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Vorderbruggen M, Velázquez-Martínez CA, Natarajan A, Karpf AR. PROTACs in Ovarian Cancer: Current Advancements and Future Perspectives. Int J Mol Sci 2024; 25:5067. [PMID: 38791105 PMCID: PMC11121112 DOI: 10.3390/ijms25105067] [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: 04/04/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy. The majority of patients diagnosed with advanced ovarian cancer will relapse, at which point additional therapies can be administered but, for the most part, these are not curative. As such, a need exists for the development of novel therapeutic options for ovarian cancer patients. Research in the field of targeted protein degradation (TPD) through the use of proteolysis-targeting chimeras (PROTACs) has significantly increased in recent years. The ability of PROTACs to target proteins of interest (POI) for degradation, overcoming limitations such as the incomplete inhibition of POI function and the development of resistance seen with other inhibitors, is of particular interest in cancer research, including ovarian cancer research. This review provides a synopsis of PROTACs tested in ovarian cancer models and highlights PROTACs characterized in other types of cancers with potential high utility in ovarian cancer. Finally, we discuss methods that will help to enable the selective delivery of PROTACs to ovarian cancer and improve the pharmacodynamic properties of these agents.
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Affiliation(s)
- Makenzie Vorderbruggen
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | | | - Amarnath Natarajan
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Adam R. Karpf
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA; (M.V.); (A.N.)
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
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2
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Dugo E, Piva F, Giulietti M, Giannella L, Ciavattini A. Copy number variations in endometrial cancer: from biological significance to clinical utility. Int J Gynecol Cancer 2024:ijgc-2024-005295. [PMID: 38677776 DOI: 10.1136/ijgc-2024-005295] [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: 04/29/2024] Open
Abstract
The molecular basis of endometrial cancer, which is the most common malignancy of the female reproductive organs, relies not only on onset of mutations but also on copy number variations, the latter consisting of gene gains or losses. In this review, we introduce copy number variations and discuss their involvement in endometrial cancer to determine the perspectives of clinical applicability. We performed a literature analysis on PubMed of publications over the past 30 years and annotated clinical information, including histological and molecular subtypes, adopted molecular techniques for identification of copy number variations, their locations, and the genes involved. We highlight correlations between the presence of some specific copy number variations and myometrial invasion, lymph node metastasis, advanced International Federation of Gynecology and Obstetrics (FIGO) stage, high grade, drug response, and cancer progression. In particular, type I endometrial cancer cells have few copy number variations and are mainly located in 8q and 1q, while type II, high grade, and advanced FIGO stage endometrial cancer cells are aneuploid and have a greater number of copy number variations. As expected, the higher the number of copy number variations the worse the prognosis, especially if they amplify CCNE1, ERBB2, KRAS, MYC, and PIK3CA oncogenes. Great variability in copy number and location among patients with the same endometrial cancer histological or molecular subtype emerged, making them interesting candidates to be explored for the improvement of patient stratification. Copy number variations have a role in endometrial cancer progression, and therefore their detection may be useful for more accurate prediction of prognosis. Unfortunately, only a few studies have been carried out on the role of copy number variations according to the molecular classification of endometrial cancer, and even fewer have explored the correlation with drugs. For these reasons, further studies, also using single cell RNA sequencing, are needed before reaching a clinical application.
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Affiliation(s)
- Erica Dugo
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luca Giannella
- Woman's Health Sciences Department, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Ciavattini
- Woman's Health Sciences Department, Polytechnic University of Marche, Ancona, Italy
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Adamson AW, Ding YC, Steele L, Leong LA, Morgan R, Wakabayashi MT, Han ES, Dellinger TH, Lin PS, Hakim AA, Wilczynski S, Warden CD, Tao S, Bedell V, Cristea MC, Neuhausen SL. Genomic analyses of germline and somatic variation in high-grade serous ovarian cancer. J Ovarian Res 2023; 16:141. [PMID: 37460928 PMCID: PMC10351177 DOI: 10.1186/s13048-023-01234-x] [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: 02/15/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND High-grade serous ovarian cancers (HGSCs) display a high degree of complex genetic alterations. In this study, we identified germline and somatic genetic alterations in HGSC and their association with relapse-free and overall survival. Using a targeted capture of 557 genes involved in DNA damage response and PI3K/AKT/mTOR pathways, we conducted next-generation sequencing of DNA from matched blood and tumor tissue from 71 HGSC participants. In addition, we performed the OncoScan assay on tumor DNA from 61 participants to examine somatic copy number alterations (SCNA). RESULTS Approximately one-third of tumors had loss-of-function (LOF) germline (18/71, 25.4%) or somatic (7/71, 9.9%) variants in the DNA homologous recombination repair pathway genes BRCA1, BRCA2, CHEK2, MRE11A, BLM, and PALB2. LOF germline variants also were identified in other Fanconi anemia genes and in MAPK and PI3K/AKT/mTOR pathway genes. Most tumors harbored somatic TP53 variants (65/71, 91.5%). Using the OncoScan assay on tumor DNA from 61 participants, we identified focal homozygous deletions in BRCA1, BRCA2, MAP2K4, PTEN, RB1, SLX4, STK11, CREBBP, and NF1. In total, 38% (27/71) of HGSC patients harbored pathogenic variants in DNA homologous recombination repair genes. For patients with multiple tissues from the primary debulking or from multiple surgeries, the somatic mutations were maintained with few newly acquired point mutations suggesting that tumor evolution was not through somatic mutations. There was a significant association of LOF variants in homologous recombination repair pathway genes and high-amplitude somatic copy number alterations. Using GISTIC analysis, we identified NOTCH3, ZNF536, and PIK3R2 in these regions that were significantly associated with an increase in cancer recurrence and a reduction in overall survival. CONCLUSIONS From 71 patients with HGCS, we performed targeted germline and tumor sequencing and provided a comprehensive analysis of these 557 genes. We identified germline and somatic genetic alterations including somatic copy number alterations and analyzed their associations with relapse-free and overall survival. This single-site long-term follow-up study provides additional information on genetic alterations related to occurrence and outcome of HGSC. Our findings suggest that targeted treatments based on both variant and SCNA profile potentially could improve relapse-free and overall survival.
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Affiliation(s)
- A W Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, CA, Duarte, USA
| | - Y C Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, CA, Duarte, USA
| | - L Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, CA, Duarte, USA
| | - L A Leong
- Formerly, Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - R Morgan
- Formerly, Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - M T Wakabayashi
- Currently at Regeneron Pharmaceuticals Inc, Formerly City of Hope National Medical Center, Duarte, CA, USA
- Formerly, Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - E S Han
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - T H Dellinger
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - P S Lin
- Formerly, Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - A A Hakim
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - S Wilczynski
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - C D Warden
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - S Tao
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - V Bedell
- Cytogenetics Core, City of Hope National Medical Center, Duarte, CA, USA
| | - M C Cristea
- Formerly, Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
- Currently at Regeneron Pharmaceuticals Inc, Formerly City of Hope National Medical Center, Duarte, CA, USA
| | - S L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, CA, Duarte, USA.
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Adamson AW, Ding YC, Steele L, Leong LA, Morgan R, Wakabayashi MT, Han ES, Dellinger TH, Lin PS, Hakim AA, Wilczynski S, Warden CD, Tao S, Bedell V, Cristea MC, Neuhausen SL. Genomic Analyses of Germline and Somatic Variation in High-Grade Serous Ovarian Cancer. RESEARCH SQUARE 2023:rs.3.rs-2592107. [PMID: 36865331 PMCID: PMC9980206 DOI: 10.21203/rs.3.rs-2592107/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Background High-grade serous ovarian cancers (HGSCs) display a high degree of complex genetic alterations. In this study, we identified germline and somatic genetic alterations in HGSC and their association with relapse-free and overall survival. Using a targeted capture of 577 genes involved in DNA damage response and PI3K/AKT/mTOR pathways, we conducted next-generation sequencing of DNA from matched blood and tumor tissue from 71 HGSC participants. In addition, we performed the OncoScan assay on tumor DNA from 61 participants to examine somatic copy number alterations. Results Approximately one-third of tumors had loss-of-function germline (18/71, 25.4%) or somatic (7/71, 9.9%) variants in the DNA homologous recombination repair pathway genes BRCA1, BRCA2, CHEK2, MRE11A, BLM , and PALB2 . Loss-of-function germline variants also were identified in other Fanconi anemia genes and in MAPK and PI3K/AKT/mTOR pathway genes. Most tumors harbored somatic TP53 variants (65/71, 91.5%). Using the OncoScan assay on tumor DNA from 61 participants, we identified focal homozygous deletions in BRCA1, BRCA2, MAP2K4, PTEN, RB1, SLX4, STK11, CREBBP , and NF1 . In total, 38% (27/71) of HGSC patients harbored pathogenic variants in DNA homologous recombination repair genes. For patients with multiple tissues from the primary debulking or from multiple surgeries, the somatic mutations were maintained with few newly acquired point mutations suggesting that tumor evolution was not through somatic mutations. There was a significant association of loss-of-function variants in homologous recombination repair pathway genes and high-amplitude somatic copy number alterations. Using GISTIC analysis, we identified NOTCH3, ZNF536 , and PIK3R2 in these regions that were significantly associated with an increase in cancer recurrence and a reduction in overall survival. Conclusions From 71 patients with HGCS, we performed targeted germline and tumor sequencing and provided a comprehensive analysis of these 577 genes. We identified germline and somatic genetic alterations including somatic copy number alterations and analyzed their associations with relapse-free and overall survival. This single-site long-term follow-up study provides additional information on genetic alterations related to occurrence and outcome of HGSC. Our findings suggest that targeted treatments based on both variant and SCNA profile potentially could improve relapse-free and overall survival.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Shu Tao
- City Of Hope National Medical Center
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5
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Lai X, Gao L, Zhou G, Xu X, Wang J. Copy number variations: A novel molecular marker for papillary thyroid cancer. Heliyon 2022; 8:e11107. [PMID: 36299525 PMCID: PMC9589167 DOI: 10.1016/j.heliyon.2022.e11107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/15/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Background We aimed to screen tumor-associated functional genes on a large scale through copy number variation (CNV) analysis of papillary thyroid cancer (PTC). Methods We analyzed 74 tissue samples from 41 patients with thyroid nodules. The samples were subjected to whole-genome resequencing and then analyzed by the ‘WISECONDOR’ method. Potential chromosome CNV regions were identified between the different sample groups. Results Of the 74 samples from 41 patients, 28 were PTC tissue samples, 29 were para-carcinoma tissue samples, 13 were benign tumor tissue samples and 4 were para-benign tumor tissue samples. According to our findings, PTC can be identified by CNVs at the corresponding positions on chromosomes 5, 7, 8, 10, and 17. For carcinoma tissue, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy and area under the curve (AUC) of the test method were 100%, 66.7%, 87.5%, 100.0%, 90.0% and 0.83 (95% confidence interval [CI], 0.67–1.00) and for para-carcinoma tissue, these values were 96.6%, 75.0%, 96.6%, 75.0%, 93.9% and 0.86 (95% CI, 0.60–1.00). Conclusion CNV analysis assays involving high-volume sequencing analysis can increase the identification of PTC, potentially avoiding errors caused by position deflection in sampling. Thyroid nodules can be identified by CNVs at the corresponding positions on chromosomes 5, 7, 8, 10, and 17. The identification rate of PTC can be greatly increased through high-volume CNV sequencing analysis.
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Affiliation(s)
- Xingjian Lai
- Department of Ultrasound, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Luying Gao
- Department of Ultrasound, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Gaoying Zhou
- Beijing Longer Gene Technology Co., Ltd., Beijing, China
| | - Xiequn Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Corresponding author.
| | - Jinhui Wang
- Department of Gynecology and Obstetrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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6
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FAK in Cancer: From Mechanisms to Therapeutic Strategies. Int J Mol Sci 2022; 23:ijms23031726. [PMID: 35163650 PMCID: PMC8836199 DOI: 10.3390/ijms23031726] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 01/25/2023] Open
Abstract
Focal adhesion kinase (FAK), a non-receptor tyrosine kinase, is overexpressed and activated in many cancer types. FAK regulates diverse cellular processes, including growth factor signaling, cell cycle progression, cell survival, cell motility, angiogenesis, and the establishment of immunosuppressive tumor microenvironments through kinase-dependent and kinase-independent scaffolding functions in the cytoplasm and nucleus. Mounting evidence has indicated that targeting FAK, either alone or in combination with other agents, may represent a promising therapeutic strategy for various cancers. In this review, we summarize the mechanisms underlying FAK-mediated signaling networks during tumor development. We also summarize the recent progress of FAK-targeted small-molecule compounds for anticancer activity from preclinical and clinical evidence.
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Dawson JC, Serrels A, Stupack DG, Schlaepfer DD, Frame MC. Targeting FAK in anticancer combination therapies. Nat Rev Cancer 2021; 21:313-324. [PMID: 33731845 PMCID: PMC8276817 DOI: 10.1038/s41568-021-00340-6] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
Focal adhesion kinase (FAK) is both a non-receptor tyrosine kinase and an adaptor protein that primarily regulates adhesion signalling and cell migration, but FAK can also promote cell survival in response to stress. FAK is commonly overexpressed in cancer and is considered a high-value druggable target, with multiple FAK inhibitors currently in development. Evidence suggests that in the clinical setting, FAK targeting will be most effective in combination with other agents so as to reverse failure of chemotherapies or targeted therapies and enhance efficacy of immune-based treatments of solid tumours. Here, we discuss the recent preclinical evidence that implicates FAK in anticancer therapeutic resistance, leading to the view that FAK inhibitors will have their greatest utility as combination therapies in selected patient populations.
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Affiliation(s)
- John C Dawson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Alan Serrels
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego Moores Cancer Centre, La Jolla, CA, USA
| | - David D Schlaepfer
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego Moores Cancer Centre, La Jolla, CA, USA
| | - Margaret C Frame
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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Ibragimova MK, Tsyganov MM, Slonimskaya EM, Litviakov NV. Aberrations of the number of copies (CNA) in the genome of luminal B breast tumor. BULLETIN OF SIBERIAN MEDICINE 2020. [DOI: 10.20538/1682-0363-2020-3-22-28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M. K. Ibragimova
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| | - M. M. Tsyganov
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| | | | - N. V. Litviakov
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
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Taniguchi-Ponciano K, Huerta-Padilla V, Baeza-Xochihua V, Ponce-Navarrete G, Salcedo E, Gomez-Apo E, Chavez-Macias L, Aviles-Duran J, Ruiz-Sanchez H, Valdivia A, Peralta R, Romero-Anduaga H, Rosas-Vargas H, Quijano F, Salcedo M, Marrero-Rodríguez D. Revisiting the Genomic and Transcriptomic Landscapes from Female Malignancies Could Provide Molecular Markers and Targets for Precision Medicine. Arch Med Res 2019; 50:428-436. [PMID: 31783305 DOI: 10.1016/j.arcmed.2019.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 11/14/2019] [Indexed: 12/17/2022]
Abstract
AIMS Gynaecological malignancies such as breast, ovarian and cervical cancers have become an important public health problem. Detection of molecular alterations in cancer research is fundamental since it can reveal specific pathogenic patterns and genes that could serve as markers. Our aim was to characterize common genomic and transcriptomic signatures for the three gynaecologic malignancies with the highest incidence and mortality to try to identify new molecular markers, therapeutic targets and molecular signatures. METHODS Here we analysed a total of 723 microarray libraries corresponding to equal number of breast, ovary and cervical cancer and non-cancer patient samples. Copy number variation (CNV) was carried out using 428 libraries and transcriptomic analysis using the 295 remaining samples. RESULTS Our results showed that breast, ovary and cervical malignancies are characterized by gain of 1q chromosome. At transcriptomic level, they share 351 coding and non-coding genes, which could represent core transcriptome of gynaecological malignancies. Pathway analysis from the resulting gene lists from CNV and expression showed participation in cell cycle, metabolism, and cell adhesion molecules among others. CONCLUSIONS Chromosome 1q characterize the gynaecological malignancies, which could harbour a richness of genetic repertoire to mine for molecular markers and targets, particular gynaecologic expression profile, containing FANCI, FH and MIR155HG among others, could represent part of the transcriptomic core for diagnostic test and attractive therapeutic targets. It may not be long before every human cancer sample is profiled for a detections test to ascertain a molecular diagnosis and prognosis and to define an optimal and precise treatment strategy.
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Affiliation(s)
- Keiko Taniguchi-Ponciano
- Laboratorio de Neuroendocrinología Comparada, Departamento de Ecología y Recursos Naturales, Biología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico; Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Victor Huerta-Padilla
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico; Laboratorio de Quimioterapia Experimental, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Victor Baeza-Xochihua
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Gustavo Ponce-Navarrete
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Emmanuel Salcedo
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Erick Gomez-Apo
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México Dr. Eduardo Liceaga, Ciudad de México, Mexico
| | - Laura Chavez-Macias
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México Dr. Eduardo Liceaga, Ciudad de México, Mexico; Facultad de Medicina, Universidad Nacional Autonoma de México, Ciudad de México, Mexico
| | - Julio Aviles-Duran
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Hilario Ruiz-Sanchez
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Alejandra Valdivia
- Escuela Superior de Enfermería y Obstetricia, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Raul Peralta
- Centro de Investigación en Dinámica Celular, Universidad Autónoma de Morelos, Cuernavaca, Morelos, Mexico
| | - Hugo Romero-Anduaga
- Servicio de Radioterapia, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Felix Quijano
- Jefatura de Investigación y Enseñanza, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Mauricio Salcedo
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Daniel Marrero-Rodríguez
- CONACyT-Laboratorio de Endocrinología Experimental, Unidad de Investigación Medica en Endocrinología Experimental, Hospital de Especialidades, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico.
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10
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Diaz Osterman CJ, Ozmadenci D, Kleinschmidt EG, Taylor KN, Barrie AM, Jiang S, Bean LM, Sulzmaier FJ, Jean C, Tancioni I, Anderson K, Uryu S, Cordasco EA, Li J, Chen XL, Fu G, Ojalill M, Rappu P, Heino J, Mark AM, Xu G, Fisch KM, Kolev VN, Weaver DT, Pachter JA, Győrffy B, McHale MT, Connolly DC, Molinolo A, Stupack DG, Schlaepfer DD. FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy. eLife 2019; 8:e47327. [PMID: 31478830 PMCID: PMC6721800 DOI: 10.7554/elife.47327] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/01/2019] [Indexed: 12/19/2022] Open
Abstract
Gene copy number alterations, tumor cell stemness, and the development of platinum chemotherapy resistance contribute to high-grade serous ovarian cancer (HGSOC) recurrence. Stem phenotypes involving Wnt-β-catenin, aldehyde dehydrogenase activities, intrinsic platinum resistance, and tumorsphere formation are here associated with spontaneous gains in Kras, Myc and FAK (KMF) genes in a new aggressive murine model of ovarian cancer. Adhesion-independent FAK signaling sustained KMF and human tumorsphere proliferation as well as resistance to cisplatin cytotoxicity. Platinum-resistant tumorspheres can acquire a dependence on FAK for growth. Accordingly, increased FAK tyrosine phosphorylation was observed within HGSOC patient tumors surviving neo-adjuvant chemotherapy. Combining a FAK inhibitor with platinum overcame chemoresistance and triggered cell apoptosis. FAK transcriptomic analyses across knockout and reconstituted cells identified 135 targets, elevated in HGSOC, that were regulated by FAK activity and β-catenin including Myc, pluripotency and DNA repair genes. These studies reveal an oncogenic FAK signaling role supporting chemoresistance.
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Affiliation(s)
- Carlos J Diaz Osterman
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Duygu Ozmadenci
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Elizabeth G Kleinschmidt
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Kristin N Taylor
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Allison M Barrie
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Shulin Jiang
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Lisa M Bean
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Florian J Sulzmaier
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Christine Jean
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Isabelle Tancioni
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Kristen Anderson
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Sean Uryu
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Edward A Cordasco
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life SciencesXiamen UniversityXiamenChina
| | - Xiao Lei Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life SciencesXiamen UniversityXiamenChina
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cellular Signaling Network, School of Life SciencesXiamen UniversityXiamenChina
| | | | - Pekka Rappu
- Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Jyrki Heino
- Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Adam M Mark
- Department of MedicineUCSD Center for Computational Biology & BioinformaticsLa JollaUnited States
| | - Guorong Xu
- Department of MedicineUCSD Center for Computational Biology & BioinformaticsLa JollaUnited States
| | - Kathleen M Fisch
- Department of MedicineUCSD Center for Computational Biology & BioinformaticsLa JollaUnited States
| | | | | | | | - Balázs Győrffy
- Institute of EnzymologyHungarian Academy of SciencesBudapestHungary
- 2nd Department of PediatricsSemmelweis UniversityBudapestHungary
| | - Michael T McHale
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | | | - Alfredo Molinolo
- Department of PathologyMoores UCSD Cancer CenterLa JollaUnited States
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
| | - David D Schlaepfer
- Department of Obstetrics, Gynecology and Reproductive SciencesMoores UCSD Cancer CenterLa JollaUnited States
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In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma. Int J Mol Sci 2019; 20:ijms20143582. [PMID: 31336658 PMCID: PMC6679006 DOI: 10.3390/ijms20143582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/06/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
Understanding the gene regulatory network governing cancer initiation and progression is necessary, although it remains largely unexplored. Enhancer elements represent the center of this regulatory circuit. The study aims to identify the gene expression change driven by copy number variation in enhancer elements of pancreatic adenocarcinoma (PAAD). The pancreatic tissue specific enhancer and target gene data were taken from EnhancerAtlas. The gene expression and copy number data were taken from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) and copy number variations (CNVs) were identified between matched tumor-normal samples of PAAD. Significant CNVs were matched onto enhancer coordinates by using genomic intersection functionality from BEDTools. By combining the gene expression and CNV data, we identified 169 genes whose expression shows a positive correlation with the CNV of enhancers. We further identified 16 genes which are regulated by a super enhancer and 15 genes which have high prognostic potential (Z-score > 1.96). Cox proportional hazard analysis of these genes indicates that these are better predictors of survival. Taken together, our integrative analytical approach identifies enhancer CNV-driven gene expression change in PAAD, which could lead to better understanding of PAAD pathogenesis and to the design of enhancer-based cancer treatment strategies.
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Characterizing functional consequences of DNA copy number alterations in breast and ovarian tumors by spaceMap. J Genet Genomics 2018; 45:361-371. [PMID: 30057342 DOI: 10.1016/j.jgg.2018.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 01/18/2023]
Abstract
We propose a novel conditional graphical model - spaceMap - to construct gene regulatory networks from multiple types of high dimensional omic profiles. A motivating application is to characterize the perturbation of DNA copy number alterations (CNAs) on downstream protein levels in tumors. Through a penalized multivariate regression framework, spaceMap jointly models high dimensional protein levels as responses and high dimensional CNAs as predictors. In this setup, spaceMap infers an undirected network among proteins together with a directed network encoding how CNAs perturb the protein network. spaceMap can be applied to learn other types of regulatory relationships from high dimensional molecular profiles, especially those exhibiting hub structures. Simulation studies show spaceMap has greater power in detecting regulatory relationships over competing methods. Additionally, spaceMap includes a network analysis toolkit for biological interpretation of inferred networks. We applies spaceMap to the CNAs, gene expression and proteomics data sets from CPTAC-TCGA breast (n=77) and ovarian (n=174) cancer studies. Each cancer exhibits disruption of 'ion transmembrane transport' and 'regulation from RNA polymerase II promoter' by CNA events unique to each cancer. Moreover, using protein levels as a response yields a more functionally-enriched network than using RNA expressions in both cancer types. The network results also help to pinpoint crucial cancer genes and provide insights on the functional consequences of important CNA in breast and ovarian cancers. The R package spaceMap - including vignettes and documentation - is hosted on https://topherconley.github.io/spacemap.
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Correction to: A systematic comparison of copy number alterations in four types of female cancer. BMC Cancer 2018; 18:80. [PMID: 29338700 PMCID: PMC5769487 DOI: 10.1186/s12885-017-3766-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022] Open
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