peiyu Gao
- Department of Thoracic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Tingyi Sun
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
| | - Lingfei Kong
- Department of Pathology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R China
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20
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Wagener-Ryczek S, Pappesch R. Targeted RNA-sequencing for the evaluation of gene fusions in lung tumors: current status and future prospects. Expert Rev Mol Diagn 2021; 21:531-534. [PMID: 33887162 DOI: 10.1080/14737159.2021.1920399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Svenja Wagener-Ryczek
- Institute for Pathology and Center for Integrated Oncology (CIO), University Hospital Cologne, Cologne, Germany
| | - Roberto Pappesch
- Institute for Pathology and Center for Integrated Oncology (CIO), University Hospital Cologne, Cologne, Germany
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21
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Denkert C, Untch M, Benz S, Schneeweiss A, Weber KE, Schmatloch S, Jackisch C, Sinn HP, Golovato J, Karn T, Marmé F, Link T, Budczies J, Nekljudova V, Schmitt WD, Stickeler E, Müller V, Jank P, Parulkar R, Heinmöller E, Sanborn JZ, Schem C, Sinn BV, Soon-Shiong P, van Mackelenbergh M, Fasching PA, Rabizadeh S, Loibl S. Reconstructing tumor history in breast cancer: signatures of mutational processes and response to neoadjuvant chemotherapy ⋆. Ann Oncol 2021; 32:500-511. [PMID: 33418062 DOI: 10.1016/j.annonc.2020.12.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/13/2020] [Accepted: 12/20/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Different endogenous and exogenous mutational processes act over the evolutionary history of a malignant tumor, driven by abnormal DNA editing, mutagens or age-related DNA alterations, among others, to generate the specific mutational landscape of each individual tumor. The signatures of these mutational processes can be identified in large genomic datasets. We investigated the hypothesis that genomic patterns of mutational signatures are associated with the clinical behavior of breast cancer, in particular chemotherapy response and survival, with a particular focus on therapy-resistant disease. PATIENTS AND METHODS Whole exome sequencing was carried out in 405 pretherapeutic samples from the prospective neoadjuvant multicenter GeparSepto study. We analyzed 11 mutational signatures including biological processes such as APOBEC-mutagenesis, homologous recombination deficiency (HRD), mismatch repair deficiency and also age-related or tobacco-induced alterations. RESULTS Different subgroups of breast carcinomas were defined mainly by differences in HRD-related and APOBEC-related mutational signatures and significant differences between hormone-receptor (HR)-negative and HR-positive tumors as well as correlations with age, Ki-67 and immunological parameters were observed. We could identify mutational processes that were linked to increased pathological complete response rates to neoadjuvant chemotherapy with high significance. In univariate analyses for HR-positive tumors signatures, S3 (HRD, P < 0.001) and S13 (APOBEC, P = 0.001) as well as exonic mutation rate (P = 0.002) were significantly correlated with increased pathological complete response rates. The signatures S3 (HRD, P = 0.006) and S4 (tobacco, P = 0.011) were prognostic for reduced disease-free survival of patients with chemotherapy-resistant tumors. CONCLUSION The results of this investigation suggest that the clinical behavior of a tumor, in particular, response to neoadjuvant chemotherapy and disease-free survival of therapy-resistant tumors, could be predicted by the composition of mutational signatures as an indicator of the individual genomic history of a tumor. After additional validations, mutational signatures might be used to identify tumors with an increased response rate to neoadjuvant chemotherapy and to define therapy-resistant subgroups for future therapeutic interventions.
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Affiliation(s)
- C Denkert
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg (UK-GM), Marburg, Germany; Charité - Universitätsmedizin Berlin, Institute of Pathology, Berlin, Germany.
| | - M Untch
- Helios Klinikum Berlin-Buch, Department of Obstetrics and Gynaecology, Berlin, Germany
| | - S Benz
- NantOmics, LLC, Culver City, USA
| | - A Schneeweiss
- Nationales Centrum für Tumorerkrankungen, Universitätsklinikum und Deutsches Krebsforschungszentrum Heidelberg, Heidelberg, Germany
| | - K E Weber
- German Breast Group (GBG), Neu-Isenburg, Germany
| | - S Schmatloch
- Brustzentrum Kassel, Elisabeth Krankenhaus, Kassel, Germany
| | - C Jackisch
- Department of Obstetrics and Gynecology and Breast Cancer Center, Sana Klinikum Offenbach, Offenbach, Germany
| | - H P Sinn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; German Cancer consortium (DKTK), Heidelberg, Germany
| | | | - T Karn
- Klinik für Frauenheilkunde und Geburtshilfe, Goethe Universität, Frankfurt, Germany
| | - F Marmé
- Universitätsfrauenklinik Mannheim, Mannheim, Germany
| | - T Link
- Department of Gynecology and Obstetrics, Technische Universität Dresden, Dresden, Germany
| | - J Budczies
- Charité - Universitätsmedizin Berlin, Institute of Pathology, Berlin, Germany; Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; German Cancer consortium (DKTK), Heidelberg, Germany
| | - V Nekljudova
- German Breast Group (GBG), Neu-Isenburg, Germany
| | - W D Schmitt
- Charité - Universitätsmedizin Berlin, Institute of Pathology, Berlin, Germany
| | - E Stickeler
- Department of Gynecology, RWTH Aachen, Aachen, Germany
| | - V Müller
- Department of Gynecology, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - P Jank
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg (UK-GM), Marburg, Germany; Charité - Universitätsmedizin Berlin, Institute of Pathology, Berlin, Germany
| | | | | | | | - C Schem
- Mammazentrum Hamburg am Krankenhaus Jerusalem, Hamburg, Germany
| | - B V Sinn
- Charité - Universitätsmedizin Berlin, Institute of Pathology, Berlin, Germany
| | | | - M van Mackelenbergh
- Universitätsklinikum Schleswig-Holstein, Klinik für Gynäkologie und Geburtshilfe, Kiel, Germany
| | - P A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | | | - S Loibl
- German Breast Group (GBG), Neu-Isenburg, Germany; University of Frankfurt, Frankfurt am Main, Germany
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