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Hein KZ, Stephen B, Fu S. Therapeutic Role of Synthetic Lethality in ARID1A-Deficient Malignancies. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2024; 7:41-52. [PMID: 38327752 PMCID: PMC10846636 DOI: 10.36401/jipo-22-37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/28/2023] [Accepted: 09/21/2023] [Indexed: 02/09/2024]
Abstract
AT-rich interaction domain 1A (ARID1A), a mammalian switch/sucrose nonfermenting complex subunit, modulates several cellular processes by regulating chromatin accessibility. It is encoded by ARID1A, an immunosuppressive gene frequently disrupted in a many tumors, affecting the proliferation, migration, and invasion of cancer cells. Targeting molecular pathways and epigenetic regulation associated with ARID1A loss, such as inhibiting the PI3K/AKT pathway or modulating Wnt/β-catenin signaling, may help suppress tumor growth and progression. Developing epigenetic drugs like histone deacetylase or DNA methyltransferase inhibitors could restore normal chromatin structure and function in cells with ARID1A loss. As ARID1A deficiency correlates with enhanced tumor mutability, microsatellite instability, high tumor mutation burden, increased programmed death-ligand 1 expression, and T-lymphocyte infiltration, ARID1A-deficient cells can be a potential therapeutic target for immune checkpoint inhibitors that warrants further exploration. In this review, we discuss the role of ARID1A in carcinogenesis, its crosstalk with other signaling pathways, and strategies to make ARID1A-deficient cells a potential therapeutic target for patients with cancer.
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Affiliation(s)
- Kyaw Z. Hein
- Department of Internal Medicine, HCA Florida Westside Hospital, Plantation, FL, USA
| | - Bettzy Stephen
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Tsai YF, Huang CC, Hsu CY, Feng CJ, Lin YS, Chao TC, Lai JI, Lien PJ, Liu CY, Chiu JH, Tseng LM. Genomic Alterations of Tumors in HER2-Low Breast Cancers. Int J Mol Sci 2024; 25:1318. [PMID: 38279318 PMCID: PMC10816179 DOI: 10.3390/ijms25021318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
The aim of this study was to elucidate molecular profiling in HER2-low tumors based on a promising dataset. A total of 615 consecutive HER2-negative breast cancer samples were assayed. The genomic mutations in the two groups with different HER2 expression levels (HER2-0 vs. HER2-low) were compared. The mutation types obtained via next-generation targeted sequencing were correlated with the clinicopathological features of the patients with HER2-0 and HER2-low breast cancer. The results showed that there was a significantly higher percentage of receptor-positive (ER/PR) tumors and more low-level Ki-67 tumors, but a lower incidence of stage I/II tumors in the HER2-low group compared to the HER2-0 group. There was a significantly higher frequency of 17.62% (65/369) for PIK3CA_SNA in the HER2-low group than in the HER2-0 group, which had a frequency of only 9.35% (23/246) (p = 0.006). When the called gene alterations in the triple-negative breast cancer (TNBC) group were compared with those in the luminal-like breast cancer group, there was a significantly high frequency of 28.17% (140/497) for ERBB2_SNA in a luminal-like group than in the TNBC group(16.95% (20/118)).We conclude that the early detection of PIK3CA mutations is likely to be important and might help therapeutic decision making in patients with HER2-low tumors.
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Affiliation(s)
- Yi-Fang Tsai
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112201, Taiwan;
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- School of Public Health, College of Public Health, National Taiwan University, Taipei 112201, Taiwan
| | - Chih-Yi Hsu
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112201, Taiwan;
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- College of Nursing, National Taipei University of Nursing and Health Sciences, Taipei 112201, Taiwan
| | - Chin-Jung Feng
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112201, Taiwan;
- Division of Plastic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Yen-Shu Lin
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Ta-Chung Chao
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112201, Taiwan;
- Division of Chemotherapy, Department of Oncology, Taipei 112201, Taiwan
| | - Jiun-I Lai
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112201, Taiwan;
- Division of Chemotherapy, Department of Oncology, Taipei 112201, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Chun-Yu Liu
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112201, Taiwan;
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Division of General Surgery, Department of Surgery, Cheng-Hsin General Hospital, Taipei 112201, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan; (Y.-F.T.); (C.-C.H.); (C.-J.F.); (Y.-S.L.); (T.-C.C.); (J.-I.L.); (P.-J.L.); (C.-Y.L.); (L.-M.T.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112201, Taiwan;
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Cheng HF, Tsai YF, Liu CY, Hsu CY, Lien PJ, Lin YS, Chao TC, Lai JI, Feng CJ, Chen YJ, Chen BF, Chiu JH, Tseng LM, Huang CC. Prevalence of BRCA1, BRCA2, and PALB2 genomic alterations among 924 Taiwanese breast cancer assays with tumor-only targeted sequencing: extended data analysis from the VGH-TAYLOR study. Breast Cancer Res 2023; 25:152. [PMID: 38098088 PMCID: PMC10722686 DOI: 10.1186/s13058-023-01751-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The homologous recombination (HR) repair pathway for DNA damage, particularly the BRCA1 and BRCA2 genes, has become a target for cancer therapy, with poly ADP-ribose polymerase (PARP) inhibitors showing significant outcomes in treating germline BRCA1/2 (gBRCA1/2) mutated breast cancer. Recent studies suggest that some patients with somatic BRCA1/2 (sBRCA1/2) mutation or mutations in HR-related genes other than BRCA1/2 may benefit from PARP inhibitors as well, particularly those with PALB2 mutations. The current analysis aims to evaluate the prevalence of genetic alterations specific to BRCA1, BRCA2, and PALB2 in a large cohort of Taiwanese breast cancer patients through tumor-targeted sequencing. METHODS A total of 924 consecutive assays from 879 Taiwanese breast cancer patients underwent tumor-targeted sequencing (Thermo Fisher Oncomine Comprehensive Assay v3). We evaluated BRCA1, BRCA2, and PALB2 mutational profiles, with variants annotated and curated by the ClinVAR, the Oncomine™ Knowledgebase Reporter, and the OncoKB™. We also conducted reflex germline testing using either whole exome sequencing (WES) or whole genome sequencing (WGS), which is ongoing. RESULTS Among the 879 patients analyzed (924 assays), 130 had positive mutations in BRCA1 (3.1%), BRCA2 (8.6%), and PALB2 (5.2%), with a total of 14.8% having genetic alterations. Co-occurrence was noted between BRCA1/BRCA2, BRCA1/PALB2, and BRCA2/PALB2 mutations. In BRCA1-mutated samples, only p.K654fs was observed in three patients, while other variants were observed no more than twice. For BRCA2, p.N372H was the most common (26 patients), followed by p.S2186fs, p.V2466A, and p.X159_splice (5 times each). For PALB2, p.I887fs was the most common mutation (30 patients). This study identified 176 amino acid changes; 60.2% (106) were not documented in either ClinVAR or the Oncomine™ Knowledgebase Reporter. Using the OncoKB™ for annotation, 171 (97.2%) were found to have clinical implications. For the result of reflex germline testing, three variants (BRCA1 c.1969_1970del, BRCA1 c.3629_3630del, BRCA2 c.8755-1G > C) were annotated as Pathogenic/Likely pathogenic (P/LP) variants by ClinVar and as likely loss-of-function or likely oncogenic by OncoKB; while one variant (PALB2 c.448C > T) was not found in ClinVar but was annotated as likely loss-of-function or likely oncogenic by OncoKB. CONCLUSION Our study depicted the mutational patterns of BRCA1, BRCA2, and PALB2 in Taiwanese breast cancer patients through tumor-only sequencing. This highlights the growing importance of BRCA1/2 and PALB2 alterations in breast cancer susceptibility risk and the treatment of index patients. We also emphasized the need to meticulously annotate variants in cancer-driver genes as well as actionable mutations across multiple databases.
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Affiliation(s)
- Han-Fang Cheng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
| | - Yi-Fang Tsai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
| | - Chun-Yu Liu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
| | - Chih-Yi Hsu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- Department of Nurse, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
| | - Yen-Shu Lin
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
| | - Ta-Chung Chao
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
| | - Jiun-I Lai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
| | - Chin-Jung Feng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
- Division of Plastic and Reconstruction Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
| | - Yen-Jen Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
| | - Bo-Fang Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
- Center for Traditional Medicine, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC
- Institue of Traditional Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC.
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan, ROC.
- Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC.
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan, ROC.
- Institute of Epidemiology and Preventive Medicine, College of Medicine, National Taiwan University, Taipei City, Taiwan, ROC.
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Huang CC, Tsai YF, Liu CY, Lien PJ, Lin YS, Chao TC, Feng CJ, Chen YJ, Lai JI, Cheng HF, Chen BF, Hsu CY, Chiu JH, Tseng LM. Concordance of Targeted Sequencing from Circulating Tumor DNA and Paired Tumor Tissue for Early Breast Cancer. Cancers (Basel) 2023; 15:4475. [PMID: 37760445 PMCID: PMC10526508 DOI: 10.3390/cancers15184475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
In this study, we evaluated the concordance of targeted sequencing between paired ctDNA and matched tumor samples from early breast cancers treated with curative intention. Molecular profiling was performed using the Oncomine Comprehensive Assay v3 and the Oncomine Breast cfDNA Assay v2. The liquid biopsy detection rate was 39% (all-stage breast cancers, n = 612). Among 246 early-stage patients assayed for both ctDNA and matched tumor, the cfDNA assay detected 73 (29.6%) and the comprehensive assay detected 201 (81.7%) breast cancers with at least one alteration (χ2 test, p = 0.001). In total, 67 (25.6%) cases tested positive on both platforms, while the cfDNA and comprehensive assays detected an additional 10 (4%) and 138 (56%) cases, respectively. The most prevalent mutant genes were TP53 (68.3%) and KRAS (53.5%), while the PIK3CA (39.4%), AKT1 (45.9%), and ERBB2 (17.1%) mutations constituted biomarkers for FDA-approved therapeutics. Our study showed that tumor tissue should be the source of actionable mutation detection for early breast cancers, considering that the concordance rate between tumor and liquid biopsy was only one-quarter.
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Affiliation(s)
- Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Fang Tsai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Chun-Yu Liu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yen-Shu Lin
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Ta-Chung Chao
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Division of Chemotherapy, Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chin-Jung Feng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yen-Jen Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Jiun-I Lai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan
| | - Han-Fang Cheng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
| | - Bo-Fang Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chih-Yi Hsu
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Traditional Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (C.-C.H.); (Y.-F.T.); (C.-Y.L.); (P.-J.L.); (Y.-S.L.); (T.-C.C.); (C.-J.F.); (Y.-J.C.); (J.-I.L.); (H.-F.C.); (B.-F.C.); (J.-H.C.)
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan;
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Functional regulations between genetic alteration-driven genes and drug target genes acting as prognostic biomarkers in breast cancer. Sci Rep 2022; 12:10641. [PMID: 35739271 PMCID: PMC9226112 DOI: 10.1038/s41598-022-13835-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/30/2022] [Indexed: 12/19/2022] Open
Abstract
Differences in genetic molecular features including mutation, copy number alterations and DNA methylation, can explain interindividual variability in response to anti-cancer drugs in cancer patients. However, identifying genetic alteration-driven genes and characterizing their functional mechanisms in different cancer types are still major challenges for cancer studies. Here, we systematically identified functional regulations between genetic alteration-driven genes and drug target genes and their potential prognostic roles in breast cancer. We identified two mutation and copy number-driven gene pairs (PARP1-ACSL1 and PARP1-SRD5A3), three DNA methylation-driven gene pairs (PRLR-CDKN1C, PRLR-PODXL2 and PRLR-SRD5A3), six gene pairs between mutation-driven genes and drug target genes (SLC19A1-SLC47A2, SLC19A1-SRD5A3, AKR1C3-SLC19A1, ABCB1-SRD5A3, NR3C2-SRD5A3 and AKR1C3-SRD5A3), and four copy number-driven gene pairs (ADIPOR2-SRD5A3, CASP12-SRD5A3, SLC39A11-SRD5A3 and GALNT2-SRD5A3) that all served as prognostic biomarkers of breast cancer. In particular, RARP1 was found to be upregulated by simultaneous copy number amplification and gene mutation. Copy number deletion and downregulated expression of ACSL1 and upregulation of SRD5A3 both were observed in breast cancers. Moreover, copy number deletion of ACSL1 was associated with increased resistance to PARP inhibitors. PARP1-ACSL1 pair significantly correlated with poor overall survival in breast cancer owing to the suppression of the MAPK, mTOR and NF-kB signaling pathways, which induces apoptosis, autophagy and prevents inflammatory processes. Loss of SRD5A3 expression was also associated with increased sensitivity to PARP inhibitors. The PARP1-SRD5A3 pair significantly correlated with poor overall survival in breast cancer through regulating androgen receptors to induce cell proliferation. These results demonstrate that genetic alteration-driven gene pairs might serve as potential biomarkers for the prognosis of breast cancer and facilitate the identification of combination therapeutic targets for breast cancers.
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Huang CC, Tseng LM. ASO Author Reflections: Broaden the Targeted Population of Synthetic Lethality for Taiwanese Breast Cancer. Ann Surg Oncol 2022; 29:3591-3592. [PMID: 35391610 DOI: 10.1245/s10434-022-11407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/18/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors selectively cause the failure of DNA single-stranded break (SSB) repair but do not affect double-stranded break (DSB) repair. Furthermore, antitumor activities have been reported for breast cancer, with germline BRCA1/2 mutations. The prevalence of germline BRCA1/2 mutations never exceed one-tenth; beyond BRCA1/2, genes recurrently altered (more than 5%) in the homologous repair pathway are ARID1A, PALB2, and PTEN. Altered homologous recombination repair genes can total up to one-quarter based on different definitions, and the potential of PARP inhibitors will be elucidated when further studies unraveling the impact of individual homologous recombination genes are conducted.
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Affiliation(s)
- Chi-Cheng Huang
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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