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Zhang J, Simpson CM, Berner J, Chong HB, Fang J, Ordulu Z, Weiss-Sadan T, Possemato AP, Harry S, Takahashi M, Yang TY, Richter M, Patel H, Smith AE, Carlin AD, Hubertus de Groot AF, Wolf K, Shi L, Wei TY, Dürr BR, Chen NJ, Vornbäumen T, Wichmann NO, Mahamdeh MS, Pooladanda V, Matoba Y, Kumar S, Kim E, Bouberhan S, Oliva E, Rueda BR, Soberman RJ, Bardeesy N, Liau BB, Lawrence M, Stokes MP, Beausoleil SA, Bar-Peled L. Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway. Cell 2023; 186:2361-2379.e25. [PMID: 37192619 PMCID: PMC10225361 DOI: 10.1016/j.cell.2023.04.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
Multiple anticancer drugs have been proposed to cause cell death, in part, by increasing the steady-state levels of cellular reactive oxygen species (ROS). However, for most of these drugs, exactly how the resultant ROS function and are sensed is poorly understood. It remains unclear which proteins the ROS modify and their roles in drug sensitivity/resistance. To answer these questions, we examined 11 anticancer drugs with an integrated proteogenomic approach identifying not only many unique targets but also shared ones-including ribosomal components, suggesting common mechanisms by which drugs regulate translation. We focus on CHK1 that we find is a nuclear H2O2 sensor that launches a cellular program to dampen ROS. CHK1 phosphorylates the mitochondrial DNA-binding protein SSBP1 to prevent its mitochondrial localization, which in turn decreases nuclear H2O2. Our results reveal a druggable nucleus-to-mitochondria ROS-sensing pathway-required to resolve nuclear H2O2 accumulation and mediate resistance to platinum-based agents in ovarian cancers.
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Affiliation(s)
- Junbing Zhang
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | | | - Jacqueline Berner
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison B Chong
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Jiafeng Fang
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Zehra Ordulu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Tommy Weiss-Sadan
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Stefan Harry
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Mariko Takahashi
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Tzu-Yi Yang
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Marianne Richter
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Himani Patel
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Abby E Smith
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander D Carlin
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Konstantin Wolf
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Lei Shi
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Ting-Yu Wei
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Benedikt R Dürr
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas J Chen
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Tristan Vornbäumen
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Nina O Wichmann
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Mohammed S Mahamdeh
- Division of Cardiology, Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Venkatesh Pooladanda
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA; Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Yusuke Matoba
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA; Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Shaan Kumar
- Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Eugene Kim
- Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Sara Bouberhan
- Division of Hematology/Oncology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Bo R Rueda
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA; Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Roy J Soberman
- Division of Nephrology, Harvard Medical School, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nabeel Bardeesy
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Michael Lawrence
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | - Liron Bar-Peled
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.
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2
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Kang HG, Hwangbo H, Kim MJ, Kim S, Lee EJ, Park MJ, Kim JW, Kim BG, Cho EH, Chang S, Lee JY, Choi JK. Aberrant Transcript Usage Is Associated with Homologous Recombination Deficiency and Predicts Therapeutic Response. Cancer Res 2022; 82:142-154. [PMID: 34711610 PMCID: PMC9397646 DOI: 10.1158/0008-5472.can-21-2023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/15/2021] [Accepted: 10/25/2021] [Indexed: 01/07/2023]
Abstract
BRCA1/2 mutations account for only a small fraction of homologous recombination (HR) deficiency (HRD) cases. Recently developed genomic HRD (gHRD) tests suffer confounding factors that cause low precision in predicting samples that will respond to PARP inhibitors and DNA damaging agents. Here we present molecular and clinical evidence of transcriptional HRD (tHRD) that is based on aberrant transcript usage (aTU) of minor isoforms. Specifically, increased TU of nonfunctional isoforms of DNA repair genes was prevalent in breast and ovarian cancer with gHRD. Functional assays validated the association of aTU with impaired HR activity. Machine learning-based tHRD detection by the transcript usage (TU) pattern of key genes was superior to directly screening for gHRD or BRCA1/2 mutations in accurately predicting responses of cell lines and patients with cancer to PARP inhibitors and genotoxic drugs. This approach demonstrated the capability of tHRD status to reflect functional HR status, including in a cohort of olaparib-treated ovarian cancer with acquired platinum resistance. Diagnostic tests based on tHRD are expected to broaden the clinical utility of PARP inhibitors. SIGNIFICANCE: A novel but widespread transcriptional mechanism by which homologous recombination deficiency arises independently of BRCA1/2 mutations can be utilized as a companion diagnostic for PARP inhibitors.
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Affiliation(s)
- Hyeon Gu Kang
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Haeun Hwangbo
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Myung Ji Kim
- Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sinae Kim
- Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eun Ji Lee
- Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Min Ji Park
- Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jae-Weon Kim
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Byoung-Gie Kim
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eun-Hae Cho
- Genome Research Center, GC Genome, GC Labs, Yongin-si, Gyeonggi-do, Republic of Korea.,Corresponding Authors: Eun-Hae Cho, GC Genome, GC Labs, 107 Ihyeonro, 30beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do 16924, Republic of Korea. Phone: 82-31-260-9216; E-mail: ; Suhwan Chang, Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Pungnap 2(i)-dong, Songpa-gu, Seoul, Republic of Korea. Phone: 82-2-3010-2095; E-mail: ; Jung-Yun Lee, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea. Phone: 82-2-2228-2237; E-mail: ; and Jung Kyoon Choi, YBS Building (E16-1), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea. Phone: 82-42-350-4327; E-mail:
| | - Suhwan Chang
- Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Corresponding Authors: Eun-Hae Cho, GC Genome, GC Labs, 107 Ihyeonro, 30beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do 16924, Republic of Korea. Phone: 82-31-260-9216; E-mail: ; Suhwan Chang, Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Pungnap 2(i)-dong, Songpa-gu, Seoul, Republic of Korea. Phone: 82-2-3010-2095; E-mail: ; Jung-Yun Lee, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea. Phone: 82-2-2228-2237; E-mail: ; and Jung Kyoon Choi, YBS Building (E16-1), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea. Phone: 82-42-350-4327; E-mail:
| | - Jung-Yun Lee
- Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Corresponding Authors: Eun-Hae Cho, GC Genome, GC Labs, 107 Ihyeonro, 30beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do 16924, Republic of Korea. Phone: 82-31-260-9216; E-mail: ; Suhwan Chang, Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Pungnap 2(i)-dong, Songpa-gu, Seoul, Republic of Korea. Phone: 82-2-3010-2095; E-mail: ; Jung-Yun Lee, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea. Phone: 82-2-2228-2237; E-mail: ; and Jung Kyoon Choi, YBS Building (E16-1), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea. Phone: 82-42-350-4327; E-mail:
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.,PentaMedix Co., Ltd., Seongnam-si, Gyeonggi-do, Republic of Korea.,Corresponding Authors: Eun-Hae Cho, GC Genome, GC Labs, 107 Ihyeonro, 30beon-gil, Giheung-gu, Yongin-si, Gyeonggi-do 16924, Republic of Korea. Phone: 82-31-260-9216; E-mail: ; Suhwan Chang, Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Pungnap 2(i)-dong, Songpa-gu, Seoul, Republic of Korea. Phone: 82-2-3010-2095; E-mail: ; Jung-Yun Lee, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea. Phone: 82-2-2228-2237; E-mail: ; and Jung Kyoon Choi, YBS Building (E16-1), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea. Phone: 82-42-350-4327; E-mail:
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Hussain A, Voisin V, Poon S, Karamboulas C, Bui NHB, Meens J, Dmytryshyn J, Ho VW, Tang KH, Paterson J, Clarke BA, Bernardini MQ, Bader GD, Neel BG, Ailles LE. Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21. J Exp Med 2021; 217:151793. [PMID: 32434219 PMCID: PMC7398174 DOI: 10.1084/jem.20191094] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/06/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Recent studies indicate that cancer-associated fibroblasts (CAFs) are phenotypically and functionally heterogeneous. However, little is known about CAF subtypes, the roles they play in cancer progression, and molecular mediators of the CAF “state.” Here, we identify a novel cell surface pan-CAF marker, CD49e, and demonstrate that two distinct CAF states, distinguished by expression of fibroblast activation protein (FAP), coexist within the CD49e+ CAF compartment in high-grade serous ovarian cancers. We show for the first time that CAF state influences patient outcomes and that this is mediated by the ability of FAP-high, but not FAP-low, CAFs to aggressively promote proliferation, invasion and therapy resistance of cancer cells. Overexpression of the FAP-low–specific transcription factor TCF21 in FAP-high CAFs decreases their ability to promote invasion, chemoresistance, and in vivo tumor growth, indicating that it acts as a master regulator of the CAF state. Understanding CAF states in more detail could lead to better patient stratification and novel therapeutic strategies.
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Affiliation(s)
- Ali Hussain
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Poon
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Christina Karamboulas
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ngoc Hoang Bao Bui
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jalna Meens
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Julia Dmytryshyn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Victor W Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kwan Ho Tang
- Laura and Isaac Perlmutter Cancer Center, New York Langone Health, New York, NY
| | - Joshua Paterson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Blaise A Clarke
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Marcus Q Bernardini
- Division of Gynaecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin G Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Laura and Isaac Perlmutter Cancer Center, New York Langone Health, New York, NY
| | - Laurie E Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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4
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The Dawning of the Age of Personalized Medicine in Gynecologic Oncology. Cancers (Basel) 2020; 12:cancers12113135. [PMID: 33120871 PMCID: PMC7693675 DOI: 10.3390/cancers12113135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
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5
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Lorenzi C, Barriere S, Villemin JP, Dejardin Bretones L, Mancheron A, Ritchie W. iMOKA: k-mer based software to analyze large collections of sequencing data. Genome Biol 2020; 21:261. [PMID: 33050927 PMCID: PMC7552494 DOI: 10.1186/s13059-020-02165-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/10/2020] [Indexed: 01/24/2023] Open
Abstract
iMOKA (interactive multi-objective k-mer analysis) is a software that enables comprehensive analysis of sequencing data from large cohorts to generate robust classification models or explore specific genetic elements associated with disease etiology. iMOKA uses a fast and accurate feature reduction step that combines a Naïve Bayes classifier augmented by an adaptive entropy filter and a graph-based filter to rapidly reduce the search space. By using a flexible file format and distributed indexing, iMOKA can easily integrate data from multiple experiments and also reduces disk space requirements and identifies changes in transcript levels and single nucleotide variants. iMOKA is available at https://github.com/RitchieLabIGH/iMOKA and Zenodo https://doi.org/10.5281/zenodo.4008947 .
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Affiliation(s)
- Claudio Lorenzi
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Sylvain Barriere
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Jean-Philippe Villemin
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | | | | | - William Ritchie
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France.
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6
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Penson RT, Valencia RV, Cibula D, Colombo N, Leath CA, Bidziński M, Kim JW, Nam JH, Madry R, Hernández C, Mora PAR, Ryu SY, Milenkova T, Lowe ES, Barker L, Scambia G. Olaparib Versus Nonplatinum Chemotherapy in Patients With Platinum-Sensitive Relapsed Ovarian Cancer and a Germline BRCA1/2 Mutation (SOLO3): A Randomized Phase III Trial. J Clin Oncol 2020; 38:1164-1174. [PMID: 32073956 PMCID: PMC7145583 DOI: 10.1200/jco.19.02745] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE A phase II study (ClinicalTrials.gov identifier: NCT00628251) showed activity of olaparib capsules versus pegylated liposomal doxorubicin in patients with germline BRCA-mutated platinum-resistant or partially platinum-sensitive relapsed ovarian cancer. We conducted a phase III trial (SOLO3) of olaparib tablets versus nonplatinum chemotherapy in patients with germline BRCA-mutated platinum-sensitive relapsed ovarian cancer who had received at least 2 prior lines of platinum-based chemotherapy. PATIENTS AND METHODS In this randomized, open-label trial, patients were randomly assigned 2:1 to olaparib 300 mg twice a day or physician's choice single-agent nonplatinum chemotherapy (pegylated liposomal doxorubicin, paclitaxel, gemcitabine, or topotecan). The primary end point was objective response rate (ORR) in the measurable disease analysis set assessed by blinded independent central review (BICR). The key secondary end point was progression-free survival (PFS) assessed by BICR in the intent-to-treat population. RESULTS Of 266 randomly assigned patients, 178 were assigned to olaparib and 88 to chemotherapy. In patients with measurable disease (olaparib, n = 151; chemotherapy, n = 72), the BICR-assessed ORR was significantly higher with olaparib than with chemotherapy (72.2% v 51.4%; odds ratio [OR], 2.53 [95% CI, 1.40 to 4.58]; P = .002). In the subgroup who had received 2 prior lines of treatment, the ORR was 84.6% with olaparib and 61.5% with chemotherapy (OR, 3.44 [95% CI, 1.42 to 8.54]). BICR-assessed PFS also significantly favored olaparib versus chemotherapy (hazard ratio, 0.62 [95% CI, 0.43 to 0.91]; P = .013; median, 13.4 v 9.2 months). Adverse events were consistent with the established safety profiles of olaparib and chemotherapy. CONCLUSION Olaparib resulted in statistically significant and clinically relevant improvements in ORR and PFS compared with nonplatinum chemotherapy in patients with germline BRCA-mutated platinum-sensitive relapsed ovarian cancer who had received at least 2 prior lines of platinum-based chemotherapy.
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Affiliation(s)
- Richard T Penson
- Harvard Medical School and Massachusetts General Hospital, Boston, MA
| | | | - David Cibula
- First Faculty of Medicine, Charles University and General University, Prague, Czech Republic
| | - Nicoletta Colombo
- University of Milan-Bicocca and IEO European Institute of Oncology IRCCS, Milan, Italy
| | | | - Mariusz Bidziński
- Faculty of Medicine and Health Sciences, Jan Kochanowski University, Kielce, Poland
| | - Jae-Weon Kim
- Seoul National University Hospital, Seoul, South Korea
| | | | - Radoslaw Madry
- Medical University K. Marcinkowski and Clinical Hospital of the Transfiguration, Poznań, Poland
| | | | - Paulo A R Mora
- Instituto COI de Educação e Pesquisa, Rio de Janeiro, Brazil
| | - Sang Young Ryu
- Korea Institute of Radiological and Medical Sciences, Seoul, South Korea
| | | | | | | | - Giovanni Scambia
- Università Cattolica del Sacro Cuore-Fondazione Policlinico A. Gemelli, IRCCS, Rome, Italy
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7
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Song X, Ji J, Gleason KJ, Yang F, Martignetti JA, Chen LS, Wang P. Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis. Mol Cell Proteomics 2019; 18:S52-S65. [PMID: 31227599 PMCID: PMC6692782 DOI: 10.1074/mcp.ra118.001220] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 06/19/2019] [Indexed: 12/19/2022] Open
Abstract
In this work, we propose iProFun, an integrative analysis tool to screen for proteogenomic functional traits perturbed by DNA copy number alterations (CNAs) and DNA methylations. The goal is to characterize functional consequences of DNA copy number and methylation alterations in tumors and to facilitate screening for cancer drivers contributing to tumor initiation and progression. Specifically, we consider three functional molecular quantitative traits: mRNA expression levels, global protein abundances, and phosphoprotein abundances. We aim to identify those genes whose CNAs and/or DNA methylations have cis-associations with either some or all three types of molecular traits. Compared with analyzing each molecular trait separately, the joint modeling of multi-omics data enjoys several benefits: iProFun experienced enhanced power for detecting significant cis-associations shared across different omics data types, and it also achieved better accuracy in inferring cis-associations unique to certain type(s) of molecular trait(s). For example, unique associations of CNAs/methylations to global/phospho protein abundances may imply posttranslational regulations.We applied iProFun to ovarian high-grade serous carcinoma tumor data from The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium and identified CNAs and methylations of 500 and 121 genes, respectively, affecting the cis-functional molecular quantitative traits of the corresponding genes. We observed substantial power gain via the joint analysis of iProFun. For example, iProFun identified 117 genes whose CNAs were associated with phosphoprotein abundances by leveraging mRNA expression levels and global protein abundances. By comparison, analyses based on phosphoprotein data alone identified none. A network analysis of these 117 genes revealed the known oncogene AKT1 as a key hub node interacting with many of the rest. In addition, iProFun identified one gene, BIN2, whose DNA methylation has cis-associations with its mRNA expression, global protein, and phosphoprotein abundances. These and other genes identified by iProFun could serve as potential drug targets for ovarian cancer.
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Affiliation(s)
- Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kevin J Gleason
- Department of Public Health Sciences, The University of Chicago, Chicago, IL
| | - Fan Yang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Anschutz Medical Campus, Aurora, CO
| | - John A Martignetti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lin S Chen
- Department of Public Health Sciences, The University of Chicago, Chicago, IL.
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.
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