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Palovcak A, Yuan F, Verdun R, Luo L, Zhang Y. Fanconi anemia associated protein 20 (FAAP20) plays an essential role in homology-directed repair of DNA double-strand breaks. Commun Biol 2023; 6:873. [PMID: 37620397 PMCID: PMC10449828 DOI: 10.1038/s42003-023-05252-9] [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: 12/19/2022] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
FAAP20 is a Fanconi anemia (FA) protein that associates with the FA core complex to promote FANCD2/FANCI monoubiquitination and activate the damage response to interstrand crosslink damage. Here, we report that FAAP20 has a marked role in homologous recombination at a DNA double-strand break not associated with an ICL and separable from its binding partner FANCA. While FAAP20's role in homologous recombination is not dependent on FANCA, we found that FAAP20 stimulates FANCA's biochemical activity in vitro and participates in the single-strand annealing pathway of double-strand break repair in a FANCA-dependent manner. This indicates that FAAP20 has roles in several homology-directed repair pathways. Like other homology-directed repair factors, FAAP20 loss causes a reduction in nuclear RAD51 Irradiation-induced foci; and sensitizes cancer cells to ionizing radiation and PARP inhibition. In summary, FAAP20 participates in DNA double strand break repair by supporting homologous recombination in a non-redundant manner to FANCA, and single-strand annealing repair via FANCA-mediated strand annealing activity.
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Affiliation(s)
- Anna Palovcak
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Ramiro Verdun
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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2
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Lyu F, Shang SY, Gao XS, Ma MW, Xie M, Ren XY, Liu MZ, Chen JY, Li SS, Huang L. Uncovering the Secrets of Prostate Cancer's Radiotherapy Resistance: Advances in Mechanism Research. Biomedicines 2023; 11:1628. [PMID: 37371723 PMCID: PMC10296152 DOI: 10.3390/biomedicines11061628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/20/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Prostate cancer (PCa) is a critical global public health issue with its incidence on the rise. Radiation therapy holds a primary role in PCa treatment; however, radiation resistance has become increasingly challenging as we uncover more about PCa's pathogenesis. Our review aims to investigate the multifaceted mechanisms underlying radiation therapy resistance in PCa. Specifically, we will examine how various factors, such as cell cycle regulation, DNA damage repair, hypoxic conditions, oxidative stress, testosterone levels, epithelial-mesenchymal transition, and tumor stem cells, contribute to radiation therapy resistance. By exploring these mechanisms, we hope to offer new insights and directions towards overcoming the challenges of radiation therapy resistance in PCa. This can also provide a theoretical basis for the clinical application of novel ultra-high-dose-rate (FLASH) radiotherapy in the era of PCa.
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Affiliation(s)
- Feng Lyu
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
| | - Shi-Yu Shang
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
- First Clinical Medical School, Hebei North University, Zhangjiakou 075000, China
| | - Xian-Shu Gao
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
| | - Ming-Wei Ma
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
| | - Mu Xie
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
| | - Xue-Ying Ren
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
| | - Ming-Zhu Liu
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
| | - Jia-Yan Chen
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
| | - Shan-Shi Li
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
| | - Lei Huang
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China; (F.L.); (S.-Y.S.); (M.-W.M.); (M.X.); (X.-Y.R.); (M.-Z.L.); (J.-Y.C.); (S.-S.L.); (L.H.)
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3
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Maslov DV, Sember Q, Cham J, Bhangoo M. A review of treatments targeting DNA-repair gene defects in metastatic castration resistant prostate cancer. Front Oncol 2023; 13:1150777. [PMID: 36998466 PMCID: PMC10046303 DOI: 10.3389/fonc.2023.1150777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
Prostate cancer is the most common cancer in men. About 6% of those diagnosed will develop metastatic disease. Unfortunately, metastatic prostate cancer is fatal. Prostate cancer can be castration sensitive or castration resistant. Many treatments have been shown to improve progression free survival and overall survival in metastatic castration resistant prostate cancer (mCRPC). In recent years, studies have been exploring targeting mutations in the DNA Damage Repair (DDR) response that may amplify oncogenes. In this paper, we aim to discuss DDR, new approved targeted therapies, and the most recent clinical trials in the setting of metastatic CRPC.
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Affiliation(s)
- Diana V. Maslov
- Department of Hematology/Oncology, Scripps Health System, San Diego, CA, United States
- *Correspondence: Diana V. Maslov,
| | - Quinne Sember
- Department of Hematology/Oncology, Scripps Health System, San Diego, CA, United States
| | - Jason Cham
- Scripps Clinic/Green Hospital, Department of Internal Medicine, San Diego, CA, United States
| | - Munveer Bhangoo
- Department of Hematology/Oncology, Scripps Health System, San Diego, CA, United States
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4
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Sora V, Laspiur AO, Degn K, Arnaudi M, Utichi M, Beltrame L, De Menezes D, Orlandi M, Stoltze UK, Rigina O, Sackett PW, Wadt K, Schmiegelow K, Tiberti M, Papaleo E. RosettaDDGPrediction for high-throughput mutational scans: From stability to binding. Protein Sci 2023; 32:e4527. [PMID: 36461907 PMCID: PMC9795540 DOI: 10.1002/pro.4527] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Reliable prediction of free energy changes upon amino acid substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein-protein interaction. Advances in experimental mutational scans allow high-throughput studies thanks to multiplex techniques. On the other hand, genomics initiatives provide a large amount of data on disease-related variants that can benefit from analyses with structure-based methods. Therefore, the computational field should keep the same pace and provide new tools for fast and accurate high-throughput ΔΔG calculations. In this context, the Rosetta modeling suite implements effective approaches to predict folding/unfolding ΔΔGs in a protein monomer upon amino acid substitutions and calculate the changes in binding free energy in protein complexes. However, their application can be challenging to users without extensive experience with Rosetta. Furthermore, Rosetta protocols for ΔΔG prediction are designed considering one variant at a time, making the setup of high-throughput screenings cumbersome. For these reasons, we devised RosettaDDGPrediction, a customizable Python wrapper designed to run free energy calculations on a set of amino acid substitutions using Rosetta protocols with little intervention from the user. Moreover, RosettaDDGPrediction assists with checking completed runs and aggregates raw data for multiple variants, as well as generates publication-ready graphics. We showed the potential of the tool in four case studies, including variants of uncertain significance in childhood cancer, proteins with known experimental unfolding ΔΔGs values, interactions between target proteins and disordered motifs, and phosphomimetics. RosettaDDGPrediction is available, free of charge and under GNU General Public License v3.0, at https://github.com/ELELAB/RosettaDDGPrediction.
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Affiliation(s)
- Valentina Sora
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Adrian Otamendi Laspiur
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Matteo Arnaudi
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Mattia Utichi
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Ludovica Beltrame
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Dayana De Menezes
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Matteo Orlandi
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Ulrik Kristoffer Stoltze
- Department of Clinical GeneticsCopenhagen University Hospital RigshospitaletCopenhagenDenmark
- Department of Pediatrics and Adolescent MedicineUniversity Hospital RigshospitaletCopenhagenDenmark
- Institute of Clinical Medicine, Faculty of MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Olga Rigina
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Peter Wad Sackett
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
| | - Karin Wadt
- Department of Clinical GeneticsCopenhagen University Hospital RigshospitaletCopenhagenDenmark
- Institute of Clinical Medicine, Faculty of MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent MedicineUniversity Hospital RigshospitaletCopenhagenDenmark
- Institute of Clinical Medicine, Faculty of MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research CenterCopenhagenDenmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and TechnologyTechnical University of DenmarkLyngbyDenmark
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5
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Trendowski MR, Sample C, Baird T, Sadeghpour A, Moon D, Ruterbusch JJ, Beebe-Dimmer JL, Cooney KA. Germline Variants in DNA Damage Repair Genes and HOXB13 Among Black Patients With Early-Onset Prostate Cancer. JCO Precis Oncol 2022; 6:e2200460. [PMID: 36446039 PMCID: PMC9812633 DOI: 10.1200/po.22.00460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Genetic studies of prostate cancer susceptibility have predominantly focused on non-Hispanic White men, despite the observation that Black men are more likely to develop prostate cancer and die from the disease. Therefore, we sought to identify genetic variants in Black patients diagnosed with early-onset prostate cancer. METHODS Whole-exome sequencing of germline DNA from a population-based cohort of Black men diagnosed with prostate cancer at age 62 years or younger was performed. Analysis was focused on a panel of DNA damage repair (DDR) genes and HOXB13. All discovered variants were ranked according to their pathogenic potential based upon REVEL score, evidence from existing literature, and prevalence in the cohort. Logistic regression was used to investigate associations between mutation status and relevant clinical characteristics. RESULTS Among 743 Black prostate cancer patients, we identified 26 unique pathogenic (P) or likely pathogenic (LP) variants in 14 genes (including HOXB13, BRCA1/2, BRIP1, ATM, CHEK2, and PALB2) among 30 men, or approximately 4.0% of the patient population. We also identified 33 unique variants of unknown significance in 16 genes among 39 men. Because of the rarity of these variants in the population, most associations between clinical characteristics did not achieve statistical significance. However, our results suggest that carriers for P or LP (P/LP) variants were more likely to have a first-degree relative diagnosed with DDR gene-associated cancer, have a higher prostate-specific antigen at time of diagnosis, and be diagnosed with metastatic disease. CONCLUSION Variants in DDR genes and HOXB13 may be important cancer risk factors for Black men diagnosed with early-onset prostate cancer, and are more frequently observed in men with a family history of cancer.
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Affiliation(s)
| | | | - Tara Baird
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI,Barbara Ann Karmanos Cancer Institute, Detroit, MI
| | - Azita Sadeghpour
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - David Moon
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Julie J. Ruterbusch
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI,Barbara Ann Karmanos Cancer Institute, Detroit, MI
| | - Jennifer L. Beebe-Dimmer
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI,Barbara Ann Karmanos Cancer Institute, Detroit, MI,Jennifer L. Beebe-Dimmer, MPH, PhD, Karmanos Cancer Institute, 4100 John R, MM04, Detroit, MI 48201; e-mail:
| | - Kathleen A. Cooney
- Department of Medicine, Duke University School of Medicine, Durham, NC,Duke Cancer Institute, Durham, NC
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Gruber JJ, Afghahi A, Timms K, DeWees A, Gross W, Aushev VN, Wu HT, Balcioglu M, Sethi H, Scott D, Foran J, McMillan A, Ford JM, Telli ML. A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes. NATURE CANCER 2022; 3:1181-1191. [PMID: 36253484 PMCID: PMC9586861 DOI: 10.1038/s43018-022-00439-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 08/29/2022] [Indexed: 11/09/2022]
Abstract
Talazoparib, a PARP inhibitor, is active in germline BRCA1 and BRCA2 (gBRCA1/2)-mutant advanced breast cancer, but its activity beyond gBRCA1/2 is poorly understood. We conducted Talazoparib Beyond BRCA ( NCT02401347 ), an open-label phase II trial, to evaluate talazoparib in patients with pretreated advanced HER2-negative breast cancer (n = 13) or other solid tumors (n = 7) with mutations in homologous recombination (HR) pathway genes other than BRCA1 and BRCA2. In patients with breast cancer, four patients had a Response Evaluation Criteria in Solid Tumors (RECIST) partial response (overall response rate, 31%), and three additional patients had stable disease of ≥6 months (clinical benefit rate, 54%). All patients with germline mutations in PALB2 (gPALB2; encoding partner and localizer of BRCA2) had treatment-associated tumor regression. Tumor or plasma circulating tumor DNA (ctDNA) HR deficiency (HRD) scores were correlated with treatment outcomes and were increased in all gPALB2 tumors. In addition, a gPALB2-associated mutational signature was associated with tumor response. Thus, talazoparib has been demonstrated to have efficacy in patients with advanced breast cancer who have gPALB2 mutations, showing activity in the context of HR pathway gene mutations beyond gBRCA1/2.
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Affiliation(s)
- Joshua J Gruber
- Department of Internal Medicine and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Anosheh Afghahi
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | | | - Alyssa DeWees
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Wyatt Gross
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | | | - Danika Scott
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jessica Foran
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Alex McMillan
- Department of Statistics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - James M Ford
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Melinda L Telli
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.
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7
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Harindran VD, Sadanandan VS, Sreedath PV, Prashanth P, Sajeevan K, Sreedharan P, Warrier N. Therapy for Recurrent High-Grade Epithelial Ovarian Cancer—The Current Status and Future Trends. Indian J Med Paediatr Oncol 2022. [DOI: 10.1055/s-0042-1742321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
AbstractOvarian malignancy is the seventh most frequently diagnosed cancer among women. The most common type is epithelial ovarian cancer. Several subtypes with distinct biological and molecular properties exist, and there is inconsistency in availability of and access to different modalities of treatment. The standard first-line management is combining surgery and platinum-based chemotherapy. Most of them are diagnosed at an advanced stage due to which they have poor outcomes. The existing screening tests have a low predictive value. Even with the best available upfront treatment, high rates of recurrences are observed. As a result, there have been major advances in the treatment of recurrences with the development of anti-angiogenic agents and PARP inhibitors. It has led to the improvement in survival and quality of life among the relapsed epithelial ovarian cancers. This review is focused on the management of recurrent epithelial ovarian cancers and future directions based on current evidence. The application of a personalized and structured approach will meaningfully bring changes in the paradigm of care in these groups of patients.
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Affiliation(s)
| | - V.P. Sanudev Sadanandan
- Department of Medical Oncology, MVR Cancer Centre and Research Institute, Calicut, Kerala, India
| | - P. Vishnu Sreedath
- Department of Medical Oncology, MVR Cancer Centre and Research Institute, Calicut, Kerala, India
| | - Parameswaran Prashanth
- Department of Medical Oncology, MVR Cancer Centre and Research Institute, Calicut, Kerala, India
| | - K.V. Sajeevan
- Department of Medical Oncology, MVR Cancer Centre and Research Institute, Calicut, Kerala, India
| | - P.S. Sreedharan
- Department of Medical Oncology, MVR Cancer Centre and Research Institute, Calicut, Kerala, India
| | - Narayanankutty Warrier
- Department of Medical Oncology, MVR Cancer Centre and Research Institute, Calicut, Kerala, India
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8
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Garner IM, Brown R. Is There a Role for Epigenetic Therapies in Modulating DNA Damage Repair Pathways to Enhance Chemotherapy and Overcome Drug Resistance? Cancers (Basel) 2022; 14:cancers14061533. [PMID: 35326684 PMCID: PMC8946236 DOI: 10.3390/cancers14061533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/09/2022] [Accepted: 03/12/2022] [Indexed: 02/01/2023] Open
Abstract
Epigenetic therapies describe drug molecules such as DNA methyltransferase, histone methyltransferase and histone acetylase/deacetylase inhibitors, which target epigenetic mechanisms such as DNA methylation and histone modifications. Many DNA damage response (DDR) genes are epigenetically regulated in cancer leading to transcriptional silencing and the loss of DNA repair capacity. Epigenetic marks at DDR genes, such as DNA methylation at gene promoters, have the potential to be used as stratification biomarkers, identifying which patients may benefit from particular chemotherapy treatments. For genes such as MGMT and BRCA1, promoter DNA methylation is associated with chemosensitivity to alkylating agents and platinum coordination complexes, respectively, and they have use as biomarkers directing patient treatment options. In contrast to epigenetic change leading to chemosensitivity, DNA methylation of DDR genes involved in engaging cell death responses, such as MLH1, are associated with chemoresistance. This contrasting functional effect of epigenetic modification on chemosensitivity raises challenges in using DNA-demethylating agents, and other epigenetic approaches, to sensitise tumours to DNA-damaging chemotherapies and molecularly targeted agents. Demethylation of MGMT/BRCA1 could lead to drug resistance whereas demethylation of MLH1 could sensitise cells to chemotherapy. Patient selection based on a solid understanding of the disease pathway will be one means to tackle these challenges. The role of epigenetic modification of DDR genes during tumour development, such as causing a mutator phenotype, has different selective pressures and outcomes compared to epigenetic adaptation during treatment. The prevention of epigenetic adaptation during the acquisition of drug resistance will be a potential strategy to improve the treatment of patients using epigenetic therapies.
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9
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Qian B, Leng W, Yan Z, Lu J, Chen S, Yi H, Jiang Z. Clinical Benefit With PARP Inhibitor for Pathogenic Germline FANCA-Mutated Relapsed Epithelial Ovarian Cancer: A Case Report. Front Oncol 2022; 12:778545. [PMID: 35280757 PMCID: PMC8913585 DOI: 10.3389/fonc.2022.778545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/18/2022] [Indexed: 01/05/2023] Open
Abstract
Background PARP inhibitors have been approved as targeted therapy for BRCA-deficient metastatic ovarian cancer (OC). Fanconi anemia complementation group A (FANCA), one of the homologous recombination repair pathway genes, is a susceptibility gene to breast cancer and OC. Therefore, it is interesting to investigate whether germline FANCA-mutated relapsed epithelial OC could achieve clinical benefit from the treatment of PARP inhibitor. Case Presentation A 49-year-old female patient without a family history of cancer was diagnosed with epithelial OC. This patient underwent surgical resection plus platinum-based treatment twice in 2016 and 2018, successively. After the second relapse in July 2019, the patient underwent another radical resection. The next-generation sequencing analysis results revealed a germline FANCA mutation in the tumor tissue. Subsequently, the third-line treatment of liposomal doxorubicin hydrochloride plus lobaplatin was administrated for five cycles with the patient’s consent. Then, oral niraparib (200 mg daily) was given for maintenance treatment. During the follow-up, no evidence of tumor recurrence was observed. Currently, the survival with no evidence of disease has already exceeded 21 months, and the treatment is still going on. Conclusions This case highlighted that OC patients harboring pathogenic gene alterations in the homologous recombination pathway might achieve clinical benefit from PARP inhibitors, which should be confirmed in further studies.
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Affiliation(s)
- Bing Qian
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Wenshu Leng
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zhengqing Yan
- Department of Medical Affairs, The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Jin Lu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Shiqing Chen
- Department of Medical Affairs, The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Huan Yi
- Department of Medical Affairs, The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Zhi Jiang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Zhi Jiang,
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10
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Kneubil M, Goulart K, Brollo J, Coelho G, Mandelli J, Orlandin B, Corso L, Roesch-Ely M, Henriques J. Predictive value of DNA repair gene expression for response to neoadjuvant chemotherapy in breast cancer. Braz J Med Biol Res 2022; 55:e11857. [PMID: 35293552 PMCID: PMC8922549 DOI: 10.1590/1414-431x2021e11857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/17/2021] [Indexed: 11/22/2022] Open
Abstract
Genome-wide analysis using microarrays has revolutionized breast cancer (BC)
research. A substantial body of evidence supports the clinical utility of the
21-gene assay (Oncotype DX) and 70-gene assay (MammaPrint) to predict BC
recurrence and the magnitude of benefit from chemotherapy. However, there is
currently no genetic tool able to predict chemosensitivity and chemoresistance
to neoadjuvant chemotherapy (NACT) during BC treatment. In this study, we
explored the predictive value of DNA repair gene expression in the neoadjuvant
setting. We selected 98 patients with BC treated with NACT. We assessed DNA
repair expression in 98 formalin-fixed, paraffin-embedded core biopsy fragments
used at diagnosis and in 32 formalin-fixed, paraffin-embedded post-NACT residual
tumors using quantitative reverse transcription-polymerase chain reaction. The
following genes were selected: BRCA1, PALB2,
RAD51C, BRCA2, ATM,
FANCA, MSH2, XPA,
ERCC1, PARP1, and SNM1.
Of 98 patients, 33 (33.7%) achieved pathologic complete response (pCR). The DNA
expression of 2 genes assessed in pre-NACT biopsies (PALB2 and
ERCC1) was lower in pCR than in non-pCR patients (P=0.005
and P=0.009, respectively). There was no correlation between molecular subtype
and expression of DNA repair genes. The genes BRCA2 (P=0.009),
ATM (P=0.004), FANCA (P=0.001), and
PARP1 (P=0.011) showed a lower expression in post-NACT
residual tumor samples (n=32) than in pre-NACT biopsy samples (n=98). The
expression of 2 genes (PALB2 and ERCC1) was
lower in pCR patients. These alterations in DNA repair could be considered
suitable targets for cancer therapy.
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Affiliation(s)
- M.C. Kneubil
- Universidade de Caxias do Sul, Brasil; Universidade de Caxias do Sul, Brasil
| | | | - J. Brollo
- Universidade de Caxias do Sul, Brasil
| | | | | | | | - L.L. Corso
- Universidade de Caxias do Sul, Brasil; Instituto Hercílio Randon, Brasil
| | | | - J.A.P. Henriques
- Universidade de Caxias do Sul, Brasil; Universidade do Vale do Taquari - UNIVATES, Brasil
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11
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Chen YX, Tan LM, Gong JP, Huang MS, Yin JY, Zhang W, Zhou HH, Liu ZQ. Response prediction biomarkers and drug combinations of PARP inhibitors in prostate cancer. Acta Pharmacol Sin 2021; 42:1970-1980. [PMID: 33589795 PMCID: PMC8632930 DOI: 10.1038/s41401-020-00604-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/20/2020] [Indexed: 01/31/2023] Open
Abstract
PARP inhibitors are a group of inhibitors targeting poly(ADP-ribose) polymerases (PARP1 or PARP2) involved in DNA repair and transcriptional regulation, which may induce synthetic lethality in BRCAness tumors. Systematic analyzes of genomic sequencing in prostate cancer show that ~10%-19% of patients with primary prostate cancer have inactivated DNA repair genes, with a notably higher proportion of 23%-27% in patients with metastatic castration-resistant prostate cancer (mCRPC). These characteristic genomic alterations confer possible vulnerability to PARP inhibitors in patients with mCRPC who benefit only modestly from other therapies. However, only a small proportion of patients with mCRPC shows sensitivity to PARP inhibitors, and these sensitive patients cannot be fully identified by existing response prediction biomarkers. In this review, we provide an overview of the potential response prediction biomarkers and synergistic combinations studied in the preclinical and clinical stages, which may expand the population of patients with prostate cancer who may benefit from PARP inhibitors.
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Affiliation(s)
- Yi-Xin Chen
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha, 410078, China
| | - Li-Ming Tan
- Department of Pharmacy, The Second People's Hospital of Huaihua City, Huaihua, 418000, China
| | - Jian-Ping Gong
- Department of Pharmacy, The Second People's Hospital of Huaihua City, Huaihua, 418000, China
| | - Ma-Sha Huang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha, 410078, China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha, 410078, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha, 410078, China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha, 410078, China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Institute of Clinical Pharmacology, Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Central South University, Changsha, 410078, China.
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12
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Multiparametric Circulating Tumor Cell Analysis to Select Targeted Therapies for Breast Cancer Patients. Cancers (Basel) 2021; 13:cancers13236004. [PMID: 34885114 PMCID: PMC8657376 DOI: 10.3390/cancers13236004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Liquid biopsies may act as a dynamic tool for identification of targets for precision therapy while circumventing limitations of tissue biopsies. In opposite to most liquid biopsy-related studies that analyze limited patient material for only one parameter, this study is based on a longitudinal and multiparametric analysis of circulating tumor cells (CTCs). A metastatic breast cancer patient was followed over a period of three years and analyses of the genome, RNA profiling, and in vitro drug testing on cultured CTCs were performed in a unique manner. We show that combining the strengths of multiple technologies for analysis yielded maximum information on the ongoing disease and, eventually, allowed choosing an effective therapy, which led to a massive reduction in CTC numbers. This approach provides a concept for future detailed longitudinal and multiparametric CTC analyses. Abstract Background: The analysis of liquid biopsies, e.g., circulating tumor cells (CTCs) is an appealing diagnostic concept for targeted therapy selection. In this proof-of-concept study, we aimed to perform multiparametric analyses of CTCs to select targeted therapies for metastatic breast cancer patients. Methods: First, CTCs of five metastatic breast cancer patients were analyzed by whole exome sequencing (WES). Based on the results, one patient was selected and monitored by longitudinal and multiparametric liquid biopsy analyses over more than three years, including WES, RNA profiling, and in vitro drug testing of CTCs. Results: Mutations addressable by targeted therapies were detected in all patients, including mutations that were not detected in biopsies of the primary tumor. For the index patient, the clonal evolution of the tumor cells was retraced and resistance mechanisms were identified. The AKT1 E17K mutation was uncovered as the driver of the metastatic process. Drug testing on the patient’s CTCs confirmed the efficacy of drugs targeting the AKT1 pathway. During a targeted therapy chosen based on the CTC characterization and including the mTOR inhibitor everolimus, CTC numbers dropped by 97.3% and the disease remained stable as determined by computer tomography/magnetic resonance imaging. Conclusion: These results illustrate the strength of a multiparametric CTC analysis to choose and validate targeted therapies to optimize cancer treatment in the future. Furthermore, from a scientific point of view, such studies promote the understanding of the biology of CTCs during different treatment regimens.
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13
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Krushkal J, Negi S, Yee LM, Evans JR, Grkovic T, Palmisano A, Fang J, Sankaran H, McShane LM, Zhao Y, O'Keefe BR. Molecular genomic features associated with in vitro response of the NCI-60 cancer cell line panel to natural products. Mol Oncol 2021; 15:381-406. [PMID: 33169510 PMCID: PMC7858122 DOI: 10.1002/1878-0261.12849] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/29/2020] [Accepted: 11/06/2020] [Indexed: 12/17/2022] Open
Abstract
Natural products remain a significant source of anticancer chemotherapeutics. The search for targeted drugs for cancer treatment includes consideration of natural products, which may provide new opportunities for antitumor cytotoxicity as single agents or in combination therapy. We examined the association of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with in vitro response to treatment with 1302 small molecules which included natural products, semisynthetic natural product derivatives, and synthetic compounds based on a natural product pharmacophore from the Developmental Therapeutics Program of the US National Cancer Institute's database. These compounds were obtained from a variety of plant, marine, and microbial species. Molecular information utilized for the analysis included expression measures for 23059 annotated transcripts, lncRNAs, and miRNAs, and data on protein-changing single nucleotide variants in 211 cancer-related genes. We found associations of expression of multiple genes including SLFN11, CYP2J2, EPHX1, GPC1, ELF3, and MGMT involved in DNA damage repair, NOTCH family members, ABC and SLC transporters, and both mutations in tyrosine kinases and BRAF V600E with NCI-60 responses to specific categories of natural products. Hierarchical clustering identified groups of natural products, which correlated with a specific mechanism of action. Specifically, several natural product clusters were associated with SLFN11 gene expression, suggesting that potential action of these compounds may involve DNA damage. The associations between gene expression or genome alterations of functionally relevant genes with the response of cancer cells to natural products provide new information about potential mechanisms of action of these identified clusters of compounds with potentially similar biological effects. This information will assist in future drug discovery and in design of new targeted cancer chemotherapy agents.
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Affiliation(s)
- Julia Krushkal
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Simarjeet Negi
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Laura M. Yee
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Jason R. Evans
- Natural Products BranchDevelopmental Therapeutics ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteFrederickMDUSA
| | - Tanja Grkovic
- Natural Products Support GroupFrederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Alida Palmisano
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
- General Dynamics Information Technology (GDIT)Falls ChurchVAUSA
| | - Jianwen Fang
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Hari Sankaran
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Lisa M. McShane
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Yingdong Zhao
- Biometric Research ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteNIHRockvilleMDUSA
| | - Barry R. O'Keefe
- Natural Products BranchDevelopmental Therapeutics ProgramDivision of Cancer Treatment and DiagnosisNational Cancer InstituteFrederickMDUSA
- Molecular Targets ProgramCenter for Cancer ResearchNational Cancer InstituteFrederickMDUSA
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14
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Risdon EN, Chau CH, Price DK, Sartor O, Figg WD. PARP Inhibitors and Prostate Cancer: To Infinity and Beyond BRCA. Oncologist 2021; 26:e115-e129. [PMID: 32790034 PMCID: PMC7794174 DOI: 10.1634/theoncologist.2020-0697] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/04/2020] [Indexed: 12/18/2022] Open
Abstract
The U.S. Food and Drug Administration recently approved two poly-adenosine diphosphate-ribose polymerase (PARP) inhibitors, olaparib and rucaparib, for treatment of biomarker-positive metastatic castrate resistant prostate cancer. The benefits of PARP inhibition have been well characterized in patients who have BRCA1 and BRCA2 mutations in several forms of cancer. BRCA1 and BRCA2 occupy key roles in DNA damage repair, which is comprised of several different pathways with numerous participants. Patients with mutations in other key genes within the DNA damage repair pathway may also respond to treatment with PARP inhibitors, and identification of these alterations could significantly increase the percentage of patients that may benefit from PARP inhibition. This review focuses on the potential for synthetically lethal interactions between PARP inhibitors and non-BRCA DNA damage repair genes. IMPLICATIONS FOR PRACTICE: The treatment potential of PARP inhibition has been well characterized in patients with BRCA1 and BRCA2 mutations, but there is compelling evidence for expanding the use of PARP inhibitors to mutations of other non-BRCA DNA damage repair (DDR) genes. This could increase the percentage of patients that may benefit from treatment with PARP inhibitors alone or in combination with other therapies. Understanding the significance of PARP inhibitor-sensitizing alterations in other common non-BRCA DDR genes will help guide clinical decisions to provide targeted treatment options to a wider population of patients.
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Affiliation(s)
- Emily N. Risdon
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Cindy H. Chau
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Douglas K. Price
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | | | - William D. Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
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15
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Jang A, Sartor O, Barata PC, Paller CJ. Therapeutic Potential of PARP Inhibitors in the Treatment of Metastatic Castration-Resistant Prostate Cancer. Cancers (Basel) 2020; 12:E3467. [PMID: 33233320 PMCID: PMC7700539 DOI: 10.3390/cancers12113467] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023] Open
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) is an incurable malignancy with a poor prognosis. Up to 30% of patients with mCRPC have mutations in homologous recombination repair (HRR) genes. Poly (ADP-ribose) polymerase (PARP) inhibitors take advantage of HRR deficiency to kill tumor cells based on the concept of synthetic lethality. Several PARP inhibitors (PARPis) have been successful in various malignancies with HRR gene mutations including BRCA1/2, especially in breast cancer and ovarian cancer. More recently, olaparib and rucaparib were approved for mCRPC refractory to novel hormonal therapies, and other PARPis will likely follow. This article highlights the mechanism of action of PARPis at the cellular level, the preclinical data regarding a proposed mechanism of action and the effectiveness of PARPis in cancer cell lines and animal models. The article expands on the clinical development of PARPis in mCRPC, discusses potential biomarkers that may predict successful tumor control, and summarizes present and future clinical research on PARPis in the metastatic disease landscape.
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Affiliation(s)
- Albert Jang
- Deming Department of Medicine, Hematology-Oncology Section, Tulane University School of Medicine, New Orleans, LA 70112, USA; (A.J.); (O.S.); (P.C.B.)
| | - Oliver Sartor
- Deming Department of Medicine, Hematology-Oncology Section, Tulane University School of Medicine, New Orleans, LA 70112, USA; (A.J.); (O.S.); (P.C.B.)
- Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Pedro C. Barata
- Deming Department of Medicine, Hematology-Oncology Section, Tulane University School of Medicine, New Orleans, LA 70112, USA; (A.J.); (O.S.); (P.C.B.)
- Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Channing J. Paller
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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16
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Xia Q, Zhao LY, Yan YD, Liao Y, Di YS, Xiao XY. A Multiple Primary Malignancy Patient With FANCA Gene Mutation: A Case Report and Literature Review. Front Oncol 2020; 10:1199. [PMID: 32850347 PMCID: PMC7420727 DOI: 10.3389/fonc.2020.01199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/12/2020] [Indexed: 01/14/2023] Open
Abstract
Background: Multiple primary malignancies (MPMs) refer to two or more primary malignant tumors in the same individual, the prevalence of which ranges from 0. 734 to 11.7%. The risk factors for MPMs vary and include both genetic and environmental causes. FANCA gene mutation might be a predisposition to the development of a second primary cancer. Here, we report a case in which a patient with a FANCA mutation developed thyroid papillary carcinoma and gastric adenocarcinoma. Case Presentation: A 48-year-old woman was diagnosed with thyroid cancer underwent resection in 2006. In 2008, the patient developed gastric adenocarcinoma and underwent radical gastrectomy. Gastric cancer was completely remitted after radiochemotherapy, but metastasis developed, and she received immunotherapy. The patient died on October 27, 2019. Peripheral blood gene detection showed germline FANCA mutation. Conclusions: Gene detection is of great importance in cancer patients, especially in those with MPMs. FANCA mutation is a predisposition to tumorigenesis that can increase the risk of developing MPMs. Patients with heterozygous FANCA gene mutations have poorer outcomes.
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Affiliation(s)
- Qing Xia
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ling-Yi Zhao
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Basic Medical Sciences, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Dan Yan
- Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Liao
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Ying-San Di
- Department of Oncology, Baoshan Branch Hospital, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiu-Ying Xiao
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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17
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Sailer V, Eng KW, Zhang T, Bareja R, Pisapia DJ, Sigaras A, Bhinder B, Romanel A, Wilkes D, Sticca E, Cyrta J, Rao R, Sahota S, Pauli C, Beg S, Motanagh S, Kossai M, Fontugne J, Puca L, Rennert H, Xiang JZ, Greco N, Kim R, MacDonald TY, McNary T, Blattner-Johnson M, Schiffman MH, Faltas BM, Greenfield JP, Rickman D, Andreopoulou E, Holcomb K, Vahdat LT, Scherr DS, van Besien K, Barbieri CE, Robinson BD, Fine HA, Ocean AJ, Molina A, Shah MA, Nanus DM, Pan Q, Demichelis F, Tagawa ST, Song W, Mosquera JM, Sboner A, Rubin MA, Elemento O, Beltran H. Integrative Molecular Analysis of Patients With Advanced and Metastatic Cancer. JCO Precis Oncol 2019; 3:PO.19.00047. [PMID: 31592503 PMCID: PMC6778956 DOI: 10.1200/po.19.00047] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
PURPOSE We developed a precision medicine program for patients with advanced cancer using integrative whole-exome sequencing and transcriptome analysis. PATIENTS AND METHODS Five hundred fifteen patients with locally advanced/metastatic solid tumors were prospectively enrolled, and paired tumor/normal sequencing was performed. Seven hundred fifty-nine tumors from 515 patients were evaluated. RESULTS Most frequent tumor types were prostate (19.4%), brain (16.5%), bladder (15.4%), and kidney cancer (9.2%). Most frequently altered genes were TP53 (33%), CDKN2A (11%), APC (10%), KTM2D (8%), PTEN (8%), and BRCA2 (8%). Pathogenic germline alterations were present in 10.7% of patients, most frequently CHEK2 (1.9%), BRCA1 (1.5%), BRCA2 (1.5%), and MSH6 (1.4%). Novel gene fusions were identified, including a RBM47-CDK12 fusion in a metastatic prostate cancer sample. The rate of clinically relevant alterations was 39% by whole-exome sequencing, which was improved by 16% by adding RNA sequencing. In patients with more than one sequenced tumor sample (n = 146), 84.62% of actionable mutations were concordant. CONCLUSION Integrative analysis may uncover informative alterations for an advanced pan-cancer patient population. These alterations are consistent in spatially and temporally heterogeneous samples.
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Affiliation(s)
| | | | - Tuo Zhang
- Weill Cornell Medicine, New York, NY
| | | | | | | | | | | | | | | | | | - Rema Rao
- Weill Cornell Medicine, New York, NY
| | | | | | | | | | | | | | | | | | | | | | - Rob Kim
- Weill Cornell Medicine, New York, NY
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Qiulu Pan
- Weill Cornell Medicine, New York, NY
| | | | | | - Wei Song
- Weill Cornell Medicine, New York, NY
| | | | | | | | | | - Himisha Beltran
- Weill Cornell Medicine, New York, NY,Himisha Beltran, MD, Weill Cornell Medicine, 413 E. 69th Street, New York, NY 10021; e-mail:
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18
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Mani C, Jonnalagadda S, Lingareddy J, Awasthi S, Gmeiner WH, Palle K. Prexasertib treatment induces homologous recombination deficiency and synergizes with olaparib in triple-negative breast cancer cells. Breast Cancer Res 2019; 21:104. [PMID: 31492187 PMCID: PMC6729044 DOI: 10.1186/s13058-019-1192-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022] Open
Abstract
Background Breast cancer remains as one of the most lethal types of cancer in women. Among various subtypes, triple-negative breast cancer (TNBC) is the most aggressive and hard to treat type of breast cancer. Mechanistically, increased DNA repair and cell cycle checkpoint activation remain as the foremost reasons behind TNBC tumor resistance to chemotherapy and disease recurrence. Methods We evaluated the mechanism of prexasertib-induced regulation of homologous recombination (HR) proteins using 20S proteasome inhibitors and RT-PCR. HR efficiency and DNA damages were evaluated using Dr-GFP and comet assays. DNA morphology and DNA repair focus studies were analyzed using immunofluorescence. UALCAN portal was used to evaluate the expression of RAD51 and survival probability based on tumor stage, subtype, and race in breast cancer patients. Results Our results show that prexasertib treatment promotes both post-translational and transcriptional mediated regulation of BRCA1 and RAD51 proteins. Additionally, prexasertib-treated TNBC cells revealed over 55% reduction in HR efficiency compared to control cells. Based on these results, we hypothesized that prexasertib treatment induced homologous recombination deficiency (HRD) and thus should synergize with PARP inhibitors (PARPi) in TNBC cells. As predicted, combined treatment of prexasertib and PARPi olaparib increased DNA strand breaks, γH2AX foci, and nuclear disintegration relative to single-agent treatment. Further, the prexasertib and olaparib combination was synergistic in multiple TNBC cell lines, as indicated by combination index (CI) values. Analysis of TCGA data revealed elevated RAD51 expression in breast tumors compared to normal breast tissues, especially in TNBC subtype. Interestingly, there was a discrepancy in RAD51 expression in racial groups, with African-American and Asian breast cancer patients showing elevated RAD51 expression compared to Caucasian breast cancer patients. Consistent with these observations, African-American and Asian TNBC patients show decreased survival. Conclusions Based on these data, RAD51 could be a biomarker for aggressive TNBC and for racial disparity in breast cancer. As positive correlation exists between RAD51 and CHEK1 expression in breast cancer, the in vitro preclinical data presented here provides additional mechanistic insights for further evaluation of the rational combination of prexasertib and olaparib for improved outcomes and reduced racial disparity in TNBC.
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Affiliation(s)
- Chinnadurai Mani
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, TX, 79430, USA
| | - Shirisha Jonnalagadda
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, TX, 79430, USA
| | - Jojireddy Lingareddy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, TX, 79430, USA.,Present Address: Loyola Academic Degree PG College, Old Alwal, Secunderabad, Telangana, 500010, India
| | - Sanjay Awasthi
- Department of Internal Medicine, Texas Tech University Health Sciences Centre, Lubbock, TX, 79430, USA
| | - William H Gmeiner
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Komaraiah Palle
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, TX, 79430, USA.
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19
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Engel NW, Schliffke S, Schüller U, Frenzel C, Bokemeyer C, Kubisch C, Lessel D. Fatal Myelotoxicity Following Palliative Chemotherapy With Cisplatin and Gemcitabine in a Patient With Stage IV Cholangiocarcinoma Linked to Post Mortem Diagnosis of Fanconi Anemia. Front Oncol 2019; 9:420. [PMID: 31192125 PMCID: PMC6540739 DOI: 10.3389/fonc.2019.00420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Unrecognized genome instability syndromes can potentially impede the rational treatment of cancer in rare patients. Identification of cancer patients with a hereditary condition is a compelling necessity for oncologists, giving varying hypersensitivities to various chemotherapeutic agents or radiation, depending on the underlying genetic cause. Omission of genetic testing in the setting of an overlooked hereditary syndrome may lead to unexpected and unbearable toxicity from oncological standard approaches. We present a case of a 33-year-old man with an early-onset stage IV intrahepatic cholangiocarcinoma, who experienced unusual bone marrow failure and neutropenic fever syndrome as a consequence of palliative chemotherapy containing cisplatin and gemcitabine, leading to a fatal outcome on day 25 of his first chemotherapeutic cycle. The constellation of bone marrow failure after exposure to the platinum-based agent cisplatin, the presence of an early-onset solid malignancy and the critical appraisal of further phenotypical features raised suspicion of a hereditary genome instability syndrome. Whole-exome sequencing from buccal swab DNA enabled the post mortem diagnosis of Fanconi anemia, most likely linked to the fatal outcome due to utilization of the DNA crosslinking agent cisplatin. The patient's phenotype was exceptional, as he never displayed significant hematologic abnormalities, which is the hallmark of Fanconi anemia. As such, this case stresses the importance to at least question the possibility of a hereditary basis in cases of relatively early-onset malignancy before defining an oncological treatment strategy.
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Affiliation(s)
- Nils W Engel
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Schliffke
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Christian Frenzel
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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20
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Platinum Resistance in Ovarian Cancer: Role of DNA Repair. Cancers (Basel) 2019. [PMID: 30669514 DOI: 10.3390/cancers11010119]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynecological cancer. It is initially responsive to cisplatin and carboplatin, two DNA damaging agents used in first line therapy. However, almost invariably, patients relapse with a tumor resistant to subsequent treatment with platinum containing drugs. Several mechanisms associated with the development of acquired drug resistance have been reported. Here we focused our attention on DNA repair mechanisms, which are fundamental for recognition and removal of platinum adducts and hence for the ability of these drugs to exert their activity. We analyzed the major DNA repair pathways potentially involved in drug resistance, detailing gene mutation, duplication or deletion as well as polymorphisms as potential biomarkers for drug resistance development. We dissected potential ways to overcome DNA repair-associated drug resistance thanks to the development of new combinations and/or drugs directly targeting DNA repair proteins or taking advantage of the vulnerability arising from DNA repair defects in EOCs.
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21
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Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynecological cancer. It is initially responsive to cisplatin and carboplatin, two DNA damaging agents used in first line therapy. However, almost invariably, patients relapse with a tumor resistant to subsequent treatment with platinum containing drugs. Several mechanisms associated with the development of acquired drug resistance have been reported. Here we focused our attention on DNA repair mechanisms, which are fundamental for recognition and removal of platinum adducts and hence for the ability of these drugs to exert their activity. We analyzed the major DNA repair pathways potentially involved in drug resistance, detailing gene mutation, duplication or deletion as well as polymorphisms as potential biomarkers for drug resistance development. We dissected potential ways to overcome DNA repair-associated drug resistance thanks to the development of new combinations and/or drugs directly targeting DNA repair proteins or taking advantage of the vulnerability arising from DNA repair defects in EOCs.
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Platinum Resistance in Ovarian Cancer: Role of DNA Repair. Cancers (Basel) 2019; 11:cancers11010119. [PMID: 30669514 PMCID: PMC6357127 DOI: 10.3390/cancers11010119] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/15/2019] [Accepted: 01/17/2019] [Indexed: 12/22/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynecological cancer. It is initially responsive to cisplatin and carboplatin, two DNA damaging agents used in first line therapy. However, almost invariably, patients relapse with a tumor resistant to subsequent treatment with platinum containing drugs. Several mechanisms associated with the development of acquired drug resistance have been reported. Here we focused our attention on DNA repair mechanisms, which are fundamental for recognition and removal of platinum adducts and hence for the ability of these drugs to exert their activity. We analyzed the major DNA repair pathways potentially involved in drug resistance, detailing gene mutation, duplication or deletion as well as polymorphisms as potential biomarkers for drug resistance development. We dissected potential ways to overcome DNA repair-associated drug resistance thanks to the development of new combinations and/or drugs directly targeting DNA repair proteins or taking advantage of the vulnerability arising from DNA repair defects in EOCs.
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23
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Warner EW, Yip SM, Chi KN, Wyatt AW. DNA repair defects in prostate cancer: impact for screening, prognostication and treatment. BJU Int 2018; 123:769-776. [PMID: 30281887 DOI: 10.1111/bju.14576] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Failure of effective DNA damage repair is a hallmark of cancer, but was previously underappreciated as a driver of aggressive prostate cancer. However, recent international sequencing efforts have revealed that both germline and somatic alterations within the homologous recombination and mismatch repair pathways are relatively common in lethal metastatic disease. BRCA2 gene alterations are particularly prevalent and are linked to poor prognosis as well as poor responses to systemic therapy for castration-resistant prostate cancer, although there is conflicting support for the latter. Defective DNA repair contributes to tumour heterogeneity, evolution and progression, but there are high hopes that management of this aggressive subset will be transformed by biomarker-driven use of poly-ADP ribose polymerase (PARP) inhibitors and platinum-based chemotherapy. In this review, we detail the relationship between DNA repair defects and prostate cancer, highlighting the prevalence of mutations in key genes and their controversial association with clinical outcomes.
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Affiliation(s)
- Evan W Warner
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Steven M Yip
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Kim N Chi
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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24
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Huang JP, Lin J, Tzen CY, Huang WY, Tsai CC, Chen CJ, Lu YJ, Chou KF, Su YW. FANCA D1359Y mutation in a patient with gastric polyposis and cancer susceptibility: A case report and review of literature. World J Gastroenterol 2018; 24:4412-4418. [PMID: 30344425 PMCID: PMC6189845 DOI: 10.3748/wjg.v24.i38.4412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/02/2018] [Accepted: 08/24/2018] [Indexed: 02/06/2023] Open
Abstract
Gastric polyposis is a rare disease. Not all polyps progress to cancer. Monoallelic mutation in Fanconi anemia (FA) genes, unlike biallelic gene mutations that causes typical FA phenotype, can increase risks of cancers in a sporadic manner. Aberrations in the FA pathway were reported in all molecular subtypes of gastric cancer. We studied a patient with synchronous gastric cancer from gastric polyposis by conducting a 13-year long-term follow up. Via pathway-driven massive parallel genomic sequencing, a germline mutation at FANCA D1359Y was identified. We identified several recurrent mutations in DNA methylation (TET1, V873I), the β-catenin pathway (CTNNB1, S45F) and RHO signaling pathway (PLEKHG5, R203C) by comparing the genetic events between benign and malignant gastric polyps. Furthermore, we revealed gastric polyposis susceptible genes and genetic events promoting malignant transformation using pathway-driven targeted gene sequencing.
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Affiliation(s)
- Jeffrey Peng Huang
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mackay Memorial Hospital, Taipei 10491, Taiwan
| | - Johnson Lin
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mackay Memorial Hospital, Taipei 10491, Taiwan
| | - Chi-Yuan Tzen
- Department of Pathology, Mackay Memorial Hospital, Taipei 10491, Taiwan
| | - Wen-Yu Huang
- Laboratory of Good Clinical Research Center, Mackay Memorial Hospital, Tamsui Branch, New Taipei City 25160, Taiwan
| | - Chia-Chi Tsai
- Department of General Surgery, Mackay Memorial Hospital, Taipei 10491, Taiwan
| | - Chih-Jen Chen
- Division of Gastroenterology, Department of Internal Medicine, Mackay Memorial Hospital, Taipei 10491, Taiwan
| | - Yen-Jung Lu
- ACT Genomics Co., Ltd., Taipei 11494, Taiwan
| | - Kuei-Fang Chou
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mackay Memorial Hospital, Taipei 10491, Taiwan
| | - Ying-Wen Su
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mackay Memorial Hospital, Taipei 10491, Taiwan
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25
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Cava C, Bertoli G, Colaprico A, Olsen C, Bontempi G, Castiglioni I. Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis. BMC Genomics 2018; 19:25. [PMID: 29304754 PMCID: PMC5756345 DOI: 10.1186/s12864-017-4423-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/27/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Modern high-throughput genomic technologies represent a comprehensive hallmark of molecular changes in pan-cancer studies. Although different cancer gene signatures have been revealed, the mechanism of tumourigenesis has yet to be completely understood. Pathways and networks are important tools to explain the role of genes in functional genomic studies. However, few methods consider the functional non-equal roles of genes in pathways and the complex gene-gene interactions in a network. RESULTS We present a novel method in pan-cancer analysis that identifies de-regulated genes with a functional role by integrating pathway and network data. A pan-cancer analysis of 7158 tumour/normal samples from 16 cancer types identified 895 genes with a central role in pathways and de-regulated in cancer. Comparing our approach with 15 current tools that identify cancer driver genes, we found that 35.6% of the 895 genes identified by our method have been found as cancer driver genes with at least 2/15 tools. Finally, we applied a machine learning algorithm on 16 independent GEO cancer datasets to validate the diagnostic role of cancer driver genes for each cancer. We obtained a list of the top-ten cancer driver genes for each cancer considered in this study. CONCLUSIONS Our analysis 1) confirmed that there are several known cancer driver genes in common among different types of cancer, 2) highlighted that cancer driver genes are able to regulate crucial pathways.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090 Milan, Segrate-Milan Italy
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090 Milan, Segrate-Milan Italy
| | - Antonio Colaprico
- Interuniversity Institute of Bioinformatics in Brussels (IB)2, 1050 Brussels, Belgium
- Machine Learning Group (MLG), Department d’Informatique, Universite libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Catharina Olsen
- Interuniversity Institute of Bioinformatics in Brussels (IB)2, 1050 Brussels, Belgium
- Machine Learning Group (MLG), Department d’Informatique, Universite libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels (IB)2, 1050 Brussels, Belgium
- Machine Learning Group (MLG), Department d’Informatique, Universite libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090 Milan, Segrate-Milan Italy
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