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Wu M, Zhou S. Harnessing tumor immunogenomics: Tumor neoantigens in ovarian cancer and beyond. Biochim Biophys Acta Rev Cancer 2023; 1878:189017. [PMID: 37935309 DOI: 10.1016/j.bbcan.2023.189017] [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: 08/27/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Ovarian cancer is a major cause of death among gynecological cancers due to its highly aggressive nature. Immunotherapy has emerged as a promising avenue for ovarian cancer treatment, offering targeted approaches with reduced off-target effects. With the advent of next-generation sequencing, it has become possible to identify genomic alterations that can serve as potential targets for immunotherapy. Furthermore, immunogenomics research has revealed the importance of genetic alterations in shaping the cancer immune responses. However, the heterogeneity of immunogenicity and the low tumor mutation burden pose challenges for neoantigen-based immunotherapies. Further research is needed to identify neoantigen-specific tumor-infiltrating lymphocytes (TIL) and establish guidelines for patient inclusion criteria in TIL-based therapy. The study of neoantigens and their implications in ovarian cancer immunotherapy holds great promise, and efforts focused on personalized treatment strategies, refined neoantigen selection, and optimized therapeutic combinations will contribute to improving patient outcomes in the future.
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Affiliation(s)
- Mengrui Wu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, PR China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, PR China.
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2
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Quintanilha JC, Storandt MH, Graf RP, Li G, Keller R, Lin DI, Ross JS, Huang RS, Schrock AB, Oxnard GR, Chakrabarti S, Mahipal A. Tumor Mutational Burden in Real-World Patients With Pancreatic Cancer: Genomic Alterations and Predictive Value for Immune Checkpoint Inhibitor Effectiveness. JCO Precis Oncol 2023; 7:e2300092. [PMID: 37410975 PMCID: PMC10581638 DOI: 10.1200/po.23.00092] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/05/2023] [Accepted: 05/26/2023] [Indexed: 07/08/2023] Open
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is largely considered a nonimmunogenic malignancy; however, approximately 1%, of patients may have tumors with deficient mismatch repair, high microsatellite instability, or high tumor mutational burden (TMB ≥10 mutations/Mb), which may be predictive of response to immune checkpoint inhibitor (ICI) therapy. We sought to analyze outcomes of patients with high-TMB and pathogenic genomic alterations observed in this population. METHODS This study included patients with PDAC who underwent comprehensive genomic profiling (CGP) at Foundation Medicine (Cambridge, MA). Clinical data were obtained from a US-wide real-world clinicogenomic pancreatic database. We report genomic alterations in those with high and low TMB, and compare outcomes on the basis of receipt of single-agent ICI or therapy regimens not containing ICI. RESULTS We evaluated 21,932 patients with PDAC who had tissue CGP data available, including 21,639 (98.7%) with low-TMB and 293 (1.3%) with high-TMB. Among patients with high-TMB, a greater number of alterations were observed in BRCA2, BRAF, PALB2, and genes of the mismatch repair pathway, whereas fewer alterations were observed in KRAS. Among patients who received an ICI (n = 51), those with high-TMB had more favorable median overall survival when compared with the low-TMB subset (25.7 v 5.2 months; hazard ratio, 0.32; 95% CI, 0.11 to 0.91; P = .034). CONCLUSION Longer survival was observed in patients with high-TMB receiving ICI compared with those with low-TMB. This supports the role of high-TMB as a predictive biomarker for efficacy of ICI therapy in PDAC. Additionally, we report higher rates of BRAF and BRCA2 mutations and lower rates of KRAS mutation among patients with PDAC and high-TMB, which to our knowledge, is a novel finding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Sakti Chakrabarti
- University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Amit Mahipal
- University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH
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3
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Al-Rawi DH, Rusk N, Friedman CF. The Search for Genomic Biomarkers of Response to Immunotherapy in Ovarian Cancer. Clin Cancer Res 2023; 29:1645-1647. [PMID: 36826422 PMCID: PMC10159911 DOI: 10.1158/1078-0432.ccr-23-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023]
Abstract
Immune checkpoint blockade has been ineffective in ovarian cancer, and there is an ongoing effort to identify biomarkers of therapeutic benefit. Despite promising preclinical data, a substudy of the IMagyn050 trial found that patients with homologous recombination deficient tumors did not have improved progression-free survival with the addition of the PD-L1 inhibitor atezolizumab. See related article by Landen et al., p. 1698.
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Affiliation(s)
- Duaa H Al-Rawi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Claire F Friedman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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Parisi R, Patel RR, Rood G, Bowden A, Turco G, Korones DN, Andolina JR, Comito M, Barth M, Weintraub L. Multi-institution analysis of tumor mutational burden and outcomes in pediatric central nervous system tumor patients. Pediatr Blood Cancer 2023; 70:e30139. [PMID: 36573296 DOI: 10.1002/pbc.30139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Pediatric central nervous system (CNS) tumors are the leading cause of pediatric cancer mortality. Research addressing genomic biomarkers and clinical outcomes is needed to inform therapeutic decision-making. METHODS We conducted a retrospective analysis of pediatric patients (age <21) diagnosed with a primary CNS tumor at four upstate New York hospitals from 2008 to 2021. Clinical and histopathologic data were identified from each patient, including genomic analysis of somatic mutations and tumor mutational burden (TMB) where available. These variables were each compared with overall survival using Cox regression analyses. Multivariable analysis was conducted to identify patient characteristics that may independently predict survival. RESULTS We identified 119 patients. Common tumor types included low-grade glioma (N = 51), high-grade glioma (N = 29), and medulloblastoma (N = 11). Common driver mutations included TP53 inactivation (N = 16), BRAF-KIAA1549 fusion (N = 16), FGFR1 amplification (N = 12), BRAF V600E mutation (N = 12), NF1 loss (N = 12), and H3F3A K28M mutation (N = 6). Median TMB was one mutation/megabase (mut/Mb, range = 0-132). Overall survival was 79.9%. Variables associated with poorer survival on univariable analysis were higher TMB (p = .002, HR 4.97), high-grade tumors (p = .009, HR 84.3), and high-grade glioma histology (p = .021, HR 3.14). Multivariable analyses further identified TMB (p = .011, HR 4.46) and high-grade histology (p = .015, HR 5.28) as independently predictive of worse survival. Tumor progression was more common in high-TMB (N = 15, 44%) than in low-TMB tumors (N = 19, 35%). CONCLUSIONS High TMB is correlated with higher rates of progression and death as compared to low-TMB tumors. These findings may help identify patients who may benefit from alternative treatments, such as immunotherapies.
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Affiliation(s)
- Rose Parisi
- Albany Medical College, Albany, New York, USA
| | - Roshal R Patel
- Albany Medical College, Albany, New York, USA.,Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gavrielle Rood
- Upstate Medical University College of Medicine, Syracuse, New York, USA
| | - Acacia Bowden
- University of Rochester School of Medicine, Rochester, New York, USA
| | - George Turco
- Pediatric Hematology/Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - David N Korones
- Pediatric Hematology/Oncology, University of Rochester Medical Center, Rochester, New York, USA
| | - Jeffrey R Andolina
- Pediatric Hematology/Oncology, University of Rochester Medical Center, Rochester, New York, USA
| | - Melanie Comito
- Pediatric Hematology/Oncology, Upstate University Hospital, Syracuse, New York, USA
| | - Matthew Barth
- Pediatric Hematology/Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Lauren Weintraub
- Pediatric Hematology/Oncology, Albany Medical Center, Albany, New York, USA
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Liang W, Zhou C, Wang J, Zhao J, Liu F, Wang G, Xu C, Zhang Y, Wang W, Cai S, Han Y, Chang L, Zhang P. A prognostic signature based on adenosine metabolism related genes for ovarian cancer. Front Oncol 2022; 12:1003512. [PMID: 36518306 PMCID: PMC9742553 DOI: 10.3389/fonc.2022.1003512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/14/2022] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Ovarian cancer is one of the most common cause of cancer death in women due to its late diagnosis and susceptibility to drug resistance. Adenosine (ADO) signaling plays a key role in immune activity and tumor progression. In this study, we constructed a signature of ADO metabolism related genes expression in patients with ovarian cancer. METHODS A total of 372 ovarian cancer patients from TCGA was used as training set and 1,137 patients from six GEO datasets were as validation set. The gene expression and drug response inhibitory concentration values for ovarian cancer cell line from GDSC were used for drug sensitivity analysis. The non-negative matrix factorization algorithm and ssGSVA were used to construct the ADO score. RESULTS Patients with high ADO score had shorter overall survival (OS) than those with low ADO score in both training set (HR = 1.42, 95% CI, 1.06-1.88) and validation sets (pooled HR = 1.24, 95% CI = 1.02-1.51). In GSEA analysis, genes in ATP synthesis related pathways were enriched in the low ADO score group (adjusted P value = 0.02). Further, we observed that the high ADO score group had significantly higher levels of most cancer hallmark signatures (all adjusted P values < 0.01) and T cell dysfunction and exclusion signatures than the low ADO score group (all adjusted P values < 0.001). Patients with lower ADO score tended to be sensitive to common drugs including Olaparib and Paclitaxel (adjusted P values = 0.05 and 0.04, respectively). CONCLUSIONS In conclusion, the established ADO signature could be used as a prognostic biomarker to stratify ovarian cancer patients and had the potential to guide the drug exploitation and personalized therapy selection.
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Affiliation(s)
- Weifeng Liang
- Department of Gynecology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, China
| | - Chao Zhou
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Jingshu Wang
- Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Jing Zhao
- Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Fang Liu
- Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Guoqiang Wang
- Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Chunwei Xu
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yuzi Zhang
- Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Wenxian Wang
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
| | - Shangli Cai
- Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Yusheng Han
- Medical Department, Burning Rock Biotech, Guangzhou, China
| | - Lei Chang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Peihai Zhang
- Department of Gynecology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, China
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Barresi V, Musmeci C, Rinaldi A, Condorelli DF. Transcript-Targeted Therapy Based on RNA Interference and Antisense Oligonucleotides: Current Applications and Novel Molecular Targets. Int J Mol Sci 2022; 23:ijms23168875. [PMID: 36012138 PMCID: PMC9408055 DOI: 10.3390/ijms23168875] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/03/2022] [Accepted: 08/07/2022] [Indexed: 12/28/2022] Open
Abstract
The development of novel target therapies based on the use of RNA interference (RNAi) and antisense oligonucleotides (ASOs) is growing in an exponential way, challenging the chance for the treatment of the genetic diseases and cancer by hitting selectively targeted RNA in a sequence-dependent manner. Multiple opportunities are taking shape, able to remove defective protein by silencing RNA (e.g., Inclisiran targets mRNA of protein PCSK9, permitting a longer half-life of LDL receptors in heterozygous familial hypercholesteremia), by arresting mRNA translation (i.e., Fomivirsen that binds to UL123-RNA and blocks the translation into IE2 protein in CMV-retinitis), or by reactivating modified functional protein (e.g., Eteplirsen able to restore a functional shorter dystrophin by skipping the exon 51 in Duchenne muscular dystrophy) or a not very functional protein. In this last case, the use of ASOs permits modifying the expression of specific proteins by modulating splicing of specific pre-RNAs (e.g., Nusinersen acts on the splicing of exon 7 in SMN2 mRNA normally not expressed; it is used for spinal muscular atrophy) or by downregulation of transcript levels (e.g., Inotersen acts on the transthryretin mRNA to reduce its expression; it is prescribed for the treatment of hereditary transthyretin amyloidosis) in order to restore the biochemical/physiological condition and ameliorate quality of life. In the era of precision medicine, recently, an experimental splice-modulating antisense oligonucleotide, Milasen, was designed and used to treat an 8-year-old girl affected by a rare, fatal, progressive form of neurodegenerative disease leading to death during adolescence. In this review, we summarize the main transcriptional therapeutic drugs approved to date for the treatment of genetic diseases by principal regulatory government agencies and recent clinical trials aimed at the treatment of cancer. Their mechanism of action, chemical structure, administration, and biomedical performance are predominantly discussed.
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Clinical Characteristics in the Prediction of Posttreatment Survival of Patients with Ovarian Cancer. DISEASE MARKERS 2022; 2022:3321014. [PMID: 35571616 PMCID: PMC9098309 DOI: 10.1155/2022/3321014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/15/2022] [Indexed: 12/14/2022]
Abstract
Objective To determine the efficacy of clinical characteristics in the prediction of prognosis in patients with ovarian cancer. Methods Clinical data were collected from 3 datasets from TCGA database, including 1680 cases of ovarian serous cystadenocarcinoma, and were analyzed. Patients with ovarian cancer admitted to our hospital in 2016 were retrieved and followed up for prognosis analysis. Results From the datasets, for patients > 75 years old at the time of diagnosis, histologic grade and mutation count were good predictors for disease-free survival, while for patients > 50 years old at the time of diagnosis, histologic grade, race, fraction genome altered, and mutation count were good predictors for overall survival. In the patients (n = 38) retrieved from our hospital, the longest dimension of lesion (cm) and body weight at admission were good predictors for overall survival. Conclusions Those clinical factors, together with the two predictive equations, could be used to comprehensively predict the long-term prognosis of patients with ovarian cancer.
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Takamatsu S, Brown JB, Yamaguchi K, Hamanishi J, Yamanoi K, Takaya H, Kaneyasu T, Mori S, Mandai M, Matsumura N. Utility of Homologous Recombination Deficiency Biomarkers Across Cancer Types. JCO Precis Oncol 2022; 6:e2200085. [PMID: 35613413 PMCID: PMC9200383 DOI: 10.1200/po.22.00085] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Homologous recombination DNA repair deficiency (HRD) is associated with sensitivity to platinum and poly (ADP-ribose) polymerase inhibitors in certain cancer types, including breast, ovarian, pancreatic, and prostate. In these cancers, BRCA1/2 alterations and genomic scar signatures are useful indicators for assessing HRD. However, alterations in other homologous recombination repair (HRR)-related genes and their clinical significance in other cancer types have not been adequately and systematically investigated. A comprehensive pan-cancer analysis on the clinical significance of homologous recombination deficiency![]()
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Affiliation(s)
- Shiro Takamatsu
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - J B Brown
- Life Science Informatics Research Unit, Department of Molecular Biosciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Yamaguchi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junzo Hamanishi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Yamanoi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisamitsu Takaya
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Tomoko Kaneyasu
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Mori
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Noriomi Matsumura
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
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Ellegate J, Mastri M, Isenhart E, Krolewski JJ, Chatta G, Kauffman E, Moffitt M, Eng KH. Loss of MAGEC3 Expression Is Associated with Prognosis in Advanced Ovarian Cancers. Cancers (Basel) 2022; 14:cancers14030731. [PMID: 35158998 PMCID: PMC8833712 DOI: 10.3390/cancers14030731] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Familial studies connect variants in the X-linked gene MAGEC3 to early-onset ovarian cancers. In this retrospective cohort study, we determined that, unlike other MAGE family members, the MAGEC3 protein is normally expressed in ovarian tissue but is lost in half of the ovarian cancers. Similar to other predisposition genes like BRCA2, survival modeling suggests that expression loss is associated with favorable progression-free survival, and continued expression is associated with response to platinum therapy. Because of the assumed antigenicity of MAGE genes, we tested and observed associations with lymphocyte infiltration, NY-ESO-1 seropositivity, and the co-expression of tumor antigens at Xq28. Using transcriptomic modeling, we predicted that MAGEC3 expression is associated with stress-related cell cycle stalling and DNA repair pathway expression. Abstract Rare variants in MAGEC3 are associated with BRCA negative, early-onset ovarian cancers. Given this association, we evaluated the impact of MAGEC3 protein expression on prognosis and transcription. We quantified normal and tumor protein expression of MAGEC3 via immunohistochemistry in n = 394 advanced ovarian cancers, assessed the correlation of these values with clinicopathologic and immunological features and modeled survival using univariate and multivariate models. To extend these results, we quantified MAGEC3 protein expression in n = 180 cancers and used matching RNA sequencing data to determine MAGEC3-associated differentially expressed genes and to build an RNA-based model of MAGEC3 protein levels. This model was tested in a third independent cohort of patients from TCGA’s OV dataset (n = 282). MAGEC3 protein was sporadically lost in ovarian cancers, with half of the cases falling below the 9.5th percentile of normal tissue expression. Cases with MAGEC3 loss demonstrated better progression-free survival [HR = 0.71, p = 0.004], and analyses performed on predicted protein scores were consistent [HR = 0.57 p = 0.002]. MAGEC3 protein was correlated with CD8 protein expression [Pearson’s r = 0.176, p = 0.011], NY-ESO-1 seropositivity, and mRNA expression of tumor antigens at Xq28. Results of gene set enrichment analysis showed that genes associated with MAGEC3 protein expression cluster around G2/M checkpoint (NES = 3.20, FDR < 0.001) and DNA repair (NES = 2.28, FDR < 0.001) hallmark pathways. These results show that MAGEC3 is a prognostic biomarker in ovarian cancer.
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Affiliation(s)
- James Ellegate
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.E.J.); (M.M.); (E.I.); (J.J.K.)
| | - Michalis Mastri
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.E.J.); (M.M.); (E.I.); (J.J.K.)
| | - Emily Isenhart
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.E.J.); (M.M.); (E.I.); (J.J.K.)
| | - John J. Krolewski
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.E.J.); (M.M.); (E.I.); (J.J.K.)
| | - Gurkamal Chatta
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Eric Kauffman
- Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Melissa Moffitt
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Kevin H. Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.E.J.); (M.M.); (E.I.); (J.J.K.)
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Correspondence:
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Yang H, Yu M, Zhong S, You Y, Feng F. Neoantigens and the tumor microenvironment play important roles in the prognosis of high-grade serous ovarian cancer. J Ovarian Res 2022; 15:18. [PMID: 35093146 PMCID: PMC8801100 DOI: 10.1186/s13048-022-00955-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
Background Despite the consistency of patient age, disease stage and treatment options, the prognosis of different high-grade serous ovarian carcinoma (HGSOC) patients is different. Here, we sought to measure predictive biomarkers for distinct responses to platinum-based chemotherapy and immunotherapy benefits. Methods Sixteen HGSOC patients receiving debulking surgery and adjuvant first-line combination chemotherapy at Peking Union Medical College Hospital (PUMCH) were enrolled. Whole exome sequencing (WES) and RNA-seq were performed on tumor and normal tissues of these patients. Results The tumor mutational burden (TMB) and intratumoral heterogeneity (ITH) of the platinum-resistant group were significantly higher than those of the platinum-sensitive group (P=0.0321 and P=0.0452, respectively). TMB, neoantigen and ITH had certain predictive value according to the area under the receiver operating characteristic (ROC) curve (AUC 0.7778 for TMB, 0.7619 for neoantigen, 0.7778 for ITH). The infiltration of other immune cells in tumor tissues was different between the two groups, but the difference was not significant. Univariate Cox proportional hazard analysis revealed poorer progression-free survival (PFS) for those patients who carried a higher number of neoantigens (P =0.0069), higher TMB (P =0.0083), and higher ITH (P =0.0249). Further Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis indicated the Differentially expressed genes (DEGs) in platinum-resistant and platinum-sensitive patients were mainly enriched in the phosphatidylinositol 3-kinase-Akt (PI3K-Akt) signaling pathway and focal adhesion pathway, which are associated with platinum resistance. Conclusions Higher TMB, neoantigen and ITH may account for the worse prognosis of patients with platinum-based chemotherapy and higher TMB was observed in the platinum-resistant group, which could make the patients in the platinum-resistant group to be the better candidates for immunotherapy. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-022-00955-9.
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Wen Y, Ouyang D, Chen Q, Zeng L, Luo N, He H, Anwar M, Qu L, Zou Q, Yi W. Prognostic value of tumor mutation burden and the relationship between tumor mutation burden and immune infiltration in HER2+ breast cancer: a gene expression-based study. Gland Surg 2022; 11:100-114. [PMID: 35242673 PMCID: PMC8825527 DOI: 10.21037/gs-21-594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/16/2021] [Indexed: 08/02/2023]
Abstract
BACKGROUND Whether tumor mutation burden (TMB) correlated with improved survival outcomes or promotion of immunotherapies remained controversy in various malignancies. We aimed to explore the prognostic value of TMB and the relationship between TMB and immune infiltration in human epidermal growth factor receptor 2-positive (HER2+) breast cancer (BC). METHODS We downloaded somatic mutation data and clinical information for 216 HER2+ BC patients from the The Cancer Genome Atlas (TCGA) and cBioPortal databases. Patients were divided into high- and low-TMB groups through TMB calculation. Cox regression analysis was used to establish an immune- and mutant-related risk model based on 5-hub genes. The relationship between 5-hub genes mutants and the level of immune infiltration, as well as the relationship between the risk model and the immune microenvironment were analyzed by "TIMER" database. RESULTS TMB was negatively correlated with overall survival (OS) and disease-free survival (DFS), and high TMB may inhibit immune infiltration in HER2+ BC. Furthermore, risk score classified effectively patients into low- and high-risk groups in training and validation cohorts. The infiltration of CD4+ T cells and NK cells and the levels of immune checkpoint pathway genes were lower in the high-risk group, which indicated a poor prognosis. CONCLUSIONS Higher TMB correlated with poor survival outcomes and might inhibit the immune infiltrates in HER2+ BC. The 5-hub TMB-related signature conferred lower immune cells infiltration which deserved further validation.
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Affiliation(s)
- Ying Wen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Dengjie Ouyang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qitong Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Liyun Zeng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Na Luo
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hongye He
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Munawar Anwar
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Limeng Qu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qiongyan Zou
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
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Wu ZH, Li ZW, Yang DL, Liu J. Development and Validation of a Pyroptosis-Related Long Non-coding RNA Signature for Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:713925. [PMID: 34869306 PMCID: PMC8634266 DOI: 10.3389/fcell.2021.713925] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/05/2021] [Indexed: 01/07/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a highly aggressive malignant disease, and numerous studies have demonstrated that an inflammatory environment can induce normal cells to transform into cancerous. Methods: We integrated genomic data to comprehensively assess the association between pyroptosis and tumor microenvironment (TME) cell-infiltrating characteristics in HCC, as well as the potential molecular function and clinical significance of lncRNA. Results: The analysis of CNV alteration frequency displayed that CNV changes were common in 33 PRGs, and most were focused on copy number amplification. As a result of lasso regression analysis, nine differentially expressed lncRNAs (AL031985.3, NRAV, OSMR-AS1, AC073611.1, MKLN1-AS, AL137186.2, AL049840.4, MIR4435-2HG, and AL118511.1) were selected as independent prognosis factors of HCC patients. Patients at high risk have poorer survival than those in the low-risk group in training and testing cohorts. A low-risk score was significantly associated with an IC50 of chemotherapeutics such as bortezomib (p < 0.001), but a high-risk score was significantly linked to docetaxel (p < 0.001), implying that signature served as a prospective predictor for chemosensitivity. Conclusion: This work suggests pyroptosis-related lncRNAs features and their potential mechanisms on tumor microenvironment. The exploration may assist in identifying novel biomarkers and assist patients in predicting their prognosis, clinical diagnosis, and management.
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Affiliation(s)
- Zeng-Hong Wu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zi-Wei Li
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dong-Liang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Liu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Funingana IG, Reinius MAV, Petrillo A, Ang JE, Brenton JD. Can integrative biomarker approaches improve prediction of platinum and PARP inhibitor response in ovarian cancer? Semin Cancer Biol 2021; 77:67-82. [PMID: 33607245 DOI: 10.1016/j.semcancer.2021.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/06/2021] [Accepted: 02/10/2021] [Indexed: 12/28/2022]
Abstract
Epithelial ovarian carcinoma (EOC) encompasses distinct histological, molecular and genomic entities that determine intrinsic sensitivity to platinum-based chemotherapy. Current management of each subtype is determined by factors including tumour grade and stage, but only a small number of biomarkers can predict treatment response. The recent incorporation of PARP inhibitors into routine clinical practice has underscored the need to personalise ovarian cancer treatment based on tumour biology. In this article, we review the strengths and limitations of predictive biomarkers in current clinical practice and highlight integrative strategies that may inform the development of future personalised medicine programs and composite biomarkers.
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Affiliation(s)
- Ionut-Gabriel Funingana
- Department of Oncology, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK; Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Marika A V Reinius
- Department of Oncology, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK; Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Angelica Petrillo
- Medical Oncology Unit, Ospedale del Mare, Naples, Italy; University of Study of Campania "L.Vanvitelli", Naples, Italy.
| | - Joo Ern Ang
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK; Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - James D Brenton
- Department of Oncology, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK; Department of Oncology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
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Lu N, Liu J, Xu M, Liang J, Wang Y, Wu Z, Xing Y, Diao F. CSMD3 is Associated with Tumor Mutation Burden and Immune Infiltration in Ovarian Cancer Patients. Int J Gen Med 2021; 14:7647-7657. [PMID: 34764678 PMCID: PMC8575319 DOI: 10.2147/ijgm.s335592] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Background Globally, ovarian cancer (OC), the deadliest gynecologic malignancy, remains a major cause of mortality, with a rising number of cases in many low- and middle-income countries. Immunotherapy has been proven to be promising for OC. There is increasing awareness of the vital role that tumor mutation burden (TMB) plays in predicting the efficacy of immunotherapy. Women with a family history of OC are at higher risk of the disease due to gene mutations. However, whether these gene mutations are related to immune response and TMB remains to be explored. Methods Our present work analyzed genetic mutation data of OC patients obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) cohorts, and we identified 11 frequently mutated genes, namely, APOB, CSMD3, DST, FAT3, FLG, HMCN1, MUC16, RYR1, TP53, TTN, and USH2A, in accordance with the overlap of two databases. Results A statistically higher TMB was detected by whole-exome sequencing in patients with OC with CSMD3 mutation than in those with mutations in the other frequently mutated genes. Prognosis analysis performed with patients from the TCGA cohort revealed that those with CSMD3 mutation had an overall survival (OS) that was inferior to that of those with wild-type CSMD3. Gene set enrichment analysis (GSEA) and CIBERSORT analysis indicated that OC samples with CSMD3 mutations had significant involvement of pathways related to the immune response. Conclusion In summary, we found that CSMD3 mutation is highly correlated with increased TMB and poor clinical prognosis and that it might function as a biomarker for predicting prognosis and choosing an immunotherapy regimen.
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Affiliation(s)
- Nan Lu
- Department of Reproduction, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Mengting Xu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Jianqiang Liang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Yichun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Zhipeng Wu
- Department of Urology, The Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yan Xing
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Feiyang Diao
- Department of Reproduction, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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Multiomics analysis of tumor mutational burden across cancer types. Comput Struct Biotechnol J 2021; 19:5637-5646. [PMID: 34745455 PMCID: PMC8531462 DOI: 10.1016/j.csbj.2021.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Whether tumor mutational burden (TMB) is related to improved survival outcomes or the promotion of immunotherapy in various malignant tumors remains controversial, and we lack a comprehensive understanding of TMB across cancers. Based on the data obtained from The Cancer Genome Atlas (TCGA), we conducted a multiomics analysis of TMB across 21 cancer types to identify characteristics related to TMB and determine the mechanism as it relates to prognosis, gene expression, gene mutation and signaling pathways. In our study, TMB was found to have a significant relationship with prognosis for 21 tumors, and the relationship was different in different tumors. TMB may also be related to different outcomes for patients with different tumor subtypes. TMB was confirmed to be correlated with clinical information, such as age and sex. Mutations in GATA3 and MAP3K1 in beast invasive carcinoma (BRCA), TCF7L2 in colon adenocarcinoma (COAD), NFE2L2 in esophageal carcinoma (ESCA), CIC and IDH1 in brain lower grade glioma (LGG), CDH1 in stomach adenocarcinoma (STAD), and TP53 in uterine corpus endometrial carcinoma (UCEC) were demonstrated to be correlated with lower TMB. Moreover, we identified differentially expressed genes (DEGs) and differentially methylated regions (DMRs) according to different TMB levels in 21 cancers. We also investigated the correlation between enrichment of signaling pathways, immune cell infiltration and TMB. In conclusion, we identified multiomic characteristics related to the TMB in 21 tumors, providing support for a comprehensive understanding of the role of TMB in different tumors.
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16
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Takamatsu S, Brown J, Yamaguchi K, Hamanishi J, Yamanoi K, Takaya H, Kaneyasu T, Mori S, Mandai M, Matsumura N. Utility of Homologous Recombination Deficiency Biomarkers Across Cancer Types. JCO Precis Oncol 2021; 5:PO.21.00141. [PMID: 34423229 PMCID: PMC8373547 DOI: 10.1200/po.21.00141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/07/2021] [Accepted: 07/06/2021] [Indexed: 12/24/2022] Open
Abstract
Homologous recombination DNA repair deficiency (HRD) is associated with sensitivity to platinum and poly (ADP-ribose) polymerase inhibitors in certain cancer types, including breast, ovarian, pancreatic, and prostate. In these cancers, BRCA1/2 alterations and genomic scar signatures are useful indicators for assessing HRD. However, alterations in other homologous recombination repair (HRR)-related genes and their clinical significance in other cancer types have not been adequately and systematically investigated. METHODS We obtained data sets of all solid tumors in The Cancer Genome Atlas and Cancer Cell Line Encyclopedia, and comprehensively analyzed HRR pathway gene alterations, their loss-of-heterozygosity status, and per-sample genomic scar scores, that is, the HRD score and mutational signature 3 ratio, DNA methylation profiles, gene expression profiles, somatic TP53 mutations, sex, and clinical or in vitro response to chemical exposure. RESULTS Biallelic alterations in HRR genes other than BRCA1/2 were also associated with elevated genomic scar scores. The association between HRR-related gene alterations and genomic scar scores differed significantly by sex and the presence of somatic TP53 mutations. HRD tumors determined by a combination of indices also showed HRD features in gene expression analysis and exhibited significantly higher sensitivity to DNA-damaging agents than non-HRD cases in both clinical samples and cell lines. CONCLUSION This study provides evidence for the usefulness of HRD analysis in all cancer types, improves chemotherapy decision making and its efficacy in clinical settings, and represents a substantial advancement in precision oncology.A comprehensive pan-cancer analysis on the clinical significance of homologous recombination deficiency.
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Affiliation(s)
- Shiro Takamatsu
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - J.B. Brown
- Life Science Informatics Research Unit, Department of Molecular Biosciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Yamaguchi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junzo Hamanishi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Yamanoi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisamitsu Takaya
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Tomoko Kaneyasu
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Mori
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Noriomi Matsumura
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
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17
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Fan L, Lei H, Lin Y, Zhou Z, Shu G, Yan Z, Chen H, Zhang T, Yin G. Identification of a Gene Set Correlated With Immune Status in Ovarian Cancer by Transcriptome-Wide Data Mining. Front Mol Biosci 2021; 8:670666. [PMID: 34395521 PMCID: PMC8363306 DOI: 10.3389/fmolb.2021.670666] [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: 03/16/2021] [Accepted: 07/16/2021] [Indexed: 12/26/2022] Open
Abstract
Immune checkpoint blocking (ICB) immunotherapy has achieved great success in the treatment of various malignancies. Although not have been approved for the treatment of ovarian cancer (OC), it has been actively tested for the treatment of OC. However, biomarkers that could indicate the immune status of OC and predict the response to ICB are rare. We downloaded RNAseq and clinical data of OC from The Cancer Genome Atlas (TCGA). Data analysis revealed both TMBhigh and immunityhigh were significantly related to better survival of OC. Up-regulated differentially expressed genes (Up-DEGs) were identified by analyzing the gene expression levels. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed in the "GSVA" and "limma" package in R software. The correlation of genes with overall survival was also analyzed by conducted Kaplan-Meier survival analysis. Four genes, CXCL13, FCRLA, MS4A1, and PLA2G2D were found positively correlated with better prognosis of OC and mainly involved in immune response-related pathways. Finally, TIMER and TIDE were used to predict gene immune function and its association with immunotherapy. We found that these four genes were positively correlated with better response to immune checkpoint blockade-based immunotherapy. Altogether, CXCL13, FCRLA, MS4A1, and PLA2G2D may be used as potential therapeutic genes for reflecting OC immune status and predicting response to immunotherapy.
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Affiliation(s)
- Lili Fan
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China.,School of Traditional Chinese Medicine, Jinan University, Guangzhou, China
| | - Han Lei
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Ying Lin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhengwei Zhou
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Guang Shu
- School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhipeng Yan
- Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Haotian Chen
- School of Basic Medical Sciences, Central South University, Changsha, China
| | - Tianxiang Zhang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
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18
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Sun T, He Y, Li W, Liu G, Li L, Wang L, Xiao Z, Han X, Wen H, Liu Y, Chen Y, Wang H, Li J, Fan Y, Zhang W, Zhang J. neoDL: a novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival. BMC Bioinformatics 2021; 22:382. [PMID: 34301201 PMCID: PMC8299600 DOI: 10.1186/s12859-021-04301-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/07/2021] [Indexed: 12/18/2022] Open
Abstract
Background Neoantigen based personalized immune therapies achieve promising results in melanoma and lung cancer, but few neoantigen based models perform well in IDH wild-type GBM, and the association between neoantigen intrinsic features and prognosis remain unclear in IDH wild-type GBM. We presented a novel neoantigen intrinsic feature-based deep learning model (neoDL) to stratify IDH wild-type GBMs into subgroups with different survivals. Results We first derived intrinsic features for each neoantigen associated with survival, followed by applying neoDL in TCGA data cohort(AUC = 0.988, p value < 0.0001). Leave one out cross validation (LOOCV) in TCGA demonstrated that neoDL successfully classified IDH wild-type GBMs into different prognostic subgroups, which was further validated in an independent data cohort from Asian population. Long-term survival IDH wild-type GBMs identified by neoDL were found characterized by 12 protective neoantigen intrinsic features and enriched in development and cell cycle. Conclusions The model can be therapeutically exploited to identify IDH wild-type GBM with good prognosis who will most likely benefit from neoantigen based personalized immunetherapy. Furthermore, the prognostic intrinsic features of the neoantigens inferred from this study can be used for identifying neoantigens with high potentials of immunogenicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04301-6.
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Affiliation(s)
- Ting Sun
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yufei He
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Wendong Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Guang Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Lin Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Lu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Zixuan Xiao
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Xiaohan Han
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Hao Wen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yong Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yifan Chen
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Haoyu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Jing Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
| | - Wei Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, People's Republic of China. .,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 South Fourth Ring Road West, Fengtai District, Beijing, 100070, People's Republic of China.
| | - Jing Zhang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, No.37 Xueyuan Road, Haidian District, Beijing, 100083, People's Republic of China.
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Lawlor RT, Mattiolo P, Mafficini A, Hong SM, Piredda ML, Taormina SV, Malleo G, Marchegiani G, Pea A, Salvia R, Kryklyva V, Shin JI, Brosens LA, Milella M, Scarpa A, Luchini C. Tumor Mutational Burden as a Potential Biomarker for Immunotherapy in Pancreatic Cancer: Systematic Review and Still-Open Questions. Cancers (Basel) 2021; 13:cancers13133119. [PMID: 34206554 PMCID: PMC8269341 DOI: 10.3390/cancers13133119] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Tumor mutational burden (TMB) represents the number of mutations per megabase (muts/Mb) harbored by tumor cells in a given neoplasm, and can be determined with next-generation sequencing. High values are an indicator of potential response to immunotherapy. With this systematic review, we assessed its role in pancreatic ductal adenocarcinoma (PDAC). Our main findings can be summarized as: (i) high-TMB can be found in about 1% of PDAC; (ii) it is associated with mucinous/colloid and medullary histology; (iii) high-TMB PDAC frequently harbor other actionable alterations, with microsatellite instability as the most common; (iv) immunotherapy has shown promising results in high-TMB PDAC. Abstract Tumor mutational burden (TMB) is a numeric index that expresses the number of mutations per megabase (muts/Mb) harbored by tumor cells in a neoplasm. TMB can be determined using different approaches based on next-generation sequencing. In the case of high values, it indicates a potential response to immunotherapy. In this systematic review, we assessed the potential predictive role of high-TMB in pancreatic ductal adenocarcinoma (PDAC), as well as the histo-molecular features of high-TMB PDAC. High-TMB appeared as a rare but not-negligible molecular feature in PDAC, being present in about 1.1% of cases. This genetic condition was closely associated with mucinous/colloid and medullary histology (p < 0.01). PDAC with high-TMB frequently harbored other actionable alterations, with microsatellite instability/defective mismatch repair as the most common. Immunotherapy has shown promising results in high-TMB PDAC, but the sample size of high-TMB PDAC treated so far is quite small. This study highlights interesting peculiarities of PDAC harboring high-TMB and may represent a reliable starting point for the assessment of TMB in the clinical management of patients affected by pancreatic cancer.
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Affiliation(s)
- Rita T. Lawlor
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
| | - Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy;
| | - Andrea Mafficini
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy;
| | - Seung-Mo Hong
- Asan Medical Center, Department of Pathology, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Maria L. Piredda
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
| | - Sergio V. Taormina
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
| | - Giuseppe Malleo
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy; (G.M.); (G.M.); (A.P.); (R.S.)
| | - Giovanni Marchegiani
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy; (G.M.); (G.M.); (A.P.); (R.S.)
| | - Antonio Pea
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy; (G.M.); (G.M.); (A.P.); (R.S.)
| | - Roberto Salvia
- Department of Surgery, The Pancreas Institute, University and Hospital Trust of Verona, 37134 Verona, Italy; (G.M.); (G.M.); (A.P.); (R.S.)
| | - Valentyna Kryklyva
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (V.K.); (L.A.B.)
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul 120-752, Korea;
| | - Lodewijk A. Brosens
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (V.K.); (L.A.B.)
- Department of Pathology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Michele Milella
- Department of Medicine, Section of Oncology, University and Hospital Trust of Verona, 37134 Verona, Italy;
| | - Aldo Scarpa
- ARC-Net Research Center, University and Hospital Trust of Verona, 37134 Verona, Italy; (R.T.L.); (A.M.); (M.L.P.); (S.V.T.)
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy;
- Correspondence: (A.S.); (C.L.); Tel.: +39-045-812-7458 (A.S.); +39-045-812-4835 (C.L.)
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy;
- Correspondence: (A.S.); (C.L.); Tel.: +39-045-812-7458 (A.S.); +39-045-812-4835 (C.L.)
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TP53 variant allele frequency correlates with the chemotherapy response score in ovarian/fallopian tube/peritoneal high-grade serous carcinoma. Hum Pathol 2021; 115:76-83. [PMID: 34153306 DOI: 10.1016/j.humpath.2021.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 11/23/2022]
Abstract
Molecular findings in ovarian, fallopian tube, and peritoneal high-grade serous carcinoma (HGSCa) are emerging as potential prognostic indicators. The chemotherapy response score (CRS) has been proposed as a histologic-based prognostic factor in patients with HGSCa treated with neoadjuvant chemotherapy (NACT). No study details the relationship between the mutational landscape of HGSCa and the CRS. This study addresses this issue using next-generation sequencing (NGS). We retrospectively identified 25 HGSCas treated with NACT and pathology material available to calculate the CRS. All cases had NGS on the primary debulking specimen post-NACT. The three-tier Böhm CRS was applied to the omentum or adnexa and calculated as a combined score. Tumor mutation burden (TMB) and TP53 variant allele frequency (VAF) were calculated and used in correlative analysis. All cases had at least one mutation, most commonly TP53 (25 cases, 100%). Other mutations were BRCA2 (one case, 4%), ARID1A (two cases, 8%), and 1 (4%) of each of the following: ERBB2, NTRK3, STK11, NTRK2, TSC1, PIK3CA, NF1, NOTCH3, CDK2, SMAD4, and PMS2. TMB ranged from 2.58 to 7.75 (median 3.84). There was no statistically significant relationship between the TMB and omental CRS, R-squared = 0.011 (P = 0.62); adnexal CRS, R-squared = 0.005 (P = 0.74); or with the combined CRS, R-squared = 0.009 (P = 0.65). Statistically significant correlation was found between the TP53 VAF and the omental CRS (R-squared = 0.28, P = 0.007), adnexal CRS (R-squared = 0.26, P = 0.01), and the combined CRS (R-squared = 0.33, P = 0.0026). The TP53 VAF was adjusted for percent of tumor present on the slide resulting in an average per cell TP53 mutational load, resulting in similar results with a statistically significant correlation between the average per cell TP53 mutational load and the omental CRS (R-squared = 0.27, P = 0.02), adnexal CRS (R-squared = 0.16, P = 0.05), and the combined CRS (R-squared = 0.23, P = 0.02). In summary, NGS confirmed TP53 mutations in all cases of HGSCa. TMB showed no correlation with the CRS. TP53 VAF and average per cell TP53 mutational load showed significant correlation with the CRS, whether graded on the adnexa or omentum or as a combined score, indicating concordance between molecular and histological findings following NACT.
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The RAD51-FFPE Test; Calibration of a Functional Homologous Recombination Deficiency Test on Diagnostic Endometrial and Ovarian Tumor Blocks. Cancers (Basel) 2021; 13:cancers13122994. [PMID: 34203855 PMCID: PMC8232577 DOI: 10.3390/cancers13122994] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Rapid and reliable identification of patients with homologous recombination deficient (HRD) tumors is important for treatment choice as these tumors tend to respond well to platinum-based chemotherapy and PARP inhibitors (PARPi). In this study, a RAD51-based functional HRD test that can be performed on routine diagnostic formalin-fixed paraffin-embedded (FFPE) tissues (RAD51-FFPE test), was further improved and optimal test parameters were determined. The RAD51-FFPE test was able to determine tumor HR status with high sensitivity and specificity, making it an attractive test to be applied as routine diagnostic tool in the near future. Abstract PARP inhibitor (PARPi) sensitivity is related to tumor-specific defects in homologous recombination (HR). Therefore, there is great clinical interest in tests that can rapidly and reliably identify HR deficiency (HRD). Functional HRD tests determine the actual HR status by using the (dis)ability to accumulate RAD51 protein at sites of DNA damage as read-out. In this study, we further improved and calibrated a previously described RAD51-based functional HRD test on 74 diagnostic formalin-fixed paraffin-embedded (FFPE) specimens (RAD51-FFPE test) from endometrial cancer (EC n = 25) and epithelial ovarian cancer (OC n = 49) patients. We established optimal parameters with regard to RAD51 foci cut-off (≥2) and HRD threshold (15%) using matched endometrial and ovarian carcinoma specimens for which HR status had been established using a RAD51-based test that required ex vivo irradiation of fresh tissue (RECAP test). The RAD51-FFPE test detected BRCA deficient tumors with 90% sensitivity and RECAP-HRD tumors with 87% sensitivity, indicating that it is an attractive alternative to DNA-based tests with the potential to be applied in routine diagnostic pathology.
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Oh SY, Rahman S, Sparano JA. Perspectives on PARP inhibitors as pharmacotherapeutic strategies for breast cancer. Expert Opin Pharmacother 2021; 22:981-1003. [PMID: 33646064 DOI: 10.1080/14656566.2021.1876662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction Approximately 10% of all breast cancer cases occur in individuals who have germline pathogenic variants of the BRCA 1, BRCA 2, and other genes associated with impaired DNA damage repair that is associated with an increased risk of breast, ovarian, and other cancers. Inhibitors of poly-ADP ribose polymerase (PARP) induce synthetic lethality in cancer cells harboring such pathogenic variants.Area covered In this review, the authors review the mechanisms of action, antitumor activity, and adverse events associated with PARP inhibitors for the treatment of advanced breast cancer. The authors then summarize the area and provide their expert perspectives on the area.Expert opinion Two PARP inhibitors are approved in metastatic breast cancer, including olaparib and talozaparib. Both agents were approved based on phase III trials demonstrating that they were associated with improved progression-free survival compared with treatment of physician's choice in patients receiving second-third line therapy for locally advanced, inoperable, or metastatic breast cancer in patients with germline pathogenic BRCA 1 or BRCA2 variants.
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Affiliation(s)
- Sun Young Oh
- Department of Hematology and Oncology, Montefiore-Einstein center for cancer care, Albert Einstein College of Medicine, Bronx, NY
| | - Shafia Rahman
- Department of Hematology and Oncology, Montefiore-Einstein center for cancer care, Albert Einstein College of Medicine, Bronx, NY
| | - Joseph A Sparano
- Department of Hematology and Oncology, Montefiore-Einstein center for cancer care, Albert Einstein College of Medicine, Bronx, NY
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van Wilpe S, Tolmeijer SH, Koornstra RHT, de Vries IJM, Gerritsen WR, Ligtenberg M, Mehra N. Homologous Recombination Repair Deficiency and Implications for Tumor Immunogenicity. Cancers (Basel) 2021; 13:cancers13092249. [PMID: 34067105 PMCID: PMC8124836 DOI: 10.3390/cancers13092249] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 01/06/2023] Open
Abstract
Homologous recombination repair deficiency (HRD) can be observed in virtually all cancer types. Although HRD sensitizes tumors to DNA-damaging chemotherapy and poly(ADP-ribose) polymerase (PARP) inhibitors, all patients ultimately develop resistance to these therapies. Therefore, it is necessary to identify therapeutic regimens with a more durable efficacy. HRD tumors have been suggested to be more immunogenic and, therefore, more susceptible to treatment with checkpoint inhibitors. In this review, we describe how HRD might mechanistically affect antitumor immunity and summarize the available translational evidence for an association between HRD and antitumor immunity across multiple tumor types. In addition, we give an overview of all available clinical data on the efficacy of checkpoint inhibitors in HRD tumors and describe the evidence for using treatment strategies that combine checkpoint inhibitors with PARP inhibitors.
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Affiliation(s)
- Sandra van Wilpe
- Department of Medical Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (S.v.W.); (S.H.T.); (W.R.G.)
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Sofie H. Tolmeijer
- Department of Medical Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (S.v.W.); (S.H.T.); (W.R.G.)
| | | | - I. Jolanda M. de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Winald R. Gerritsen
- Department of Medical Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (S.v.W.); (S.H.T.); (W.R.G.)
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Marjolijn Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (S.v.W.); (S.H.T.); (W.R.G.)
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
- Correspondence:
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PEG3 mutation is associated with elevated tumor mutation burden and poor prognosis in breast cancer. Biosci Rep 2021; 40:225944. [PMID: 32729618 PMCID: PMC7419805 DOI: 10.1042/bsr20201648] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Breast cancer is the second most common malignancy in women and considered as a severe health burden. PEG3 mutations have been observed in several cancers. However, the associations of PEG3 mutation with tumor mutation burden (TMB) and prognosis in breast cancer have not been investigated. Methods: In our study, the somatic mutation data of 986 breast cancer patients from The Cancer Genome Atlas (TCGA) were analyzed. Results: It showed that PEG3 had a relatively high mutation rate (2%). After calculated the TMB in PEG3 mutant and PEG3 wild-type groups, we found the TMB value was significantly higher in PEG3 mutant samples than that in PEG3 wild-type samples (P = 5.6e-07), which was independent of the confounding factors including age, stage, mutations of BRCA1, BRCA2 and POLE (odd ratio, 0.45; 95% CI, 0.20–0.98; P=0.044). Survival analysis revealed that PEG3 mutant samples had inferior survival outcome compared with the PEG3 wild-type samples after adjusted for the confounding factors above (hazard ratio, 0.27; 95% CI: 0.12–0.57; P<0.001). Conclusion: These results illustrated that PEG3 mutation was associated with high TMB and inferior prognosis, suggesting PEG3 mutation might play a guiding role in prognosis prediction and immunotherapy selection in breast cancer.
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25
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Eskander RN, Powell MA. Immunotherapy as a treatment strategy in advanced stage and recurrent endometrial cancer: review of current phase III immunotherapy clinical trials. Ther Adv Med Oncol 2021; 13:17588359211001199. [PMID: 33796152 PMCID: PMC7970168 DOI: 10.1177/17588359211001199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022] Open
Abstract
The treatment of advanced stage, metastatic or recurrent endometrial cancer remains a clinically difficult scenario. Although combination carboplatin and paclitaxel is an effective standard-of-care regimen, alternate strategies have shown promise, particularly in biomarker select populations. In an effort to improve oncologic outcomes, investigators are exploring novel immunotherapy combinations. In this review, we discuss the clinical rationale and design of current phase III immuno-oncology clinical trials in patients with advanced stage or recurrent endometrial cancer.
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Affiliation(s)
- Ramez N. Eskander
- Department of Obstetrics, Gynecology and
Reproductive Sciences, Division of Gynecologic Oncology, University of
California San Diego Moores Cancer Center, 3855 Health Sciences Drive, La
Jolla, CA 92093, USA
| | - Matthew A. Powell
- Department of Obstetrics and Gynecology,
Division of Gynecologic Oncology, Washington University School of Medicine,
St. Louis, MO, USA
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26
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Li Y, Zhang X, Gao Y, Shang C, Yu B, Wang T, Su J, Huang C, Wu Y, Guo H, Ha C. Development of a Genomic Signatures-Based Predictor of Initial Platinum-Resistance in Advanced High-Grade Serous Ovarian Cancer Patients. Front Oncol 2021; 10:625866. [PMID: 33747898 PMCID: PMC7977004 DOI: 10.3389/fonc.2020.625866] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/30/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND High grade serous ovarian cancer (HGSOC) is the most common subtype of ovarian cancer. Although platinum-based chemotherapy has been the cornerstone for HGSOC treatment, nearly 25% of patients would have less than 6 months of interval since the last platinum chemotherapy, referred to as platinum-resistance. Currently, no precise tools to predict platinum resistance have been developed yet. METHODS Ninety-nine HGSOC patients, who have finished cytoreductive surgery and platinum-based chemotherapy in Peking University Third Hospital from 2018 to 2019, were enrolled. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) were performed on the collected tumor tissue samples to establish a platinum-resistance predictor in a discovery cohort of 57 patients, and further validated in another 42 HGSOC patients. RESULTS A high prevalence of alterations in DNA damage repair (DDR) pathway, including BRCA1/2, was identified both in the platinum-sensitive and resistant HGSOC patients. Compared with the resistant subgroup, there was a trend of higher prevalence of homologous recombination deficiency (HRD) in the platinum-sensitive subgroup (78.95% vs. 47.37%, p=0.0646). Based on the HRD score, microhomology insertions and deletions (MHID), copy number changes load, duplication load of 1-100 kb, single nucleotide variants load, and eight other mutational signatures, a combined predictor of platinum-resistance, named as DRDscore, was established. DRDscore outperformed in predicting the platinum-sensitivity than the previously reported biomarkers with a predictive accuracy of 0.860 at a threshold of 0.7584. The predictive performance of DRDscore was validated in an independent cohort of 42 HGSOC patients with a sensitivity of 90.9%. CONCLUSIONS A multi-genomic signature-based analysis enabled the prediction of initial platinum resistance in advanced HGSOC patients, which may serve as a novel assessment of platinum resistance, provide therapeutic guidance, and merit further validation.
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Affiliation(s)
- Yuan Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Xiaolan Zhang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yan Gao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Chunliang Shang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Bo Yu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Tongxia Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Junyan Su
- Lifehealthcare Clinical Laboratories, Hangzhou, China
| | - Cuiyu Huang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Hongyan Guo
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Chunfang Ha
- Department of Gynecology and Obstetrics Department, General Hospital of Ningxia Medical University, Yinchuan, China
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27
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Yu C, Zhou L, Zhang Q. Identification of unanimous immune subtypes for different hormone receptor phenotypes of human breast cancer with potential prognostic significance. Int Immunopharmacol 2021; 94:107473. [PMID: 33611062 DOI: 10.1016/j.intimp.2021.107473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/06/2021] [Accepted: 01/28/2021] [Indexed: 12/19/2022]
Abstract
The immunogenicity of the breast tumor microenvironment is clinically heterogeneous. The insight into the role of tumor-infiltrating lymphocytes (TILs) might serve as a biomarker to predict a survival benefit and enable optimal patient selection for immunotherapy. In this study, we aimed at characterizing the breast cancer immune subtypes linked to CD8 T cells and associating with the patient characteristics and clinical outcomes. We analyzed the immune gene signatures of human breast cancer using The Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) database profiling of 1092 breast tumor patients. We performed hierarchical clustering to the immune gene expression by applying hormone receptor status including triple negative breast cancer to categorize 66 immune-related genes in breast tumors. The separation was characterized by dividing the breast tumors into two major immune subtypes: predominant immune (PI) subtype and low immune subtype (LI). Our results showed that both PI and LI subtypes can be observed in the different hormone receptor phenotypes of breast tumors, and PI subtype accounted for 16% and LI subtype 20% in the breast tumor patients. The estimated odds for LI subtype breast tumors were significantly higher than PI subtype breast tumors in primary tumor stages. Our data demonstrated that the PI subtype breast tumors have significantly improved survival compared with LI subtype. Our findings provide a novel perspective of breast cancer immune subtypes linked to CD8 T cells. The immune subtypes will be a valuable resource for future research to identify clinically relevant biomarkers for precision immunotherapy.
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Affiliation(s)
- ChenWei Yu
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, China.
| | - Linlin Zhou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, China.
| | - Qiuyu Zhang
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian, China.
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28
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Li N, Li B, Zhan X. Comprehensive Analysis of Tumor Microenvironment Identified Prognostic Immune-Related Gene Signature in Ovarian Cancer. Front Genet 2021; 12:616073. [PMID: 33679883 PMCID: PMC7928403 DOI: 10.3389/fgene.2021.616073] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
Background Accumulating evidence demonstrated that tumor microenvironmental cells played important roles in predicting clinical outcomes and therapeutic efficacy. We aimed to develop a reliable immune-related gene signature for predicting the prognosis of ovarian cancer (OC). Methods Single sample gene-set enrichment analysis (ssGSEA) of immune gene-sets was used to quantify the relative abundance of immune cell infiltration and develop high- and low-abundance immune subtypes of 308 OC samples. The presence of infiltrating stromal/immune cells in OC tissues was calculated as an estimate score. We estimated the correlation coefficients among the immune subtype, clinicopathological feature, immune score, distribution of immune cells, and tumor mutation burden (TMB). The differentially expressed immune-related genes between high- and low-abundance immune subtypes were further used to construct a gene signature of a prognostic model in OC with lasso regression analysis. Results The ssGSEA analysis divided OC samples into high- and low-abundance immune subtypes based on the abundance of immune cell infiltration, which was significantly related to the estimate score and clinical characteristics. The distribution of immune cells was also significantly different between high- and low-abundance immune subtypes. The correlation analysis showed the close relationship between TMB and the estimate score. The differentially expressed immune-related genes between high- and low-abundance immune subtypes were enriched in multiple immune-related pathways. Some immune checkpoints (PDL1, PD1, and CTLA-4) were overexpressed in the high-abundance immune subtype. Furthermore, the five-immune-related-gene-signature prognostic model (CCL18, CXCL13, HLA-DOB, HLA-DPB2, and TNFRSF17)-based high-risk and low-risk groups were significantly related to OC overall survival. Conclusion Immune-related genes were the promising predictors of prognosis and survival, and the comprehensive landscape of tumor microenvironmental cells of OC has potential for therapeutic schedule monitoring.
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Affiliation(s)
- Na Li
- Science and Technology Innovation Center, Shandong First Medical University, Jinan, China.,Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China.,State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Biao Li
- Science and Technology Innovation Center, Shandong First Medical University, Jinan, China.,Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China.,State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Xianquan Zhan
- Science and Technology Innovation Center, Shandong First Medical University, Jinan, China.,Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China.,State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China.,Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
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29
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Zhang Y, Shi X, Zhang J, Chen X, Zhang P, Liu A, Zhu T. A comprehensive analysis of somatic alterations in Chinese ovarian cancer patients. Sci Rep 2021; 11:387. [PMID: 33432021 PMCID: PMC7801677 DOI: 10.1038/s41598-020-79694-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
Ovarian cancer is one of the most common cancers in women and is often diagnosed as advanced stage because of the subtle symptoms of early ovarian cancer. To identify the somatic alterations and new biomarkers for the diagnosis and targeted therapy of Chinese ovarian cancer patients, a total of 65 Chinese ovarian cancer patients were enrolled for detection of genomic alterations. The most commonly mutated genes in ovarian cancers were TP53 (86.15%, 56/65), NF1 (13.85%, 9/65), NOTCH3 (10.77%, 7/65), and TERT (10.77%, 7/65). Statistical analysis showed that TP53 and LRP1B mutations were associated with the age of patients, KRAS, TP53, and PTEN mutations were significantly associated with tumor differentiation, and MED12, LRP2, PIK3R2, CCNE1, and LRP1B mutations were significantly associated with high tumor mutational burden. The mutation frequencies of LRP2 and NTRK3 in metastatic ovarian cancers were higher than those in primary tumors, but the difference was not significant (P = 0.072, for both). Molecular characteristics of three patients responding to olapanib supported that BRCA mutation and HRD related mutations is the target of olaparib in platinum sensitive patients. In conclusion we identified the somatic alterations and suggested a group of potential biomarkers for Chinese ovarian cancer patients. Our study provided a basis for further exploration of diagnosis and molecular targeted therapy for Chinese ovarian cancer patients.
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Affiliation(s)
- Yingli Zhang
- Department of Gynecologic Oncology, Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Science, Hangzhou, People's Republic of China.,Department of Gynecological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, People's Republic of China.,Department of Gynecological Surgery, Zhejiang Cancer Hospital, No 1, East Banshan Road, Gongshu District, Hangzhou, 310022, People's Republic of China
| | - Xiaoliang Shi
- OrigiMed Co. Ltd, Shanghai, 201114, People's Republic of China
| | - Jiejie Zhang
- Department of Gynecologic Oncology, Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Science, Hangzhou, People's Republic of China.,Department of Gynecological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, People's Republic of China.,Department of Gynecological Surgery, Zhejiang Cancer Hospital, No 1, East Banshan Road, Gongshu District, Hangzhou, 310022, People's Republic of China
| | - Xi Chen
- Department of Gynecologic Oncology, Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Science, Hangzhou, People's Republic of China.,Department of Gynecological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, People's Republic of China.,Department of Gynecological Surgery, Zhejiang Cancer Hospital, No 1, East Banshan Road, Gongshu District, Hangzhou, 310022, People's Republic of China
| | - Peng Zhang
- OrigiMed Co. Ltd, Shanghai, 201114, People's Republic of China
| | - Angen Liu
- OrigiMed Co. Ltd, Shanghai, 201114, People's Republic of China
| | - Tao Zhu
- Department of Gynecologic Oncology, Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Science, Hangzhou, People's Republic of China. .,Department of Gynecological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, People's Republic of China. .,Department of Gynecological Surgery, Zhejiang Cancer Hospital, No 1, East Banshan Road, Gongshu District, Hangzhou, 310022, People's Republic of China.
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30
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Oza J, Doshi SD, Hao L, Musi E, Schwartz GK, Ingham M. Homologous recombination repair deficiency as a therapeutic target in sarcoma. Semin Oncol 2020; 47:380-389. [DOI: 10.1053/j.seminoncol.2020.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/29/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
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31
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Limaye S, Kumar P, Pragya R, Sambath J, Patil D, Srinivasan A, Apurva S, Srivastava N, Patil S, Patil R, Datta V, Akolkar D, Datar R. A case report of androgen receptor inhibitor therapy in recurrent high-grade serous ovarian cancer. Oncotarget 2020; 11:4358-4363. [PMID: 33245722 PMCID: PMC7679039 DOI: 10.18632/oncotarget.27809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/27/2020] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer is common gynaecological malignancy and a leading cause of death among women. Despite the advances in treatment strategies, majority of patients present with recurrence after first- or second-line treatment. Targeted therapy that has proven to be effective in other advanced or metastatic solid tumors have also demonstrated its efficacy in ovarian cancer. Recent studies have shown that the androgen receptor (AR) signalling is involved in pathogenicity and progression of cancer. Current observations suggest AR could be a potential target in managing the disease. In this case report we present a patient with high grade serous ovarian cancer (HGSOC) with multiple relapses with excellent disease control on AR inhibition with bicalutamide.
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Affiliation(s)
- Sewanti Limaye
- Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute, Mumbai, Maharashtra, India
| | - Prashant Kumar
- Datar Cancer Genetics Limited, Nasik, Maharashtra, India.,Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ramya Pragya
- Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute, Mumbai, Maharashtra, India
| | - Janani Sambath
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Darshana Patil
- Datar Cancer Genetics Limited, Nasik, Maharashtra, India
| | | | - Sachin Apurva
- Datar Cancer Genetics Limited, Nasik, Maharashtra, India
| | | | - Sanket Patil
- Datar Cancer Genetics Limited, Nasik, Maharashtra, India
| | - Revati Patil
- Datar Cancer Genetics Limited, Nasik, Maharashtra, India
| | - Vineet Datta
- Datar Cancer Genetics Limited, Nasik, Maharashtra, India
| | | | - Rajan Datar
- Datar Cancer Genetics Limited, Nasik, Maharashtra, India
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32
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Mi JL, Xu M, Liu C, Wang RS. Interactions between tumor mutation burden and immune infiltration in ovarian cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:2513-2523. [PMID: 33165430 PMCID: PMC7642696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
The aim of the study was to evaluate the relationship between tumor mutational burden (TMB) and immune infiltration in ovarian cancer. We extracted somatic mutational data and gene expression profiles of ovarian cancer from The Cancer Genome Atlas (TCGA). The samples were separated into low and high TMB groups. Correlations between TMB and cancer prognosis were analyzed and immune cell infiltration in the high and low TMB subgroups was calculated using the CIBERSORT package software. High TMB was significantly related to an improved survival rate. We identified 4 TMB-related core genes that were significantly associated with prognosis. Furthermore, mutations in the 4 genes were associated with immune cell infiltration. We also found a high proportion of naive B cells and activated NK cells in the high TMB group, while increased proportions of memory B cells and plasma cells were found in the low TMB group. Overall, our study indicated that patients with a higher TMB level experienced a favorable survival outcome and this may influence immune infiltration in ovarian cancer. Furthermore, the 4 TMB-related core genes were highly correlated with prognosis and the level of immune cell infiltration.
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Affiliation(s)
- Jing-Lin Mi
- Department of Radiotherapy Oncology Clinical Medical Research Center, Guangxi Medical UniversityNanning, People’s Republic of China
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, People’s Republic of China
| | - Meng Xu
- Department of Radiotherapy Oncology Clinical Medical Research Center, Guangxi Medical UniversityNanning, People’s Republic of China
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, People’s Republic of China
| | - Chang Liu
- Department of Radiotherapy Oncology Clinical Medical Research Center, Guangxi Medical UniversityNanning, People’s Republic of China
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, People’s Republic of China
| | - Ren-Sheng Wang
- Department of Radiotherapy Oncology Clinical Medical Research Center, Guangxi Medical UniversityNanning, People’s Republic of China
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, People’s Republic of China
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Riviere P, Goodman AM, Okamura R, Barkauskas DA, Whitchurch TJ, Lee S, Khalid N, Collier R, Mareboina M, Frampton GM, Fabrizio D, Sharabi AB, Kato S, Kurzrock R. High Tumor Mutational Burden Correlates with Longer Survival in Immunotherapy-Naïve Patients with Diverse Cancers. Mol Cancer Ther 2020; 19:2139-2145. [PMID: 32747422 PMCID: PMC7541603 DOI: 10.1158/1535-7163.mct-20-0161] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/29/2020] [Accepted: 07/20/2020] [Indexed: 01/02/2023]
Abstract
Higher tumor mutational burden (TMB) has been correlated with response to checkpoint blockade immunotherapy. However, it is unclear whether TMB independently serves as a prognostic biomarker for outcomes in immunotherapy-naïve patients. Here, we evaluated the relationship between TMB and overall survival in 1,415 immunotherapy-naïve patients with diverse advanced malignancies. TMB was studied both as a tiered variable (low ≤5 mutations/Mb, intermediate >5 and <20, high ≥20 and <50, and very high ≥50) and as a continuous variable. Interestingly, we observed a parabolic correlation between TMB and overall survival, in which intermediate-range TMB correlated with decreased survival, whereas low and very high TMB correlated with improved outcomes (median survival: 238, 174, 195, and 350 weeks for low, intermediate, high, and very high TMB, respectively; multivariate P < 0.01). This corresponded to an HR of 1.29 (95% confidence interval, 1.07-1.54; P < 0.01) for intermediate-range TMB on multivariable survival analysis correcting for known confounders, including primary tumor of origin. These results demonstrate that TMB may have utility as a prognostic biomarker in immunotherapy-naïve patients, with a protective effect at higher TMBs, and that studies of survival in immunotherapy-treated patients may need to stratify or randomize by TMB in a nonlinear fashion to account for this confounding.
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Affiliation(s)
- Paul Riviere
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California
| | - Aaron M Goodman
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
- Division of Blood and Marrow Transplantation, University of California, Moores Cancer Center, La Jolla, California
| | - Ryosuke Okamura
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
| | - Donald A Barkauskas
- Biostatistics Division, Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Theresa J Whitchurch
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
| | - Suzanna Lee
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
| | - Noor Khalid
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
| | - Rachel Collier
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
| | - Manvita Mareboina
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
| | | | | | - Andrew B Sharabi
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California
| | - Shumei Kato
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, Department of Medicine, University of California, Moores Cancer Center, La Jolla, California.
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Shao C, Li G, Huang L, Pruitt S, Castellanos E, Frampton G, Carson KR, Snow T, Singal G, Fabrizio D, Alexander BM, Jin F, Zhou W. Prevalence of High Tumor Mutational Burden and Association With Survival in Patients With Less Common Solid Tumors. JAMA Netw Open 2020; 3:e2025109. [PMID: 33119110 PMCID: PMC7596577 DOI: 10.1001/jamanetworkopen.2020.25109] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
IMPORTANCE Tumor mutational burden (TMB) is a potential biomarker associated with response to immune checkpoint inhibitor therapies. The prognostic value associated with TMB in the absence of immunotherapy is uncertain. OBJECTIVE To assess the prevalence of high TMB (TMB-H) and its association with overall survival (OS) among patients not treated with immunotherapy with the same 10 tumor types from the KEYNOTE-158 study. DESIGN, SETTING, AND PARTICIPANTS This retrospective cohort study evaluated the prognostic value of TMB-H, assessed by Foundation Medicine (FMI) and defined as at least 10 mutations/megabase (mut/Mb) in the absence of immunotherapy. Data were sourced from the deidentified Flatiron Health-FMI clinicogenomic database collected up to July 31, 2018. Eligible patients were aged 18 years or older with any of the following solid cancer types: anal, biliary, endometrial, cervical, vulvar, small cell lung, thyroid, salivary gland, mesothelioma, or neuroendocrine tumor. Patients with microsatellite instability-high tumors were excluded from primary analysis. For OS analysis, patients were excluded if immunotherapy started on the FMI report date or earlier or if patients died before January 1, 2012, and patients were censored if immunotherapy was started later than the FMI report date. Data were analyzed from November 2018 to February 2019. MAIN OUTCOMES AND MEASURES Overall survival was analyzed using the Kaplan-Meier method and Cox proportional hazards model, adjusting for age, sex, cancer types, practice type, and albumin level. RESULTS Of 2589 eligible patients, 1671 (64.5%) were women, and the mean (SD) age was 63.7 (11.7) years. Median (interquartile range) TMB was 2.6 (1.7-6.1) mut/Mb, and 332 patients (12.8%) had TMB-H (≥10 mut/Mb). Prevalence of TMB-H was highest among patients with small cell lung cancer (40.0%; 95% CI, 34.7%-45.6%) and neuroendocrine tumor (29.3%; 95% CI, 22.8%-36.6%) and lowest was among patients with mesothelioma (1.2%; 95% CI, 0.3%-4.4%) and thyroid cancer (2.7%; 95% CI, 1.2%-5.7%). Adjusted hazard ratio for OS of patients not treated with immunotherapy with TMB-H vs those without TMB-H was 0.94 (95% CI, 0.77-1.13). Comparable results were observed when including patients with high microsatellite instability tumors and calculating OS from first observed antineoplastic treatment date. CONCLUSIONS AND RELEVANCE These findings suggest that prevalence of TMB-H varies widely depending on tumor type and TMB-H does not appear to be a factor associated with OS among patients across these cancer types treated in the absence of immunotherapy.
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Affiliation(s)
| | - Gerald Li
- Foundation Medicine, Cambridge, Massachusetts
| | | | | | | | | | | | | | | | | | | | - Fan Jin
- Merck and Co, Kenilworth, New Jersey
| | - Wei Zhou
- Merck and Co, Kenilworth, New Jersey
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van Wijk LM, Vermeulen S, Meijers M, van Diest MF, ter Haar NT, de Jonge MM, Solleveld-Westerink N, van Wezel T, van Gent DC, Kroep JR, Bosse T, Gaarenstroom KN, Vrieling H, Vreeswijk MPG. The RECAP Test Rapidly and Reliably Identifies Homologous Recombination-Deficient Ovarian Carcinomas. Cancers (Basel) 2020; 12:E2805. [PMID: 33003546 PMCID: PMC7650677 DOI: 10.3390/cancers12102805] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022] Open
Abstract
Recent studies have shown that the efficacy of PARP inhibitors in epithelial ovarian carcinoma (EOC) is related to tumor-specific defects in homologous recombination (HR) and extends beyond BRCA1/2 deficient EOC. A robust method with which to identify HR-deficient (HRD) carcinomas is therefore of utmost clinical importance. In this study, we investigated the proficiency of a functional HR assay based on the detection of RAD51 foci, the REcombination CAPacity (RECAP) test, in identifying HRD tumors in a cohort of prospectively collected epithelial ovarian carcinomas (EOCs). Of the 39 high-grade serous ovarian carcinomas (HGSOC), the RECAP test detected 26% (10/39) to be HRD, whereas ovarian carcinomas of other histologic subtypes (n = 10) were all HR-proficient (HRP). Of the HRD tumors that could be sequenced, 8/9 showed pathogenic BRCA1/2 variants or BRCA1 promoter hypermethylation, indicating that the RECAP test reliably identifies HRD, including but not limited to tumors related to BRCA1/2 deficiency. Furthermore, we found a trend towards better overall survival (OS) of HGSOC patients with RECAP-identified HRD tumors compared to patients with HRP tumors. This study shows that the RECAP test is an attractive alternative to DNA-based HRD tests, and further development of a clinical grade RECAP test is clearly warranted.
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Affiliation(s)
- Lise M. van Wijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Sylvia Vermeulen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Matty Meijers
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Manuela F. van Diest
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Natalja T. ter Haar
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Marthe M. de Jonge
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Nienke Solleveld-Westerink
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Dik C. van Gent
- Department of Molecular Genetics, Erasmus MC, 3000 CA Rotterdam, The Netherlands;
| | - Judith R. Kroep
- Department of Medical Oncology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (N.T.t.H.); (M.M.d.J.); (N.S.-W.); (T.v.W.); (T.B.)
| | - Katja N. Gaarenstroom
- Department of Gynecology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
| | - Maaike P. G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (L.M.v.W.); (S.V.); (M.M.); (M.F.v.D.); (H.V.)
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Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
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Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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Gbolahan O, Hashemi-Sadraei N, O'Neil B. Prolonged Response to Anti-PD-1 Antibody Therapy in Chemotherapy-Refractory Cholangiocarcinoma With High Tumor Mutational Burden. J Natl Compr Canc Netw 2020; 17:644-648. [PMID: 31200359 DOI: 10.6004/jnccn.2019.7304] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/29/2019] [Indexed: 12/16/2022]
Abstract
Management of advanced intrahepatic cholangiocarcinoma (iCCA) is challenging and overall survival is poor. Progress in the development of new therapeutic options for metastatic cholangiocarcinoma (CCA) has been slow; hence, to date, there are no approved second-line agents in this setting. Although the development of immune checkpoint inhibitors has significantly improved overall survival in a variety of malignancies, there has not been a clinically important impact in CCA. This report presents a 66-year-old patient with chemotherapy-refractory iCCA who experienced a prolonged response to immunotherapy. Tumor genome profiling revealed a high tumor mutation burden of 17 mutations per megabase in the absence of microsatellite instability. He was started on immunotherapy with nivolumab and has experienced an ongoing response for 16 months without clinical symptoms and only minimal radiologic disease.
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Affiliation(s)
- Olumide Gbolahan
- University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | | | - Bert O'Neil
- Indiana University School of Medicine, Indianapolis, Indiana
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Yu QJ, Liang YZ, Mei XP, Fang TY. Tumor mutation burden associated with miRNA-gene interaction outcome mediates the survival of patients with liver hepatocellular carcinoma. EXCLI JOURNAL 2020; 19:861-871. [PMID: 32665773 PMCID: PMC7355149 DOI: 10.17179/excli2020-1224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023]
Abstract
Tumor mutation burden (TMB) is associated with immunogenic responses and the survival of cancer patients. This study demonstrates how TMB levels impact the immune-related cells, genes, and miRNAs, and how miRNA/gene interactions respond to variations in the survival rate of patients with liver hepatocellular carcinoma (LIHC). LIHC patients were divided into two groups, either a low TMB (< median) or a high TMB (≥ median) group. We found that high TMB plays a positive role in immune-mediated infiltration, generating more CD4 T-cells and memory B cells. Among the 21 immune genes that altered significantly, only C9orf24 and CYP1A1 were expected to up-regulate in LIHC patients with high TMB. A total of 19 miRNAs, which regulate various functional pathways, were significantly altered in patients with LIHC. One of the miRNA/gene pair, hsa-miR-33a/ALDH1A3 was significantly associated with the survival rate of LIHC patients. Our results suggest that LIHC patients with high TMB can be treated more effectively with immunotherapy.
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Affiliation(s)
- Qing-Jiang Yu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Jiaxing University, Jiaxing 314000, China
| | - Yi-Zhi Liang
- Department of Gastroenterology, Second Affiliated Hospital, Fujian Medical University, Quanzhou 362000, China
| | - Xiao-Ping Mei
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Jiaxing University, Jiaxing 314000, China
| | - Tai-Yong Fang
- Department of Gastroenterology, Second Affiliated Hospital, Fujian Medical University, Quanzhou 362000, China
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Xu LB, Zhao ZG, Xu SF, Zhang XX, Liu T, Jing CY, Zhang SG, Yu SJ. The landscape of gene mutations and clinical significance of tumor mutation burden in patients with soft tissue sarcoma who underwent surgical resection and received conventional adjuvant therapy. Int J Biol Markers 2020; 35:14-22. [PMID: 32520634 DOI: 10.1177/1724600820925095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The aim of this study was to evaluate the landscape of gene mutations and the clinical significance of tumor mutation burden (TMB) in patients with soft tissue sarcoma who underwent surgical resection and received conventional adjuvant therapy. METHODS A total of 68 patients with soft tissue sarcoma were included. Postoperative tumor tissue specimens from the patients were collected for DNA extraction. Targeted next-generation sequencing of cancer-relevant genes was performed for the detection of gene mutations and the analysis of TMB. Univariate analysis between TMB status and prognosis was carried out using the Kaplan-Meier survival analysis, and multivariate analysis was adjusted by the Cox regression model. RESULTS No specific genetic mutations associated with soft tissue sarcoma were found. The mutation frequency of TP53, PIK3C2G, NCOR1, and KRAS of the 68 patients with soft tissue sarcoma were observed in 19 cases (27.94%), 15 cases (22.06%), 14 cases (20.59%), and 14 cases (20.59%), respectively. With regard to the analysis of TMB, the overall TMB of the 68 patients with soft tissue sarcoma was relatively low (median: 2.05 per Mb (range: 0∼15.5 per Mb)). Subsequently, TMB status was divided into TMB-Low and TMB-Middle according to the median TMB. Patients with TMB-Low and TMB-Middle were 37 cases (54.41%) and 31 cases (45.59%), respectively. Overall survival analysis indicated that the median overall survival of patients with TMB-Low and TMB-Middle was not reached, and 4.5 years, respectively (P=0.015). CONCLUSION This study characterizes the genetic background of patients with STS soft tissue sarcoma. The TMB was of clinical significance for patients with soft tissue sarcoma who underwent surgical resection and received conventional adjuvant therapy.
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Affiliation(s)
- Li-Bin Xu
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhen-Guo Zhao
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Song-Feng Xu
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin-Xin Zhang
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Liu
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chang-You Jing
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shu-Guang Zhang
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sheng-Ji Yu
- Department of Orthopedic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Tumor mutational burden and immune infiltration as independent predictors of response to neoadjuvant immune checkpoint inhibition in early TNBC in GeparNuevo. Ann Oncol 2020; 31:1216-1222. [PMID: 32461104 DOI: 10.1016/j.annonc.2020.05.015] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/27/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The predictive value of tumor mutational burden (TMB), alone or in combination with an immune gene expression profile (GEP), for response to neoadjuvant therapy in early triple negative breast cancer (TNBC) is currently not known, either for immune checkpoint blockade (ICB) or conventional chemotherapy. PATIENTS AND METHODS We obtained both whole exome sequencing and RNA-Seq data from pretreatment samples of 149 TNBC of the recent neoadjuvant ICB trial, GeparNuevo. In a predefined analysis, we assessed the predictive value of TMB and a previously developed immune GEP for pathological complete remission (pCR). RESULTS Median TMB was 1.52 mut/Mb (range 0.02-7.65) and was significantly higher in patients with pCR (median 1.87 versus 1.39; P = 0.005). In multivariate analysis, odds ratios for pCR per mut/Mb were 2.06 [95% confidence intervals (CI) 1.33-3.20, P = 0.001] among all patients, 1.77 (95% CI 1.00-3.13, P = 0.049) in the durvalumab treatment arm, and 2.82 (95% CI 1.21-6.54, P = 0.016) in the placebo treatment arm, respectively. We also found that both continuous TMB and immune GEP (or tumor infiltrating lymphocytes) independently predicted pCR. When we stratified patients in groups based on the upper tertile of TMB and median GEP, we observed a pCR rate of 82% (95% CI 60% to 95%) in the group with both high TMB and GEP in contrast to only 28% (95% CI 16% to 43%) in the group with both low TMB and GEP. CONCLUSIONS TMB and immune GEP add independent value for pCR prediction. Our results recommend further analysis of TMB in combination with immune parameters to individually tailor therapies in breast cancer.
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Clinical Implications of DNA Repair Defects in High-Grade Serous Ovarian Carcinomas. Cancers (Basel) 2020; 12:cancers12051315. [PMID: 32455819 PMCID: PMC7281678 DOI: 10.3390/cancers12051315] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
Despite significant improvements in surgical and medical management, high grade serous ovarian cancer (HGSOC) still represents the deadliest gynecologic malignancy and the fifth most frequent cause of cancer-related mortality in women in the USA. Since DNA repair alterations are regarded as the “the Achille’s heel” of HGSOC, both DNA homologous recombination and DNA mismatch repair deficiencies have been explored and targeted in epithelial ovarian cancers in the latest years. In this review, we aim at focusing on the therapeutic issues deriving from a faulty DNA repair machinery in epithelial ovarian cancers, starting from existing and well-established treatments and investigating new therapeutic approaches which could possibly improve ovarian cancer patients’ survival outcomes in the near future. In particular, we concentrate on the role of both Poly (ADP-ribose) Polymerase (PARP) inhibitors (PARPis) and immune checkpoint inhibitors in HGSOC, highlighting their activity in relation to BRCA1/2 mutational status and homologous recombination deficiency (HRD). We investigate the biological rationale supporting their use in the clinical setting, pointing at tracking their route from the laboratory bench to the patient’s bedside. Finally, we deal with the onset of mechanisms of primary and acquired resistance to PARPis, reporting the pioneering strategies aimed at converting homologous-recombination (HR) proficient tumors into homologous recombination (HR)-deficient HGSOC.
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Chen G, Wang L, Diao T, Chen Y, Cao C, Zhang X. Analysis of immune-related signatures of colorectal cancer identifying two different immune phenotypes: Evidence for immune checkpoint inhibitor therapy. Oncol Lett 2020; 20:517-524. [PMID: 32565977 PMCID: PMC7285802 DOI: 10.3892/ol.2020.11605] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/05/2020] [Indexed: 12/24/2022] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy has revolutionized the treatment of numerous types of cancer, including colorectal cancer (CRC). Patients with CRC and deficient mismatch repair or high microsatellite instability could benefit from ICI treatment, although the response rate of most patients is low. Therefore, the immune subtyping of patients with CRC is required in order to determine the subtypes suitable for ICI treatment. The present study used a cohort of patients with CRC from The Cancer Genome Atlas (TCGA) to perform molecular subtyping, with results validated in three CRC cohorts from the Gene Expression Omnibus. Non-negative matrix factorization was used to achieve consensus molecular subtyping. The tumor immune dysfunction and exclusion algorithm was used to predict potential ICI therapy responses and gene set enrichment analysis was performed to define different pathways associated with the immune response. Two distinct subtypes of CRC were finally identified in TCGA cohorts, which were characterized as significantly different prognostic subtypes (low-risk and high-risk subtypes). Higher expression of programmed death-ligand 1, higher proportion of tumor-infiltrating lymphocytes and tumor mutation burden were significantly enriched in the low-risk subtype. Further pathway analysis revealed that the low-risk subtype was associated with immune response activation and signaling pathways involved in ‘antigen processing and presentation’. Three independent CRC cohorts were used to validate the above findings. In summary, two clinical CRC subtypes were identified, which are characterized by significantly different survival outcomes and immune infiltration patterns. The findings of the present study suggest that ICI treatment may be more effective in the low-risk CRC subtype.
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Affiliation(s)
- Gang Chen
- Department of Anal and Intestinal Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Lin Wang
- Department of Surgery Operating Room, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Tongwei Diao
- Department of Anal and Intestinal Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Ying Chen
- Department of Anal and Intestinal Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Chengbo Cao
- Department of Anal and Intestinal Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
| | - Xindong Zhang
- Department of Pathology, Tengzhou Central People's Hospital, Tengzhou, Shandong 277500, P.R. China
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43
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Huang Z, Johnson TS, Han Z, Helm B, Cao S, Zhang C, Salama P, Rizkalla M, Yu CY, Cheng J, Xiang S, Zhan X, Zhang J, Huang K. Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations. BMC Med Genomics 2020; 13:41. [PMID: 32241264 PMCID: PMC7118823 DOI: 10.1186/s12920-020-0686-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Recent advances in kernel-based Deep Learning models have introduced a new era in medical research. Originally designed for pattern recognition and image processing, Deep Learning models are now applied to survival prognosis of cancer patients. Specifically, Deep Learning versions of the Cox proportional hazards models are trained with transcriptomic data to predict survival outcomes in cancer patients. METHODS In this study, a broad analysis was performed on TCGA cancers using a variety of Deep Learning-based models, including Cox-nnet, DeepSurv, and a method proposed by our group named AECOX (AutoEncoder with Cox regression network). Concordance index and p-value of the log-rank test are used to evaluate the model performances. RESULTS All models show competitive results across 12 cancer types. The last hidden layers of the Deep Learning approaches are lower dimensional representations of the input data that can be used for feature reduction and visualization. Furthermore, the prognosis performances reveal a negative correlation between model accuracy, overall survival time statistics, and tumor mutation burden (TMB), suggesting an association among overall survival time, TMB, and prognosis prediction accuracy. CONCLUSIONS Deep Learning based algorithms demonstrate superior performances than traditional machine learning based models. The cancer prognosis results measured in concordance index are indistinguishable across models while are highly variable across cancers. These findings shedding some light into the relationships between patient characteristics and survival learnability on a pan-cancer level.
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Affiliation(s)
- Zhi Huang
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Electrical and Computer Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Travis S Johnson
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhi Han
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Bryan Helm
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sha Cao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Chi Zhang
- Department of Electrical and Computer Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, 46202, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Paul Salama
- Department of Electrical and Computer Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Maher Rizkalla
- Department of Electrical and Computer Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Christina Y Yu
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Jun Cheng
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Shunian Xiang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xiaohui Zhan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Department of Electrical and Computer Engineering, Indiana University - Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
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Le Saux O, Dubois B, Stern MH, Terme M, Tartour E, Classe JM, Chopin N, Trédan O, Caux C, Ray-Coquard I. [Current advances in immunotherapy in ovarian cancer]. Bull Cancer 2020; 107:465-473. [PMID: 32089245 DOI: 10.1016/j.bulcan.2019.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 01/06/2023]
Abstract
Ovarian cancers express highly immunogenic tissue-specific antigens. The resulting immune infiltration is a major prognostic factor. There is therefore a strong biological rationale for the development of immunotherapy in ovarian cancer. However, based on Phase I and II clinical trials data, the efficacy of anti-PD-1 and anti-PD-L1 immune checkpoint inhibitors (ICPIs) remains limited in monotherapy in heavily pre-treated patients. Currently, the identification of predictive biomarkers of response and resistance is one of the major areas of research. Identifying effective combination of anti-PD-1 or anti-PD-L1 with other anticancer agents is another clinical need. Several combinations were evaluated. The association of ICPIs with chemotherapy (anthracyclines or carboplatin+paclitaxel) is disappointing (JAVELIN studies). The association with PARP inhibitors, anti-angiogenic agents and CTLA-4 inhibitors seems promising. Other immune therapies such as cell therapies (adoptive transfer of intra-tumor lymphocytes, CAR T cells or vaccines from dendritic cells) could be the future of immunotherapy in ovarian cancer but only early phase studies clinical data is available at this time.
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Affiliation(s)
- Olivia Le Saux
- Hospices civils de Lyon, service d'oncologie médicale, 165, chemin du grand Revoyet, 69495 Pierre-Bénite, France; Université Claude-Bernard Lyon I, centre de recherche en cancérologie de Lyon, CNRS 5286, centre Léon-Bérard, Inserm 1052, 69008 Lyon, France.
| | - Bertrand Dubois
- Université Claude-Bernard Lyon I, centre de recherche en cancérologie de Lyon, CNRS 5286, centre Léon-Bérard, Inserm 1052, 69008 Lyon, France
| | - Marc-Henri Stern
- Université de recherche PSL, institut Curie, DNA repair and uveal melanoma (D.R.U.M.), équipe labellisée par la Ligue nationale contre le cancer, Inserm U830, 75248 Paris, France; Institut Curie, département de biologie des tumeurs, Paris, France
| | - Magali Terme
- PARCC (Paris-Cardiovascular Research Center), Inserm U970, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, faculté de médecine, Paris, France
| | - Eric Tartour
- PARCC (Paris-Cardiovascular Research Center), Inserm U970, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, faculté de médecine, Paris, France; AP-HP, Hôpital Européen Georges-Pompidou, service d'immunologie biologique, Paris, France
| | - Jean-Marc Classe
- Institut de cancérologie de l'Ouest, Saint-Herblain, départment de chirurgie carcinologique, Loire Atlantique, France
| | | | | | - Christophe Caux
- Université Claude-Bernard Lyon I, centre de recherche en cancérologie de Lyon, CNRS 5286, centre Léon-Bérard, Inserm 1052, 69008 Lyon, France
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45
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Zhu G, Pei L, Li Y, Gou X. EP300 mutation is associated with tumor mutation burden and promotes antitumor immunity in bladder cancer patients. Aging (Albany NY) 2020; 12:2132-2141. [PMID: 32012118 PMCID: PMC7041765 DOI: 10.18632/aging.102728] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/02/2020] [Indexed: 02/05/2023]
Abstract
Bladder cancer is a leading cause of morbidity and mortality worldwide. Currently, immunotherapy has become a worthwhile therapy for bladder cancer. Tumor mutation burden (TMB) has been regarded as the most prevalent biomarker to predict immunotherapy. Bladder cancer is reported to have the third highest mutation rate. However, whether these gene mutations are related to TMB and immune response remain unknown. In this study, we downloaded somatic mutation data of bladder cancer from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets, and found 11 frequently mutated genes were covered by both two cohorts including FGFR3, TTN, XIRP2, CREBBP, PIK3CA, TP53, MUC16, EP300 (E1A binding protein P300), ARID1A, ERBB2, and KDM6A. Among them, EP300 mutation was associated with higher TMB and indicated a favorable clinical prognosis. Furthermore, based on Gene set enrichment analysis (GSEA) and CIBERSORT algorithm, we observed that EP300 mutation upregulated signaling pathways involved in immune system and enhanced antitumor immune response. In conclusion, EP300 is frequently mutated in bladder cancer, and its mutation is associated with increased TMB and promotes antitumor immunity, which may serve as a biomarker to predict immune response.
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Affiliation(s)
- Gongmin Zhu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lijiao Pei
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Li
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Gou
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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46
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Noguchi T, Sakai K, Iwahashi N, Matsuda K, Matsukawa H, Yahata T, Toujima S, Nishio K, Ino K. Changes in the gene mutation profiles of circulating tumor DNA detected using CAPP-Seq in neoadjuvant chemotherapy-treated advanced ovarian cancer. Oncol Lett 2020; 19:2713-2720. [PMID: 32218822 PMCID: PMC7068231 DOI: 10.3892/ol.2020.11356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/03/2019] [Indexed: 01/09/2023] Open
Abstract
Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) is a novel ultrasensitive next-generation sequencing-based approach that is used to detect circulating tumor DNA (ctDNA). The aim of the present study was to compare the gene mutation profiles and blood tumor mutation burden (bTMB) measured between pre- and post-neoadjuvant chemotherapy (NAC), utilizing CAPP-seq for plasma ctDNA in patients with advanced ovarian cancer. The current study included 10 patients (6 NAC-sensitive and 4 NAC-resistant) clinically diagnosed as having stage III or IV ovarian cancer and were administered NAC between May 2017 and February 2019. The plasma ctDNA samples were collected at pre- and post-NAC, and comprehensive gene mutation analysis was performed using CAPP-seq. In 5 out of 6 NAC-sensitive cases, the variant allele frequency (VAF) of non-synonymous somatic mutations decreased following NAC. In 2 out of the 4 NAC-resistant cases, the VAF of non-synonymous somatic mutations increased, and new somatic mutations emerged following NAC. In regard to TP53 mutation, the rate of TP53 mutation in the NAC-resistant cases was significantly higher compared with NAC-sensitive cases. Finally, the bTMB decreased significantly after NAC treatment in the NAC-sensitive cases, even though there were no significant differences in the pretreatment bTMB levels between the NAC-sensitive and NAC-resistant cases. These results indicated that gene mutation can be profiled and monitored using liquid biopsy-based CAPP-Seq in patients with advanced ovarian cancer with NAC treatment, and TP53 mutation in the ctDNA and bTMB may be novel biomarkers that can be used for patient monitoring during NAC treatment.
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Affiliation(s)
- Tomoko Noguchi
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Naoyuki Iwahashi
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kaho Matsuda
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Hitomi Matsukawa
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Tamaki Yahata
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Saori Toujima
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuhiko Ino
- Department of Obstetrics and Gynecology, Wakayama Medical University, Wakayama, Wakayama 641-0012, Japan
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47
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Tian W, Shan B, Zhang Y, Ren Y, Liang S, Zhao J, Zhao Z, Wang G, Zhao X, Peng D, Bi R, Cai S, Bai Y, Wang H. Association between DNA damage repair gene somatic mutations and immune-related gene expression in ovarian cancer. Cancer Med 2020; 9:2190-2200. [PMID: 31991061 PMCID: PMC7064027 DOI: 10.1002/cam4.2849] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/02/2020] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Defects in DNA damage repair (DDR) system may lead to genomic instability and manifest as increased immunogenicity. DDR deficiency is prevalent in ovarian cancer (OvCa); however, the association of DDR mutation with immune profiles in OvCa remains largely unknown. This knowledge will provide an essential basis to the rational design of biomarker-guided immune combination therapy of OvCa in the future. METHODS Whole-exome sequencing data of 587 OvCa from The Cancer Genome Atlas (TCGA) were used to determine the expression profiles of 47 immune-related genes and the abundance of tumor-infiltrating immune cells. A Chinese OvCa cohort (n = 220) tested by next-generation sequencing (NGS) was used to validate the association between DDR status and tumor mutation burden (TMB). RESULTS A total of 19.3% in TCGA cohort and 25.9% in Chinese cohort harbored at least one DDR somatic mutation. DDR deficiency exhibited a distinct immune profile with significant higher expression levels of PTPRCAP, CCL5, IFI16, LAG3, IL15RA, and GBP1 in OvCa in the TCGA cohort. Different DDR pathway deficiency displayed various immune profiles. Increased levels of Th1 cells, TMB, and neoantigen were also observed in DDR-deficient tumors. CONCLUSIONS DDR deficiency was associated with specific immune signatures in OvCa. Our findings emphasize the urgent need for biomarker-guided rational immune combination therapy to maximize the OvCa patients who could benefit from immunotherapy.
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Affiliation(s)
- Wenjuan Tian
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Boer Shan
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yuzi Zhang
- The Medical Department, 3D Medicines Inc, Shanghai, People's Republic of China
| | - Yulan Ren
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Shanhui Liang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Jing Zhao
- The Medical Department, 3D Medicines Inc, Shanghai, People's Republic of China
| | - Zhengyi Zhao
- The Medical Department, 3D Medicines Inc, Shanghai, People's Republic of China
| | - Guoqiang Wang
- The Medical Department, 3D Medicines Inc, Shanghai, People's Republic of China
| | - Xiaochen Zhao
- The Medical Department, 3D Medicines Inc, Shanghai, People's Republic of China
| | - Dongxian Peng
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangdong, People's Republic of China
| | - Rui Bi
- Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Shangli Cai
- The Medical Department, 3D Medicines Inc, Shanghai, People's Republic of China
| | - Yuezong Bai
- The Medical Department, 3D Medicines Inc, Shanghai, People's Republic of China
| | - Huaying Wang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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48
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Liu J, Xu W, Li S, Sun R, Cheng W. Multi-omics analysis of tumor mutational burden combined with prognostic assessment in epithelial ovarian cancer based on TCGA database. Int J Med Sci 2020; 17:3200-3213. [PMID: 33173439 PMCID: PMC7646107 DOI: 10.7150/ijms.50491] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Tumor mutation burden (TMB) is considered as a novel biomarker of response to immunotherapy and correlated with survival outcomes in various malignancies. Here, TMB-related genes (TRGs) expression signatures were constructed to investigate the association between TMB and prognosis in epithelial ovarian cancer (EOC), and the potential mechanism in immunoregulation was also explored. Methods: Based on somatic mutation data of 436 EOC samples from The Cancer Genome Atlas database, we examined the relationship between TMB level and overall survival (OS), as well as disease-free survival (DFS). Next, the TRGs signatures were constructed and validated. Differential abundance of immune cell infiltration, expression levels of immunomodulators and functional enrichment in high- and low-risk groups were also analyzed. Results: Higher TMB level revealed better OS and DFS, and correlated with earlier clinical stages in EOCs (P = 2.796e-04). The OS-related prognostic model constructed based on seven TRGs (B3GALT1, LIN7B, ANGPT2, D2HGDH, TAF13, PFDN4 and DNAJC19) significantly stratified EOC patients into high- and low-risk groups (P < 0.001). The AUC values of the seven-gene prognostic signature at 1 year, 3 years, and 5 years were 0.703, 0.758 and 0.777. While the DFS-related prognostic model was constructed based on the 4 TRGs (LPIN3, PXYLP1, IGSF23 and B3GALT1), with AUCs of 0.617, 0.756, and 0.731, respectively. Functional analysis indicated that immune-related pathways were enriched in low-risk groups. When considering the infiltration patterns of immune cells, we found higher proportions of follicular helper T (Tfh) cell and M1 macrophage, while lower infiltration of M0 macrophage in low-risk groups (P < 0.05). Accordingly, TMB levels of low-risk patients were significantly higher both in OS and DFS model (P < 0.01). Conclusions: Our TRGs-based models are reliable predictive tools for OS and DFS. High TMB may confer with an immunogenic microenvironment and predict favorable outcomes in EOCs.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Wei Xu
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Siyue Li
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Rui Sun
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Wenjun Cheng
- Department of Gynecology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
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Kim W, Zhao F, Wu R, Qin S, Nowsheen S, Huang J, Zhou Q, Chen Y, Deng M, Guo G, Luo K, Lou Z, Yuan J. ZFP161 regulates replication fork stability and maintenance of genomic stability by recruiting the ATR/ATRIP complex. Nat Commun 2019; 10:5304. [PMID: 31757956 PMCID: PMC6876566 DOI: 10.1038/s41467-019-13321-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/23/2019] [Indexed: 12/03/2022] Open
Abstract
DNA replication stress-mediated activation of the ATR kinase pathway is important for maintaining genomic stability. In this study, we identified a zinc finger protein, ZFP161 that functions as a replication stress response factor in ATR activation. Mechanistically, ZFP161 acts as a scaffolding protein to facilitate the interaction between RPA and ATR/ATRIP. ZFP161 binds to RPA and ATR/ATRIP through distinct regions and stabilizes the RPA–ATR–ATRIP complex at stalled replication forks. This function of ZFP161 is important to the ATR signaling cascade and genome stability maintenance. In addition, ZFP161 knockout mice showed a defect in ATR activation and genomic instability. Furthermore, low expression of ZFP161 is associated with higher cancer risk and chromosomal instability. Overall, these findings suggest that ZFP161 coordinates ATR/Chk1 pathway activation and helps maintain genomic stability. The ATR pathway is active during DNA replication stress to maintain genome stability. Here the authors reveal the role of the zinc finger containing protein 161 (ZFP161) to facilitate replication fork stability by acting as a scaffold to facilitate the interaction between RPA and ATR/ATRIP.
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Affiliation(s)
- Wootae Kim
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fei Zhao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rentian Wu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sisi Qin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Somaira Nowsheen
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.,Mayo Clinic Medical Scientist Training Program, Mayo Clinic Alix School Of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinzhou Huang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qin Zhou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yuping Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai, 200120, China.,Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai, 200120, China
| | - Min Deng
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guijie Guo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kuntian Luo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA. .,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai, 200120, China. .,Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai, 200120, China.
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50
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Choosing wisely: Selecting PARP inhibitor combinations to promote anti-tumor immune responses beyond BRCA mutations. Gynecol Oncol 2019; 156:488-497. [PMID: 31630846 DOI: 10.1016/j.ygyno.2019.09.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/29/2022]
Abstract
PARP inhibitors have transformed the management of advanced high-grade serous ovarian cancer. Despite the overwhelming success of PARP inhibition, particularly in BRCA-mutated ovarian cancer, several limitations and unanswered questions remain. With PARP inhibitors now being used in earlier treatment settings, the issue of both de novo and acquired resistance mechanisms and appropriate post-PARP management are pressing concerns. In addition, the population appropriate to target with PARP inhibitors and their use in patients without BRCA mutations is controversial and evolving. In this review we will discuss exciting PARP combinations and biologic rationale for the development and selection of PARP inhibitor combinations.
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