1
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Kim JY, Park K, Park WY, Ahn JS, Im YH, Lee JE, Kim SW, Nam SJ, Yu J, Park YH. Prognostic value of structural variants in early breast cancer patients. NPJ Breast Cancer 2024; 10:64. [PMID: 39068172 PMCID: PMC11283467 DOI: 10.1038/s41523-024-00669-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
Genomic analysis of structural variants(SVs) in breast cancer (BC) patients has been conducted, but the relationship between genomic alterations and BC prognosis remains unclear. We performed RNA sequencing of 297 early BC fresh-frozen tissues. We identified SVs using three tools (STAR.Arriba, STAR.fusion, and STAR.SEQR) with the COSMIC and Mitelman databases as guide references. We found a median of five to eight fusions per sample. In BC intrinsic subtypes, normal subtype had the fewest fusions (median: 1, interquartile range [IQR]: 0, 3) followed by luminal A (median: 5.5, IQR: 2.75, 10.25), luminal B (median: 9, IQR: 6, 16.5), HER2-enriched (median: 9, IQR: 6, 16.5) and basal (median 10, IQR: 6, 15.5) subtypes (p < 0.05). Intrachromosomal fusion was more frequent observed rather than interchromosomal fusion. In location, chromosome 17 had the most fusions followed by chromosome 1 and 11. When samples were divided into high and low fusion groups based on a cut-off value of 11 fusions, five-year event-free survival (5Y-EFS) was 68.1% in the high fusion group (n = 72) and 80.1% in the low fusion group (n = 125) (p = 0.024) while 75.6% among all patients (95% confidence interval: 0.699, 0.819). Among BC subtype, TNBCs with more fusions had shorter EFS compared to those with fewer fusions (5Y-EFS rate: 65.1% vs. 85.7%; p = 0.013) but no EFS differences were observed in other BC subtypes. ESTIMATE ImmuneScore was also associated with the number of fusions in TNBC (p < 0.005) and TNBCs with high ImmuneScore had better 5Y-EFS compared to those with low ImmuneScore (p = 0.041). In conclusion, diverse fusions were observed by BC subtype, and the number of fusions was associated with BC survival outcome and immune status in TNBC.
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Affiliation(s)
- Ji-Yeon Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyunghee Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Hyuck Im
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Won Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Nam
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jonghan Yu
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Korea.
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2
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Kurimoto-Nishiguchi M, Muraoka K, Inaba Y, Kunimoto K, Yamamoto Y, Kumegawa S, Ueno K, Asamura S, Nakatani Y, Sawamura S, Makino K, Jinnin M. Glycoprotein M6A upregulation detected by transcriptome analysis controls the proliferation of keloidal fibroblasts. J Dermatol 2023; 50:1170-1179. [PMID: 37365986 DOI: 10.1111/1346-8138.16861] [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: 01/10/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Hypertrophic scars and keloids are fibroproliferative disorders caused by abnormal wound healing. Their exact cause has not been found, but abnormalities during the wound healing process including inflammatory, immune, genetic, and other factors are thought to predispose an individual to excessive scarring. In the present study, we performed transcriptome analysis of established keloid cell lines (KEL FIB), focusing on gene expression analysis and fusion gene detection for the first time. For gene expression analysis, fragments per kilobase per million map read values were calculated, which were validated by real-time PCR and immunohistochemistry. Fusion genes were predicted by transcriptome sequence, and validated by Sanger sequence and G-banding. As a result, GPM6A was shown in the expression analysis to be upregulated in KEL FIB compared with normal fibroblasts. The GPM6A upregulation in KEL FIB was confirmed by real-time PCR, and GPM6A messenger ribonucleic acid expression was consistently significantly elevated in the tissues of hypertrophic scar and keloid compared to normal skin. Immunohistochemistry also revealed that the number of fibroblast-like spindle-shaped cells positive for GPM6A was significantly increased in keloidal tissues. GPM6A inhibition by small interfering ribonucleic acid significantly reduced the number of KEL FIB. On the other hand, although we hypothesized that fusion genes are involved in the pathogenesis of keloids, the transcriptome analysis could not prove the presence of fusion genes in KEL FIB. Taken together, GPM6A upregulation may have an inducible effect on cell proliferation in keloidal fibroblasts. GPM6A can be a novel therapeutic target in hypertrophic scars and keloids. The inflammatory nature may be more prominent in the pathogenesis of keloids, rather than being skin tumors, as proposed by Ogawa et al. Future studies using several cell lines will be required.
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Affiliation(s)
| | - Kyoko Muraoka
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Yutaka Inaba
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Kayo Kunimoto
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Yuki Yamamoto
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Shinji Kumegawa
- Department of Plastic Surgery, Wakayama Medical University, Wakayama, Japan
| | - Kazuki Ueno
- Department of Plastic Surgery, Wakayama Medical University, Wakayama, Japan
| | - Shinichi Asamura
- Department of Plastic Surgery, Wakayama Medical University, Wakayama, Japan
| | - Yumi Nakatani
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Soichiro Sawamura
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Katsunari Makino
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masatoshi Jinnin
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
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3
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Cristiano L. The pseudogenes of eukaryotic translation elongation factors (EEFs): Role in cancer and other human diseases. Genes Dis 2022; 9:941-958. [PMID: 35685457 PMCID: PMC9170609 DOI: 10.1016/j.gendis.2021.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/29/2021] [Indexed: 02/06/2023] Open
Abstract
The eukaryotic translation elongation factors (EEFs), i.e. EEF1A1, EEF1A2, EEF1B2, EEF1D, EEF1G, EEF1E1 and EEF2, are coding-genes that play a central role in the elongation step of translation but are often altered in cancer. Less investigated are their pseudogenes. Recently, it was demonstrated that pseudogenes have a key regulatory role in the cell, especially via non-coding RNAs, and that the aberrant expression of ncRNAs has an important role in cancer development and progression. The present review paper, for the first time, collects all that published about the EEFs pseudogenes to create a base for future investigations. For most of them, the studies are in their infancy, while for others the studies suggest their involvement in normal cell physiology but also in various human diseases. However, more investigations are needed to understand their functions in both normal and cancer cells and to define which can be useful biomarkers or therapeutic targets.
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Affiliation(s)
- Luigi Cristiano
- R&D Division, Prestige, 18 via Vecchia, Terranuova Bracciolini, AR 52028, Italy
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4
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Loo SK, Yates ME, Yang S, Oesterreich S, Lee AV, Wang X. Fusion-Associated Carcinomas of the Breast: Diagnostic, Prognostic, and Therapeutic Significance. Genes Chromosomes Cancer 2022; 61:261-273. [PMID: 35106856 DOI: 10.1002/gcc.23029] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Recurrent gene fusions comprise a class of viable genetic targets in solid tumors that have culminated several recent break-through cancer therapies. Their role in breast cancer, however, remains largely underappreciated due to the complexity of genomic rearrangements in breast malignancy. Just recently, we and others have identified several recurrent gene fusions in breast cancer with important clinical and biological implications. Examples of the most significant recurrent gene fusions to date include 1) ESR1-CCDC170 gene fusions in luminal B and endocrine resistant breast cancer that exert oncogenic function via modulating the HER2/HER3/SRC complex, 2) ESR1 exon 6 fusions in metastatic disease that drive estrogen-independent ER transcriptional activity, 3) BCL2L14-ETV6 fusions in a more aggressive form of the triple negative subtype that prime epithelial-mesenchymal transition and endow paclitaxel resistance, 4) the ETV6-NTRK3 fusion in secretory breast carcinoma that constitutively activates NTRK3 kinase, 5) the oncogenic MYB-NFIB fusion as a genetic driver underpinning adenoid cystic carcinomas of the breast that activates MYB pathway, and 6) the NOTCH/MAST kinase gene fusions that activate NOTCH and MAST signaling. Importantly, these fusions are enriched in more aggressive and lethal breast cancer presentations and appear to confer therapeutic resistance. Thus, these gene fusions could be utilized as genetic biomarkers to identify patients that require more intensive treatment and surveillance. In addition, kinase fusions are currently being evaluated in breast cancer clinical trials and on-going mechanistic investigation is exposing therapeutic vulnerabilities in patients with fusion positive disease. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Megan E Yates
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA.,Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Steffi Oesterreich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
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5
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Dameri M, Ferrando L, Cirmena G, Vernieri C, Pruneri G, Ballestrero A, Zoppoli G. Multi-Gene Testing Overview with a Clinical Perspective in Metastatic Triple-Negative Breast Cancer. Int J Mol Sci 2021; 22:7154. [PMID: 34281208 PMCID: PMC8268401 DOI: 10.3390/ijms22137154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) is the technology of choice for the routine screening of tumor samples in clinical practice. In this setting, the targeted sequencing of a restricted number of clinically relevant genes represents the most practical option when looking for genetic variants associated with cancer, as well as for the choice of targeted treatments. In this review, we analyze available NGS platforms and clinical applications of multi-gene testing in breast cancer, with a focus on metastatic triple-negative breast cancer (mTNBC). We make an overview of the clinical utility of multi-gene testing in mTNBC, and then, as immunotherapy is emerging as a possible targeted therapy for mTNBC, we also briefly report on the results of the latest clinical trials involving immune checkpoint inhibitors (ICIs) and TNBC, where NGS could play a role for the potential predictive utility of homologous recombination repair deficiency (HRD) and tumor mutational burden (TMB).
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Affiliation(s)
- Martina Dameri
- Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; (M.D.); (L.F.); (G.C.); (A.B.)
| | - Lorenzo Ferrando
- Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; (M.D.); (L.F.); (G.C.); (A.B.)
| | - Gabriella Cirmena
- Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; (M.D.); (L.F.); (G.C.); (A.B.)
| | - Claudio Vernieri
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
- IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Giancarlo Pruneri
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
- School of Medicine, University of Milan, 20122 Milan, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; (M.D.); (L.F.); (G.C.); (A.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; (M.D.); (L.F.); (G.C.); (A.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
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6
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Yan Z, Fan G, Li H, Jiao Y, Fu W, Weng J, Huo R, Wang J, Xu H, Wang S, Cao Y, Zhao J. The CTSC-RAB38 Fusion Transcript Is Associated With the Risk of Hemorrhage in Brain Arteriovenous Malformations. J Neuropathol Exp Neurol 2021; 80:71-78. [PMID: 33120410 DOI: 10.1093/jnen/nlaa126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Brain arteriovenous malformations (bAVMs) are congenital anomalies of blood vessels that cause intracranial hemorrhage in children and young adults. Chromosomal rearrangements and fusion genes play an important role in tumor pathogenesis, though the role of fusion genes in bAVM pathophysiological processes is unclear. The aim of this study was to identify fusion transcripts in bAVMs and analyze their effects. To identify fusion transcripts associated with bAVM, RNA sequencing was performed on 73 samples, including 66 bAVM and 7 normal cerebrovascular samples, followed by STAR-Fusion analysis. Reverse transcription polymerase chain reaction and Sanger sequencing were applied to verify fusion transcripts. Functional pathway analysis was performed to identify potential effects of different fusion types. A total of 21 fusion transcripts were detected. Cathepsin C (CTSC)-Ras-Related Protein Rab-38 (RAB38) was the most common fusion and was detected in 10 of 66 (15%) bAVM samples. In CTSC-RAB38 fusion-positive samples, CTSC and RAB38 expression was significantly increased and activated immune/inflammatory signaling. Clinically, CTSC-RAB38 fusion bAVM cases had a higher hemorrhage rate than non-CTSC-RAB38 bAVM cases (p < 0.05). Our study identified recurrent CTSC-RAB38 fusion transcripts in bAVMs, which may be associated with bAVM hemorrhage by promoting immune/inflammatory signaling.
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Affiliation(s)
- Zihan Yan
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Guangming Fan
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease.,Chaoyang Central Hospital, Liaoning Province, China
| | - Hao Li
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Yuming Jiao
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Weilun Fu
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Jiancong Weng
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Ran Huo
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Jie Wang
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Hongyuan Xu
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Shuo Wang
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Yong Cao
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease
| | - Jizong Zhao
- From the Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University.,China National Clinical Research Center for Neurological Diseases.,Center of Stroke, Beijing Institute for Brain Disorders.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease.,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, China
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7
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Liu X, Li YG, Tan F, Liu J, Yi R, Zhao X. Three functional polymorphisms in CCDC170 were associated with osteoporosis phenotype. Biol Open 2021; 10:bio.050930. [PMID: 33785515 PMCID: PMC8061906 DOI: 10.1242/bio.050930] [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: 01/20/2020] [Accepted: 07/26/2020] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) play essential roles in regulating bone formation and homeostasis. Genomic variations within miRNA target sites may therefore be important sources of genetic differences in osteoporosis risk. The function of CCDC170 in bone biology is still unclear. To verify the function of CCDC170, we knocked down CCDC170 in cells and mice and searched for miRNA recognition sites within CCDC170 using the TargetScan, miRNASNP, and miRBase databases. In this study, our results demonstrated that CCDC170 plays an important role in the positive regulation of bone formation. MiR-153-3p, miR-374b-3p, miR-4274, miR-572 and miR-2964a-5p inhibited CCDC170 expression in an allele-specific manner by binding GWAS lead SNPs rs6932603, rs3757322 and rs3734806. These findings may improve our understanding of the association between CCDC170, miRNAs, GWAS lead SNPs, and osteoporosis pathogenesis and may provide a potential therapeutic target for osteoporosis therapy. Summary: CCDC170 may provide a potential therapeutic target for osteoporosis therapy.
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Affiliation(s)
- Xinhong Liu
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China.,College of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, China
| | - Yu-Gang Li
- Department of Orthopedics, the First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, China
| | - Fang Tan
- Department of Public Health, Our Lady of Fatima University, Valenzuela 838, Philippines
| | - Jia Liu
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China
| | - Ruokun Yi
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China
| | - Xin Zhao
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China
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8
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Jeong JH, Yun JW, Kim HY, Heo CY, Lee S. Elucidation of Novel Therapeutic Targets for Breast Cancer with ESR1-CCDC170 Fusion. J Clin Med 2021; 10:jcm10040582. [PMID: 33557149 PMCID: PMC7913953 DOI: 10.3390/jcm10040582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/09/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022] Open
Abstract
Among the various types of breast cancer, the luminal B subtype is the most common in young women, and ESR1-CCDC170 (E:C) fusion is the most frequent oncogenic fusion driver of the luminal B subtype. Nevertheless, treatments targeting E:C fusion has not been well established yet. Hence, the aim of this study is to investigate potential therapies targeting E:C fusion based on systematic bioinformatical analysis of the Cancer Genome Atlas (TCGA) data. One thousand related genes were extracted using transcriptome analysis, and major signaling pathways associated with breast cancer were identified with over-representation analysis. Then, we conducted drug-target network analysis based on the OncoKB and CIViC databases, and finally selected potentially applicable drug candidates. Six major cancer-related signaling pathways (p53, ATR/ATM, FOXM1, hedgehog, cell cycle, and Aurora B) were significantly altered in E:C fusion-positive cases of breast cancer. Further investigation revealed that nine genes (AURKB, HDAC2, PLK1, CENPA, CHEK1, CHEK2, RB1, CCNA2, and MDM2) in coordination with E:C fusion were found to be common denominators in three or more of these pathways, thereby making them promising gene biomarkers for target therapy. Among the 21 putative actionable drugs inferred by drug-target network analysis, palbociclib, alpelisib, ribociclib, dexamethasone, checkpoint kinase inhibitor AXD 7762, irinotecan, milademetan tosylate, R05045337, cisplatin, prexasertib, and olaparib were considered promising drug candidates targeting genes involved in at least two E:C fusion-related pathways.
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Affiliation(s)
- Jae Heon Jeong
- Integrated Major in Innovative Medical Science, College of Medicine, Seoul National University, Seoul 08826, Korea;
- Interdisciplinary Program for Bioengineering, College of Engineering, Seoul National University, Seoul 08826, Korea;
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Jae Won Yun
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul 08826, Korea;
| | - Ha Young Kim
- Interdisciplinary Program for Bioengineering, College of Engineering, Seoul National University, Seoul 08826, Korea;
| | - Chan Yeong Heo
- Interdisciplinary Program for Bioengineering, College of Engineering, Seoul National University, Seoul 08826, Korea;
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam 13620, Korea
- Department of Plastic and Reconstructive Surgery, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (C.Y.H.); (S.L.); Tel.: +82-31-787-8124 (S.L.)
| | - Sejoon Lee
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam 13620, Korea
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
- Correspondence: (C.Y.H.); (S.L.); Tel.: +82-31-787-8124 (S.L.)
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9
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Liu CC, Veeraraghavan J, Tan Y, Kim JA, Wang X, Loo SK, Lee S, Hu Y, Wang XS. A Novel Neoplastic Fusion Transcript, RAD51AP1-DYRK4, Confers Sensitivity to the MEK Inhibitor Trametinib in Aggressive Breast Cancers. Clin Cancer Res 2021; 27:785-798. [PMID: 33172895 PMCID: PMC7934498 DOI: 10.1158/1078-0432.ccr-20-2769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/18/2020] [Accepted: 11/04/2020] [Indexed: 01/19/2023]
Abstract
PURPOSE Luminal B breast tumors are more aggressive estrogen receptor-positive (ER+) breast cancers characterized by aggressive clinical behavior and a high risk of metastatic dissemination. The underlying pathologic molecular events remain poorly understood with a paucity of actionable genetic drivers, which hinders the development of new treatment strategies. EXPERIMENTAL DESIGN We performed large-scale RNA sequencing analysis to identify chimerical transcripts preferentially expressed in luminal B breast cancer. The lead candidate was validated by reverse transcription PCR in breast cancer tissues. The effects of inducible ectopic expression or genetic silencing were assessed by phenotypic assays such as MTS, transwell, and transendothelial migration assays, and by clonogenic assays to assess MEK inhibitor sensitivity. Subcellular fractionation, Western blots, and immunoprecipitation were performed to characterize the protein products and elucidate the engaged mechanisms. RESULTS Here we report a novel tumor-specific chimeric transcript RAD51AP1-DYRK4 preferentially expressed in luminal B tumors. Analysis of 200 ER+ breast tumors detected RAD51AP1-DYRK4 overexpression in 19 tumors (9.5%), which is markedly enriched in the luminal B tumors (17.5%). Ectopic expression of RAD51AP1-DYRK4, but not wild-type RAD51AP1, leads to marked activation of MEK/ERK signaling, and endows increased cell motility and transendothelial migration. More importantly, RAD51AP1-DYRK4 appears to endow increased sensitivity to the MEK inhibitor trametinib through attenuating compensatory activation of HER2/PI3K/AKT under MEK inhibition. CONCLUSIONS This discovery sheds light on a new area of molecular pathobiology of luminal B tumors and implies potential new therapeutic opportunities for more aggressive breast tumors overexpressing this fusion.
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Affiliation(s)
- Chia-Chia Liu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jamunarani Veeraraghavan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ying Tan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jin-Ah Kim
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xian Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yiheng Hu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania.
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
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10
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Li L, Lin L, Veeraraghavan J, Hu Y, Wang X, Lee S, Tan Y, Schiff R, Wang XS. Therapeutic role of recurrent ESR1-CCDC170 gene fusions in breast cancer endocrine resistance. Breast Cancer Res 2020; 22:84. [PMID: 32771039 PMCID: PMC7414578 DOI: 10.1186/s13058-020-01325-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 07/27/2020] [Indexed: 01/07/2023] Open
Abstract
Background Endocrine therapy is the most common treatment for estrogen receptor (ER)-positive breast cancer, but its effectiveness is limited by high rates of primary and acquired resistance. There are likely many genetic causes, and recent studies suggest the important role of ESR1 mutations and fusions in endocrine resistance. Previously, we reported a recurrent ESR1 fusion called ESR1-CCDC170 in 6–8% of the luminal B breast cancers that has a worse clinical outcome after endocrine therapy. Despite being the most frequent ESR1 fusion, its functional role in endocrine resistance has not been studied in vivo, and the engaged mechanism and therapeutic relevance remain uncharacterized. Methods The endocrine sensitivities of HCC1428 or T47D breast cancer cells following genetic perturbations of ESR1-CCDC170 were assessed using clonogenic assays and/or xenograft mouse models. The underlying mechanisms were investigated by reverse phase protein array, western blotting, immunoprecipitation, and bimolecular fluorescence complementation assays. The sensitivity of ESR1-CCDC170 expressing breast cancer cells to concomitant treatments of tamoxifen and HER/SRC inhibitors was assessed by clonogenic assays. Results Our results suggested that different ESR1-CCDC170 fusions endow different levels of reduced endocrine sensitivity in vivo, resulting in significant survival disadvantages. Further investigation revealed a novel mechanism that ESR1-CCDC170 binds to HER2/HER3/SRC and activates SRC/PI3K/AKT signaling. Silencing of ESR1-CCDC170 in the fusion-positive cell line, HCC1428, downregulates HER2/HER3, represses pSRC/pAKT, and improves endocrine sensitivity. More important, breast cancer cells expressing ectopic or endogenous ESR1-CCDC170 are highly sensitive to treatment regimens combining endocrine agents with the HER2 inhibitor lapatinib and/or the SRC inhibitor dasatinib. Conclusion ESR1-CCDC170 may endow breast cancer cell survival under endocrine therapy via maintaining/activating HER2/HER3/SRC/AKT signaling which implies a potential therapeutic strategy for managing these fusion positive tumors.
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Affiliation(s)
- Li Li
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Women's Cancer Research Center, Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA.,Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ling Lin
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Women's Cancer Research Center, Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Jamunarani Veeraraghavan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yiheng Hu
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Women's Cancer Research Center, Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA.,Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xian Wang
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.,Women's Cancer Research Center, Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA.,Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sanghoon Lee
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206, USA
| | - Ying Tan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rachel Schiff
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiao-Song Wang
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA. .,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15261, USA. .,Women's Cancer Research Center, Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA. .,Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206, USA.
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11
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Lee S, Hu Y, Loo SK, Tan Y, Bhargava R, Lewis MT, Wang XS. Landscape analysis of adjacent gene rearrangements reveals BCL2L14-ETV6 gene fusions in more aggressive triple-negative breast cancer. Proc Natl Acad Sci U S A 2020; 117:9912-9921. [PMID: 32321829 PMCID: PMC7211963 DOI: 10.1073/pnas.1921333117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) accounts for 10 to 20% of breast cancer, with chemotherapy as its mainstay of treatment due to lack of well-defined targets, and recent genomic sequencing studies have revealed a paucity of TNBC-specific mutations. Recurrent gene fusions comprise a class of viable genetic targets in solid tumors; however, their role in breast cancer remains underappreciated due to the complexity of genomic rearrangements in this cancer. Our interrogation of the whole-genome sequencing data for 215 breast tumors catalogued 99 recurrent gene fusions, 57% of which are cryptic adjacent gene rearrangements (AGRs). The most frequent AGRs, BCL2L14-ETV6, TTC6-MIPOL1, ESR1-CCDC170, and AKAP8-BRD4, were preferentially found in the more aggressive forms of breast cancers that lack well-defined genetic targets. Among these, BCL2L14-ETV6 was exclusively detected in TNBC, and interrogation of four independent patient cohorts detected BCL2L14-ETV6 in 4.4 to 12.2% of TNBC tumors. Interestingly, these fusion-positive tumors exhibit more aggressive histopathological features, such as gross necrosis and high tumor grade. Amid TNBC subtypes, BCL2L14-ETV6 is most frequently detected in the mesenchymal entity, accounting for ∼19% of these tumors. Ectopic expression of BCL2L14-ETV6 fusions induce distinct expression changes from wild-type ETV6 and enhance cell motility and invasiveness of TNBC and benign breast epithelial cells. Furthermore, BCL2L14-ETV6 fusions prime partial epithelial-mesenchymal transition and endow resistance to paclitaxel treatment. Together, these data reveal AGRs as a class of underexplored genetic aberrations that could be pathological in breast cancer, and identify BCL2L14-ETV6 as a recurrent gene fusion in more aggressive form of TNBC tumors.
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Affiliation(s)
- Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232
| | - Yiheng Hu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15232
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15232
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232
| | - Ying Tan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Rohit Bhargava
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232
| | - Michael T Lewis
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
- Department of Radiology, Baylor College of Medicine, Houston, TX 77030
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232;
- Women's Cancer Research Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15232
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
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12
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Abstract
Supplemental Digital Content is available in the text Background: Fusion genes may play an important role in tumorigenesis, prognosis, and drug resistance; however, studies on fusion genes in endometrial cancer (EC) are rare. This study aimed to identify new fusion genes and to explore their clinical significance in EC. Methods: A total of 28 patients diagnosed with EC were enrolled in this study. RNA sequencing was used to obtain entire genomes and transcriptomes. STAR-comparison and STAR-fusion prediction were applied to predict the fusion genes. Chi-square tests and Student t tests were used to verify the clinical significance with SPSS 13.0 software. Results: New fusion genes were found, and the number of fusion genes varied from 3 to 110 among all patients with EC. The type of fusion genes varied and included messenger RNA (mRNA)-mRNA, long non-coding RNA (lncRNA)-lncRNA, and lncRNA-mRNA. There were six fusion genes with high fusion rates, namely, RP11–123O10.4–GRIP1, RP11–444D3.1–SOX5, RP11–680G10.1–GSE1, NRIP1–AF127936.7, RP11–96H19.1–RP11–446N19.1, and DPH7–PTP4A3. Further studies showed that these fusion genes are related to stage, grade, and recurrence, in which NRIP1–AF127936.7 and DPH7–PTP4A3 were found only in stage III patients with EC. DPH7–PTP4A3 was found in grades 2 and 3, and recurrent patients with EC. Conclusion: Fusion genes play an essential role in EC. Six genes that are overexpressed with high fusion rates are identified. NRIP1–AF127936.7 and DPH7–PTP4A3 might be related to stage, and DPH7–PTP4A3 be related to grade and recurrence.
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13
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Eismann J, Heng YJ, Waldschmidt JM, Vlachos IS, Gray KP, Matulonis UA, Konstantinopoulos PA, Murphy CJ, Nabavi S, Wulf GM. Transcriptome analysis reveals overlap in fusion genes in a phase I clinical cohort of TNBC and HGSOC patients treated with buparlisib and olaparib. J Cancer Res Clin Oncol 2019; 146:503-514. [PMID: 31745703 PMCID: PMC6985087 DOI: 10.1007/s00432-019-03078-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/02/2019] [Indexed: 01/05/2023]
Abstract
PURPOSE Fusion genes can be therapeutically relevant if they result in constitutive activation of oncogenes or repression of tumor suppressors. However, the prevalence and role of fusion genes in female cancers remain largely unexplored. Here, we investigate the fusion gene landscape in triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSOC), two subtypes of female cancers with high molecular similarity but limited treatment options at present. METHODS RNA-seq was utilized to identify fusion genes in a cohort of 18 TNBC and HGSOC patients treated with the PI3K inhibitor buparlisib and the PARP inhibitor olaparib in a phase I clinical trial (NCT01623349). Differential gene expression analysis was performed to assess the function of fusion genes in silico. Finally, these findings were correlated with the reported clinical outcomes. RESULTS A total of 156 fusion genes was detected, whereof 44/156 (28%) events occurred in more than one patient. Low recurrence across samples indicated that the majority of fusion genes were private passenger events. The long non-coding RNA MALAT1 was involved in 97/156 (62%) fusion genes, followed in prevalence by MUC16, FOXP1, WWOX and XIST. Gene expression of FOXP1 was significantly elevated in patients with vs. without FOXP1 fusion (P= 0.02). From a clinical perspective, FOXP1 fusions were associated with a favorable overall survival. CONCLUSIONS In summary, this study provides the first characterization of fusion genes in a cohort of TNBC and HGSOC patients. An improved mechanistic understanding of fusion genes will support the future identification of innovative therapeutic approaches for these challenging diseases.
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Affiliation(s)
- Julia Eismann
- Department of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Department of Obstetrics and Gynecology, University Medical Center Freiburg, Freiburg, Germany
| | - Yujing J Heng
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Johannes M Waldschmidt
- Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ioannis S Vlachos
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn P Gray
- Harvard Medical School, Boston, MA, USA.,Biostatic Core, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ursula A Matulonis
- Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Charles J Murphy
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA
| | - Sheida Nabavi
- Department of Computer Science and Engineering, Institute of System Genomics, University of Connecticut, Storrs, USA
| | - Gerburg M Wulf
- Department of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
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14
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Mutation Profiling of Premalignant Colorectal Neoplasia. Gastroenterol Res Pract 2019; 2019:2542640. [PMID: 31781186 PMCID: PMC6875414 DOI: 10.1155/2019/2542640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
Accumulation of allelic variants in genes that regulate cellular proliferation, differentiation, and apoptosis may result in expansion of the aberrant intestinal epithelium, generating adenomas. Herein, we compared the mutation profiles of conventional colorectal adenomas (CNADs) across stages of progression towards early carcinoma. DNA was isolated from 17 invasive adenocarcinomas (ACs) and 58 large CNADs, including 19 with low-grade dysplasia (LGD), 21 with LGD adjacent to areas of high-grade dysplasia and/or carcinoma (LGD-H), and 28 with high-grade dysplasia (HGD). Ion AmpliSeq Comprehensive Cancer Panel libraries were prepared and sequenced on the Ion Proton. We identified 956 unique allelic variants; of these, 499 were considered nonsynonymous variants. Eleven genes (APC, KRAS, SYNE1, NOTCH4, BLNK, FBXW7, GNAS, KMT2D, TAF1L, TCF7L2, and TP53) were mutated in at least 15% of all samples. Out of frequently mutated genes, TP53 and BCL2 had a consistent trend in mutation prevalence towards malignancy, while two other genes (HNF1A and FBXW7) exhibited the opposite trend. HGD adenomas had significantly higher mutation rates than LGD adenomas, while LGD-H adenomas exhibited mutation frequencies similar to those of LGD adenomas. A significant increase in copy number variant frequency was observed from LGD through HGD to malignant samples. The profiling of advanced CNADs demonstrated variations in mutation patterns among colorectal premalignancies. Only limited numbers of genes were repeatedly mutated while the majority were altered in single cases. Most genetic alterations in adenomas can be considered early contributors to colorectal carcinogenesis.
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15
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Parl FF, Dupont WD, Crooke PS. Interchromosomal Translocations as a Means to Map Chromosome Territories in Breast Cancer. Cancer Inform 2019; 18:1176935119842573. [PMID: 31019364 PMCID: PMC6469281 DOI: 10.1177/1176935119842573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/17/2019] [Indexed: 02/01/2023] Open
Abstract
The genome-wide identification of mutated genes is an important advance in our understanding of tumor biology, but several fundamental questions remain open. How do these genes act together to promote cancer development and, a related question, how are they spatially arranged in the nucleus to allow coordinated expression? We examined the nuclear topography of mutated genes in breast cancer and their relation to chromosome territories (CTs). We performed a literature review and analyzed 1 type of mutation, interchromosomal translocations, in 1546 primary breast cancers to infer the spatial arrangement of chromosomes. The cosegregation of all observed fusion genes was used to create a matrix of genome-wide CT contacts and develop a tentative CT map of breast cancer. Regression analysis was performed to determine the association between CTs and all types of mutations. Chromosomes 17, 11, 8, and 1 had the majority of interchromosomal fusions and are presumably clustered in the nuclear center, whereas chromosomes 22, 21, X, and 18 had the lowest number of contacts, likely reflecting a more peripheral position. Regression analysis revealed that there was no significant association between chromosome length indicated by the number of base pairs per chromosome and the number of total (inter- and intrachromosomal) translocations, point mutations, or copy number aberrations (CNAs). The gene density of chromosomes (genes/Mb) was significantly correlated with total translocations (P = .02), but not with point mutations P = .19 and CNAs P = .62. Finally, the association of the 3 genetic alterations with the CT map deduced from the interchromosomal fusions was significant, ie, total translocations P = 7 × 10-11, point mutations P = .01, CNAs P = .002. In conclusion, we developed a tentative CT map and observed a spatial association with genetic alterations in breast cancer.
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Affiliation(s)
- Fritz F Parl
- Department of Pathology, Microbiology
and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William D Dupont
- Department of Biostatistics, Vanderbilt
University, Nashville, TN, USA
| | - Philip S Crooke
- Department of Mathematics, Vanderbilt
University, Nashville, TN, USA
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