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Morla-Barcelo PM, Laguna-Macarrilla D, Cordoba O, Matheu G, Oliver J, Roca P, Nadal-Serrano M, Sastre-Serra J. Unraveling malignant phenotype of peritumoral tissue: transcriptomic insights into early-stage breast cancer. Breast Cancer Res 2024; 26:89. [PMID: 38831458 PMCID: PMC11145834 DOI: 10.1186/s13058-024-01837-2] [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] [Received: 12/12/2023] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Early-stage invasive ductal carcinoma displays high survival rates due to early detection and treatments. However, there is still a chance of relapse of 3-15% after treatment. The aim of this study was to uncover the distinctive transcriptomic characteristics and monitoring prognosis potential of peritumoral tissue in early-stage cases. METHODS RNA was isolated from tumoral, peritumoral, and non-tumoral breast tissue from surgical resection of 10 luminal early-stage invasive ductal carcinoma patients. Transcriptome expression profiling for differentially expressed genes (DEGs) identification was carried out through microarray analysis. Gene Ontology and KEGG pathways enrichment analysis were explored for functional characterization of identified DEGs. Protein-Protein Interactions (PPI) networks analysis was performed to identify hub nodes of peritumoral tissue alterations and correlated with Overall Survival and Relapse Free Survival. RESULTS DEGs closely related with cell migration, extracellular matrix organization, and cell cycle were upregulated in peritumoral tissue compared to non-tumoral. Analyzing PPI networks, we observed that the proximity to tumor leads to the alteration of gene modules involved in cell proliferation and differentiation signaling pathways. In fact, in the peritumoral area were identified the top ten upregulated hub nodes including CDK1, ESR1, NOP58, PCNA, EZH2, PPP1CA, BUB1, TGFBR1, CXCR4, and CCND1. A signature performed by four of these hub nodes (CDK1, PCNA, EZH2, and BUB1) was associated with relapse events in untreated luminal breast cancer patients. CONCLUSIONS In conclusion, our study characterizes in depth breast peritumoral tissue providing clues on the changes that tumor signaling could cause in patients with early-stage breast cancer. We propose that the use of a four gene signature could help to predict local relapse. Overall, our results highlight the value of peritumoral tissue as a potential source of new biomarkers for early detection of relapse and improvement in invasive ductal carcinoma patient's prognosis.
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MESH Headings
- Humans
- Female
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/mortality
- Breast Neoplasms/metabolism
- Gene Expression Profiling
- Transcriptome
- Gene Expression Regulation, Neoplastic
- Neoplasm Staging
- Prognosis
- Protein Interaction Maps/genetics
- Middle Aged
- Biomarkers, Tumor/genetics
- Gene Regulatory Networks
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/metabolism
- Phenotype
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Aged
- Adult
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Affiliation(s)
- Pere Miquel Morla-Barcelo
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d'Investigació en Ciéncies de la Salut (IUNICS), Universitat de les Illes Balears, Palma, Illes Balears, Spain
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, Edificio S, Palma, Illes Balears, Spain
| | - David Laguna-Macarrilla
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, Edificio S, Palma, Illes Balears, Spain
- Departamento de Patología, Hospital Universitari Son Espases, Palma, Illes Balears, Spain
| | - Octavi Cordoba
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, Edificio S, Palma, Illes Balears, Spain
- Servicio de Obstetricia y Ginecología, Hospital Universitari de Son Espases, Palma, Illes Balears, Spain
- Facultat de Medicina, Universitat de les Illes Balears, Palma, Illes Balears, Spain
| | - Gabriel Matheu
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, Edificio S, Palma, Illes Balears, Spain
- Departamento de Patología, Hospital Universitari Son Espases, Palma, Illes Balears, Spain
| | - Jordi Oliver
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d'Investigació en Ciéncies de la Salut (IUNICS), Universitat de les Illes Balears, Palma, Illes Balears, Spain
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, Edificio S, Palma, Illes Balears, Spain
- CIBER Fisiopatología Obesidad y Nutrición, Instituto Salud Carlos III, Madrid, Spain
| | - Pilar Roca
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d'Investigació en Ciéncies de la Salut (IUNICS), Universitat de les Illes Balears, Palma, Illes Balears, Spain
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, Edificio S, Palma, Illes Balears, Spain
- CIBER Fisiopatología Obesidad y Nutrición, Instituto Salud Carlos III, Madrid, Spain
| | - Mercedes Nadal-Serrano
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d'Investigació en Ciéncies de la Salut (IUNICS), Universitat de les Illes Balears, Palma, Illes Balears, Spain.
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, Edificio S, Palma, Illes Balears, Spain.
| | - Jorge Sastre-Serra
- Grupo Multidisciplinar de Oncología Traslacional, Institut Universitari d'Investigació en Ciéncies de la Salut (IUNICS), Universitat de les Illes Balears, Palma, Illes Balears, Spain
- Instituto de Investigación Sanitaria de las Islas Baleares (IdISBa), Hospital Universitario Son Espases, Edificio S, Palma, Illes Balears, Spain
- CIBER Fisiopatología Obesidad y Nutrición, Instituto Salud Carlos III, Madrid, Spain
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Sverchkova A, Burkholz S, Rubsamen R, Stratford R, Clancy T. Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response. BMC Med Genomics 2024; 17:37. [PMID: 38281021 PMCID: PMC10821267 DOI: 10.1186/s12920-024-01808-8] [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: 07/05/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND The HLA complex is the most polymorphic region of the human genome, and its improved characterization can help us understand the genetics of human disease as well as the interplay between cancer and the immune system. The main function of HLA genes is to recognize "non-self" antigens and to present them on the cell surface to T cells, which instigate an immune response toward infected or transformed cells. While sequence variation in the antigen-binding groove of HLA may modulate the repertoire of immunogenic antigens presented to T cells, alterations in HLA expression can significantly influence the immune response to pathogens and cancer. METHODS RNA sequencing was used here to accurately genotype the HLA region and quantify and compare the level of allele-specific HLA expression in tumors and patient-matched adjacent normal tissue. The computational approach utilized in the study types classical and non-classical Class I and Class II HLA alleles from RNA-seq while simultaneously quantifying allele-specific or personalized HLA expression. The strategy also uses RNA-seq data to infer immune cell infiltration into tumors and the corresponding immune cell composition of matched normal tissue, to reveal potential insights related to T cell and NK cell interactions with tumor HLA alleles. RESULTS The genotyping method outperforms existing RNA-seq-based HLA typing tools for Class II HLA genotyping. Further, we demonstrate its potential for studying tumor-immune interactions by applying the method to tumor samples from two different subtypes of breast cancer and their matched normal breast tissue controls. CONCLUSIONS The integrative RNA-seq-based HLA typing approach described in the study, coupled with HLA expression analysis, neoantigen prediction and immune cell infiltration, may help increase our understanding of the interplay between a patient's tumor and immune system; and provide further insights into the immune mechanisms that determine a positive or negative outcome following treatment with immunotherapy such as checkpoint blockade.
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Affiliation(s)
- Angelina Sverchkova
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Scott Burkholz
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
| | - Reid Rubsamen
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
- University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Richard Stratford
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
| | - Trevor Clancy
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway.
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Lau HSH, Tan VKM, Tan BKT, Sim Y, Quist J, Thike AA, Tan PH, Pervaiz S, Grigoriadis A, Sabapathy K. Adipose-enriched peri-tumoral stroma, in contrast to myofibroblast-enriched stroma, prognosticates poorer survival in breast cancers. NPJ Breast Cancer 2023; 9:84. [PMID: 37863888 PMCID: PMC10589339 DOI: 10.1038/s41523-023-00590-7] [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: 02/22/2023] [Accepted: 10/02/2023] [Indexed: 10/22/2023] Open
Abstract
Despite our understanding of the genetic basis of intra-tumoral heterogeneity, the role of stromal heterogeneity arising from an altered tumor microenvironment in affecting tumorigenesis is poorly understood. In particular, extensive study on the peri-tumoral stroma in the morphologically normal tissues surrounding the tumor is lacking. Here, we examine the heterogeneity in tumors and peri-tumoral stroma from 8 ER+/PR+/HER2- invasive breast carcinomas, through multi-region transcriptomic profiling by microarray. We describe the regional heterogeneity observed at the intrinsic molecular subtype, pathway enrichment, and cell type composition levels within each tumor and its peri-tumoral region, up to 7 cm from the tumor margins. Moreover, we identify a pro-inflammatory adipose-enriched peri-tumoral subtype which was significantly associated with poorer overall survival in breast cancer patients, in contrast to an adaptive immune cell- and myofibroblast-enriched subtype. These data together suggest that peri-tumoral heterogeneity may be an important determinant of the evolution and treatment of breast cancers.
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Affiliation(s)
- Hannah Si Hui Lau
- Divisions of Cellular & Molecular Research, National Cancer Centre Singapore, Singapore, 168583, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Veronique Kiak Mien Tan
- Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
- Department of Breast Surgery, Singapore General Hospital, Singapore, 168753, Singapore
| | - Benita Kiat Tee Tan
- Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
- Department of Breast Surgery, Singapore General Hospital, Singapore, 168753, Singapore
- Department of General Surgery, Sengkang General Hospital, Singapore, 544886, Singapore
| | - Yirong Sim
- Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
- Department of Breast Surgery, Singapore General Hospital, Singapore, 168753, Singapore
| | - Jelmar Quist
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aye Aye Thike
- Division of Pathology, Singapore General Hospital, Singapore, 169856, Singapore
| | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore, 169856, Singapore
| | - Shazib Pervaiz
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Kanaga Sabapathy
- Divisions of Cellular & Molecular Research, National Cancer Centre Singapore, Singapore, 168583, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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Brito Baleeiro R, Liu P, Chard Dunmall LS, Di Gioia C, Nagano A, Cutmore L, Wang J, Chelala C, Nyambura LW, Walden P, Lemoine N, Wang Y. Personalized neoantigen viro-immunotherapy platform for triple-negative breast cancer. J Immunother Cancer 2023; 11:e007336. [PMID: 37586771 PMCID: PMC10432671 DOI: 10.1136/jitc-2023-007336] [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] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) corresponds to approximately 20% of all breast tumors, with a high propensity for metastasis and a poor prognosis. Because TNBC displays a high mutational load compared with other breast cancer types, a neoantigen-based immunotherapy strategy could be effective. One major bottleneck in the development of a neoantigen-based vaccine for TNBC is the selection of the best targets, that is, tumor-specific neoantigens which are presented at the surface of tumor cells and capable of eliciting robust immune responses. In this study, we aimed to set up a platform for identification and delivery of immunogenic neoantigens in a vaccine regimen for TNBC using oncolytic vaccinia virus (VV). METHODS We used bioinformatic tools and cell-based assays to identify immunogenic neoantigens in TNBC patients' samples, human and murine cell lines. Immunogenicity of the neoantigens was tested in vitro (human) and ex vivo (murine) in T-cell assays. To assess the efficacy of our regimen, we used a preclinical model of TNBC where we treated tumor-bearing mice with neoantigens together with oncolytic VV and evaluated the effect on induction of neoantigen-specific CD8+T cells, tumor growth and survival. RESULTS We successfully identified immunogenic neoantigens and generated neoantigen-specific CD8+T cells capable of recognizing a human TNBC cell line expressing the mutated gene. Using a preclinical model of TNBC, we showed that our tumor-specific oncolytic VV was able to change the tumor microenvironment, attracting and maintaining mature cross-presenting CD8α+dendritic cells and effector T-cells. Moreover, when delivered in a prime/boost regimen together with oncolytic VV, long peptides encompassing neoantigens were able to induce neoantigen-specific CD8+T cells, slow tumor growth and increase survival. CONCLUSIONS Our study provides a promising approach for the development of neoantigen-based immunotherapies for TNBC. By identifying immunogenic neoantigens and developing a delivery system through tumor-specific oncolytic VV, we have demonstrated that neoantigen-based vaccines could be effective in inducing neoantigen-specific CD8+T cells response with significant impact on tumor growth. Further studies are needed to determine the safety and efficacy of this approach in clinical trials.
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Affiliation(s)
- Renato Brito Baleeiro
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Peng Liu
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Louisa S Chard Dunmall
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Carmela Di Gioia
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Ai Nagano
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Lauren Cutmore
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Jun Wang
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
| | - Lydon Wainaina Nyambura
- Department of Dermatology, Venerology and Allergology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Walden
- Department of Dermatology, Venerology and Allergology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nicholas Lemoine
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
- Zhengzhou University, Zhengzhou, Henan, China
| | - Yaohe Wang
- Centre for Cancer Biomarkers and Biotherapeutics, Queen Mary University of London, London, UK
- Zhengzhou University, Zhengzhou, Henan, China
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5
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Arat S, Huynh R, Kumpf S, Qian J, Shoieb A, Virgen-Slane R, Voigt F, Xie Z, Jakubczak JL. Effects of donor source on transcriptomic profiles of human kidney tissue. FASEB J 2023; 37:e22804. [PMID: 36753402 DOI: 10.1096/fj.202201754r] [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: 11/03/2022] [Revised: 12/27/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023]
Abstract
Normal human tissue is a critical reference control in biomedical research. However, the type of tissue donor can significantly affect the underlying biology of the samples. We investigated the impact of tissue donor source type by performing transcriptomic analysis on healthy kidney tissue from three donor source types: cadavers, organ donors, and normal-adjacent tissue from surgical resections of clear cell renal cell carcinomas, and we compared the gene expression profiles to those of clear cell renal cell carcinoma samples. Comparisons among the normal samples revealed general similarity, with notable differences in gene expression pathways involving immune system and inflammatory processes, response to extracellular stimuli, ion transport, and metabolism. When compared to tumors, the transcriptomic profiles of the normal adjacent tissue were highly similar to the profiles from cadaveric and organ donor tissue samples, arguing against the presence of a field cancerization effect in clear cell renal cell carcinoma. We conclude that all three normal source types are suitable for reference kidney control samples, but important differences must be noted for particular research areas and tissue banking strategies.
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Affiliation(s)
- Seda Arat
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Renee Huynh
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Steven Kumpf
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Jessie Qian
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Ahmed Shoieb
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Richard Virgen-Slane
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., La Jolla, California, USA
| | - Frank Voigt
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
| | - Zhiyong Xie
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Cambridge, Massachusetts, USA
| | - John L Jakubczak
- Drug Safety Research and Development, Worldwide Research, Development and Medical, Pfizer Inc., Groton, Connecticut, USA
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6
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Dynamic Biobanking for Advancing Breast Cancer Research. J Pers Med 2023; 13:jpm13020360. [PMID: 36836597 PMCID: PMC9959444 DOI: 10.3390/jpm13020360] [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: 01/23/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Longitudinal patient biospecimens and data advance breast cancer research through enabling precision medicine approaches for identifying risk, early diagnosis, improved disease management and targeted therapy. Cancer biobanks must evolve to provide not only access to high-quality annotated biospecimens and rich associated data, but also the tools required to harness these data. We present the Breast Cancer Now Tissue Bank centre at the Barts Cancer Institute as an exemplar of a dynamic biobanking ecosystem that hosts and links longitudinal biospecimens and multimodal data including electronic health records, genomic and imaging data, offered alongside integrated data sharing and analytics tools. We demonstrate how such an ecosystem can inform precision medicine efforts in breast cancer research.
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7
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Kostecka A, Nowikiewicz T, Olszewski P, Koczkowska M, Horbacz M, Heinzl M, Andreou M, Salazar R, Mair T, Madanecki P, Gucwa M, Davies H, Skokowski J, Buckley PG, Pęksa R, Śrutek E, Szylberg Ł, Hartman J, Jankowski M, Zegarski W, Tiemann-Boege I, Dumanski JP, Piotrowski A. High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing. NPJ Breast Cancer 2022; 8:76. [PMID: 35768433 PMCID: PMC9243094 DOI: 10.1038/s41523-022-00443-9] [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: 09/29/2021] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 × 10-2- 5.2 × 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.
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Affiliation(s)
- Anna Kostecka
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
| | - Tomasz Nowikiewicz
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland.
- Department of Breast Cancer and Reconstructive Surgery, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland.
| | - Paweł Olszewski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Koczkowska
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Horbacz
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Heinzl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Maria Andreou
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Renato Salazar
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gucwa
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jarosław Skokowski
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | | | - Rafał Pęksa
- Department of Patomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Śrutek
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Perinatology, Gynaecology and Gynaecologic, Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
- MedTech Labs, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Michał Jankowski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Wojciech Zegarski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | | | - Jan P Dumanski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arkadiusz Piotrowski
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
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8
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Filipowicz N, Drężek K, Horbacz M, Wojdak A, Szymanowski J, Rychlicka-Buniowska E, Juhas U, Duzowska K, Nowikiewicz T, Stańkowska W, Chojnowska K, Andreou M, Ławrynowicz U, Wójcik M, Davies H, Śrutek E, Bieńkowski M, Milian-Ciesielska K, Zdrenka M, Ambicka A, Przewoźnik M, Harazin-Lechowska A, Adamczyk A, Kowalski J, Bała D, Wiśniewski D, Tkaczyński K, Kamecki K, Drzewiecka M, Wroński P, Siekiera J, Ratnicka I, Jankau J, Wierzba K, Skokowski J, Połom K, Przydacz M, Bełch Ł, Chłosta P, Matuszewski M, Okoń K, Rostkowska O, Hellmann A, Sasim K, Remiszewski P, Sierżęga M, Hać S, Kobiela J, Kaska Ł, Jankowski M, Hodorowicz-Zaniewska D, Jaszczyński J, Zegarski W, Makarewicz W, Pęksa R, Szpor J, Ryś J, Szylberg Ł, Piotrowski A, Dumanski JP. Comprehensive cancer-oriented biobanking resource of human samples for studies of post-zygotic genetic variation involved in cancer predisposition. PLoS One 2022; 17:e0266111. [PMID: 35390022 PMCID: PMC8989288 DOI: 10.1371/journal.pone.0266111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
The progress in translational cancer research relies on access to well-characterized samples from a representative number of patients and controls. The rationale behind our biobanking are explorations of post-zygotic pathogenic gene variants, especially in non-tumoral tissue, which might predispose to cancers. The targeted diagnoses are carcinomas of the breast (via mastectomy or breast conserving surgery), colon and rectum, prostate, and urinary bladder (via cystectomy or transurethral resection), exocrine pancreatic carcinoma as well as metastases of colorectal cancer to the liver. The choice was based on the high incidence of these cancers and/or frequent fatal outcome. We also collect age-matched normal controls. Our still ongoing collection originates from five clinical centers and after nearly 2-year cooperation reached 1711 patients and controls, yielding a total of 23226 independent samples, with an average of 74 donors and 1010 samples collected per month. The predominant diagnosis is breast carcinoma, with 933 donors, followed by colorectal carcinoma (383 donors), prostate carcinoma (221 donors), bladder carcinoma (81 donors), exocrine pancreatic carcinoma (15 donors) and metachronous colorectal cancer metastases to liver (14 donors). Forty percent of the total sample count originates from macroscopically healthy cancer-neighboring tissue, while contribution from tumors is 12%, which adds to the uniqueness of our collection for cancer predisposition studies. Moreover, we developed two program packages, enabling registration of patients, clinical data and samples at the participating hospitals as well as the central system of sample/data management at coordinating center. The approach used by us may serve as a model for dispersed biobanking from multiple satellite hospitals. Our biobanking resource ought to stimulate research into genetic mechanisms underlying the development of common cancers. It will allow all available "-omics" approaches on DNA-, RNA-, protein- and tissue levels to be applied. The collected samples can be made available to other research groups.
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Affiliation(s)
| | - Kinga Drężek
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Horbacz
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Agata Wojdak
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Jakub Szymanowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Bioenit Jakub Szymanowski, Gdańsk, Poland
| | | | - Ulana Juhas
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Tomasz Nowikiewicz
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | | | | | - Maria Andreou
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Magdalena Wójcik
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ewa Śrutek
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Jacek Kowalski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Dariusz Bała
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Dorian Wiśniewski
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Karol Tkaczyński
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Krzysztof Kamecki
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Marta Drzewiecka
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Paweł Wroński
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Jerzy Siekiera
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Izabela Ratnicka
- Department of Plastic Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Jerzy Jankau
- Department of Plastic Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Wierzba
- Department of Internal Medicine, Connective Tissue Diseases and Geriatrics, Medical University of Gdańsk, Gdańsk, Poland
| | - Jarosław Skokowski
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
- Department of Medical Laboratory Diagnostics-Biobank, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Połom
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Mikołaj Przydacz
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Łukasz Bełch
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Piotr Chłosta
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Marcin Matuszewski
- Department and Clinic of Urology, Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Okoń
- Department of Pathomorphology, Jagiellonian University Medical College, Kraków, Poland
| | - Olga Rostkowska
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Andrzej Hellmann
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Sasim
- Clinic of Urology and Oncological Urology, Specialist Hospital of Kościerzyna, Kościerzyna, Poland
| | - Piotr Remiszewski
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Marek Sierżęga
- Department of General, Oncological, and Gastrointestinal Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Stanisław Hać
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Jarosław Kobiela
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Łukasz Kaska
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Jankowski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Diana Hodorowicz-Zaniewska
- Department of General, Oncological, and Gastrointestinal Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Janusz Jaszczyński
- Department of Urology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Wojciech Zegarski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Makarewicz
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Kościerzyna, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Joanna Szpor
- Department of Pathomorphology, Jagiellonian University Medical College, Kraków, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
| | - Jan P. Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
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9
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Gadaleta E, Thorn GJ, Ross-Adams H, Jones LJ, Chelala C. Field cancerization in breast cancer. J Pathol 2022; 257:561-574. [PMID: 35362092 PMCID: PMC9322418 DOI: 10.1002/path.5902] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Breast cancer affects one in seven women worldwide during their lifetime. Widespread mammographic screening programs and education campaigns allow for early detection of the disease, often during its asymptomatic phase. Current practice in treatment and recurrence monitoring is based primarily on pathological evaluations but can also encompass genomic evaluations, both of which focus on the primary tumor. Although breast cancer is one of the most studied cancers, patients still recur at a rate of up to 15% within the first 10 years post‐surgery. Local recurrence was originally attributed to tumor cells contaminating histologically normal (HN) tissues beyond the surgical margin, but advances in technology have allowed for the identification of distinct aberrations that exist in the peri‐tumoral tissues themselves. One leading theory to explain this phenomenon is the field cancerization theory. Under this hypothesis, tumors arise from a field of molecularly altered cells that create a permissive environment for malignant evolution, which can occur with or without morphological changes. The traditional histopathology paradigm dictates that molecular alterations are reflected in the tissue phenotype. However, the spectrum of inter‐patient variability of normal breast tissue may obfuscate recognition of a cancerized field during routine diagnostics. In this review, we explore the concept of field cancerization focusing on HN peri‐tumoral tissues: we present the pathological and molecular features of field cancerization within these tissues and discuss how the use of peri‐tumoral tissues can affect research. Our observations suggest that pathological and molecular evaluations could be used synergistically to assess risk and guide the therapeutic management of patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Emanuela Gadaleta
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Graeme J Thorn
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helen Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Louise J Jones
- Centre for Tumour Biology Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
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