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Calabrese A, von Arx C, Tafuti AA, Pensabene M, De Laurentiis M. Prevention, diagnosis and clinical management of hereditary breast cancer beyond BRCA1/2 genes. Cancer Treat Rev 2024; 129:102785. [PMID: 38870570 DOI: 10.1016/j.ctrv.2024.102785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/18/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
Abstract
The detection of germline pathogenic variants (gPVs) in BRCA1/2 and other breast cancer (BC) genes is rising exponentially thanks to the advent of multi-gene panel testing. This promising technology, coupled with the availability of specific therapies for BC BRCA-related, has increased the number of patients eligible for genetic testing. Implementing multi-gene panel testing for hereditary BC screening holds promise to maximise benefits for patients at hereditary risk of BC. These benefits range from prevention programs to antineoplastic-targeted therapies. However, the clinical management of these patients is complex and requires guidelines based on recent evidence. Furthermore, applying multi-gene panel testing into clinical practice increases the detection of variants of uncertain significance (VUSs). This augments the complexity of patients' clinical management, becoming an unmet need for medical oncologists. This review aims to collect updated evidence on the most common BC-related genes besides BRCA1/2, from their biological role in BC development to their potential impact in tailoring prevention and treatment strategies.
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Affiliation(s)
- A Calabrese
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy
| | - C von Arx
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy.
| | - A A Tafuti
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy
| | - M Pensabene
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy
| | - M De Laurentiis
- Department Breast and Thoracic Oncology, Istituto Nazionale Tumori - IRCCS, 'Fondazione G. Pascale', Via Mariano Semmola, 53, 80131 Napoli, NA, Italy
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2
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Veerla S, Staaf J. Kataegis in clinical and molecular subgroups of primary breast cancer. NPJ Breast Cancer 2024; 10:32. [PMID: 38658600 PMCID: PMC11043427 DOI: 10.1038/s41523-024-00640-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024] Open
Abstract
Kataegis is a hypermutation phenomenon characterized by localized clusters of single base pair substitution (SBS) reported in multiple cancer types. Despite a high frequency in breast cancer, large-scale analyses of kataegis patterns and associations with clinicopathological and molecular variables in established breast cancer subgroups are lacking. Therefore, WGS profiled primary breast cancers (n = 791) with associated clinical and molecular data layers, like RNA-sequencing data, were analyzed for kataegis frequency, recurrence, and associations with genomic contexts and functional elements, transcriptional patterns, driver alterations, homologous recombination deficiency (HRD), and prognosis in tumor subgroups defined by ER, PR, and HER2/ERBB2 status. Kataegis frequency was highest in the HER2-positive(p) subgroups, including both ER-negative(n)/positive(p) tumors (ERnHER2p/ERpHER2p). In TNBC, kataegis was neither associated with PAM50 nor TNBC mRNA subtypes nor with distant relapse in chemotherapy-treated patients. In ERpHER2n tumors, kataegis was associated with aggressive characteristics, including PR-negativity, molecular Luminal B subtype, higher mutational burden, higher grade, and expression of proliferation-associated genes. Recurrent kataegis loci frequently targeted regions commonly amplified in ER-positive tumors, while few recurrent loci were observed in TNBC. SBSs in kataegis loci appeared enriched in regions of open chromatin. Kataegis status was not associated with HRD in any subgroup or with distinct transcriptional patterns in unsupervised or supervised analysis. In summary, kataegis is a common hypermutation phenomenon in established breast cancer subgroups, particularly in HER2p subgroups, coinciding with an aggressive tumor phenotype in ERpHER2n disease. In TNBC, the molecular implications and associations of kataegis are less clear, including its prognostic value.
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Affiliation(s)
- Srinivas Veerla
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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3
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Castellano G, Giugliano F, Curigliano G, Marra A. Clinical utility of genomic signatures for the management of early and metastatic triple-negative breast cancer. Curr Opin Oncol 2023; 35:479-490. [PMID: 37621170 DOI: 10.1097/cco.0000000000000989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
PURPOSE OF REVIEW This comprehensive review aims to provide timely and relevant insights into the current therapeutic landscape for triple-negative breast cancer (TNBC) and the molecular features underlying this subtype. It emphasizes the need for more reliable biomarkers to refine prognostication and optimize therapy, considering the aggressive nature of TNBC and its limited targeted treatment options. RECENT FINDINGS The review explores the multidisciplinary management of early TNBC, which typically involves systemic chemotherapy, surgery, and radiotherapy. It highlights the emergence of immune checkpoint inhibitors (ICIs), poly(ADP-ribose) polymerase (PARP) inhibitors, and antibody-drug conjugates (ADCs) as promising therapeutic strategies for TNBC. Recent clinical trials investigating the use of ICIs in combination with chemotherapy and the approval of pembrolizumab and atezolizumab for PD-L1-positive metastatic TNBC are discussed. The efficacy of PARP inhibitors and ADCs in treating TNBC patients with specific genetic alterations is also highlighted. SUMMARY The findings discussed in this review have significant implications for clinical practice and research in TNBC. The identification of distinct molecular subtypes through gene expression profiling has enabled a better understanding of TNBC heterogeneity and its clinical implications. This knowledge has the potential to guide treatment decisions, as different subtypes display varying responses to neoadjuvant chemotherapy. Furthermore, the review emphasizes the importance of developing reliable genomic and transcriptomic signatures as biomarkers to refine patient prognostication and optimize therapy selection in TNBC. Integrating these signatures into clinical practice may lead to more personalized treatment approaches, improving outcomes for TNBC patients.
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Affiliation(s)
- Grazia Castellano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Federica Giugliano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Antonio Marra
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS
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Ma J, Chan JJ, Toh CH, Yap YS. Emerging systemic therapy options beyond CDK4/6 inhibitors for hormone receptor-positive HER2-negative advanced breast cancer. NPJ Breast Cancer 2023; 9:74. [PMID: 37684290 PMCID: PMC10491615 DOI: 10.1038/s41523-023-00578-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Endocrine therapy (ET) with cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) is currently the standard first-line treatment for most patients with hormone receptor (HR) positive, human epidermal growth factor receptor (HER2) negative advanced breast cancer. However, resistance to ET and CDK4/6i inevitably ensues. The optimal post-progression treatment regimens and their sequencing continue to evolve in the rapidly changing treatment landscape. In this review, we summarize the mechanisms of resistance to ET and CDK4/6i, which can be broadly classified as alterations affecting cell cycle mediators and activation of alternative signaling pathways. Recent clinical trials have been directed at the targets and pathways implicated, including estrogen and androgen receptors, PI3K/AKT/mTOR and MAPK pathways, tyrosine kinase receptors such as FGFR and HER2, homologous recombination repair pathway, other components of the cell cycle and cell death. We describe the findings from these clinical trials using small molecule inhibitors, antibody-drug conjugates and immunotherapy, providing insights into how these novel strategies may circumvent treatment resistance, and discuss how some have not translated into clinical benefit. The challenges posed by tumor heterogeneity, adaptive rewiring of signaling pathways and dose-limiting toxicities underscore the need to elucidate the latest tumor biology in each patient, and develop treatments with improved therapeutic index in the era of precision medicine.
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Affiliation(s)
- Jun Ma
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Jack Junjie Chan
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
- Oncology Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ching Han Toh
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore.
- Oncology Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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5
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Ascrizzi S, Arillotta GM, Grillone K, Caridà G, Signorelli S, Ali A, Romeo C, Tassone P, Tagliaferri P. Lynch Syndrome Biopathology and Treatment: The Potential Role of microRNAs in Clinical Practice. Cancers (Basel) 2023; 15:3930. [PMID: 37568746 PMCID: PMC10417124 DOI: 10.3390/cancers15153930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Lynch syndrome (LS), also known as Hereditary Non-Polyposis Colorectal Cancer (HNPCC), is an autosomal dominant cancer syndrome which causes about 2-3% of cases of colorectal carcinoma. The development of LS is due to the genetic and epigenetic inactivation of genes involved in the DNA mismatch repair (MMR) system, causing an epiphenomenon known as microsatellite instability (MSI). Despite the fact that the genetics of the vast majority of MSI-positive (MSI+) cancers can be explained, the etiology of this specific subset is still poorly understood. As a possible new mechanism, it has been recently demonstrated that the overexpression of certain microRNAs (miRNAs, miRs), such as miR-155, miR-21, miR-137, can induce MSI or modulate the expression of the genes involved in LS pathogenesis. MiRNAs are small RNA molecules that regulate gene expression at the post-transcriptional level by playing a critical role in the modulation of key oncogenic pathways. Increasing evidence of the link between MSI and miRNAs in LS prompted a deeper investigation into the miRNome involved in these diseases. In this regard, in this study, we discuss the emerging role of miRNAs as crucial players in the onset and progression of LS as well as their potential use as disease biomarkers and therapeutic targets in the current view of precision medicine.
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Affiliation(s)
- Serena Ascrizzi
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
| | - Grazia Maria Arillotta
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
| | - Giulio Caridà
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
| | - Stefania Signorelli
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
| | - Asad Ali
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
| | - Caterina Romeo
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
- Medical Oncology and Translational Medical Oncology Units, University Hospital Renato Dulbecco, 88100 Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (S.A.); (G.M.A.); (K.G.); (G.C.); (S.S.); (A.A.); (C.R.); (P.T.)
- Medical Oncology and Translational Medical Oncology Units, University Hospital Renato Dulbecco, 88100 Catanzaro, Italy
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Porta FM, Sajjadi E, Venetis K, Frascarelli C, Cursano G, Guerini-Rocco E, Fusco N, Ivanova M. Immune Biomarkers in Triple-Negative Breast Cancer: Improving the Predictivity of Current Testing Methods. J Pers Med 2023; 13:1176. [PMID: 37511789 PMCID: PMC10381494 DOI: 10.3390/jpm13071176] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Triple-negative breast cancer (TNBC) poses a significant challenge in terms of prognosis and disease recurrence. The limited treatment options and the development of resistance to chemotherapy make it particularly difficult to manage these patients. However, recent research has been shifting its focus towards biomarker-based approaches for TNBC, with a particular emphasis on the tumor immune landscape. Immune biomarkers in TNBC are now a subject of great interest due to the presence of tumor-infiltrating lymphocytes (TILs) in these tumors. This characteristic often coincides with the presence of PD-L1 expression on both neoplastic cells and immune cells within the tumor microenvironment. Furthermore, a subset of TNBC harbor mismatch repair deficient (dMMR) TNBC, which is frequently accompanied by microsatellite instability (MSI). All of these immune biomarkers hold actionable potential for guiding patient selection in immunotherapy. To fully capitalize on these opportunities, the identification of additional or complementary biomarkers and the implementation of highly customized testing strategies are of paramount importance in TNBC. In this regard, this article aims to provide an overview of the current state of the art in immune-related biomarkers for TNBC. Specifically, it focuses on the various testing methodologies available and sheds light on the immediate future perspectives for patient selection. By delving into the advancements made in understanding the immune landscape of TNBC, this study aims to contribute to the growing body of knowledge in the field. The ultimate goal is to pave the way for the development of more personalized testing strategies, ultimately improving outcomes for TNBC patients.
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Affiliation(s)
- Francesca Maria Porta
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, 20122 Milan, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, 20122 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, 20122 Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, 20122 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, 20122 Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, 20122 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, 20122 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, 20122 Milan, Italy
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7
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Farmanbar A, Kneller R, Firouzi S. Mutational signatures reveal mutual exclusivity of homologous recombination and mismatch repair deficiencies in colorectal and stomach tumors. Sci Data 2023; 10:423. [PMID: 37393385 PMCID: PMC10314920 DOI: 10.1038/s41597-023-02331-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Decomposing somatic mutation spectra into mutational signatures and their corresponding etiologies provides a powerful approach for investigating the mechanism of DNA damage and repair. Assessing microsatellite (in)stability (MSI/MSS) status and interpreting their clinical relevance in different malignancies offers significant diagnostic and prognostic value. However, little is known about microsatellite (in)stability and its interactions with other DNA repair mechanisms such as homologous recombination (HR) in different cancer types. Based on whole-genome/exome mutational signature analysis, we showed HR deficiency (HRd) and mismatch repair deficiency (MMRd) occur in a significantly mutually exclusive manner in stomach and colorectal adenocarcinomas. ID11 signature with currently unknown etiology was prevalent in MSS tumors, co-occurred with HRd and was mutually exclusive with MMRd. Apolipoprotein B mRNA editing enzyme, Catalytic polypeptide-like (APOBEC) signature co-occurred with HRd and was mutually exclusive with MMRd in stomach tumors. The HRd signature in MSS tumors and the MMRd signature in MSI tumors were the first or second dominant signatures wherever detected. HRd may drive a distinct subgroup of MSS tumors and lead to poor clinical outcome. These analyses offer insight into mutational signatures in MSI and MMS tumors and reveal opportunities for improved clinical diagnosis and personalized treatment of MSS tumors.
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Affiliation(s)
- Amir Farmanbar
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Research Center for Advanced Science and Technology, University of Tokyo, Minato-ku, Tokyo, 153-8904, Japan
| | - Robert Kneller
- Research Center for Advanced Science and Technology, University of Tokyo, Minato-ku, Tokyo, 153-8904, Japan
| | - Sanaz Firouzi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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8
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Pan L, Han J, Lin M. Targeting breast cancer stem cells directly to treat refractory breast cancer. Front Oncol 2023; 13:981247. [PMID: 37251931 PMCID: PMC10213424 DOI: 10.3389/fonc.2023.981247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/02/2023] [Indexed: 05/31/2023] Open
Abstract
For patients with refractory breast cancer (BC), integrative immunotherapies are emerging as a critical component of treatment. However, many patients remain unresponsive to treatment or relapse after a period. Different cells and mediators in the tumor microenvironment (TME) play important roles in the progression of BC, and cancer stem cells (CSCs) are deemed the main cause of relapse. Their characteristics depend on their interactions with their microenvironment as well as on the inducing factors and elements in this environment. Strategies to modulate the immune system in the TME of BC that are aimed at reversing the suppressive networks within it and eradicating residual CSCs are, thus, essential for improving the current therapeutic efficacy of BC. This review focuses on the development of immunoresistance in BCs and discusses the strategies that can modulate the immune system and target breast CSCs directly to treat BC including immunotherapy with immune checkpoint blockades.
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Affiliation(s)
- Liping Pan
- Wuhan Center for Clinical Laboratory, Wuhan, China
| | - Juan Han
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Lin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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9
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Pipek O, Alpár D, Rusz O, Bödör C, Udvarnoki Z, Medgyes-Horváth A, Csabai I, Szállási Z, Madaras L, Kahán Z, Cserni G, Kővári B, Kulka J, Tőkés AM. Genomic Landscape of Normal and Breast Cancer Tissues in a Hungarian Pilot Cohort. Int J Mol Sci 2023; 24:ijms24108553. [PMID: 37239898 DOI: 10.3390/ijms24108553] [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: 03/20/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
A limited number of studies have focused on the mutational landscape of breast cancer in different ethnic populations within Europe and compared the data with other ethnic groups and databases. We performed whole-genome sequencing of 63 samples from 29 Hungarian breast cancer patients. We validated a subset of the identified variants at the DNA level using the Illumina TruSight Oncology (TSO) 500 assay. Canonical breast-cancer-associated genes with pathogenic germline mutations were CHEK2 and ATM. Nearly all the observed germline mutations were as frequent in the Hungarian breast cancer cohort as in independent European populations. The majority of the detected somatic short variants were single-nucleotide polymorphisms (SNPs), and only 8% and 6% of them were deletions or insertions, respectively. The genes most frequently affected by somatic mutations were KMT2C (31%), MUC4 (34%), PIK3CA (18%), and TP53 (34%). Copy number alterations were most common in the NBN, RAD51C, BRIP1, and CDH1 genes. For many samples, the somatic mutational landscape was dominated by mutational processes associated with homologous recombination deficiency (HRD). Our study, as the first breast tumor/normal sequencing study in Hungary, revealed several aspects of the significantly mutated genes and mutational signatures, and some of the copy number variations and somatic fusion events. Multiple signs of HRD were detected, highlighting the value of the comprehensive genomic characterization of breast cancer patient populations.
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Affiliation(s)
- Orsolya Pipek
- Department of Physics of Complex Systems, Institute of Physics, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Donát Alpár
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Orsolya Rusz
- Department of Pathology, Forensic and Insurance Medicine, SE NAP, Brain Metastasis Research Group, Semmelweis University, 1091 Budapest, Hungary
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Zoltán Udvarnoki
- Department of Physics of Complex Systems, Institute of Physics, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Anna Medgyes-Horváth
- Department of Physics of Complex Systems, Institute of Physics, Eötvös Loránd University, 1117 Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Institute of Physics, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zoltán Szállási
- Department of Pathology, Forensic and Insurance Medicine, SE NAP, Brain Metastasis Research Group, Semmelweis University, 1091 Budapest, Hungary
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Lilla Madaras
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - Zsuzsanna Kahán
- Department of Oncotherapy, University of Szeged, 6720 Szeged, Hungary
| | - Gábor Cserni
- Department of Pathology, Albert Szent-Györgyi Medical Centre, University of Szeged, 6720 Szeged, Hungary
- Department of Pathology, Bács-Kiskun County Teaching Hospital, 6000 Kecskemét, Hungary
| | - Bence Kővári
- Department of Pathology, Albert Szent-Györgyi Medical Centre, University of Szeged, 6720 Szeged, Hungary
- Department of Pathology, Henry Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Janina Kulka
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - Anna Mária Tőkés
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
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10
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Murazawa C, Hashimoto N, Kuraishi K, Motoyama M, Hashimoto SI, Ikeuchi M, Norimura S, Matsunaga T, Teramoto K, Haba R, Abe N, Yajima T, Kontani K. Status and prognostic value of immunological biomarkers of breast cancer. Oncol Lett 2023; 25:164. [PMID: 36960188 PMCID: PMC10028224 DOI: 10.3892/ol.2023.13750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/01/2023] [Indexed: 03/25/2023] Open
Abstract
The immune response to cancer serves an important role in disease progression and patient prognosis. For triple-negative breast cancer showing aggressive behavior, immunotherapy has a good efficacy because of the potent immunogenicity of this type of cancer. However, the dominant subtype, luminal human epidermal growth factor receptor-2 (HER2)-negative breast cancer, is less immunogenic. To determine whether luminal HER2-negative cancer reacts to the anticancer immune response, the present study analyzed the status and prognostic value of the principal immunological biomarkers of breast cancer, including tumor-infiltrating lymphocytes (TILs), CD8+ T lymphocytes, the major histocompatibility complex and programmed cell death ligand-1 (PD-L1). The biomarkers were compared between patients with luminal HER2-negative breast cancer and those with immunogenic subtypes including triple-negative and HER2-overexpressed breast cancer. A total of 71 patients with primary breast cancer were classified into the immunogenic non-luminal (n=23) and less immunogenic luminal HER2-negative groups (n=48) based on immunogenicity. In the luminal HER2-negative group, compared with patients with low TIL levels, those with high TIL levels were at an advanced stage of cancer (P=0.024) and showed worse relapse-free survival (P=0.057); however, the remaining biomarkers exhibited no association with cancer progression or prognosis. In the non-luminal group, patients with high TIL levels showed significantly better RFS than those with low TIL levels (P=0.014). Compared with non-luminal patients negative for PD-L1, those positive for PD-L1 exhibited better overall survival (P=0.064). Notably, TIL status was found to exhibit contrasting prognostic predictions based on immunogenicity. In conclusion, TILs are a strong candidate for prognostic prediction in breast cancer, regardless of the subtype. PD-L1 is a potential candidate for prognostic prediction in immunogenic breast cancers, but not in the luminal HER2-negative subtype.
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Affiliation(s)
- Chisa Murazawa
- Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
| | - Nozomi Hashimoto
- Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
| | - Kana Kuraishi
- Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
| | - Mutsumi Motoyama
- Department of Diagnostic Pathology, Kagawa University Hospital, Kagawa 761-0793, Japan
| | - Shin-Ichiro Hashimoto
- Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
| | - Mayumi Ikeuchi
- Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
| | - Shoko Norimura
- Department of Surgery, Takamatsu Red Cross Hospital, Takamatsu, Kagawa 760-0017, Japan
| | - Toru Matsunaga
- Department of Diagnostic Pathology, Kagawa University Hospital, Kagawa 761-0793, Japan
| | - Koji Teramoto
- Department of Medical Oncology, Shiga University of Medical Science, Otsu, Shiga 520-2191, Japan
| | - Reiji Haba
- Department of Diagnostic Pathology, Kagawa University Hospital, Kagawa 761-0793, Japan
| | - Noriko Abe
- Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
| | - Toshiki Yajima
- Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
| | - Keiichi Kontani
- Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, Kagawa 761-0793, Japan
- Correspondence to: Dr Keiichi Kontani, Department of Thoracic, Breast and Endocrine Surgery, Faculty of Medicine, Kagawa University, 1750-1 Miki-cho, Kita-gun, Kagawa 761-0793, Japan, E-mail:
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11
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Sokolova A, Johnstone KJ, McCart Reed AE, Simpson PT, Lakhani SR. Hereditary breast cancer: syndromes, tumour pathology and molecular testing. Histopathology 2023; 82:70-82. [PMID: 36468211 PMCID: PMC10953374 DOI: 10.1111/his.14808] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 12/09/2022]
Abstract
Hereditary factors account for a significant proportion of breast cancer risk. Approximately 20% of hereditary breast cancers are attributable to pathogenic variants in the highly penetrant BRCA1 and BRCA2 genes. A proportion of the genetic risk is also explained by pathogenic variants in other breast cancer susceptibility genes, including ATM, CHEK2, PALB2, RAD51C, RAD51D and BARD1, as well as genes associated with breast cancer predisposition syndromes - TP53 (Li-Fraumeni syndrome), PTEN (Cowden syndrome), CDH1 (hereditary diffuse gastric cancer), STK11 (Peutz-Jeghers syndrome) and NF1 (neurofibromatosis type 1). Polygenic risk, the cumulative risk from carrying multiple low-penetrance breast cancer susceptibility alleles, is also a well-recognised contributor to risk. This review provides an overview of the established breast cancer susceptibility genes as well as breast cancer predisposition syndromes, highlights distinct genotype-phenotype correlations associated with germline mutation status and discusses molecular testing and therapeutic implications in the context of hereditary breast cancer.
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Affiliation(s)
- A Sokolova
- Sullivan and Nicolaides PathologyBrisbane
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - K J Johnstone
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
| | - A E McCart Reed
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - P T Simpson
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - S R Lakhani
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
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12
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Microsatellite instability detection in breast cancer using drop-off droplet digital PCR. Oncogene 2022; 41:5289-5297. [DOI: 10.1038/s41388-022-02504-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
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13
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Wang WC, Lai YC. DUSP5 and PHLDA1 mutations in mature cystic teratomas of the ovary identified on whole-exome sequencing may explain teratoma characteristics. Hum Genomics 2022; 16:50. [PMID: 36289533 PMCID: PMC9609193 DOI: 10.1186/s40246-022-00424-w] [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: 09/02/2022] [Accepted: 10/19/2022] [Indexed: 11/21/2022] Open
Abstract
Background Mature cystic teratomas of the ovary are the most common type of germ cell tumor, comprising 33% of ovarian tumors. Studying these tumors may result in a better understanding of their stepwise developmental processes and molecular bases and provide useful information for the development of tissue-engineering technologies. Methods In the present study, 9 mature cystic teratomas of the ovary were analyzed by whole-exome sequencing and the results were compared with the Catalogue of Somatic Mutations in Cancer and dbSNP databases. Results Mutations were validated in 15 genes with alterations in all 9 (100%) samples and changes in protein coding. The top 10 mutated genes were FLG, MUC17, MUC5B, RP1L1, NBPF1, GOLGA6L2, SLC29A3, SGK223, PTGFRN, and FAM186A. Moreover, 7 variants in exons with changes in protein coding are likely of importance in the development of mature cystic teratomas of the ovary, namely PTGFRN, DUSP5, MPP2, PHLDA1, PRR21, GOLGA6L2, and KRTAP4-2. Conclusions These genetic alterations may play an important etiological role in teratoma formation. Moreover, novel mutations in DUSP5 and PHLDA1 genes found on whole-exome sequencing may help to explain the characteristics of teratomas. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00424-w.
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Affiliation(s)
- Wen-Chung Wang
- grid.414969.70000 0004 0642 8534Department of Obstetrics and Gynecology, Jen-Ai Hospital, Taichung, 412 Taiwan
| | - Yen-Chein Lai
- grid.411641.70000 0004 0532 2041Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, No. 110, Sec. 1, Chien Kuo N. Road, Taichung, 402 Taiwan ,grid.411645.30000 0004 0638 9256Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
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14
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Nicolini A, Ferrari P, Carpi A. Immune Checkpoint Inhibitors and Other Immune Therapies in Breast Cancer: A New Paradigm for Prolonged Adjuvant Immunotherapy. Biomedicines 2022; 10:biomedicines10102511. [PMID: 36289773 PMCID: PMC9599105 DOI: 10.3390/biomedicines10102511] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/25/2022] [Accepted: 10/02/2022] [Indexed: 02/05/2023] Open
Abstract
Background: Breast cancer is the most common form of cancer in women worldwide. Advances in the early diagnosis and treatment of cancer in the last decade have progressively decreased the cancer mortality rate, and in recent years, immunotherapy has emerged as a relevant tool against cancer. HER2+ and triple-negative breast cancers (TNBCs) are considered more immunogenic and suitable for this kind of treatment due to the higher rate of tumor-infiltrating lymphocytes (TILs) and programmed death ligand 1 (PD-L1) expression. In TNBC, genetic aberrations further favor immunogenicity due to more neo-antigens in cancer cells. Methods: This review summarizes the principal ongoing conventional and investigational immunotherapies in breast cancer. Particularly, immune checkpoint inhibitors (ICIs) and their use alone or combined with DNA damage repair inhibitors (DDRis) are described. Then, the issue on immunotherapy with monoclonal antibodies against HER-2 family receptors is updated. Other investigational immunotherapies include a new schedule based on the interferon beta-interleukin-2 sequence that was given in ER+ metastatic breast cancer patients concomitant with anti-estrogen therapy, which surprisingly showed promising results. Results: Based on the scientific literature and our own findings, the current evaluation of tumor immunogenicity and the conventional model of adjuvant chemotherapy (CT) are questioned. Conclusions: A novel strategy based on additional prolonged adjuvant immunotherapy combined with hormone therapy or alternated with CT is proposed.
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Affiliation(s)
- Andrea Nicolini
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy
- Correspondence:
| | - Paola Ferrari
- Unit of Oncology, Department of Medical and Oncological Area, Azienda Ospedaliera-Universitaria Pisana, 56125 Pisa, Italy
| | - Angelo Carpi
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
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15
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Moradi N, Ohadian Moghadam S, Heidarzadeh S. Application of next-generation sequencing in the diagnosis of gastric cancer. Scand J Gastroenterol 2022; 57:842-855. [PMID: 35293278 DOI: 10.1080/00365521.2022.2041717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objectives: Gastric cancer (GC) is a disease with high mortality, poor prognosis and numerous risk factors. GC has an asymptomatic nature in early stages of the diseases, making timely diagnosis complicated using common conventional approaches, namely pathological examinations and imaging tests. Recently, molecular profiling of GC using next generation sequencing (NGS) has opened new doors to efficient prognostic, diagnostic, and therapeutic strategies. The current review aims to thoroughly discuss and compare the current NGS techniques and commercial platforms utilized for GC diagnosis and treatment, highlighting the most recent NGS-based GC studies. Furthermore, this review addresses the challenges of clinical implementation of NGS in GC.Materials and methods: This review was conducted according to the eligible studies identified via search of Web of Science, PubMed, Scopus, Embase and the Cochrane Library. In the present study, data on gastric cancer patients and NGS methods used to diagnose the disease were reviewed.Conclusion: Given the ever-rising advancements in NGS technologies, bioinformatics, healthcare guidelines and refined classifications, it is hoped that these technologies can actualize their advantages and optimize GC patients' experience.
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Affiliation(s)
- Narges Moradi
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Siamak Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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16
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Lamb NA, Bard JE, Loll-Krippleber R, Brown GW, Surtees JA. Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes. Genetics 2022; 221:6605222. [PMID: 35686905 PMCID: PMC9339293 DOI: 10.1093/genetics/iyac092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/24/2022] [Indexed: 12/30/2022] Open
Abstract
Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of free deoxyribonucleoside triphosphate pools by ribonucleotide reductase and repair of replication errors by the mismatch repair system. We identified genetic interactions between rnr1 alleles that skew and/or elevate deoxyribonucleoside triphosphate levels and mismatch repair gene deletions. These defects indicate that the rnr1 alleles lead to increased mutation loads that are normally acted upon by mismatch repair. We then utilized a targeted deep-sequencing approach to determine mutational profiles associated with mismatch repair pathway defects. By combining rnr1 and msh mutations to alter and/or increase deoxyribonucleoside triphosphate levels and alter the mutational load, we uncovered previously unreported specificities of Msh2-Msh3 and Msh2-Msh6. Msh2-Msh3 is uniquely able to direct the repair of G/C single-base deletions in GC runs, while Msh2-Msh6 specifically directs the repair of substitutions that occur at G/C dinucleotides. We also identified broader sequence contexts that influence variant profiles in different genetic backgrounds. Finally, we observed that the mutation profiles in double mutants were not necessarily an additive relationship of mutation profiles in single mutants. Our results have implications for interpreting mutation signatures from human tumors, particularly when mismatch repair is defective.
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Affiliation(s)
- Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jonathan E Bard
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA,University at Buffalo Genomics and Bioinformatics Core, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Raphael Loll-Krippleber
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jennifer A Surtees
- Corresponding author: Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Rm 4215, 955 Main Street, Buffalo, NY 14203, USA.
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17
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Carlino F, Diana A, Piccolo A, Ventriglia A, Bruno V, De Santo I, Letizia O, De Vita F, Daniele B, Ciardiello F, Orditura M. Immune-Based Therapy in Triple-Negative Breast Cancer: From Molecular Biology to Clinical Practice. Cancers (Basel) 2022; 14:cancers14092102. [PMID: 35565233 PMCID: PMC9103968 DOI: 10.3390/cancers14092102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 12/19/2022] Open
Abstract
Triple-negative breast cancer (TNBC) has been considered for many years an orphan disease in terms of therapeutic options, with conventional chemotherapy (CT) still representing the mainstay of treatment in the majority of patients. Although breast cancer (BC) has been historically considered a "cold tumor", exciting progress in the genomic field leading to the characterization of the molecular portrait and the immune profile of TNBC has opened the door to novel therapeutic strategies, including Immune Checkpoint Inhibitors (ICIs), Poly ADP-Ribose Polymerase (PARP) inhibitors and Antibody Drug Conjugates (ADCs). In particular, compared to standard CT, the immune-based approach has been demonstrated to improve progression-free survival (PFS) and overall survival (OS) in metastatic PD-L1-positive TNBC and the pathological complete response rate in the early setting, regardless of PD-L1 expression. To date, PD-L1 has been widely used as a predictor of the response to ICIs; however, many patients do not benefit from the addition of immunotherapy. Therefore, PD-L1 is not a reliable predictive biomarker of the response, and its accuracy remains controversial due to the lack of a consensus about the assay, the antibody, and the scoring system to adopt, as well as the spatial and temporal heterogeneity of the PD-L1 status. In the precision medicine era, there is an urgent need to identify more sensitive biomarkers in the BC immune oncology field other than just PD-L1 expression. Through the characterization of the tumor microenvironment (TME), the analysis of peripheral blood and the evaluation of immune gene signatures, novel potential biomarkers have been explored, such as the Tumor Mutational Burden (TMB), Microsatellite Instability/Mismatch Repair Deficiency (MSI/dMMR) status, genomic and epigenomic alterations and tumor-infiltrating lymphocytes (TILs). This review aims to summarize the recent knowledge on BC immunograms and on the biomarkers proposed to support ICI-based therapy in TNBC, as well as to provide an overview of the potential strategies to enhance the immune response in order to overcome the mechanisms of resistance.
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Affiliation(s)
- Francesca Carlino
- Department of Precision Medicine, Division of Medical Oncology, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (A.P.); (A.V.); (V.B.); (F.D.V.); (F.C.); (M.O.)
- Medical Oncology Unit, Ospedale Ave Gratia Plena, San Felice a Cancello, 81027 Caserta, Italy; (I.D.S.); (O.L.)
- Correspondence: ; Tel.: +39-349-5152216
| | - Anna Diana
- Medical Oncology Unit, Ospedale del Mare, 80147 Naples, Italy; (A.D.); (B.D.)
| | - Antonio Piccolo
- Department of Precision Medicine, Division of Medical Oncology, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (A.P.); (A.V.); (V.B.); (F.D.V.); (F.C.); (M.O.)
| | - Anna Ventriglia
- Department of Precision Medicine, Division of Medical Oncology, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (A.P.); (A.V.); (V.B.); (F.D.V.); (F.C.); (M.O.)
| | - Vincenzo Bruno
- Department of Precision Medicine, Division of Medical Oncology, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (A.P.); (A.V.); (V.B.); (F.D.V.); (F.C.); (M.O.)
| | - Irene De Santo
- Medical Oncology Unit, Ospedale Ave Gratia Plena, San Felice a Cancello, 81027 Caserta, Italy; (I.D.S.); (O.L.)
| | - Ortensio Letizia
- Medical Oncology Unit, Ospedale Ave Gratia Plena, San Felice a Cancello, 81027 Caserta, Italy; (I.D.S.); (O.L.)
| | - Ferdinando De Vita
- Department of Precision Medicine, Division of Medical Oncology, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (A.P.); (A.V.); (V.B.); (F.D.V.); (F.C.); (M.O.)
| | - Bruno Daniele
- Medical Oncology Unit, Ospedale del Mare, 80147 Naples, Italy; (A.D.); (B.D.)
| | - Fortunato Ciardiello
- Department of Precision Medicine, Division of Medical Oncology, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (A.P.); (A.V.); (V.B.); (F.D.V.); (F.C.); (M.O.)
| | - Michele Orditura
- Department of Precision Medicine, Division of Medical Oncology, University of Campania Luigi Vanvitelli, 80131 Naples, Italy; (A.P.); (A.V.); (V.B.); (F.D.V.); (F.C.); (M.O.)
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Zhao A, Wu F, Wang Y, Li J, Xu W, Liu H. Analysis of Genetic Alterations in Ocular Adnexal Mucosa-Associated Lymphoid Tissue Lymphoma With Whole-Exome Sequencing. Front Oncol 2022; 12:817635. [PMID: 35359413 PMCID: PMC8962736 DOI: 10.3389/fonc.2022.817635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Next-generation sequencing studies on ocular adnexal marginal zone lymphoma of mucosa-associated lymphoid tissue (OAML) have to date revealed several targets of genetic aberrations. However, most of our current understanding of the pathogenesis and prognosis of OAML is primarily based on studies conducted in populations from Europe and the US. Furthermore, the majority were based on formalin-fixed paraffin-embedded (FFPE) tissue, which generally has poor integrity and creates many sequencing artifacts. To better investigate the coding genome landscapes of OAML, especially in the Chinese population, we performed whole-exome sequencing of 21 OAML cases with fresh frozen tumor tissue and matched peripheral blood samples. IGLL5, as a novel recurrently mutated gene, was found in 24% (5/21) of patients, with a higher relapse rate (P=0.032). In addition, mutations of MSH6, DIS3, FAT1, and TMEM127 were found in 10% of cases. These novel somatic mutations indicate the existence of additional/alternative lymphomagenesis pathways in OAML. Moreover, the difference between our and previous studies suggests genetic heterogeneity of OAML between Asian and Western individuals.
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Affiliation(s)
- Andi Zhao
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Fangtian Wu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University Jiangsu Province Hospital, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yue Wang
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University Jiangsu Province Hospital, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Hu Liu, ; Wei Xu, ; Jianyong Li,
| | - Wei Xu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University Jiangsu Province Hospital, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Hu Liu, ; Wei Xu, ; Jianyong Li,
| | - Hu Liu
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- The First Clinical Medical College, Nanjing Medical University, Nanjing, China
- *Correspondence: Hu Liu, ; Wei Xu, ; Jianyong Li,
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Singh S, Singh N, Baranwal M, Sharma S. Polymorphisms in the MSH2 gene predict poor survival of North Indian lung cancer patients undergoing chemotherapy. Biomark Med 2022; 16:69-82. [PMID: 35081740 DOI: 10.2217/bmm-2021-0565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To estimate if MSH2 polymorphisms, viz. rs63749993, rs2303425, rs2303426, rs4987188, rs2303428 and rs17217772, have any association with clinical outcomes in North Indian lung cancer patients. Materials & methods: PCR-RFLP was used for genotyping 500 cases. Logistic regression and survival analysis was performed by utilizing MedCalc software. Results & conclusion: Our study concluded, adenocarcinoma subjects having heterozygous genotype for rs2303425 have increased survival time (MST = 12.43, p = 0.03). In lung cancer patients undergoing paclitaxel therapy, heterozygous carriers for the rs17217772 polymorphism have reduced survival time (MST = 7.96 vs 2.63 months; HR = 2.09; p = 0.02). For rs63749993 polymorphism undergoing irinotecan therapy, subjects having mutant genotype showed poor survival (13.26 vs 6.06 months; HR = 5.37; p = 0.0004). The results suggest that MSH2 polymorphisms are involved in decreasing overall survival for patients undergoing platinum-based chemotherapy.
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Affiliation(s)
- Sidhartha Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, 160012, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147001, India
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20
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Iyevleva AG, Aleksakhina SN, Sokolenko AP, Baskina SV, Venina AR, Anisimova EI, Bizin IV, Ivantsov AO, Belysheva YV, Chernyakova AP, Togo AV, Imyanitov EN. Somatic loss of the remaining allele occurs approximately in half of CHEK2-driven breast cancers and is accompanied by a border-line increase of chromosomal instability. Breast Cancer Res Treat 2022; 192:283-291. [PMID: 35020107 DOI: 10.1007/s10549-022-06517-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023]
Abstract
PURPOSE Germline mutations in CHEK2 gene represent the second most frequent cause of hereditary breast cancer (BC) after BRCA1/2 lesions. This study aimed to identify the molecular characteristics of CHEK2-driven BCs. METHODS Loss of heterozygosity (LOH) for the remaining CHEK2 allele was examined in 50 CHEK2-driven BCs using allele-specific PCR assays for the germline mutations and analysis of surrounding single-nucleotide polymorphisms (SNPs). Paired tumor and normal DNA samples from 25 cases were subjected to next-generation sequencing analysis. RESULTS CHEK2 LOH was detected in 28/50 (56%) BCs. LOH involved the wild-type allele in 24 BCs, mutant CHEK2 copy was deleted in 3 carcinomas, while in one case the origin of the deleted allele could not be identified. Somatic PIK3CA and TP53 mutations were present in 13/25 (52%) and 4/25 (16%) tumors, respectively. Genomic features of homologous recombination deficiency (HRD), including the HRD score ≥ 42, the predominance of BRCA-related mutational signature 3, and the high proportion of long (≥ 5 bp) indels, were observed only in 1/20 (5%) BC analyzed for chromosomal instability. Tumors with the deleted wild-type CHEK2 allele differed from LOH-negative cases by elevated HRD scores (median 23 vs. 7, p = 0.010) and higher numbers of chromosomal segments affected by copy number aberrations (p = 0.008). CONCLUSION Somatic loss of the wild-type CHEK2 allele is observed in approximately half of CHEK2-driven BCs. Tumors without CHEK2 LOH are chromosomally stable. BCs with LOH demonstrate some signs of chromosomal instability; however, its degree is significantly lower as compared to BRCA1/2-associated cancers.
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Affiliation(s)
- Aglaya G Iyevleva
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758.
| | - Svetlana N Aleksakhina
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Anna P Sokolenko
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Sofia V Baskina
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Aigul R Venina
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | | | - Ilya V Bizin
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Alexandr O Ivantsov
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Yana V Belysheva
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Alexandra P Chernyakova
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Alexandr V Togo
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758
| | - Evgeny N Imyanitov
- N.N. Petrov Institute of Oncology, Leningradskaya str. 68, Pesochny, Saint Petersburg, Russia, 197758.,St.-Petersburg State Pediatric Medical University, Saint Petersburg, Russia, 194100.,I.I. Mechnikov North-Western Medical University, Saint Petersburg, Russia, 191015
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21
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Zhu L, Liu J, Chen J, Zhou Q. The developing landscape of combinatorial therapies of immune checkpoint blockade with DNA damage repair inhibitors for the treatment of breast and ovarian cancers. J Hematol Oncol 2021; 14:206. [PMID: 34930377 PMCID: PMC8686226 DOI: 10.1186/s13045-021-01218-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/05/2021] [Indexed: 02/07/2023] Open
Abstract
The use of immune checkpoint blockade (ICB) using antibodies against programmed death receptor (PD)-1, PD ligand (PD-L)-1, and cytotoxic T-lymphocyte antigen 4 (CTLA-4) has redefined the therapeutic landscape in solid tumors, including skin, lung, bladder, liver, renal, and breast tumors. However, overall response rates to ICB therapy remain limited in PD-L1-negative patients. Thus, rational and effective combination therapies will be needed to address ICB treatment resistance in these patients, as well as in PD-L1-positive patients who have progressed under ICB treatment. DNA damage repair inhibitors (DDRis) may activate T-cell responses and trigger inflammatory cytokines release and eventually immunogenic cancer cell death by amplifying DNA damage and generating immunogenic neoantigens, especially in DDR-defective tumors. DDRi may also lead to adaptive PD-L1 upregulation, providing a rationale for PD-L1/PD-1 blockade. Thus, based on preclinical evidence of efficacy and no significant overlapping toxicity, some ICB/DDRi combinations have rapidly progressed to clinical testing in breast and ovarian cancers. Here, we summarize the available clinical data on the combination of ICB with DDRi agents for treating breast and ovarian cancers and discuss the mechanisms of action and other lessons learned from translational studies conducted to date. We also review potential biomarkers to select patients most likely to respond to ICB/DDRi combination therapy.
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Affiliation(s)
- Lingling Zhu
- Lung Cancer Center, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Jiewei Liu
- Lung Cancer Center, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Jiang Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, Zhejiang Province, China.
| | - Qinghua Zhou
- Lung Cancer Center, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan Province, China.
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22
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Fang H, Zhu X, Yang H, Oh J, Barbour JA, Wong JWH. Deficiency of replication-independent DNA mismatch repair drives a 5-methylcytosine deamination mutational signature in cancer. SCIENCE ADVANCES 2021; 7:eabg4398. [PMID: 34730999 PMCID: PMC8565909 DOI: 10.1126/sciadv.abg4398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Multiple mutational signatures have been associated with DNA mismatch repair (MMR)–deficient cancers, but the mechanisms underlying their origin remain unclear. Here, using mutation data from cancer genomes, we identify a previously unknown function of MMR that is able to protect genomes from 5-methylcytosine (5mC) deamination–induced somatic mutations in a replication-independent manner. Cancers with deficiency of MMR proteins MSH2/MSH6 (MutSα) exhibit mutational signature contributions distinct from those that are deficient in MLH1/PMS2 (MutLα). This disparity arises from unrepaired 5mC deamination–induced mismatches rather than replicative DNA polymerase errors. In cancers with biallelic loss of MBD4 DNA glycosylase, repair of 5mC deamination damage is strongly associated with H3K36me3 chromatin, implicating MutSα as the essential factor in its repair. We thus uncover a noncanonical role of MMR in the protection against 5mC deamination–induced mutation in human cancers.
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23
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Schwartz CJ, da Silva EM, Marra A, Gazzo AM, Selenica P, Rai VK, Mandelker D, Pareja F, Misyura M, D'Alfonso TM, Brogi E, Drullinsky P, Razavi P, Robson ME, Drago JZ, Wen HY, Zhang L, Weigelt B, Shia J, Reis-Filho JS, Zhang H. Morphological and genomic characteristics of breast cancers occurring in individuals with Lynch Syndrome. Clin Cancer Res 2021; 28:404-413. [PMID: 34667028 DOI: 10.1158/1078-0432.ccr-21-2027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/11/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Lynch syndrome (LS) is defined by germline pathogenic mutations involving DNA Mismatch Repair (MMR) genes and linked with the development of MMR-deficient (MMRd) colon and endometrial cancers. Whether breast cancers (BC) developing in context of LS are causally related to MMR deficiency (MMRd), remains controversial. Thus, we explored the morphological and genomic characteristics of BCs occurring in LS individuals. EXPERIMENTAL DESIGN A retrospective analysis of 20,110 cancer patients who underwent multigene panel genetic testing was performed to identify individuals with a likely pathogenic/pathogenic germline variant in MLH1, MSH2, MSH6 or PMS2 who developed BCs. The histological characteristics and immunohistochemical (IHC) assessment of BCs for MMR proteins and programmed death-ligand 1 (PD-L1) expression were assessed on cases with available materials. DNA samples from paired tumors and blood were sequenced with MSK-IMPACT ({greater than or equal to}468 key cancer genes). MSI status was assessed utilizing MSISensor. Mutational signatures were defined using SigMA. RESULTS 272 LS individuals were identified, 13 (5%) of whom had primary BCs. The majority of BCs (92%) were hormone receptor positive tumors. Five (42%) of 12 BCs displayed loss of MMR proteins by IHC. Four (36%) of 11 BCs subjected to tumor-normal sequencing showed dominant microsatellite instability mutational signatures, high tumor mutational burden and indeterminate (27%) or high MSISensor scores (9%). One patient with metastatic MMRd BC received anti-PD1 therapy and achieved a robust and durable response. CONCLUSIONS A subset of BCs developing in LS individuals are etiologically linked to MMRd and may benefit from anti-PD1/PD-L1 immunotherapy.
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Affiliation(s)
| | | | - Antonio Marra
- Division of Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS
| | - Andrea M Gazzo
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | | | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | | | - Edi Brogi
- Memorial Sloan Kettering Cancer Center
| | | | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center
| | - Mark E Robson
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center
| | | | | | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | - Hong Zhang
- Pathology, Memorial Sloan Kettering Cancer Center
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24
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Koh G, Degasperi A, Zou X, Momen S, Nik-Zainal S. Mutational signatures: emerging concepts, caveats and clinical applications. Nat Rev Cancer 2021; 21:619-637. [PMID: 34316057 DOI: 10.1038/s41568-021-00377-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/08/2021] [Indexed: 02/05/2023]
Abstract
Whole-genome sequencing has brought the cancer genomics community into new territory. Thanks to the sheer power provided by the thousands of mutations present in each patient's cancer, we have been able to discern generic patterns of mutations, termed 'mutational signatures', that arise during tumorigenesis. These mutational signatures provide new insights into the causes of individual cancers, revealing both endogenous and exogenous factors that have influenced cancer development. This Review brings readers up to date in a field that is expanding in computational, experimental and clinical directions. We focus on recent conceptual advances, underscoring some of the caveats associated with using the mutational signature frameworks and highlighting the latest experimental insights. We conclude by bringing attention to areas that are likely to see advancements in clinical applications.
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Affiliation(s)
- Gene Koh
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Andrea Degasperi
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Xueqing Zou
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Sophie Momen
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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25
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Criscitiello C, Guerini-Rocco E, Viale G, Fumagalli C, Sajjadi E, Venetis K, Piciotti R, Invernizzi M, Malapelle U, Fusco N. Immunotherapy in Breast Cancer Patients: A Focus on the Use of the Currently Available Biomarkers in Oncology. Anticancer Agents Med Chem 2021; 22:787-800. [PMID: 34229592 DOI: 10.2174/1871520621666210706144112] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/23/2021] [Accepted: 02/01/2021] [Indexed: 11/22/2022]
Abstract
Immune checkpoint inhibitors (ICIs) have remarkably modified the way solid tumors are managed, including breast cancer. Unfortunately, only a relatively small number of breast cancer patients significantly respond to these treatments. To maximize the immunotherapy benefit in breast cancer, several efforts are currently being put forward for the identification of i) the best therapeutic strategy (i.e. ICI monotherapy or in association with chemotherapy, radiotherapy, or other drugs); ii) the optimal timing for administration (e.g. early/advanced stage of disease; adjuvant/neoadjuvant setting); iii) the most effective and reliable predictive biomarkers of response (e.g. tumor-infiltrating lymphocytes, programmed death-ligand 1, microsatellite instability associated with mismatch repair deficiency, and tumor mutational burden). This article reviews the impacts and gaps in the characterization of immune-related biomarkers raised by clinical and translational research studies with immunotherapy treatments. Particular emphasis has been put on the documented evidence of significant clinical benefits of ICI in different randomized clinical trials, along with preanalytical and analytical issues in predictive biomarkers pathological assessment.
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Affiliation(s)
| | | | - Giulia Viale
- Department of Medical Oncology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Caterina Fumagalli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Elham Sajjadi
- Department of Oncology and Hemato-Oncology, University of Milan, Italy
| | | | - Roberto Piciotti
- Department of Oncology and Hemato-Oncology, University of Milan, Italy
| | - Marco Invernizzi
- Physical and Rehabilitative Medicine, Department of Health Sciences, University of Eastern Piedmont, Viale Piazza D'Armi 1, Novara, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, University of Milan, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
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26
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mmsig: a fitting approach to accurately identify somatic mutational signatures in hematological malignancies. Commun Biol 2021; 4:424. [PMID: 33782531 PMCID: PMC8007623 DOI: 10.1038/s42003-021-01938-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
Mutational signatures have emerged as powerful biomarkers in cancer patients, with prognostic and therapeutic implications. Wider clinical utility requires access to reproducible algorithms, which allow characterization of mutational signatures in a given tumor sample. Here, we show how mutational signature fitting can be applied to hematological cancer genomes to identify biologically and clinically important mutational processes, highlighting the importance of careful interpretation in light of biological knowledge. Our newly released R package mmsig comes with a dynamic error-suppression procedure that improves specificity in important clinical and biological settings. In particular, mmsig allows accurate detection of mutational signatures with low abundance, such as those introduced by APOBEC cytidine deaminases. This is particularly important in the most recent mutational signature reference (COSMIC v3.1) where each signature is more clearly defined. Our mutational signature fitting algorithm mmsig is a robust tool that can be implemented immediately in the clinic. Rustad et al. present a software package for the R statistical environment for the accurately quantify of somatic mutational signatures in hematological malignancies
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27
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Mohamed RI, Bargal SA, Mekawy AS, El-Shiekh I, Tuncbag N, Ahmed AS, Badr E, Elserafy M. The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine. PLoS One 2021; 16:e0247837. [PMID: 33662042 PMCID: PMC7932549 DOI: 10.1371/journal.pone.0247837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/14/2021] [Indexed: 12/22/2022] Open
Abstract
In the era of precision medicine, analyzing the transcriptomic profile of patients is essential to tailor the appropriate therapy. In this study, we explored transcriptional differences between two invasive breast cancer subtypes; infiltrating ductal carcinoma (IDC) and lobular carcinoma (LC) using RNA-Seq data deposited in the TCGA-BRCA project. We revealed 3854 differentially expressed genes between normal ductal tissues and IDC. In addition, IDC to LC comparison resulted in 663 differentially expressed genes. We then focused on DNA repair genes because of their known effects on patients' response to therapy and resistance. We here report that 36 DNA repair genes are overexpressed in a significant number of both IDC and LC patients' samples. Despite the upregulation in a significant number of samples, we observed a noticeable variation in the expression levels of the repair genes across patients of the same cancer subtype. The same trend is valid for the expression of miRNAs, where remarkable variations between patients' samples of the same cancer subtype are also observed. These individual variations could lie behind the differential response of patients to treatment. The future of cancer diagnostics and therapy will inevitably depend on high-throughput genomic and transcriptomic data analysis. However, we propose that performing analysis on individual patients rather than a big set of patients' samples will be necessary to ensure that the best treatment is determined, and therapy resistance is reduced.
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Affiliation(s)
- Ruwaa I. Mohamed
- Center for Informatics Sciences (CIS), Nile University, Giza, Egypt
| | - Salma A. Bargal
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Asmaa S. Mekawy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Nurcan Tuncbag
- Graduate School of Informatics, Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Alaa S. Ahmed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Eman Badr
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, Egypt
- * E-mail: (EB); (ME)
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- * E-mail: (EB); (ME)
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28
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Voutsadakis IA. High Tumor Mutation Burden and Other Immunotherapy Response Predictors in Breast Cancers: Associations and Therapeutic Opportunities. Target Oncol 2021; 15:127-138. [PMID: 31741177 DOI: 10.1007/s11523-019-00689-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The recent development of effective immunotherapies with immune checkpoint inhibitors for the treatment of cancer has rekindled the interest for the immune system and its activation for an anti-cancer response. At the same time, it has become evident that not all types of cancers respond equally to these treatments, and even within the same tumor type only a subset of patients derive clinical benefit. Biomarkers predictive of response to immunotherapy have been sought and in certain occasions incorporated in the indication for treatment. These include expression of PD-L1 and defects in DNA mismatch repair (MMR). OBJECTIVE Tumor mutation burden (TMB) has been associated with response to immune checkpoint inhibitors. The current investigation examines TMB as a biomarker of response to immunotherapy in breast cancer. PATIENTS AND METHODS Publicly available data from the breast cancer study of The Cancer Genome Atlas (TCGA) and the METABRIC study were analyzed. Parameters examined included the TMB and specific mutations that may impact on TMB. In addition, correlations with breast cancer sub-types were investigated. RESULTS The percentage of breast cancers with high TMB (more than 192 mutations per sample) was low (3.5-4.6%) in luminal and triple-negative cancers and higher (14.1%) in the HER2-positive subset. Almost all cancers with high TMB had defects in MMR proteins or the replicative polymerases POLE and POLD1. CONCLUSIONS Small sub-sets of breast cancers with high TMB exist and may present an opportunity for effective immunotherapeutic targeting.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, 750 Great Northern Road, Sault Ste Marie, ON, P6B 0A8, Canada. .,Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON, Canada.
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29
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Davies HR, Broad KD, Onadim Z, Price EA, Zou X, Sheriff I, Karaa EK, Scheimberg I, Reddy MA, Sagoo MS, Ohnuma SI, Nik-Zainal S. Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature. Cancers (Basel) 2021; 13:754. [PMID: 33670346 PMCID: PMC7918943 DOI: 10.3390/cancers13040754] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/02/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable, suggesting alternative pathways to malignancy. We used whole-genome sequencing (WGS) and transcriptomics to investigate the landscape of sporadic retinoblastomas derived from twenty patients, sought RB1 and other driver mutations and investigated mutational signatures. At least one RB1 mutation was identified in all retinoblastomas, including new mutations in addition to those previously identified by clinical screening. Ten tumours carried structural rearrangements involving RB1 ranging from relatively simple to extremely complex rearrangement patterns, including a chromothripsis-like pattern in one tumour. Bilateral tumours obtained from one patient harboured conserved germline but divergent somatic RB1 mutations, indicating independent evolution. Mutational signature analysis showed predominance of signatures associated with cell division, an absence of ultraviolet-related DNA damage and a profound platinum-related mutational signature in a chemotherapy-exposed tumour. Most RB1 mutations are identifiable by clinical screening. However, the increased resolution and ability to detect otherwise elusive rearrangements by WGS have important repercussions on clinical management and advice on recurrence risks.
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Affiliation(s)
- Helen R. Davies
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Kevin D. Broad
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, The Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (Z.O.); (E.A.P.)
| | - Elizabeth A. Price
- Retinoblastoma Genetic Screening Unit, The Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (Z.O.); (E.A.P.)
| | - Xueqing Zou
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Ibrahim Sheriff
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
| | - Esin Kotiloğlu Karaa
- Pathology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (E.K.K.); (I.S.)
| | - Irene Scheimberg
- Pathology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (E.K.K.); (I.S.)
| | - M. Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London EC1V 2PD, UK
| | - Mandeep S. Sagoo
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London EC1V 2PD, UK
| | - Shin-ichi Ohnuma
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
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30
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Gallon R, Gawthorpe P, Phelps RL, Hayes C, Borthwick GM, Santibanez-Koref M, Jackson MS, Burn J. How Should We Test for Lynch Syndrome? A Review of Current Guidelines and Future Strategies. Cancers (Basel) 2021; 13:406. [PMID: 33499123 PMCID: PMC7865939 DOI: 10.3390/cancers13030406] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
International guidelines for the diagnosis of Lynch syndrome (LS) recommend molecular screening of colorectal cancers (CRCs) to identify patients for germline mismatch repair (MMR) gene testing. As our understanding of the LS phenotype and diagnostic technologies have advanced, there is a need to review these guidelines and new screening opportunities. We discuss the barriers to implementation of current guidelines, as well as guideline limitations, and highlight new technologies and knowledge that may address these. We also discuss alternative screening strategies to increase the rate of LS diagnoses. In particular, the focus of current guidance on CRCs means that approximately half of Lynch-spectrum tumours occurring in unknown male LS carriers, and only one-third in female LS carriers, will trigger testing for LS. There is increasing pressure to expand guidelines to include molecular screening of endometrial cancers, the most frequent cancer in female LS carriers. Furthermore, we collate the evidence to support MMR deficiency testing of other Lynch-spectrum tumours to screen for LS. However, a reliance on tumour tissue limits preoperative testing and, therefore, diagnosis prior to malignancy. The recent successes of functional assays to detect microsatellite instability or MMR deficiency in non-neoplastic tissues suggest that future diagnostic pipelines could become independent of tumour tissue.
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Affiliation(s)
| | | | | | | | | | | | | | - John Burn
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK; (P.G.); (R.L.P.); (C.H.); (G.M.B.); (M.S.-K.); (M.S.J.)
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31
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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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32
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Hübschmann D, Jopp-Saile L, Andresen C, Krämer S, Gu Z, Heilig CE, Kreutzfeldt S, Teleanu V, Fröhling S, Eils R, Schlesner M. Analysis of mutational signatures with yet another package for signature analysis. Genes Chromosomes Cancer 2020; 60:314-331. [PMID: 33222322 DOI: 10.1002/gcc.22918] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022] Open
Abstract
Different mutational processes leave characteristic patterns of somatic mutations in the genome that can be identified as mutational signatures. Determining the contributions of mutational signatures to cancer genomes allows not only to reconstruct the etiology of somatic mutations, but can also be used for improved tumor classification and support therapeutic decisions. We here present the R package yet another package for signature analysis (YAPSA) to deconvolute the contributions of mutational signatures to tumor genomes. YAPSA provides in-built collections from the COSMIC and PCAWG SNV signature sets as well as the PCAWG Indel signatures and employs signature-specific cutoffs to increase sensitivity and specificity. Furthermore, YAPSA allows to determine 95% confidence intervals for signature exposures, to perform constrained stratified signature analyses to obtain enrichment and depletion patterns of the identified signatures and, when applied to whole exome sequencing data, to correct for the triplet content of individual target capture kits. With this functionality, YAPSA has proved to be a valuable tool for analysis of mutational signatures in molecular tumor boards in a precision oncology context. YAPSA is available at R/Bioconductor (http://bioconductor.org/packages/3.12/bioc/html/YAPSA.html).
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Affiliation(s)
- Daniel Hübschmann
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Pattern Recognition and Digital Medicine, Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Department of Pediatric Immunology, Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lea Jopp-Saile
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Pattern Recognition and Digital Medicine, Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Carolin Andresen
- Pattern Recognition and Digital Medicine, Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Stephen Krämer
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Zuguang Gu
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,DKFZ-HIPO (Heidelberg Center for Personalized Oncology), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Christoph E Heilig
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Simon Kreutzfeldt
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Veronica Teleanu
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Department of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Berlin, Germany.,Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Chair of Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
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33
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Deregulated estrogen receptor signaling and DNA damage response in breast tumorigenesis. Biochim Biophys Acta Rev Cancer 2020; 1875:188482. [PMID: 33260050 DOI: 10.1016/j.bbcan.2020.188482] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/05/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
Carriers of BRCA1 mutations have a higher chance of developing cancers in hormone-responsive tissues like the breast, ovary and prostate, compared to other tissues. These tumors generally exhibit basal-like characters and do not express estrogen receptor (ER) or progesterone receptor (PR). Intriguingly, BRCA1 mutated breast cancers have a less favorable clinical outcome, as they will not respond to hormone therapy. BRCA1 has been reported to exhibit ligand dependent and independent transcriptional inhibition of ER-α; however, there exists a controversy on whether BRCA1 induces or inhibits ER-α expression. The mechanisms associated with resistance of BRCA1 mutated cancers to hormone therapy, as well as the tissue restriction exhibited by BRCA1 mutated tumors are still largely unknown. BRCA1 mutated tumors possess increased DNA damages and decreased genomic integrity, as BRCA1 plays a cardinal role in high fidelity DNA damage repair pathways, like homologous recombination (HR). The existence of cross regulatory signaling networks between ER-α and BRCA1 speculates a role of ER on BRCA1 dependent DDR pathways. Thus, the loss or haploinsufficiency of BRCA1 and the consequential deregulation of ER-α signaling may result in persistence of unrepaired DNA damages, eventually leading to tumorigenesis. Therefore, understanding of this cross-talk between ER-α and BRCA1, with regard to DDR, will provide critical insights to steer drug development and therapy for breast/ovarian cancers. This review discusses the mechanisms by which estrogen and ER signaling influence BRCA1 mediated DNA damage response and repair pathways in the mammalian system.
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34
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Sorscher S. Identifying Lynch Syndrome–Related Breast Cancers. JCO Precis Oncol 2020; 4:579-580. [DOI: 10.1200/po.20.00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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35
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Fusco N, Sajjadi E, Venetis K, Gaudioso G, Lopez G, Corti C, Rocco EG, Criscitiello C, Malapelle U, Invernizzi M. PTEN Alterations and Their Role in Cancer Management: Are We Making Headway on Precision Medicine? Genes (Basel) 2020; 11:E719. [PMID: 32605290 PMCID: PMC7397204 DOI: 10.3390/genes11070719] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/27/2020] [Accepted: 06/27/2020] [Indexed: 12/15/2022] Open
Abstract
Alterations in the tumor suppressor phosphatase and tensin homolog (PTEN) occur in a substantial proportion of solid tumors. These events drive tumorigenesis and tumor progression. Given its central role as a downregulator of the phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway, PTEN is deeply involved in cell growth, proliferation, and survival. This gene is also implicated in the modulation of the DNA damage response and in tumor immune microenvironment modeling. Despite the actionability of PTEN alterations, their role as biomarkers remains controversial in clinical practice. To date, there is still a substantial lack of validated guidelines and/or recommendations for PTEN testing. Here, we provide an update on the current state of knowledge on biologic and genetic alterations of PTEN across the most frequent solid tumors, as well as on their actual and/or possible clinical applications. We focus on possible tailored schemes for cancer patients' clinical management, including risk assessment, diagnosis, prognostication, and treatment.
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Affiliation(s)
- Nicola Fusco
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (K.V.); (E.G.R.)
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Elham Sajjadi
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Konstantinos Venetis
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (K.V.); (E.G.R.)
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
- Doctoral Program in Translational Medicine, University of Milan, 20133 Milan, Italy
| | - Gabriella Gaudioso
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20131 Milan, Italy; (G.G.); (G.L.); (C.C.)
| | - Gianluca Lopez
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20131 Milan, Italy; (G.G.); (G.L.); (C.C.)
| | - Chiara Corti
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20131 Milan, Italy; (G.G.); (G.L.); (C.C.)
| | - Elena Guerini Rocco
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (K.V.); (E.G.R.)
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Carmen Criscitiello
- New Drugs and Early Drug Development for Innovative Therapies Division, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Umberto Malapelle
- Department of Public Health, University Federico II, 80138 Naples, Italy;
| | - Marco Invernizzi
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy;
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36
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Zeng Z, Vo A, Li X, Shidfar A, Saldana P, Blanco L, Xuei X, Luo Y, Khan SA, Clare SE. Somatic genetic aberrations in benign breast disease and the risk of subsequent breast cancer. NPJ Breast Cancer 2020; 6:24. [PMID: 32566745 PMCID: PMC7293275 DOI: 10.1038/s41523-020-0165-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 05/08/2020] [Indexed: 01/05/2023] Open
Abstract
It is largely unknown how the development of breast cancer (BC) is transduced by somatic genetic alterations in the benign breast. Since benign breast disease is an established risk factor for BC, we established a case-control study of women with a history of benign breast biopsy (BBB). Cases developed BC at least one year after BBB and controls did not develop BC over an average of 17 years following BBB. 135 cases were matched to 69 controls by age and type of benign change: non-proliferative or proliferation without atypia (PDWA). Whole-exome sequencing (WES) was performed for the BBB. Germline DNA (available from n = 26 participants) was utilized to develop a mutation-calling pipeline, to allow differentiation of somatic from germline variants. Among the 204 subjects, two known mutational signatures were identified, along with a currently uncatalogued signature that was significantly associated with triple negative BC (TNBC) (p = 0.007). The uncatalogued mutational signature was validated in 109 TNBCs from TCGA (p = 0.001). Compared to non-proliferative samples, PDWA harbors more abundant mutations at PIK3CA pH1047R (p < 0.001). Among the 26 BBB whose somatic copy number variation could be assessed, deletion of MLH3 is significantly associated with the mismatch repair mutational signature (p < 0.001). Matched BBB-cancer pairs were available for ten cases; several mutations were shared between BBB and cancers. This initial study of WES of BBB shows its potential for the identification of genetic alterations that portend breast oncogenesis. In future larger studies, robust personalized breast cancer risk indicators leading to novel interception paradigms can be assessed.
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Affiliation(s)
- Zexian Zeng
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T. H. Chan School of Public Health, Boston, MA USA
| | - Andy Vo
- Committee on Developmental Biology and Regenerative Medicine, The University of Chicago, Chicago, IL USA
| | - Xiaoyu Li
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Ali Shidfar
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Paulette Saldana
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luis Blanco
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Seema A. Khan
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Susan E. Clare
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL USA
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37
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Chopra N, Tovey H, Pearson A, Cutts R, Toms C, Proszek P, Hubank M, Dowsett M, Dodson A, Daley F, Kriplani D, Gevensleben H, Davies HR, Degasperi A, Roylance R, Chan S, Tutt A, Skene A, Evans A, Bliss JM, Nik-Zainal S, Turner NC. Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer. Nat Commun 2020; 11:2662. [PMID: 32471999 PMCID: PMC7260192 DOI: 10.1038/s41467-020-16142-7] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
Triple negative breast cancer (TNBC) encompasses molecularly different subgroups, with a subgroup harboring evidence of defective homologous recombination (HR) DNA repair. Here, within a phase 2 window clinical trial, RIO trial (EudraCT 2014-003319-12), we investigate the activity of PARP inhibitors in 43 patients with untreated TNBC. The primary end point, decreased Ki67, occured in 12% of TNBC. In secondary end point analyses, HR deficiency was identified in 69% of TNBC with the mutational-signature-based HRDetect assay. Cancers with HRDetect mutational signatures of HR deficiency had a functional defect in HR, assessed by impaired RAD51 foci formation on end of treatment biopsy. Following rucaparib treatment there was no association of Ki67 change with HR deficiency. In contrast, early circulating tumor DNA dynamics identified activity of rucaparib, with end of treatment ctDNA levels suppressed by rucaparib in mutation-signature HR-deficient cancers. In ad hoc analysis, rucaparib induced expression of interferon response genes in HR-deficient cancers. The majority of TNBCs have a defect in DNA repair, identifiable by mutational signature analysis, that may be targetable with PARP inhibitors.
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Affiliation(s)
- Neha Chopra
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Holly Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Alex Pearson
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Ros Cutts
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Christy Toms
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Paula Proszek
- The Centre for Molecular Pathology, The Royal Marsden Hospital, 15 Cotswold Road, Sutton, SM2 5NG, Surrey, United Kingdom
| | - Michael Hubank
- The Centre for Molecular Pathology, The Royal Marsden Hospital, 15 Cotswold Road, Sutton, SM2 5NG, Surrey, United Kingdom
| | - Mitch Dowsett
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, United Kingdom
| | - Andrew Dodson
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, United Kingdom
| | - Frances Daley
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Divya Kriplani
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Heidi Gevensleben
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
| | - Helen Ruth Davies
- Department of Medical Genetics, The Clinical School, Box 238, Level 6 Addenbrooke's Treatment Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Andrea Degasperi
- Department of Medical Genetics, The Clinical School, Box 238, Level 6 Addenbrooke's Treatment Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Rebecca Roylance
- University College London Hospitals NHS Foundation Trust, NIHR University College London Hospitals Biomedical Research Centre, London, United Kingdom
| | - Stephen Chan
- Nottingham University Hospital Trust (City Campus), Nottingham, United Kingdom
| | - Andrew Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom
- Breast Cancer Now Research Unit, Cancer Centre, Guy's Hospital, King's College London, London, United Kingdom
| | - Anthony Skene
- Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Abigail Evans
- Poole Hospital NHS Foundation Trust, Poole, United Kingdom
| | - Judith M Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Serena Nik-Zainal
- Department of Medical Genetics, The Clinical School, Box 238, Level 6 Addenbrooke's Treatment Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, United Kingdom
| | - Nicholas C Turner
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, CB2 0XZ, United Kingdom.
- Breast Unit, The Royal Marsden Hospital, Fulham Road, London, United Kingdom.
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38
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Porkka NK, Olkinuora A, Kuopio T, Ahtiainen M, Eldfors S, Almusa H, Mecklin JP, Peltomäki P. Does breast carcinoma belong to the Lynch syndrome tumor spectrum? - Somatic mutational profiles vs. ovarian and colorectal carcinomas. Oncotarget 2020; 11:1244-1256. [PMID: 32292574 PMCID: PMC7147090 DOI: 10.18632/oncotarget.27538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/14/2020] [Indexed: 12/30/2022] Open
Abstract
Inherited DNA mismatch repair (MMR) defects cause predisposition to colorectal, endometrial, ovarian, and other cancers occurring in Lynch syndrome (LS). It is unsettled whether breast carcinoma belongs to the LS tumor spectrum. We approached this question through somatic mutational analysis of breast carcinomas from LS families, using established LS-spectrum tumors for comparison. Somatic mutational profiles of 578 cancer-relevant genes were determined for LS-breast cancer (LS-BC, n = 20), non-carrier breast cancer (NC-BC, n = 10), LS-ovarian cancer (LS-OC, n = 16), and LS-colorectal cancer (LS-CRC, n = 18) from the National LS Registry of Finland. Microsatellite and MMR protein analysis stratified LS-BCs into MMR-deficient (dMMR, n = 11) and MMR-proficient (pMMR, n = 9) subgroups. All NC-BCs were pMMR and all LS-OCs and LS-CRCs dMMR. All but one dMMR LS-BCs were hypermutated (> 10 non-synonymous mutations/Mb; average 174/Mb per tumor) and the frequency of MMR-deficiency-associated signatures 6, 20, and 26 was comparable to that in LS-OC and LS-CRC. LS-BCs that were pMMR resembled NC-BCs with respect to somatic mutational loads (4/9, 44%, hypermutated with average mutation count 33/Mb vs. 3/10, 30%, hypermutated with average 88 mutations/Mb), whereas mutational signatures shared features of dMMR LS-BC, LS-OC, and LS-CRC. Epigenetic regulatory genes were significantly enriched as mutational targets in LS-BC, LS-OC, and LS-CRC. Many top mutant genes of our LS-BCs have previously been identified as drivers of unselected breast carcinomas. In conclusion, somatic mutational signatures suggest that conventional MMR status of tumor tissues is likely to underestimate the significance of the predisposing MMR defects as contributors to breast tumorigenesis in LS.
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Affiliation(s)
- Noora K. Porkka
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Teijo Kuopio
- Department of Pathology, Jyväskylä Central Hospital, Jyväskylä, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Maarit Ahtiainen
- Department of Education and Research, Jyväskylä Central Hospital and University of Eastern Finland, Jyväskylä, Finland
| | - Samuli Eldfors
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Henrikki Almusa
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Surgery, Jyväskylä Central Hospital, Jyväskylä, Finland
- Department of Education & Science, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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39
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Kutasovic JR, McCart Reed AE, Sokolova A, Lakhani SR, Simpson PT. Morphologic and Genomic Heterogeneity in the Evolution and Progression of Breast Cancer. Cancers (Basel) 2020; 12:E848. [PMID: 32244556 PMCID: PMC7226487 DOI: 10.3390/cancers12040848] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
: Breast cancer is a remarkably complex and diverse disease. Subtyping based on morphology, genomics, biomarkers and/or clinical parameters seeks to stratify optimal approaches for management, but it is clear that every breast cancer is fundamentally unique. Intra-tumour heterogeneity adds further complexity and impacts a patient's response to neoadjuvant or adjuvant therapy. Here, we review some established and more recent evidence related to the complex nature of breast cancer evolution. We describe morphologic and genomic diversity as it arises spontaneously during the early stages of tumour evolution, and also in the context of treatment where the changing subclonal architecture of a tumour is driven by the inherent adaptability of tumour cells to evolve and resist the selective pressures of therapy.
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Affiliation(s)
- Jamie R. Kutasovic
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Amy E. McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Anna Sokolova
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
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40
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Sason I, Wojtowicz D, Robinson W, Leiserson MDM, Przytycka TM, Sharan R. A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer. iScience 2020; 23:100900. [PMID: 32088392 PMCID: PMC7038582 DOI: 10.1016/j.isci.2020.100900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The characterization of mutational processes in terms of their signatures of activity relies mostly on the assumption that mutations in a given cancer genome are independent of one another. Recently, it was discovered that certain segments of mutations, termed processive groups, occur on the same DNA strand and are generated by a single process or signature. Here we provide a first probabilistic model of mutational signatures that accounts for their observed stickiness and strand coordination. The model conditions on the observed strand for each mutation and allows the same signature to generate a run of mutations. It can both use known signatures or learn new ones. We show that this model provides a more accurate description of the properties of mutagenic processes than independent-mutation achieving substantially higher likelihood on held-out data. We apply this model to characterize the processivity of mutagenic processes across multiple types of cancer.
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Affiliation(s)
- Itay Sason
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Damian Wojtowicz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | - Welles Robinson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Mark D M Leiserson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
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41
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PTEN Expression as a Complementary Biomarker for Mismatch Repair Testing in Breast Cancer. Int J Mol Sci 2020; 21:ijms21041461. [PMID: 32098071 PMCID: PMC7073136 DOI: 10.3390/ijms21041461] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Mismatch repair (MMR) analysis in breast cancer may help to inform immunotherapy decisions but it lacks breast-specific guidelines. Unlike in other neoplasms, MMR protein loss shows intra-tumor heterogeneity and it is not mirrored by microsatellite instability in the breast. Additional biomarkers can improve MMR clinical testing. Phosphatase and tensin homolog (PTEN) inactivation is an early oncogenic event that is associated with MMR deficiency (dMMR) in several tumors. Here, we sought to characterize the diagnostic utility of PTEN expression analysis for MMR status assessment in breast cancer. A total of 608 breast cancers were profiled for their MMR and PTEN status. Proteins expression and distribution were analyzed by immunohistochemistry (IHC) on tissue microarrays and confirmed on full sections; PTEN copy number alterations were detected using a real-time PCR assay. Overall, 78 (12.8%) cases were MMR-heterogeneous (hMMR), while all patterns of PTEN expression showed no intra-tumor heterogeneity. Wild-type PTEN expression was observed in 15 (18.5%) dMMR tumors (p < 0.0001). Survival analyses revealed significant correlations between MMR-proficient (pMMR), PTEN expression, and a better outcome. The positive predictive value of PTEN-retained status for pMMR ranged from 94.6% in estrogen receptor (ER)+/HER2- tumors to 100% in HER2-amplified and ER-/HER2- cases. We propose a novel diagnostic algorithm where PTEN expression analysis can be employed to identify pMMR breast cancers.
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Sorscher S, Ansley K, Delaney SD, Ramkissoon S. The implications of BRCA loss of heterozygosity (LOH) and deficient mismatch repair gene (dMMR) expression in the breast cancer of a patient with both inherited breast and ovarian cancer syndrome (BRCA2) and Lynch syndrome (MLH1). Breast Cancer Res Treat 2020; 180:511-514. [PMID: 32040686 DOI: 10.1007/s10549-020-05569-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/03/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND BRCA germline pathogenic variants represent the most common inherited mechanism predisposing individuals to breast cancer, while germline pathogenic variants in one of the mismatch repair (MMR) genes represent the most common colon cancer-predisposing inherited syndrome, known as the Lynch syndrome (LS). Individuals who harbor pathogenic germline variants for both syndromes are extremely rare. Germline testing is now done routinely for patients with breast cancer and MMR testing is recommended for nearly all patients diagnosed with colon or rectal cancer (Benson et al in NCCN clinical practice guidelines in oncology (NCCN guidelines) colon cancer (Version 4.2019-November 8, 2019). www.NCCN.org, Gradishar et al in NCCN clinical practice guidelines in oncology (NCCN guidelines) breast cancer (Version 3.2019-September 6, 2019).www.NCCN.org). We report a patient with germline mutations in both BRCA2 and the MMR gene MLH1 who developed breast cancer. The breast cancer showed loss of heterozygosity (LOH) in BRCA2 (the molecular hallmark of cancers related to inheritance of a BRCA alteration) and was also deficient in mismatch repair gene protein expression (dMMR), the hallmark of LS-related cancers. We discuss the possible mechanisms of transformation that would explain the finding that the tumor showed both BRCA2 LOH and was dMMR, each of which would generally be considered a gatekeeper event for transformation of normal cells to malignancy. RESULTS This report describes a patient with molecularly diagnosed breast and ovarian cancer syndrome (BRCA2) and LS. Next generation sequencing (NGS) and immunohistochemical (IHC) testing demonstrated her breast cancer to show BRCA2 LOH and to be dMMR. CONCLUSION The patient presented represents the first reported case where both next generation sequencing (NGS) for BRCA LOH and MMR IHC testing of her breast cancer were performed and underscores the importance of using NGS including the reported mutational allelic frequency (MAF) and IHC use to predict the likely responsiveness to the recently approved PARP inhibitors and checkpoint inhibitor therapies (Robson et al in N Engl J Med 377:523-533, 2017, Lemery et al in 377(15):1409-1412, https://doi.org/10.1056/NEJMp1709968, 2017), key because the gatekeeper transforming event for tumors related to inherited cancer syndromes is loss of normal tumor suppressor gene (TSG) protein expression.
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Affiliation(s)
- Steven Sorscher
- Oncology Division, Wake Forest School of Medicine, Medical Center Blvd, Winston-Salem, NC, 27157, USA.
| | - Katherine Ansley
- Oncology Division, Wake Forest School of Medicine, Medical Center Blvd, Winston-Salem, NC, 27157, USA
| | | | - Shakti Ramkissoon
- Foundation Medicine, Inc, Cambridge, MA, 02141, USA.,Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
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43
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Current concepts in breast cancer genomics: An evidence based review by the CGC breast cancer working group. Cancer Genet 2020; 244:11-20. [PMID: 32087595 DOI: 10.1016/j.cancergen.2020.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Genomic abnormalities in breast cancer have been described according to diverse conceptual frameworks, including histologic subtypes, clinical molecular subtypes, intrinsic DNA, RNA, and epigenetic profiles, and activated molecular pathways. METHODS The Cancer Genomics Consortium (CGC) Breast Cancer Workgroup performed an evidence based literature review to summarize current knowledge of clinically significant genomic alterations in breast cancer using CGC levels of evidence. Targetable or disease-defining alterations were prioritized. RESULTS We summarized genomic alterations in breast cancer within a framework of existing clinical tools for diagnosis, risk stratification, and therapeutic management. Using CGC levels of evidence, we catalog copy number profiles, gene expression profiles, and mutations in clinically significant genes. We also describe emerging molecular markers such as methylation profiling and immunotherapy biomarkers. CONCLUSION A summary of currently available information on breast cancer genomics will enhance precision medicine by serving as an interpretive resource for clinical laboratory geneticists, providing a foundation for future practice guidelines, and identifying knowledge gaps to address in future research.
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Abstract
Technological advances in the ability to read the human genome have accelerated the speed of sequencing, such that today we can perform whole genome sequencing (WGS) in one day. Until recently, genomic studies have largely been limited to seeking novel scientific discoveries. The application of new insights gained through cancer WGS into the clinical domain, have been relatively limited. Looking ahead, a vast amount of data can be generated by genomic studies. Of note, excellent organisation of genomic and clinical data permits the application of machine-learning methods which can lead to the development of clinical algorithms that could assist future clinicians and genomicists in the analysis and interpretation of individual cancer genomes. Here, we describe what can be gleaned from holistic whole cancer genome profiling and argue that we must build the infrastructure and educational frameworks to support the modern clinical genomicist to prepare for a future where WGS will be the norm.
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Affiliation(s)
- Serena Nik-Zainal
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, UK / Academic Laboratory of Medical Genetics, Addenbrookes Treatment Centre, Cambridge, UK
| | - Yasin Memari
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, UK / Academic Laboratory of Medical Genetics, Addenbrookes Treatment Centre, Cambridge, UK
| | - Helen R Davies
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, UK / Academic Laboratory of Medical Genetics, Addenbrookes Treatment Centre, Cambridge, UK
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45
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Abstract
Cancer classification aims to provide an accurate diagnosis of the disease and prediction of tumor behavior to facilitate oncologic decision making. Traditional breast cancer classification, mainly based on clinicopathologic features and assessment of routine biomarkers, may not capture the varied clinical courses of individual breast cancers. The underlying biology in cancer development and progression is complicated. Recent findings from high-throughput technologies added important information with regard to the underlying genetic alterations and the biological events in breast cancer. The information provides insights into new treatment strategies and patient stratifications that impact on the management of breast cancer patients. This review provides an overview of recent data on high throughput analysis of breast cancers, and it analyzes the relationship of these findings with traditional breast cancer classification and their clinical potentials.
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46
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James JL, Balko JM. Biomarker predictors for immunotherapy benefit in breast: beyond PD-L1. CURRENT BREAST CANCER REPORTS 2019; 11:217-227. [PMID: 33312343 PMCID: PMC7731906 DOI: 10.1007/s12609-019-00331-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE OF REVIEW Immune checkpoint blockade (ICB) has changed the clinical course of multiple cancer types and durable responses have now been observed in breast cancer (BC) patients. Most data suggest that, compared to other subtypes, triple-negative BC (TNBC) patients are more responsive to ICB, and anti-PD-L1 therapy is now approved in PD-L1+ metastatic TNBC, in combination with chemotherapy. RECENT FINDINGS Nearly 40% of PD-L1+ TNBC patients did not respond to this combination. Thus, additional biomarkers appear to be necessary to more precisely identify potential responders. A comprehensive analysis of the breast tumor microenvironment (TME) and peripheral blood may identify potential biomarkers for a more accurate selection of patients likely to respond to ICB. SUMMARY Herein, we summarize key features of the breast TME, and beyond, that may hold predictive power in determining immunotherapy benefit. Incorporation of these features in controlled clinical trials may help further guide personalized care for BC immunotherapy.
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Affiliation(s)
- Jamaal L. James
- Department of Medicine, Vanderbilt University Medical Center, Nashville TN
- Department of Cancer Biology Program, Vanderbilt University Medical Center, Nashville TN
| | - Justin M. Balko
- Department of Medicine, Vanderbilt University Medical Center, Nashville TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville TN
- Department of Breast Cancer Research Program, Vanderbilt University Medical Center, Nashville TN
- Department of Cancer Biology Program, Vanderbilt University Medical Center, Nashville TN
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47
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van Dessel LF, van Riet J, Smits M, Zhu Y, Hamberg P, van der Heijden MS, Bergman AM, van Oort IM, de Wit R, Voest EE, Steeghs N, Yamaguchi TN, Livingstone J, Boutros PC, Martens JWM, Sleijfer S, Cuppen E, Zwart W, van de Werken HJG, Mehra N, Lolkema MP. The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact. Nat Commun 2019; 10:5251. [PMID: 31748536 PMCID: PMC6868175 DOI: 10.1038/s41467-019-13084-7] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/17/2019] [Indexed: 12/22/2022] Open
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) has a highly complex genomic landscape. With the recent development of novel treatments, accurate stratification strategies are needed. Here we present the whole-genome sequencing (WGS) analysis of fresh-frozen metastatic biopsies from 197 mCRPC patients. Using unsupervised clustering based on genomic features, we define eight distinct genomic clusters. We observe potentially clinically relevant genotypes, including microsatellite instability (MSI), homologous recombination deficiency (HRD) enriched with genomic deletions and BRCA2 aberrations, a tandem duplication genotype associated with CDK12-/- and a chromothripsis-enriched subgroup. Our data suggests that stratification on WGS characteristics may improve identification of MSI, CDK12-/- and HRD patients. From WGS and ChIP-seq data, we show the potential relevance of recurrent alterations in non-coding regions identified with WGS and highlight the central role of AR signaling in tumor progression. These data underline the potential value of using WGS to accurately stratify mCRPC patients into clinically actionable subgroups.
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Affiliation(s)
- Lisanne F van Dessel
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Job van Riet
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Minke Smits
- Department of Medical Oncology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Yanyun Zhu
- Division on Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Paul Hamberg
- Department of Internal Medicine, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - Michiel S van der Heijden
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andries M Bergman
- Division on Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Inge M van Oort
- Department of Urology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Ronald de Wit
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emile E Voest
- Oncode Institute, Utrecht, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Neeltje Steeghs
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Takafumi N Yamaguchi
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Julie Livingstone
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
| | - Paul C Boutros
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
- Department of Human Genetics, University of California Los Angeles, Los Angeles, USA
- Department of Urology, University of California Los Angeles, Los Angeles, USA
- Jonsson Comprehensive Cancer Centre, University of California Los Angeles, Los Angeles, USA
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division on Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.
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48
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Staaf J, Glodzik D, Bosch A, Vallon-Christersson J, Reuterswärd C, Häkkinen J, Degasperi A, Amarante TD, Saal LH, Hegardt C, Stobart H, Ehinger A, Larsson C, Rydén L, Loman N, Malmberg M, Kvist A, Ehrencrona H, Davies HR, Borg Å, Nik-Zainal S. Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. Nat Med 2019; 25:1526-1533. [PMID: 31570822 PMCID: PMC6859071 DOI: 10.1038/s41591-019-0582-4] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/15/2019] [Indexed: 01/12/2023]
Abstract
Whole-genome sequencing (WGS) brings comprehensive insights to cancer genome interpretation. To explore the clinical value of WGS, we sequenced 254 triple-negative breast cancers (TNBCs) for which associated treatment and outcome data were collected between 2010 and 2015 via the population-based Sweden Cancerome Analysis Network-Breast (SCAN-B) project (ClinicalTrials.gov ID:NCT02306096). Applying the HRDetect mutational-signature-based algorithm to classify tumors, 59% were predicted to have homologous-recombination-repair deficiency (HRDetect-high): 67% explained by germline/somatic mutations of BRCA1/BRCA2, BRCA1 promoter hypermethylation, RAD51C hypermethylation or biallelic loss of PALB2. A novel mechanism of BRCA1 abrogation was discovered via germline SINE-VNTR-Alu retrotransposition. HRDetect provided independent prognostic information, with HRDetect-high patients having better outcome on adjuvant chemotherapy for invasive disease-free survival (hazard ratio (HR) = 0.42; 95% confidence interval (CI) = 0.2-0.87) and distant relapse-free interval (HR = 0.31, CI = 0.13-0.76) compared to HRDetect-low, regardless of whether a genetic/epigenetic cause was identified. HRDetect-intermediate, some possessing potentially targetable biological abnormalities, had the poorest outcomes. HRDetect-low cancers also had inadequate outcomes: ~4.7% were mismatch-repair-deficient (another targetable defect, not typically sought) and they were enriched for (but not restricted to) PIK3CA/AKT1 pathway abnormalities. New treatment options need to be considered for now-discernible HRDetect-intermediate and HRDetect-low categories. This population-based study advocates for WGS of TNBC to better inform trial stratification and improve clinical decision-making.
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Affiliation(s)
- Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.
| | - Dominik Glodzik
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ana Bosch
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Johan Vallon-Christersson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Christel Reuterswärd
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Jari Häkkinen
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Andrea Degasperi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Tauanne Dias Amarante
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Lao H Saal
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Cecilia Hegardt
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | | | - Anna Ehinger
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Clinical Genetics and Pathology, Department of Laboratory Medicine, Office for Medical Services, Lund, Sweden
| | - Christer Larsson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Lisa Rydén
- Division of Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Niklas Loman
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Department of Laboratory Medicine, Office for Medical Services, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Helen R Davies
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK.
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
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49
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Giridhar KV, Liu MC. Available and emerging molecular markers in the clinical management of breast cancer. Expert Rev Mol Diagn 2019; 19:919-928. [PMID: 31498011 DOI: 10.1080/14737159.2019.1664901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: Biomarker assessment is fundamental to managing patients with invasive breast cancer. While the assessment of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 is mandatory for all invasive breast tumors, recent advances in our understanding of tumor biology have uncovered a growing list of clinically relevant biomarkers. Areas covered: In early-stage breast cancer, we focus on dynamic changes in Ki-67 during neoadjuvant endocrine therapy and multigene prognostic assays to guide adjuvant chemotherapy decisions. In advanced breast cancer, we discuss the techniques and clinical relevance of ESR1 and PIK3CA mutations in cell-free DNA and describe therapeutically targetable germline or somatic alterations, with specific focus on BRCA mutations, microsatellite instability, and NTRK fusions. Expert opinion: Biomarkers influence breast cancer management at every stage of disease. This review summarizes recently identified tissue and blood-based biomarkers, implications on clinical management, current limitations and future developments in both early- and advanced-stage breast cancer.
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Affiliation(s)
| | - Minetta C Liu
- Department of Oncology, Mayo Clinic , Rochester , MN , USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester , MN , USA
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50
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Cheng AS, Leung SCY, Gao D, Burugu S, Anurag M, Ellis MJ, Nielsen TO. Mismatch repair protein loss in breast cancer: clinicopathological associations in a large British Columbia cohort. Breast Cancer Res Treat 2019; 179:3-10. [PMID: 31522348 PMCID: PMC6985067 DOI: 10.1007/s10549-019-05438-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022]
Abstract
Purpose Alterations to mismatch repair (MMR) pathways are a known cause of cancer, particularly colorectal and endometrial carcinomas. Recently, checkpoint inhibitors have been approved for use in MMR-deficient cancers of any type (Prasad et al. in JAMA Oncol 4:157–158, 2018). Functional studies in breast cancer have shown associations between MMR loss, resistance to aromatase inhibitors and sensitivity to palbociclib (Haricharan et al. in Cancer Discov 7:1168–1183, 2017). Herein, we investigate the clinical meaning of MMR deficiency in breast cancer by immunohistochemical assessment of MSH2, MSH6, MLH1 and PMS2 on a large series of breast cancers linked to detailed biomarker and long-term outcome data. Methods Cases were classified as MMR intact when all four markers expressed nuclear reactivity, but MMR-deficient when at least one of the four biomarkers displayed loss of nuclear staining in the presence of positive internal stromal controls on the tissue microarray core. Results Among the 1635 cases with interpretable staining, we identified 31 (1.9%) as MMR-deficient. In our cohort, MMR deficiency was present across all major breast cancer subtypes, and was associated with high-grade, low-progesterone receptor expression and high tumor-infiltrating lymphocyte counts. MMR deficiency is significantly associated with inferior overall (HR 2.29, 95% CI 1.02–5.17, p = 0.040) and disease-specific survival (HR 2.71, 95% CI 1.00–7.35, p = 0.042) in the 431 estrogen receptor-positive patients who were uniformly treated with tamoxifen as their sole adjuvant systemic therapy. Conclusion Overall, this study supports the concept that breast cancer patients with MMR deficiency as assessed by immunohistochemistry may be good candidates for alternative treatment approaches such as immune checkpoint or CDK4 inhibitors. Electronic supplementary material The online version of this article (10.1007/s10549-019-05438-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angela S Cheng
- Genetic Pathology Evaluation Centre and University of British Columbia, Vancouver, BC, Canada
| | - Samuel C Y Leung
- Genetic Pathology Evaluation Centre and University of British Columbia, Vancouver, BC, Canada
| | - Dongxia Gao
- Genetic Pathology Evaluation Centre and University of British Columbia, Vancouver, BC, Canada
| | - Samantha Burugu
- Genetic Pathology Evaluation Centre and University of British Columbia, Vancouver, BC, Canada
| | | | | | - Torsten O Nielsen
- Genetic Pathology Evaluation Centre and University of British Columbia, Vancouver, BC, Canada. .,Anatomical Pathology JPN1401 Vancouver Hospital, 855 West 12th Avenue, Vancouver, BC, V5Z 1M9, Canada.
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