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Shao C, Ren Y, Zhou H, Lee LC, Chen C, Dettman EJ, Cristescu R, Gozman A, Jin F, Zhou W. Biomarker Testing Journey Among Patients with Advanced Solid Tumors and Treatment Patterns by Homologous Recombination Repair Status: A Clinico-Genomic Database Study. Adv Ther 2024; 41:759-776. [PMID: 38169059 DOI: 10.1007/s12325-023-02734-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION Defects in the homologous recombination repair (HRR) pathway can include mutations in BRCA1 and BRCA2 (BRCAm) and other HRR genes (HRRm). These mutations are associated with a homologous recombination deficiency (HRD) phenotype. We evaluated testing journey and treatment patterns by BRCAm, HRRm, and HRD status in a real-world dataset. METHODS Deidentified data for patients who had undergone comprehensive genomic profiling using FoundationOne®CDx were collected through December 31, 2020, from a real-world multi-tumor clinico-genomic database (CGDB) capturing data from clinics in the United States. Patients eligible for inclusion in this analysis had a confirmed diagnosis with advanced or metastatic disease between January 1, 2018, and December 31, 2019, for 1 of 15 solid tumor types. Objectives were to evaluate patient treatment patterns by BRCAm, HRRm, and HRD status and to describe the timing of when (throughout disease course) comprehensive genomic profiling was performed. RESULTS Among 9457 patients included in the overall population with evaluable biomarker status, 7856 (83.1%) received ≥ 1 systemic therapy. Among the 7856 patients who received systemic therapy, 2324 (30.0%) underwent testing before first-line therapy, 4114 (52.4%) were tested after receiving first-line therapy and before receiving subsequent therapy (if any), 970 (12.3%) were tested after second-line therapy and before receiving subsequent therapy (if any), and 447 (5.7%) patients underwent testing after receiving third-line therapy. A higher proportion of patients with BRCAm, HRRm, or HRD-positive status were treated with poly(ADP-ribose) polymerase (PARP) inhibitors across all lines of therapy. There was no evidence of a meaningful difference in the proportion of patients who received other treatment (including chemotherapy and immunotherapy) by BRCAm, HRRm, or HRD status. CONCLUSION The majority of patients from this real-world dataset underwent FoundationOne®CDx testing after initiation of first-line treatment. Testing appeared to influence treatment patterns, with a higher proportion of patients with BRCAm, HRRm, and HRD-positive disease receiving PARP inhibitors.
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Affiliation(s)
- Changxia Shao
- Merck & Co., Inc., Rahway, NJ, USA.
- , Mailstop WP37A-250, 770 Sumneytown Pike, West Point, PA, 19486, USA.
| | | | | | | | - Cai Chen
- Merck & Co., Inc., Rahway, NJ, USA
| | | | | | | | - Fan Jin
- Merck & Co., Inc., Rahway, NJ, USA
| | - Wei Zhou
- Merck & Co., Inc., Rahway, NJ, USA
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Platteter E, Wulf G. Durable Response to Programmed Death 1-Directed Antibodies in a Hypermutated Triple-Negative Breast Cancer: A Case Report. Case Rep Oncol 2024; 17:392-398. [PMID: 38435448 PMCID: PMC10906999 DOI: 10.1159/000535743] [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: 09/01/2023] [Accepted: 12/06/2023] [Indexed: 03/05/2024] Open
Abstract
Introduction The advent of immune checkpoint inhibitors marks significant progress in the evolution of cancer treatment. Recent clinical trials have demonstrated the success of immune-oncologic (IO) agents like pembrolizumab (Keytruda™) in combination with chemotherapy against triple-negative breast cancer (TNBC) [Ann Oncol. 2017 Jun 1;28(6):1388-1398]. There is less literature investigating pembrolizumab in monotherapy and in cases of rare tumor mutational burden. Case Presentation Here, we report the case of a 65-year-old Native American and African American woman with previous incomplete lines of therapy diagnosed with recurrent TNBC and pulmonary metastases. Next-generation sequencing of the metastatic nodules demonstrated a significantly hypermutated tumor with rare polyploidy. The patient had a durable (14 months) response and ongoing remission of the metastatic lesions after administering the programmed cell death 1 inhibitor pembrolizumab. No serious immune checkpoint inhibitor-related toxicities or disease progression was observed during the treatment. Conclusion Our report describes recurrent TNBC with a rare amount of hypermutation and the successful use of an IO agent as a treatment.
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Affiliation(s)
- Emilie Platteter
- Phase One Cancer Clinical Trials, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Gerburg Wulf
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA, USA
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Suzuki M, Kasajima R, Yokose T, Shimizu E, Hatakeyama S, Yamaguchi K, Yokoyama K, Katayama K, Yamaguchi R, Furukawa Y, Miyano S, Imoto S, Shinozaki-Ushiku A, Ushiku T, Miyagi Y. KMT2C expression and DNA homologous recombination repair factors in lung cancers with a high-grade fetal adenocarcinoma component. Transl Lung Cancer Res 2023; 12:1738-1751. [PMID: 37691868 PMCID: PMC10483084 DOI: 10.21037/tlcr-23-137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/20/2023] [Indexed: 09/12/2023]
Abstract
Background High-grade fetal adenocarcinoma of the lung (H-FLAC) is a rare variant of pulmonary adenocarcinoma. Our previous study showed a high frequency of KMT2C mutations in lung cancers with an H-FLAC component, showing that KMT2C dysfunction may be associated with the biological features of H-FLACs. Methods In this study, we performed RNA sequencing and immunohistochemical analysis to identify the differentially expressed genes and corresponding pathways associated with H-FLACs, compared with common adenocarcinomas. Results Ingenuity pathway analysis based on RNA sequencing data revealed that DNA homologous recombination repair (HRR) pathways were significantly inactivated in H-FLAC. Expression of KMT2C, ATM, ATR, and BRCA2 was significantly lower in H-FLACs than in common adenocarcinomas, and BRCA1 expression showed a decreasing trend. Pearson correlation analyses for all cases revealed that KMT2C expression showed a strong positive correlation (R>0.7) with the expression of ATR, BRCA1, and BRCA2 genes and a moderately positive correlation with ATM expression (R=0.47). Immunohistochemical analysis showed significantly lower levels of KMT2C, ATM, ATR, and BRCA2 expression in H-FLACs than in common adenocarcinomas, and a trend of lower BRCA1 levels. Additionally, KMT2C expression showed a weak to moderate correlation with that of ATM, ATR, BRCA1, and BRCA2. Conclusions Cancers containing H-FLAC components showed lower levels of KMT2C and HRR factors than common lung adenocarcinomas, and their levels exhibited a positive correlation. These results support the hypothesis that loss of KMT2C function decreases the expression of the HRR factors in H-FLACs. H-FLACs with low KMT2C expression may be a good indication for poly (ADP-ribose) polymerase (PARP) inhibitor-based therapy.
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Affiliation(s)
- Masaki Suzuki
- Department of Pathology, The University of Tokyo, Tokyo, Japan
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Japan
| | - Rika Kasajima
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Japan
| | - Eigo Shimizu
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seira Hatakeyama
- Division of Clinical Genome Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuaki Yokoyama
- Department of Hematology/Oncology, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotoe Katayama
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Rui Yamaguchi
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Cancer Systems Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Informatics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Integrated Data Science, Medical and Dental Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Tetsuo Ushiku
- Department of Pathology, The University of Tokyo, Tokyo, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
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Menon V, Brash DE. Next-generation sequencing methodologies to detect low-frequency mutations: "Catch me if you can". MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108471. [PMID: 37716438 PMCID: PMC10843083 DOI: 10.1016/j.mrrev.2023.108471] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
Mutations, the irreversible changes in an organism's DNA sequence, are present in tissues at a variant allele frequency (VAF) ranging from ∼10-8 per bp for a founder mutation to ∼10-3 for a histologically normal tissue sample containing several independent clones - compared to 1%- 50% for a heterozygous tumor mutation or a polymorphism. The rarity of these events poses a challenge for accurate clinical diagnosis and prognosis, toxicology, and discovering new disease etiologies. Standard Next-Generation Sequencing (NGS) technologies report VAFs as low as 0.5% per nt, but reliably observing rarer precursor events requires additional sophistication to measure ultralow-frequency mutations. We detail the challenge; define terms used to characterize the results, which vary between laboratories and sometimes conflict between biologists and bioinformaticists; and describe recent innovations to improve standard NGS methodologies including: single-strand consensus sequence methods such as Safe-SeqS and SiMSen-Seq; tandem-strand consensus sequence methods such as o2n-Seq and SMM-Seq; and ultrasensitive parent-strand consensus sequence methods such as DuplexSeq, PacBio HiFi, SinoDuplex, OPUSeq, EcoSeq, BotSeqS, Hawk-Seq, NanoSeq, SaferSeq, and CODEC. Practical applications are also noted. Several methods quantify VAF down to 10-5 at a nt and mutation frequency (MF) in a target region down to 10-7 per nt. By expanding to > 1 Mb of sites never observed twice, thus forgoing VAF, other methods quantify MF < 10-9 per nt or < 15 errors per haploid genome. Clonal expansion cannot be directly distinguished from independent mutations by sequencing, so it is essential for a paper to report whether its MF counted only different mutations - the minimum independent-mutation frequency MFminI - or all mutations observed including recurrences - the larger maximum independent-mutation frequency MFmaxI which may reflect clonal expansion. Ultrasensitive methods reveal that, without their use, even mutations with VAF 0.5-1% are usually spurious.
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Affiliation(s)
- Vijay Menon
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA.
| | - Douglas E Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA; Department of Dermatology, Yale School of Medicine, New Haven, CT 06520-8059, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520-8028, USA.
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Venetis K, Sajjadi E, Ivanova M, Peccatori FA, Fusco N, Guerini-Rocco E. Characterization of the immune environment in pregnancy-associated breast cancer. Future Oncol 2023. [PMID: 37376974 DOI: 10.2217/fon-2022-1321] [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: 06/29/2023] Open
Abstract
Pregnancy-associated breast cancer (PrBC) is a rare and clinically challenging condition. Specific immune mechanisms and pathways are involved in maternal-fetal tolerance and tumor-host immunoediting. The comprehension of the molecular processes underpinning this immune synergy in PrBC is needed to improve patients' clinical management. Only a few studies focused on the immune biology of PrBC and attempted to identify bona fide biomarkers. Therefore, clinically actionable information remains extremely puzzling for these patients. In this review article, we discuss the current knowledge on the immune environment of PrBC, in comparison with pregnancy-unrelated breast cancer and in the context of maternal immune changes during pregnancy. A particular emphasis is given to the actual role of potential immune-related biomarkers for PrBC clinical management.
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Affiliation(s)
- Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Fedro Alessandro Peccatori
- Fertility & Procreation Unit, Division of Gynecologic Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
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Ban D, Housley SN, McDonald JF. The Clinical Significance of Genetic Variation in Ovarian Cancer. Int J Mol Sci 2023; 24:10823. [PMID: 37446001 DOI: 10.3390/ijms241310823] [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: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Genetic variation is a well-known contributor to the onset and progression of cancer. The goal of this study is to provide a comprehensive examination of the nucleotide and chromosomal variation associated with the onset and progression of serous ovarian cancer. Using a variety of computational and statistical methods, we examine the exome sequence profiles of genetic variants present in the primary tumors of 432 ovarian cancer patient samples to compute: (1) the tumor mutational burden for all genes and (2) the chromosomal copy number alterations associated with the onset/progression of ovarian cancer. Tumor mutational burden is reduced in the late vs. early stages, with the highest levels being associated with loss-of-function mutations in DNA-repair genes. Nucleotide variation and copy number alterations associated with known cancer driver genes are selectively favored over ovarian cancer development. The results indicate that genetic variation is a significant contributor to the onset and progression of ovarian cancer. The measurement of the relative levels of genetic variation associated with individual ovarian cancer patient tumors may be a clinically valuable predictor of potential tumor aggressiveness and resistance to chemotherapy. Tumors found to be associated with high levels of genetic variation may help in the clinical identification of high-risk ovarian cancer patients who could benefit from more frequent monitoring.
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Affiliation(s)
- Dongjo Ban
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - Stephen N Housley
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
| | - John F McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30332, USA
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Zhu Y, Duong L, Lu X, Lu X. Cancer-cell-intrinsic mechanisms shaping the immunosuppressive landscape of prostate cancer. Asian J Androl 2023; 25:171-178. [PMID: 36367020 PMCID: PMC10069702 DOI: 10.4103/aja202283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022] Open
Abstract
Although immunotherapy has revolutionized cancer treatment and achieved remarkable success across many different cancer types, only a subset of patients shows meaningful clinical responses. In particular, advanced prostate cancer exhibits overwhelming de novo resistance to immune checkpoint blockade therapy. This is primarily due to the immunosuppressive tumor microenvironment of prostate cancer. Therefore, it is paramount to understand how prostate cancer cell-intrinsic mechanisms promote immune evasion and foster an immunosuppressive microenvironment. Here, we review recent findings that reveal the roles of the genetic alterations, androgen receptor signaling, cancer cell plasticity, and oncogenic pathways in shaping the immunosuppressive microenvironment and thereby driving immunotherapy resistance. Based on preclinical and clinical observations, a variety of therapeutic strategies are being developed that may illuminate new paths to enhance immunotherapy efficacy in prostate cancer.
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Affiliation(s)
- Yini Zhu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Loan Duong
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xuemin Lu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xin Lu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN 46556, USA
- Tumor Microenvironment and Metastasis Program, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
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Predicting tumour radiosensitivity to deliver precision radiotherapy. Nat Rev Clin Oncol 2023; 20:83-98. [PMID: 36477705 DOI: 10.1038/s41571-022-00709-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
Abstract
Owing to advances in radiotherapy, the physical properties of radiation can be optimized to enable individualized treatment; however, optimization is rarely based on biological properties and, therefore, treatments are generally planned with the assumption that all tumours respond similarly to radiation. Radiation affects multiple cellular pathways, including DNA damage, hypoxia, proliferation, stem cell phenotype and immune response. In this Review, we summarize the effect of these pathways on tumour responses to radiotherapy and the current state of research on genomic classifiers designed to exploit these variations to inform treatment decisions. We also discuss whether advances in genomics have generated evidence that could be practice changing and whether advances in genomics are now ready to be used to guide the delivery of radiotherapy alone or in combination.
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Valentini V, Silvestri V, Bucalo A, Conti G, Karimi M, Di Francesco L, Pomati G, Mezi S, Cerbelli B, Pignataro MG, Nicolussi A, Coppa A, D’Amati G, Giannini G, Ottini L. Molecular profiling of male breast cancer by multigene panel testing: Implications for precision oncology. Front Oncol 2023; 12:1092201. [PMID: 36686738 PMCID: PMC9854133 DOI: 10.3389/fonc.2022.1092201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Compared with breast cancer (BC) in women, BC in men is a rare disease with genetic and molecular peculiarities. Therapeutic approaches for male BC (MBC) are currently extrapolated from the clinical management of female BC, although the disease does not exactly overlap in males and females. Data on specific molecular biomarkers in MBC are lacking, cutting out male patients from more appropriate therapeutic strategies. Growing evidence indicates that Next Generation Sequencing (NGS) multigene panel testing can be used for the detection of predictive molecular biomarkers, including Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI). Methods In this study, NGS multigene gene panel sequencing, targeting 1.94 Mb of the genome at 523 cancer-relevant genes (TruSight Oncology 500, Illumina), was used to identify and characterize somatic variants, Copy Number Variations (CNVs), TMB and MSI, in 15 Formalin-Fixed Paraffin-Embedded (FFPE) male breast cancer samples. Results and discussion A total of 40 pathogenic variants were detected in 24 genes. All MBC cases harbored at least one pathogenic variant. PIK3CA was the most frequently mutated gene, with six (40.0%) MBCs harboring targetable PIK3CA alterations. CNVs analysis showed copy number gains in 22 genes. No copy number losses were found. Specifically, 13 (86.7%) MBCs showed gene copy number gains. MYC was the most frequently amplified gene with eight (53.3%) MBCs showing a median fold-changes value of 1.9 (range 1.8-3.8). A median TMB value of 4.3 (range 0.8-12.3) mut/Mb was observed, with two (13%) MBCs showing high-TMB. The median percentage of MSI was 2.4% (range 0-17.6%), with two (13%) MBCs showing high-MSI. Overall, these results indicate that NGS multigene panel sequencing can provide a comprehensive molecular tumor profiling in MBC. The identification of targetable molecular alterations in more than 70% of MBCs suggests that the NGS approach may allow for the selection of MBC patients eligible for precision/targeted therapy.
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Affiliation(s)
- Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Agostino Bucalo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giulia Conti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Mina Karimi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Linda Di Francesco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giulia Pomati
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Silvia Mezi
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Bruna Cerbelli
- Department of Medical-Surgical Sciences and Biotechnologies Sapienza University of Rome, Rome, Italy
| | - Maria Gemma Pignataro
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Arianna Nicolussi
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Giulia D’Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy,Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy,*Correspondence: Laura Ottini,
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Vázquez-Romo R, Millan-Catalan O, Ruíz-García E, Martínez-Gutiérrez AD, Alvarado-Miranda A, Campos-Parra AD, López-Camarillo C, Jacobo-Herrera N, López-Urrutia E, Guardado-Estrada M, Cantú de León D, Pérez-Plasencia C. Pathogenic variant profile in DNA damage response genes correlates with metastatic breast cancer progression-free survival in a Mexican-mestizo population. Front Oncol 2023; 13:1146008. [PMID: 37182128 PMCID: PMC10174330 DOI: 10.3389/fonc.2023.1146008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/14/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Metastatic breast cancer causes the most breast cancer-related deaths around the world, especially in countries where breast cancer is detected late into its development. Genetic testing for cancer susceptibility started with the BRCA 1 and 2 genes. Still, recent research has shown that variations in other members of the DNA damage response (DDR) are also associated with elevated cancer risk, opening new opportunities for enhanced genetic testing strategies. Methods We sequenced BRCA1/2 and twelve other DDR genes from a Mexican-mestizo population of 40 metastatic breast cancer patients through semiconductor sequencing. Results Overall, we found 22 variants -9 of them reported for the first time- and a strikingly high proportion of variations in ARID1A. The presence of at least one variant in the ARID1A, BRCA1, BRCA2, or FANCA genes was associated with worse progression-free survival and overall survival in our patient cohort. Discussion Our results reflected the unique characteristics of the Mexican-mestizo population as the proportion of variants we found differed from that of other global populations. Based on these findings, we suggest routine screening for variants in ARID1A along with BRCA1/2 in breast cancer patients from the Mexican-mestizo population.
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Affiliation(s)
- Rafael Vázquez-Romo
- Departamento de Cirugía de Tumores Mamarios, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
| | - Oliver Millan-Catalan
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
| | - Erika Ruíz-García
- Laboratorio de Medicina Traslacional y Departamento de Tumores Gastrointestinales, Instituto Nacional de Cancerología, CDMX, Mexico
| | | | - Alberto Alvarado-Miranda
- Departamento de Cirugía de Tumores Mamarios, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
| | - Alma D. Campos-Parra
- Dirección de Investigación, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, Mexico
| | - Nadia Jacobo-Herrera
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador Zubirán (INCMNSZ), Ciudad de México, Mexico
| | - Eduardo López-Urrutia
- Laboratorio de Genómica, Unidad de Biomedicina, FES-IZTACALA, UNAM, Tlalnepantla, Mexico
| | - Mariano Guardado-Estrada
- Laboratorio de Genética, Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - David Cantú de León
- Dirección de Investigación, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
- *Correspondence: David Cantú de León, ; Carlos Pérez-Plasencia,
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, Instituto Nacional de Cancerología (INCan), Ciudad de México, Mexico
- Laboratorio de Genómica, Unidad de Biomedicina, FES-IZTACALA, UNAM, Tlalnepantla, Mexico
- *Correspondence: David Cantú de León, ; Carlos Pérez-Plasencia,
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Shi C, Qin K, Lin A, Jiang A, Cheng Q, Liu Z, Zhang J, Luo P. The role of DNA damage repair (DDR) system in response to immune checkpoint inhibitor (ICI) therapy. J Exp Clin Cancer Res 2022; 41:268. [PMID: 36071479 PMCID: PMC9450390 DOI: 10.1186/s13046-022-02469-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
As our understanding of the mechanisms of cancer treatment has increased, a growing number of studies demonstrate pathways through which DNA damage repair (DDR) affects the immune system. At the same time, the varied response of patients to immune checkpoint blockade (ICB) therapy has prompted the discovery of various predictive biomarkers and the study of combination therapy. Here, our investigation explores the interactions involved in combination therapy, accompanied by a review that summarizes currently identified and promising predictors of response to immune checkpoint inhibitors (ICIs) that are useful for classifying oncology patients. In addition, this work, which discusses immunogenicity and several components of the tumor immune microenvironment, serves to illustrate the mechanism by which higher response rates and improved efficacy of DDR inhibitors (DDRi) in combination with ICIs are achieved.
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Pinilla K, Drewett LM, Lucey R, Abraham JE. Precision Breast Cancer Medicine: Early Stage Triple Negative Breast Cancer-A Review of Molecular Characterisation, Therapeutic Targets and Future Trends. Front Oncol 2022; 12:866889. [PMID: 36003779 PMCID: PMC9393396 DOI: 10.3389/fonc.2022.866889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Personalised approaches to the management of all solid tumours are increasing rapidly, along with wider accessibility for clinicians. Advances in tumour characterisation and targeted therapies have placed triple-negative breast cancers (TNBC) at the forefront of this approach. TNBC is a highly heterogeneous disease with various histopathological features and is driven by distinct molecular alterations. The ability to tailor individualised and effective treatments for each patient is of particular importance in this group due to the high risk of distant recurrence and death. The mainstay of treatment across all subtypes of TNBC has historically been cytotoxic chemotherapy, which is often associated with off-target tissue toxicity and drug resistance. Neoadjuvant chemotherapy is commonly used as it allows close monitoring of early treatment response and provides valuable prognostic information. Patients who achieve a complete pathological response after neoadjuvant chemotherapy are known to have significantly improved long-term outcomes. Conversely, poor responders face a higher risk of relapse and death. The identification of those subgroups that are more likely to benefit from breakthroughs in the personalised approach is a challenge of the current era where several targeted therapies are available. This review presents an overview of contemporary practice, and promising future trends in the management of early TNBC. Platinum chemotherapy, DNA damage response (DDR) inhibitors, immune checkpoint inhibitors, inhibitors of the PI3K-AKT-mTOR, and androgen receptor (AR) pathways are some of the increasingly studied therapies which will be reviewed. We will also discuss the growing evidence for less-developed agents and predictive biomarkers that are likely to contribute to the forthcoming advances in this field. Finally, we will propose a framework for the personalised management of TNBC based upon the integration of clinico-pathological and molecular features to ensure that long-term outcomes are optimised.
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Affiliation(s)
- Karen Pinilla
- Precision Breast Cancer Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Lynsey M. Drewett
- Precision Breast Cancer Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Rebecca Lucey
- Precision Breast Cancer Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Jean E. Abraham
- Precision Breast Cancer Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
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13
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Scandolara TB, Valle SF, Esteves C, Scherer NDM, de Armas EM, Furtado C, Gomes R, Boroni M, Jaques HDS, Alves FM, Rech D, Panis C, Bonvicino CR. Somatic DNA Damage Response and Homologous Repair Gene Alterations and Its Association With Tumor Variant Burden in Breast Cancer Patients With Occupational Exposure to Pesticides. Front Oncol 2022; 12:904813. [PMID: 35875117 PMCID: PMC9305859 DOI: 10.3389/fonc.2022.904813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Homologous recombination is a crucial pathway that is specialized in repairing double-strand breaks; thus, alterations in genes of this pathway may lead to loss of genomic stability and cell growth suppression. Pesticide exposure potentially increases cancer risk through several mechanisms, such as the genotoxicity caused by chronic exposure, leading to gene alteration. To analyze this hypothesis, we investigated if breast cancer patients exposed to pesticides present a different mutational pattern in genes related to homologous recombination (BRCA1, BRCA2, PALB2, and RAD51D) and damage-response (TP53) concerning unexposed patients. We performed multiplex PCR-based assays and next-generation sequencing (NGS) of all coding regions and flanking splicing sites of BRCA1, BRCA2, PALB2, TP53, and RAD51D in 158 unpaired tumor samples from breast cancer patients on MiSeq (Illumina) platform. We found that exposed patients had tumors with more pathogenic and likely pathogenic variants than unexposed patients (p = 0.017). In general, tumors that harbored a pathogenic or likely pathogenic variant had a higher mutational burden (p < 0.001). We also observed that breast cancer patients exposed to pesticides had a higher mutational burden when diagnosed before 50 years old (p = 0.00978) and/or when carrying BRCA1 (p = 0.0138), BRCA2 (p = 0.0366), and/or PALB2 (p = 0.00058) variants, a result not found in the unexposed group. Our results show that pesticide exposure impacts the tumor mutational landscape and could be associated with the carcinogenesis process, therapy response, and disease progression. Further studies should increase the observation period in exposed patients to better evaluate the impact of these findings.
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Affiliation(s)
- Thalita Basso Scandolara
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Ferreira Valle
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane Esteves
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Nicole de Miranda Scherer
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Elvismary Molina de Armas
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
- Department of Informatics, Pontificia Universidade Católica (PUC)-Rio, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Renan Gomes
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | - Mariana Boroni
- Bioinformatics and Computational Biology Laboratory, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
| | | | - Fernanda Mara Alves
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
| | - Daniel Rech
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
- Francisco Beltrão Cancer Hospital, Francisco Beltrão, Brazil
| | - Carolina Panis
- Laboratory of Tumor Biology, State University of West Paraná, Francisco Beltrão, Brazil
| | - Cibele Rodrigues Bonvicino
- Department of Genetics, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Division of Genetics, Instituto Nacional de Câncer José Alencar Gomes da Silva (INCA), Rio de Janeiro, Brazil
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14
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Santa-Maria CA, Dunn SA, Ho AY. Immunotherapy Combined with Radiation Therapy in Breast Cancer: A Rapidly Evolving Landscape. Semin Radiat Oncol 2022; 32:291-297. [DOI: 10.1016/j.semradonc.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Zaarour RF, Sharda M, Azakir B, Hassan Venkatesh G, Abou Khouzam R, Rifath A, Nizami ZN, Abdullah F, Mohammad F, Karaali H, Nawafleh H, Elsayed Y, Chouaib S. Genomic Analysis of Waterpipe Smoke-Induced Lung Tumor Autophagy and Plasticity. Int J Mol Sci 2022; 23:ijms23126848. [PMID: 35743294 PMCID: PMC9225041 DOI: 10.3390/ijms23126848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
The role of autophagy in lung cancer cells exposed to waterpipe smoke (WPS) is not known. Because of the important role of autophagy in tumor resistance and progression, we investigated its relationship with WP smoking. We first showed that WPS activated autophagy, as reflected by LC3 processing, in lung cancer cell lines. The autophagy response in smokers with lung adenocarcinoma, as compared to non-smokers with lung adenocarcinoma, was investigated further using the TCGA lung adenocarcinoma bulk RNA-seq dataset with the available patient metadata on smoking status. The results, based on a machine learning classification model using Random Forest, indicate that smokers have an increase in autophagy-activating genes. Comparative analysis of lung adenocarcinoma molecular signatures in affected patients with a long-term active exposure to smoke compared to non-smoker patients indicates a higher tumor mutational burden, a higher CD8+ T-cell level and a lower dysfunction level in smokers. While the expression of the checkpoint genes tested-PD-1, PD-L1, PD-L2 and CTLA-4-remains unchanged between smokers and non-smokers, B7-1, B7-2, IDO1 and CD200R1 were found to be higher in non-smokers than smokers. Because multiple factors in the tumor microenvironment dictate the success of immunotherapy, in addition to the expression of immune checkpoint genes, our analysis explains why patients who are smokers with lung adenocarcinoma respond better to immunotherapy, even though there are no relative differences in immune checkpoint genes in the two groups. Therefore, targeting autophagy in lung adenocarcinoma patients, in combination with checkpoint inhibitor-targeted therapies or chemotherapy, should be considered in smoker patients with lung adenocarcinoma.
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Affiliation(s)
- Rania Faouzi Zaarour
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
| | - Mohak Sharda
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- School of Life Science, The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bangalore 560064, India
| | - Bilal Azakir
- Molecular and Translational Medicine Laboratory, Faculty of Medicine, Beirut Arab University, Beirut 11072809, Lebanon; (B.A.); (H.K.)
| | - Goutham Hassan Venkatesh
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
| | - Raefa Abou Khouzam
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
| | - Ayesha Rifath
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
| | - Zohra Nausheen Nizami
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
| | - Fatima Abdullah
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
| | - Fatin Mohammad
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
| | - Hajar Karaali
- Molecular and Translational Medicine Laboratory, Faculty of Medicine, Beirut Arab University, Beirut 11072809, Lebanon; (B.A.); (H.K.)
| | - Husam Nawafleh
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
| | - Yehya Elsayed
- Department of Biology, Chemistry and Environmental Sciences (BCE), American University of Sharjah, Sharjah 26666, United Arab Emirates;
| | - Salem Chouaib
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; (R.F.Z.); (G.H.V.); (R.A.K.); (A.R.); (Z.N.N.); (F.A.); (F.M.); (H.N.)
- Inserm Umr 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Faculty of Medicine, University Paris-Saclay, 94805 Villejuif, France
- Correspondence:
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16
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Hou Y, Peng Y, Li Z. Update on prognostic and predictive biomarkers of breast cancer. Semin Diagn Pathol 2022; 39:322-332. [PMID: 35752515 DOI: 10.1053/j.semdp.2022.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 11/11/2022]
Abstract
Breast cancer represents a heterogeneous group of human cancer at both histological and molecular levels. Estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) are the most commonly used biomarkers in clinical practice for making treatment plans for breast cancer patients by oncologists. Recently, PD-L1 testing plays an important role for immunotherapy for triple-negative breast cancer. With the increased understanding of the molecular characterization of breast cancer and the emergence of novel targeted therapies, more potential biomarkers are needed for the development of more personalized treatments. In this review, we summarized several main prognostic and predictive biomarkers in breast cancer at genomic, transcriptomic and proteomic levels, including hormone receptors, HER2, Ki67, multiple gene expression assays, PD-L1 testing, mismatch repair deficiency/microsatellite instability, tumor mutational burden, PIK3CA, ESR1 andNTRK and briefly introduced the roles of digital imaging analysis in breast biomarker evaluation.
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Affiliation(s)
- Yanjun Hou
- Department of Pathology, Atrium Health Wake Forest Baptist Medical Center, Winston Salem, NC
| | - Yan Peng
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Zaibo Li
- Department of pathology, The Ohio State University Wexner Medical Center, Columbus OH.
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17
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Weighted Gene Coexpression Network Analysis Identifies TBC1D10C as a New Prognostic Biomarker for Breast Cancer. Anal Cell Pathol 2022; 2022:5259187. [PMID: 35425695 PMCID: PMC9005324 DOI: 10.1155/2022/5259187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 11/30/2021] [Accepted: 03/15/2022] [Indexed: 12/09/2022] Open
Abstract
Background Immune checkpoint inhibitors are a promising therapeutic strategy for breast cancer (BRCA) patients. The tumor microenvironment (TME) can downregulate the immune response to cancer therapy. Our study is aimed at finding a TME-related biomarker to identify patients who might respond to immunotherapy. Method We downloaded raw data from several databases including TCGA and MDACC to identify TME hub genes associated with overall survival (OS) and the progression-free interval (PFI) by WGCNA. Correlations between hub genes and either tumor-infiltrating immune cells or immune checkpoints were conducted by ssGSEA. Result TME-related green and black modules were selected by WGCNA to further screen hub genes. Random forest and univariate and multivariate Cox regressions were applied to screen hub genes (MYO1G, TBC1D10C, SELPLG, and LRRC15) and construct a nomogram to predict the survival of BRCA patients. The C-index for the nomogram was 0.713. A DCA of the predictive model revealed that the net benefit of the nomogram was significantly higher than others and the calibration curve demonstrated a good performance by the nomogram. Only TBC1D10C was correlated with both OS and the PFI (both p values < 0.05). TBC1D10C also had a high positive association with tumor-infiltrating immune cells and common immune checkpoints (PD-1, CTLA-4, and TIGIT). Conclusion We constructed a TME-related gene signature model to predict the survival probability of BRCA patients. We also identified a hub gene, TBC1D10C, which was correlated with both OS and the PFI and had a high positive association with tumor-infiltrating immune cells and common immune checkpoints. TBC1D10C may be a new biomarker to select patients who may benefit from immunotherapy.
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18
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Disis ML, Cecil DL. Breast cancer vaccines for treatment and prevention. Breast Cancer Res Treat 2021; 191:481-489. [PMID: 34846625 DOI: 10.1007/s10549-021-06459-2] [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: 04/06/2021] [Accepted: 11/15/2021] [Indexed: 12/22/2022]
Abstract
Breast cancer is immunogenic and a variety of vaccines have been designed to boost immunity directed against the disease. The components of a breast cancer vaccine, the antigen, the delivery system, and the adjuvant, can have a significant impact on vaccine immunogenicity. There have been numerous immunogenic proteins identified in all subtypes of breast cancer. The majority of these antigens are weakly immunogenic nonmutated tumor-associated proteins. Mutated proteins and neoantigen epitopes are found only in a small minority of patients and are enriched in the triple negative subtype. Several vaccines have advanced to large randomized Phase II or Phase III clinical trials. None of these trials met their primary endpoint of either progression-free or overall survival. Despite these set-backs investigators have learned important lessons regarding the clinical application of breast cancer vaccines from the type of immune response needed for tumor eradication, Type I T-cell immunity, to the patient populations most likely to benefit from vaccination. Many therapeutic breast cancer vaccines are now being tested in combination with other forms of immune therapy or chemotherapy and radiation. Breast cancer vaccines as single agents are now studied in the context of the prevention of relapse or development of disease. Newer approaches are designing vaccines to prevent breast cancer by intercepting high-risk lesions such as ductal carcinoma in situ to limit the progression of these tumors to invasive cancer. There are also several efforts to develop vaccines for the primary prevention of breast cancer by targeting antigens expressed during breast cancer initiation.
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Affiliation(s)
- Mary L Disis
- Cancer Vaccine Institute, University of Washington, Seattle, WA, USA.
| | - Denise L Cecil
- Cancer Vaccine Institute, University of Washington, Seattle, WA, USA
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19
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Henriques B, Mendes F, Martins D. Immunotherapy in Breast Cancer: When, How, and What Challenges? Biomedicines 2021; 9:1687. [PMID: 34829916 PMCID: PMC8616011 DOI: 10.3390/biomedicines9111687] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022] Open
Abstract
Breast Cancer (BC) is the second most frequent cause of cancer death among women worldwide and, although there have been significant advances in BC therapies, a significant percentage of patients develop metastasis and disease recurrence. Since BC was demonstrated to be an immunogenic tumor, immunotherapy has broken through as a significant therapy strategy against BC. Over the years, immunotherapy has improved the survival rate of HER2+ BC patients due to the approval of some monoclonal antibodies (mAbs) such as Trastuzumab, Pertuzumab and, recently, Margetuximab, along with the antibody-drug conjugates (ADC) Trastuzumab-Emtansine (T-DM1) and Trastuzumab Deruxtecan. Immune checkpoint inhibitors (ICI) showed promising efficacy in triple-negative breast cancer (TNBC) treatment, namely Atezolizumab and Pembrolizumab. Despite the success of immunotherapy, some patients do not respond to immunotherapy or those who respond to the treatment relapse or progress. The main causes of these adverse events are the complex, intrinsic or extrinsic resistance mechanisms. In this review, we address the different immunotherapy approaches approved for BC and some of the mechanisms responsible for resistance to immunotherapy.
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Affiliation(s)
- Beatriz Henriques
- Politécnico de Coimbra, ESTeSC, UCPCBL, 3046-854 Coimbra, Portugal; (B.H.); (F.M.)
| | - Fernando Mendes
- Politécnico de Coimbra, ESTeSC, UCPCBL, 3046-854 Coimbra, Portugal; (B.H.); (F.M.)
- Laboratório de Investigação em Ciências Aplicadas à Saúde (LabinSaúde), Politécnico de Coimbra, ESTESC, 3046-854 Coimbra, Portugal
- Biophysics Institute of Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-504 Coimbra, Portugal
- European Association for Professions in Biomedical Sciences, B-1000 Brussels, Belgium
| | - Diana Martins
- Politécnico de Coimbra, ESTeSC, UCPCBL, 3046-854 Coimbra, Portugal; (B.H.); (F.M.)
- Laboratório de Investigação em Ciências Aplicadas à Saúde (LabinSaúde), Politécnico de Coimbra, ESTESC, 3046-854 Coimbra, Portugal
- Biophysics Institute of Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-504 Coimbra, Portugal
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20
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Using Genomic and Transcriptome Analyses to Identify the Role of the Oxidative Stress Pathway in Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5561124. [PMID: 34721758 PMCID: PMC8550864 DOI: 10.1155/2021/5561124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/31/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022]
Abstract
Oxidative stress (OS) refers to endogenous and/or exogenous stimulation when the balance between oxidation and antioxidants in the body is disrupted, resulting in excessive production of free radicals. Excessive free radicals exert a series of negative effects on the body, which can result in the oxidation of and infliction of damage on biological molecules and further cause cell death and tissue damage, which are related to many pathological processes. Pathways related to OS have always been the focus of medical research. Several studies are being conducted to develop strategies to treat cancer by exploring the OS pathways. Therefore, this study is aimed at determining the correlation between the OS pathway and kidney renal clear cell carcinoma (KIRC) through bioinformatics analysis, at proving the effect of common anticancer drugs on the OS pathway, and at constructing a prognosis model of patients with KIRC based on several genes with the strongest correlation between the OS pathway and KIRC. We first collected and analyzed gene expression and clinical information of related patients through TCGA database. Then, we divided the samples into three clusters according to their gene expression levels obtained through cluster analysis. Using these three clusters, we performed GDSC drug analysis and GSEA analysis and examined the correlation among the OS pathway, histone modification, and immune cell infiltration. We also analyzed the response of anti-PD-1 and anti-CTLA-4 to the OS pathway. Thereafter, we used LASSO regression to select the most suitable nine genes, combined with the clinicopathological characteristics to establish the prognosis model of patients with KIRC, and verified the scientific precision of the model. Finally, tumor mutational burden was calculated to verify whether patients would benefit from immunotherapy. The results of this study may provide a reference for the establishment of treatment strategies for patients with KIRC.
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21
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Cerniglia M, Xiu J, Grothey A, Pishvaian MJ, Baca Y, Hwang JJ, Marshall JL, VanderWalde AM, Shields AF, Lenz HJ, Korn WM, Salem M, Philip PA, Goldberg RM, Zeng J, Kim SS. Association of Homologous Recombination-DNA Damage Response Gene Mutations with Immune Biomarkers in Gastroesophageal Cancers. Mol Cancer Ther 2021; 21:227-236. [PMID: 34725190 DOI: 10.1158/1535-7163.mct-20-0879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/29/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022]
Abstract
The prevalence of homologous recombination-DNA damage response (HR-DDR) genetic alterations is of therapeutic interest in gastroesophageal cancers. This study is a comprehensive assessment of HR-DDR mutation prevalence across gastroesophageal adenocarcinomas and squamous cell carcinomas. Here we investigate the association of HR-DDR mutations with known predictors for immune-checkpoint inhibition [deficiency in mismatch-repair (dMMRP), tumor mutational burden (TMB), and programmed death ligand 1 (PD-L1)]. We confirmed HR-DDR mutations are present in a subset of gastroesophageal adenocarcinomas (23%) and gastroesophageal squamous cell carcinomas (20%). Biomarker expression of dMMRP (18% vs. 1%) and TMB-high with a cutoff of ≥10 mt/MB (27% vs. 9%) was significantly more prevalent in the DDR-mutated cohort compared with the non-DDR-mutated cohort. Mean combined positive score for PD-L1 in the total adenocarcinoma cohort was significantly higher in the DDR-mutated cohort compared with the non-DDR-mutated cohort (10.1 vs. 5.8). We demonstrated that alterations in ARID1A, BRCA2, PTEN, and ATM are correlated with dMMRP, TMB-high, and increased PD-L1 expression in gastroesophageal adenocarcinomas. Our findings show that a subset of gastroesophageal tumors harbor HR-DDR mutations correlated with established immune biomarkers. By better understanding the relationship between HR-DDR mutations and immune biomarkers, we may be able to develop better immunotherapy combination strategies to target these tumors.
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Affiliation(s)
| | | | | | - Michael J Pishvaian
- NCR Kimmel Cancer Center, Sibley Memorial Hospital and Johns Hopkins University School of Medicine, Washington, District of Columbia
| | | | - Jimmy J Hwang
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, North Carolina
| | - John L Marshall
- Ruesch Center for The Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | | | - Anthony F Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of, Medicine, University of Southern California, Los Angeles, California
| | | | - Mohamed Salem
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, North Carolina
| | - Philip A Philip
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | | | - Jia Zeng
- Caris Life Sciences, Phoenix, Arizona
| | - Sunnie S Kim
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, Colorado.
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22
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Kinget L, Bechter O, Punie K, Debruyne PR, Brems H, Clement P, Roussel E, Van Herck Y, Albersen M, Baldewijns M, Schöffski P, Beuselinck B. Multitumor Case Series of Germline BRCA1, BRCA2 and CHEK2-Mutated Patients Responding Favorably on Immune Checkpoint Inhibitors. ACTA ACUST UNITED AC 2021; 28:3227-3239. [PMID: 34449592 PMCID: PMC8395488 DOI: 10.3390/curroncol28050280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022]
Abstract
In recent years, immune checkpoint inhibitors (ICPI) have become widely used for multiple solid malignancies. Reliable predictive biomarkers for selection of patients who would benefit most are lacking. Several tumor types with somatic or germline alterations in genes involved in the DNA damage response (DDR) pathway harbor a higher tumor mutational burden, possibly associated with an increased tumoral neoantigen load. These neoantigens are thought to lead to stronger immune activation and enhanced response to ICPIs. We present a series of seven patients with different malignancies with germline disease-associated variants in DDR genes (BRCA1, BRCA2, CHEK2) responding favorably to ICPIs.
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Affiliation(s)
- Lisa Kinget
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (L.K.); (O.B.); (K.P.); (P.C.); (Y.V.H.); (P.S.)
| | - Oliver Bechter
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (L.K.); (O.B.); (K.P.); (P.C.); (Y.V.H.); (P.S.)
| | - Kevin Punie
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (L.K.); (O.B.); (K.P.); (P.C.); (Y.V.H.); (P.S.)
| | - Philip R. Debruyne
- Department of General Medical Oncology, AZ Groeninge, 8500 Kortrijk, Belgium;
- Medical Technology Research Centre (MTRC), School of Life Sciences, Faculty of Science and Engineering, Anglia Ruskin University, Cambridge CB1 1PT, UK
| | - Hilde Brems
- Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium;
| | - Paul Clement
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (L.K.); (O.B.); (K.P.); (P.C.); (Y.V.H.); (P.S.)
| | - Eduard Roussel
- Department of Urology, University Hospitals Leuven, 3000 Leuven, Belgium; (E.R.); (M.A.)
| | - Yannick Van Herck
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (L.K.); (O.B.); (K.P.); (P.C.); (Y.V.H.); (P.S.)
| | - Maarten Albersen
- Department of Urology, University Hospitals Leuven, 3000 Leuven, Belgium; (E.R.); (M.A.)
| | | | - Patrick Schöffski
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (L.K.); (O.B.); (K.P.); (P.C.); (Y.V.H.); (P.S.)
| | - Benoit Beuselinck
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (L.K.); (O.B.); (K.P.); (P.C.); (Y.V.H.); (P.S.)
- Correspondence: ; Tel.: +32-1634-6900
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Jones TE, Zou J, Tseng GC, Roy S, Bhargava R. The Utility of Next-Generation Sequencing in Advanced Breast and Gynecologic Cancers. Am J Clin Pathol 2021; 156:455-460. [PMID: 33728425 DOI: 10.1093/ajcp/aqaa256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Next-generation sequencing (NGS) has the potential to identify genetic alterations that are actionable with targeted therapy. Our objective was to identify the impact of NGS testing on advanced breast and gynecologic malignancies. METHODS A retrospective review of 108 patients who underwent NGS testing between 2015 and 2019 was performed. The NGS clinical action rate was calculated based on documentation of positive clinical action taken in cases with an actionable NGS result. RESULTS The 108 specimens tested included 35 breast cancers and 73 gynecologic malignancies, with most of the testing performed at Foundation Medicine (90%). Actionable mutation(s) were identified in 79 (73%) of 108 cases. The overall clinical action rate of NGS testing was 38% (30 of 79 cases). Overall, 47 (44%) of 108 patients died, all succumbing to disease. The average survival was 10.9 months. The survival difference between patients with actionable NGS result and targeted treatment, actionable NGS result but no targeted treatment, and patients with nonactionable NGS result was not significant (log-rank test, P = .5160). CONCLUSIONS NGS testing for advanced breast and gynecologic cancers at our institution has a 38% clinical action rate. However, the increased clinical action rate over the years did not translate into improved survival.
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Affiliation(s)
- Terrell E Jones
- Department of Pathology, Presbyterian University Hospital, Pittsburgh, PA, USA
| | - Jian Zou
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Somak Roy
- Department of Pathology, Presbyterian University Hospital, Pittsburgh, PA, USA
| | - Rohit Bhargava
- Department of Pathology, Magee-Womens Hospital, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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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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25
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Chiu TY, Lin RW, Huang CJ, Yeh DW, Wang YC. DNA Damage Repair Gene Set as a Potential Biomarker for Stratifying Patients with High Tumor Mutational Burden. BIOLOGY 2021; 10:biology10060528. [PMID: 34198473 PMCID: PMC8231881 DOI: 10.3390/biology10060528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 01/06/2023]
Abstract
Simple Summary Immunotherapy has been a promising therapeutic approach for cancer treatment in recent years. Although cancer immunotherapy has achieved remarkable success, treatment response is only observed in a small number of patients. As nonresponders need to endure high treatment costs and toxicities with little benefit from treatment, identifying potential predictive biomarkers is critical to optimize the benefits of immunotherapy in patients. The total number of mutations in the tumor genome is a useful biomarker. Patients with a large number of mutations tend to respond better to cancer immunotherapy. However, assessment of the total number of mutations may not be easy. In this study, we identified gene sets with only a small number of genes whose mutations serve as an indicator of the total number of mutations. These cancer-specific gene sets can be used as a cost-effective approach to stratify patients with a large number of mutations in clinical practice. Abstract Tumor mutational burden (TMB) is a promising predictive biomarker for cancer immunotherapy. Patients with a high TMB have better responses to immune checkpoint inhibitors. Currently, the gold standard for determining TMB is whole-exome sequencing (WES). However, high cost, long turnaround time, infrastructure requirements, and bioinformatics demands have prevented WES from being implemented in routine clinical practice. Panel-sequencing-based estimates of TMB have gradually replaced WES TMB; however, panel design biases could lead to overestimation of TMB. To stratify TMB-high patients better without sequencing all genes and avoid overestimating TMB, we focused on DNA damage repair (DDR) genes, in which dysfunction may increase somatic mutation rates. We extensively explored the association between the mutation status of DDR genes and TMB in different cancer types. By analyzing the mutation data from The Cancer Genome Atlas, which includes information for 33 different cancer types, we observed no single DDR gene/pathway in which mutation status was significantly associated with high TMB across all 33 cancer types. Therefore, a computational algorithm was proposed to identify a cancer-specific gene set as a surrogate for stratifying patients with high TMB in each cancer. We applied our algorithm to skin cutaneous melanoma and lung adenocarcinoma, demonstrating that the mutation status of the identified cancer-specific DDR gene sets, which included only 9 and 14 genes, respectively, was significantly associated with TMB. The cancer-specific DDR gene set can be used as a cost-effective approach to stratify patients with high TMB in clinical practice.
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Affiliation(s)
- To-Yuan Chiu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (T.-Y.C.); (R.W.L.); (C.-J.H.); (D.-W.Y.)
| | - Ryan Weihsiang Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (T.-Y.C.); (R.W.L.); (C.-J.H.); (D.-W.Y.)
- Center for Systems and Synthetic Biology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chien-Jung Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (T.-Y.C.); (R.W.L.); (C.-J.H.); (D.-W.Y.)
| | - Da-Wei Yeh
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (T.-Y.C.); (R.W.L.); (C.-J.H.); (D.-W.Y.)
| | - Yu-Chao Wang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (T.-Y.C.); (R.W.L.); (C.-J.H.); (D.-W.Y.)
- Center for Systems and Synthetic Biology, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Correspondence:
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Palmieri G, Rozzo CM, Colombino M, Casula M, Sini MC, Manca A, Pisano M, Doneddu V, Paliogiannis P, Cossu A. Are Molecular Alterations Linked to Genetic Instability Worth to Be Included as Biomarkers for Directing or Excluding Melanoma Patients to Immunotherapy? Front Oncol 2021; 11:666624. [PMID: 34026645 PMCID: PMC8132875 DOI: 10.3389/fonc.2021.666624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
The improvement of the immunotherapeutic potential in most human cancers, including melanoma, requires the identification of increasingly detailed molecular features underlying the tumor immune responsiveness and acting as disease-associated biomarkers. In recent past years, the complexity of the immune landscape in cancer tissues is being steadily unveiled with a progressive better understanding of the plethora of actors playing in such a scenario, resulting in histopathology diversification, distinct molecular subtypes, and biological heterogeneity. Actually, it is widely recognized that the intracellular patterns of alterations in driver genes and loci may also concur to interfere with the homeostasis of the tumor microenvironment components, deeply affecting the immune response against the tumor. Among others, the different events linked to genetic instability—aneuploidy/somatic copy number alteration (SCNA) or microsatellite instability (MSI)—may exhibit opposite behaviors in terms of immune exclusion or responsiveness. In this review, we focused on both prevalence and impact of such different types of genetic instability in melanoma in order to evaluate whether their use as biomarkers in an integrated analysis of the molecular profile of such a malignancy may allow defining any potential predictive value for response/resistance to immunotherapy.
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Affiliation(s)
- Giuseppe Palmieri
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Carla Maria Rozzo
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Milena Casula
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Maria Cristina Sini
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Antonella Manca
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Marina Pisano
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Valentina Doneddu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Cossu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
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Osrodek M, Wozniak M. Targeting Genome Stability in Melanoma-A New Approach to an Old Field. Int J Mol Sci 2021; 22:3485. [PMID: 33800547 PMCID: PMC8036881 DOI: 10.3390/ijms22073485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Despite recent groundbreaking advances in the treatment of cutaneous melanoma, it remains one of the most treatment-resistant malignancies. Due to resistance to conventional chemotherapy, the therapeutic focus has shifted away from aiming at melanoma genome stability in favor of molecularly targeted therapies. Inhibitors of the RAS/RAF/MEK/ERK (MAPK) pathway significantly slow disease progression. However, long-term clinical benefit is rare due to rapid development of drug resistance. In contrast, immune checkpoint inhibitors provide exceptionally durable responses, but only in a limited number of patients. It has been increasingly recognized that melanoma cells rely on efficient DNA repair for survival upon drug treatment, and that genome instability increases the efficacy of both MAPK inhibitors and immunotherapy. In this review, we discuss recent developments in the field of melanoma research which indicate that targeting genome stability of melanoma cells may serve as a powerful strategy to maximize the efficacy of currently available therapeutics.
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Affiliation(s)
| | - Michal Wozniak
- Department of Molecular Biology of Cancer, Medical University of Lodz, 92-215 Lodz, Poland;
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28
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O’Meara TA, Tolaney SM. Tumor mutational burden as a predictor of immunotherapy response in breast cancer. Oncotarget 2021; 12:394-400. [PMID: 33747355 PMCID: PMC7939529 DOI: 10.18632/oncotarget.27877] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 01/12/2023] Open
Abstract
Tumor mutational burden (TMB) is a promising tool to help define patients with triple-negative breast cancer (TNBC) most likely to benefit from immune checkpoint blockade (ICB) therapies. Roughly reflecting the degree of neo-antigens that tumors present to immune cells, TMB associates with multiple measures of tumoral immunogenicity and has proven clinically useful in cancers with relatively high mutation burden. TNBC carries higher TMB than other breast cancer subtypes, and recent data suggest that high-TMB TNBC cases may derive particular benefit from ICB in combination with chemotherapy (GeparNuevo, IMpassion130) or even ICB alone (KEYNOTE-119, TAPUR). Given the recent approval of pembrolizumab and atezolizumab in combination with chemotherapy for PD-L1-positive, metastatic TNBC, standardizing TMB calculation methods and cut-off values is of critical importance to deploy this clinical biomarker.
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Affiliation(s)
- Tess A. O’Meara
- Department of Internal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sara M. Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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29
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In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses. Int J Mol Sci 2021; 22:ijms22031097. [PMID: 33499282 PMCID: PMC7865701 DOI: 10.3390/ijms22031097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
To exploit negatively interacting pairs of cancer somatic mutations in chemotherapy responses or synthetic cytotoxicity (SC), we systematically determined mutational pairs that had significantly lower paclitaxel half maximal inhibitory concentration (IC50) values. We evaluated 407 cell lines with somatic mutation profiles and estimated their copy number and drug-inhibitory concentrations in Genomics of Drug Sensitivity in Cancer (GDSC) database. The SC effect of 142 mutated gene pairs on response to paclitaxel was successfully cross-validated using human cancer datasets for urogenital cancers available in The Cancer Genome Atlas (TCGA) database. We further analyzed the cumulative effect of increasing SC pair numbers on the TP53 tumor suppressor gene. Patients with TCGA bladder and urogenital cancer exhibited improved cancer survival rates as the number of disrupted SC partners (i.e., SYNE2, SON, and/or PRY) of TP53 increased. The prognostic effect of SC burden on response to paclitaxel treatment could be differentiated from response to other cytotoxic drugs. Thus, the concept of pairwise SC may aid the identification of novel therapeutic and prognostic targets.
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Mediratta K, El-Sahli S, D’Costa V, Wang L. Current Progresses and Challenges of Immunotherapy in Triple-Negative Breast Cancer. Cancers (Basel) 2020; 12:E3529. [PMID: 33256070 PMCID: PMC7761500 DOI: 10.3390/cancers12123529] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
With improved understanding of the immunogenicity of triple-negative breast cancer (TNBC), immunotherapy has emerged as a promising candidate to treat this lethal disease owing to the lack of specific targets and effective treatments. While immune checkpoint inhibition (ICI) has been effectively used in immunotherapy for several types of solid tumor, monotherapies targeting programmed death 1 (PD-1), its ligand PD-L1, or cytotoxic T lymphocyte-associated protein 4 (CTLA-4) have shown little efficacy for TNBC patients. Over the past few years, various therapeutic candidates have been reviewed, attempting to improve ICI efficacy on TNBC through combinatorial treatment. In this review, we describe the clinical limitations of ICI and illustrate candidates from an immunological, pharmacological, and metabolic perspective that may potentiate therapy to improve the outcomes of TNBC patients.
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Affiliation(s)
- Karan Mediratta
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (K.M.); (S.E.-S.)
- Centre for Infection, Immunity and Inflammation, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Sara El-Sahli
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (K.M.); (S.E.-S.)
- Centre for Infection, Immunity and Inflammation, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Vanessa D’Costa
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (K.M.); (S.E.-S.)
- Centre for Infection, Immunity and Inflammation, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Lisheng Wang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (K.M.); (S.E.-S.)
- Centre for Infection, Immunity and Inflammation, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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31
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Wu CE, Yeh DW, Pan YR, Huang WK, Chen MH, Chang JWC, Chen JS, Wang YC, Yeh CN. Chromosomal Instability May Not Be a Predictor for Immune Checkpoint Inhibitors from a Comprehensive Bioinformatics Analysis. Life (Basel) 2020; 10:life10110276. [PMID: 33171596 PMCID: PMC7695172 DOI: 10.3390/life10110276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/19/2020] [Accepted: 11/05/2020] [Indexed: 12/25/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have become the standard of care in various cancers, although their predictive tools have not yet completely developed. Here, we aimed to exam the role of 70-gene chromosomal instability signature (CIN70) in cancers, and its association with previous predictors, tumor mutation burden (TMB), and microsatellite instability (MSI), for patients undergoing ICIs, as well as the possible predictive value for ICIs. We examined the association of CIN70 with TMB and MSI, as well as the impact of these biomarkers on the survival of 33 cancer cohorts from The Cancer Genome Atlas (TCGA) databank. The predictive value of the ICIs of CIN70 in previously published reports was also validated. Using the TCGA dataset, CIN70 scores were frequently (either positively or negatively) associated with TMB, but were only significantly associated with MSI status in three types of cancer. In addition, our current study showed that all TMB, MSI, and CIN70 had their own prognostic values for survival in patients with various cancers, and that they could be cancer type-specific. In two validation cohorts (melanoma by Hugo et al. and urothelial cancer by Snyder et al.), no significant difference of CIN70 scores was found between responders and non-responders (p-value = 0.226 and 0.108, respectively). In addition, no overall survival difference was noted between patients with a high CIN70 and those with a low CIN70 (p-value = 0.106 and 0.222, respectively). In conclusion, the current study, through a comprehensive bioinformatics analysis, demonstrated a correlation between CIN70 and TMB, but CIN70 is not the predictor for cancer patients undergoing ICIs. Future prospective studies are warranted to validate these findings.
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Affiliation(s)
- Chiao-En Wu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou, Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (C.-E.W.); (W.-K.H.); (J.W.-C.C.); (J.-S.C.)
| | - Da-Wei Yeh
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan;
| | - Yi-Ru Pan
- Department of General Surgery and Liver Research Center, Chang Gung Memorial Hospital, Linkou branch, Chang Gung University, Taoyuan 333, Taiwan;
| | - Wen-Kuan Huang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou, Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (C.-E.W.); (W.-K.H.); (J.W.-C.C.); (J.-S.C.)
| | - Ming-Huang Chen
- Department of Oncology, Taipei Veterans General Hospital, Taipei 112, Taiwan;
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - John Wen-Cheng Chang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou, Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (C.-E.W.); (W.-K.H.); (J.W.-C.C.); (J.-S.C.)
| | - Jen-Shi Chen
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou, Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (C.-E.W.); (W.-K.H.); (J.W.-C.C.); (J.-S.C.)
| | - Yu-Chao Wang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan;
- Preventive Medicine Research Center, National Yang-Ming University, Taipei 112, Taiwan
- Correspondence: (Y.-C.W.); (C.-N.Y.)
| | - Chun-Nan Yeh
- Department of General Surgery and Liver Research Center, Chang Gung Memorial Hospital, Linkou branch, Chang Gung University, Taoyuan 333, Taiwan;
- Correspondence: (Y.-C.W.); (C.-N.Y.)
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Gordon B, Gadi VK. The Role of the Tumor Microenvironment in Developing Successful Therapeutic and Secondary Prophylactic Breast Cancer Vaccines. Vaccines (Basel) 2020; 8:vaccines8030529. [PMID: 32937885 PMCID: PMC7565925 DOI: 10.3390/vaccines8030529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer affects roughly one in eight women over their lifetime and is a leading cause of cancer-related death in women. While outcomes have improved in recent years, prognosis remains poor for patients who present with either disseminated disease or aggressive molecular subtypes. Cancer immunotherapy has revolutionized the treatment of several cancers, with therapeutic vaccines aiming to direct the cytotoxic immune program against tumor cells showing particular promise. However, these results have yet to translate to breast cancer, which remains largely refractory from such approaches. Recent evidence suggests that the breast tumor microenvironment (TME) is an important and long understudied barrier to the efficacy of therapeutic vaccines. Through an improved understanding of the complex and biologically diverse breast TME, it may be possible to advance new combination strategies to render breast carcinomas sensitive to the effects of therapeutic vaccines. Here, we discuss past and present efforts to advance therapeutic vaccines in the treatment of breast cancer, the molecular mechanisms through which the TME contributes to the failure of such approaches, as well as the potential means through which these can be overcome.
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Affiliation(s)
- Benjamin Gordon
- Department of Physiology and Biophysics, University of Illinois College of Medicine, Chicago, IL 60612, USA
- Medical Scientist Training Program, University of Illinois College of Medicine, Chicago, IL 60612, USA
- Correspondence:
| | - Vijayakrishna K. Gadi
- Division of Hematology and Oncology, University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA;
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Ravaioli S, Limarzi F, Tumedei MM, Palleschi M, Maltoni R, Bravaccini S. Are we ready to use TMB in breast cancer clinical practice? Cancer Immunol Immunother 2020; 69:1943-1945. [PMID: 32725361 DOI: 10.1007/s00262-020-02682-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
We discussed the potentialities of tumor mutation burden (TMB) as a predictive marker for immunotherapy in breast cancer, also highlighting the limits that have hindered its introduction in the clinical practice. Although some studies have demonstrated the possibility to select patients more responsive to immune-checkpoint inhibitors by evaluating TMB, some issues emerged regarding the complexity of the methodologies for its determination, the costs of the analysis, and the necessity to improve the TMB determination with that of neoantigen identification.
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Affiliation(s)
- Sara Ravaioli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Francesco Limarzi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Maria Maddalena Tumedei
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Michela Palleschi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Roberta Maltoni
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Sara Bravaccini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy.
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Pre-Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy. Cancers (Basel) 2020; 12:cancers12071943. [PMID: 32708981 PMCID: PMC7409244 DOI: 10.3390/cancers12071943] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 01/08/2023] Open
Abstract
Immunotherapy, such as anti-PD1, has improved the survival of patients with metastatic melanoma. However, predicting which patients will respond to immunotherapy remains a significant knowledge gap. In this study we analyzed pre-immunotherapy treated tumors from 52 patients with metastatic melanoma and monitored their response based on RECIST 1.1 criteria. The responders group contained 21 patients that had a complete or partial response, while the 31 non-responders had stable or progressive disease. Whole exome sequencing (WES) was used to identify biomarkers of anti-PD1 response from somatic mutations between the two groups. Variants in codons G34 and G41 in NFKBIE, a negative regulator of NFkB, were found exclusively in the responders. Mutations in NKBIE-related genes were also enriched in the responder group compared to the non-responders. Patients that harbored NFKBIE-related gene mutations also had a higher mutational burden, decreased tumor volume with treatment, and increased progression-free survival. RNA sequencing on a subset of tumor samples identified that CD83 was highly expressed in our responder group. Additionally, Gene Set Enrichment Analysis showed that the TNFalpha signaling via NFkB pathway was one of the top pathways with differential expression in responders vs. non-responders. In vitro NFkB activity assays indicated that the G34E variant caused loss-of-function of NFKBIE, and resulted in activation of NFkB signaling. Flow cytometry assays indicated that G34E variant was associated with upregulation of CD83 in human melanoma cell lines. These results suggest that NFkB activation and signaling in tumor cells contributes to a favorable anti-PD1 treatment response, and clinical screening to include aberrations in NFkB-related genes should be considered.
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