1
|
Wang Z, Lu Y, Han M, Li A, Ruan M, Tong Y, Yang C, Zhang X, Zhu C, Wang C, Shen K, Dong L, Chen X. Association between homologous recombination deficiency status and carboplatin treatment response in early triple-negative breast cancer. Breast Cancer Res Treat 2024:10.1007/s10549-024-07436-1. [PMID: 39048852 DOI: 10.1007/s10549-024-07436-1] [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: 03/27/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND The aim of this study was to assess homologous recombination deficiency (HRD) status and its correlation with carboplatin treatment response in early triple-negative breast cancer (TNBC) patients. METHODS Tumor tissues from 225 consecutive TNBC patients were evaluated with an HRD panel and homologous recombination-related (HRR) gene expression data. HRD positivity was defined as a high HRD score and/or BRCA1/2 pathogenic or likely pathogenic mutation. Clinicopathological factors, neoadjuvant treatment response, and prognosis were analyzed with respect to HRD status in these TNBC patients. RESULTS HRD positivity was found in 53.3% of patients and was significantly related to high Ki67 levels (P = 0.001). In patients who received neoadjuvant chemotherapy, HRD positivity (P = 0.005) or a high HRD score (P = 0.003) was significantly associated with a greater pathological complete response (pCR) rate, especially in those treated with carboplatin-containing neoadjuvant regimens (HRD positivity vs. negativity: 50.00% vs. 17.65%, P = 0.040). HRD positivity was associated with favorable distant metastasis-free survival (hazard ratio HR 0.49, 95% confidence interval CI 0.26-0.90, P = 0.022) and overall survival (HR 0.45, 95% CI 0.20-0.99, P = 0.049), irrespective of carboplatin treatment. CONCLUSION TNBC patients with high HRDs had high Ki67 levels and BRCA mutations. HRD-positive TNBC patients treated with carboplatin had a higher pCR rate. Patients with HRD positivity had a better prognosis, irrespective of carboplatin treatment, warranting further evaluation.
Collapse
Affiliation(s)
- Zheng Wang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Yujie Lu
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Mengyuan Han
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Anqi Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Miao Ruan
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Yiwei Tong
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Cuiyan Yang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Xiaotian Zhang
- Department of Translational Oncology, Amoy Diagnostics Co., Ltd., Xiamen, 361026, China
| | - Changbin Zhu
- Department of Translational Oncology, Amoy Diagnostics Co., Ltd., Xiamen, 361026, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
| | - Kunwei Shen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
| | - Xiaosong Chen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China.
| |
Collapse
|
2
|
Çıldır ÖŞ, Özmen Ö, Kul S, Rişvanlı A, Özalp G, Sabuncu A, Kul O. Genetic analysis of PALB2 gene WD40 domain in canine mammary tumour patients. Vet Med Sci 2024; 10:e1366. [PMID: 38527110 PMCID: PMC10962921 DOI: 10.1002/vms3.1366] [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: 05/11/2023] [Revised: 11/30/2023] [Accepted: 01/07/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND DNA repair mechanisms are essential for tumorigenesis and disruption of HR mechanism is an important predisposing factor of human breast cancers (BC). PALB2 is an important part of the HR. There are similarities between canine mammary tumours (CMT) and BCs. As its human counterpart, PALB2 mutations could be a predisposing factor of CMT. OBJECTIVES In this study, we aimed to investigate the impacts of PALB2 variants on tumorigenesis and canine mammary tumor (CMT) malignancy. METHODS We performed Sanger sequencing to detect germline mutations in the WD40 domain of the canine PALB2 gene in CMT patients. We conducted in silico analysis to investigate the variants, and compared the germline PALB2 mutations in humans that cause breast cancer (BC) with the variants detected in dogs with CMT. RESULTS We identified an intronic (c.3096+8C>G) variant, two exonic (p.A1050V and p.R1354R) variants, and a 3' UTR variant (c.4071T>C). Of these, p.R1354R and c.4071T>C novel variants were identified for the first time in this study. We found that the p.A1050V mutation had a significant effect. However, we could not determine sufficient similarity due to the differences in nucleotide/amino acid sequences between two species. Nonetheless, possible variants of human sequences in the exact location as their dog counterparts are associated with several cancer types, implying that the variants could be crucial for tumorigenesis in dogs. Our results did not show any effect of the variants on tumor malignancy. CONCLUSIONS The current project is the first study investigating the relationship between the PALB2 gene WD40 domain and CMTs. Our findings will contribute to a better understanding of the pathogenic mechanism of the PALB2 gene in CMTs. In humans, variant positions in canines have been linked to cancer-related phenotypes such as familial BC, endometrial tumor, and hereditary cancer predisposition syndrome. The results of bioinformatics analyses should be investigated through functional tests or case-control studies.
Collapse
Affiliation(s)
- Özge Şebnem Çıldır
- Department of GeneticsFaculty of Veterinary MedicineKafkas UniversityKarsTürkiye
- Department of GeneticsFaculty of Veterinary MedicineAnkara UniversityAnkaraTürkiye
| | - Özge Özmen
- Department of GeneticsFaculty of Veterinary MedicineAnkara UniversityAnkaraTürkiye
| | - Selim Kul
- Department of Animal BreedingFaculty of Veterinary MedicineYozgat Bozok UniversityYozgatTürkiye
| | - Ali Rişvanlı
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineFırat UniversityElazığTürkiye
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineKyrgyz‐Turkish Manas UniversityBishkekKyrgyzstan
| | - Gözde Özalp
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineBursa Uludağ UniversityBursaTürkiye
| | - Ahmet Sabuncu
- Department of Obstetrics and GynecologyFaculty of Veterinary Medicineİstanbul UniversityİstanbulTürkiye
| | - Oğuz Kul
- Department of PathologyFaculty of Veterinary MedicineKırıkkale UniversityKırıkkaleTürkiye
| |
Collapse
|
3
|
Her J, Zheng H, Bunting SF. RNF4 sustains Myc-driven tumorigenesis by facilitating DNA replication. J Clin Invest 2024; 134:e167419. [PMID: 38530355 PMCID: PMC11093604 DOI: 10.1172/jci167419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/20/2024] [Indexed: 03/27/2024] Open
Abstract
The mammalian SUMO-targeted E3 ubiquitin ligase Rnf4 has been reported to act as a regulator of DNA repair, but the importance of RNF4 as a tumor suppressor has not been tested. Using a conditional-knockout mouse model, we deleted Rnf4 in the B cell lineage to test the importance of RNF4 for growth of somatic cells. Although Rnf4-conditional-knockout B cells exhibited substantial genomic instability, Rnf4 deletion caused no increase in tumor susceptibility. In contrast, Rnf4 deletion extended the healthy lifespan of mice expressing an oncogenic c-myc transgene. Rnf4 activity is essential for normal DNA replication, and in its absence, there was a failure in ATR-CHK1 signaling of replication stress. Factors that normally mediate replication fork stability, including members of the Fanconi anemia gene family and the helicases PIF1 and RECQL5, showed reduced accumulation at replication forks in the absence of RNF4. RNF4 deficiency also resulted in an accumulation of hyper-SUMOylated proteins in chromatin, including members of the SMC5/6 complex, which contributes to replication failure by a mechanism dependent on RAD51. These findings indicate that RNF4, which shows increased expression in multiple human tumor types, is a potential target for anticancer therapy, especially in tumors expressing c-myc.
Collapse
Affiliation(s)
- Joonyoung Her
- Department of Molecular Biology and Biochemistry and
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | | |
Collapse
|
4
|
Pozzorini C, Andre G, Coletta T, Buisson A, Bieler J, Ferrer L, Kempfer R, Saintigny P, Harlé A, Vacirca D, Barberis M, Gilson P, Roma C, Saitta A, Smith E, Consales Barras F, Ripol L, Fritzsche M, Marques AC, Alkodsi A, Marin R, Normanno N, Grimm C, Müllauer L, Harter P, Pignata S, Gonzalez-Martin A, Denison U, Fujiwara K, Vergote I, Colombo N, Willig A, Pujade-Lauraine E, Just PA, Ray-Coquard I, Xu Z. GIInger predicts homologous recombination deficiency and patient response to PARPi treatment from shallow genomic profiles. Cell Rep Med 2023; 4:101344. [PMID: 38118421 PMCID: PMC10772634 DOI: 10.1016/j.xcrm.2023.101344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/11/2023] [Accepted: 11/23/2023] [Indexed: 12/22/2023]
Abstract
Homologous recombination deficiency (HRD) is a predictive biomarker for poly(ADP-ribose) polymerase 1 inhibitor (PARPi) sensitivity. Routine HRD testing relies on identifying BRCA mutations, but additional HRD-positive patients can be identified by measuring genomic instability (GI), a consequence of HRD. However, the cost and complexity of available solutions hamper GI testing. We introduce a deep learning framework, GIInger, that identifies GI from HRD-induced scarring observed in low-pass whole-genome sequencing data. GIInger seamlessly integrates into standard BRCA testing workflows and yields reproducible results concordant with a reference method in a multisite study of 327 ovarian cancer samples. Applied to a BRCA wild-type enriched subgroup of 195 PAOLA-1 clinical trial patients, GIInger identified HRD-positive patients who experienced significantly extended progression-free survival when treated with PARPi. GIInger is, therefore, a cost-effective and easy-to-implement method for accurately stratifying patients with ovarian cancer for first-line PARPi treatment.
Collapse
Affiliation(s)
| | | | | | - Adrien Buisson
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | | | - Loïc Ferrer
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | - Rieke Kempfer
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | - Pierre Saintigny
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France; University of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Alexandre Harlé
- Institut de Cancérologie de Lorraine, Service de Biopathologie, CNRS UMR 7039 CRAN, Vandoeuvre-lès-Nancy, France
| | | | | | - Pauline Gilson
- Institut de Cancérologie de Lorraine, Service de Biopathologie, CNRS UMR 7039 CRAN, Vandoeuvre-lès-Nancy, France
| | - Cristin Roma
- Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | | | - Ewan Smith
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | | | - Lucia Ripol
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | | | | | - Amjad Alkodsi
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | - Ray Marin
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | - Nicola Normanno
- Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | | | | | | | - Sandro Pignata
- Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, and Multicenter Italian Trials in Ovarian Cancer and Gynecologic Malignancies (MITO), Naples, Italy
| | - Antonio Gonzalez-Martin
- Cancer Center Clinica Universidad de Navarra, Madrid, Spain; GEICO, Madrid, Spain; Program In Solid Tumors, CIMA, Pamplona, Spain
| | - Ursula Denison
- Department for Gynaecology and Obstetrics, Klinik Hietzing, Vienna, Austria
| | - Keiichi Fujiwara
- Saitama Medical University International Medical Center, Saitama, Japan
| | - Ignace Vergote
- University Hospital Leuven, Leuven Cancer Institute, Leuven, Belgium
| | | | - Adrian Willig
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | | | - Pierre-Alexandre Just
- Service de Pathologie, APHM (Assistance Publique - Hôpitaux de Marseille), Marseille, Provence-Alpes-Côte d'Azur, France
| | - Isabelle Ray-Coquard
- Centre Léon BERARD, and University Claude Bernard Lyon I, Lyon, France; Groupe d'Investigateurs Nationaux pour l'Etude des Cancers Ovariens (GINECO), Lyon, France
| | - Zhenyu Xu
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
| |
Collapse
|
5
|
Lenz L, Neff C, Solimeno C, Cogan ES, Abramson VG, Boughey JC, Falkson C, Goetz MP, Ford JM, Gradishar WJ, Jankowitz RC, Kaklamani VG, Marcom PK, Richardson AL, Storniolo AM, Tung NM, Vinayak S, Hodgson DR, Lai Z, Dearden S, Hennessy BT, Mayer EL, Mills GB, Slavin TP, Gutin A, Connolly RM, Telli ML, Stearns V, Lanchbury JS, Timms KM. Identifying homologous recombination deficiency in breast cancer: genomic instability score distributions differ among breast cancer subtypes. Breast Cancer Res Treat 2023; 202:191-201. [PMID: 37589839 PMCID: PMC10504389 DOI: 10.1007/s10549-023-07046-3] [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: 06/01/2023] [Accepted: 07/07/2023] [Indexed: 08/18/2023]
Abstract
PURPOSE A 3-biomarker homologous recombination deficiency (HRD) score is a key component of a currently FDA-approved companion diagnostic assay to identify HRD in patients with ovarian cancer using a threshold score of ≥ 42, though recent studies have explored the utility of a lower threshold (GIS ≥ 33). The present study evaluated whether the ovarian cancer thresholds may also be appropriate for major breast cancer subtypes by comparing the genomic instability score (GIS) distributions of BRCA1/2-deficient estrogen receptor-positive breast cancer (ER + BC) and triple-negative breast cancer (TNBC) to the GIS distribution of BRCA1/2-deficient ovarian cancer. METHODS Ovarian cancer and breast cancer (ER + BC and TNBC) tumors from ten study cohorts were sequenced to identify pathogenic BRCA1/2 mutations, and GIS was calculated using a previously described algorithm. Pathologic complete response (pCR) to platinum therapy was evaluated in a subset of TNBC samples. For TNBC, a threshold was set and threshold validity was assessed relative to clinical outcomes. RESULTS A total of 560 ovarian cancer, 805 ER + BC, and 443 TNBC tumors were included. Compared to ovarian cancer, the GIS distribution of BRCA1/2-deficient samples was shifted lower for ER + BC (p = 0.015), but not TNBC (p = 0.35). In the subset of TNBC samples, univariable logistic regression models revealed that GIS status using thresholds of ≥ 42 and ≥ 33 were significant predictors of response to platinum therapy. CONCLUSIONS This study demonstrated that the GIS thresholds used for ovarian cancer may also be appropriate for TNBC, but not ER + BC. GIS thresholds in TNBC were validated using clinical response data to platinum therapy.
Collapse
Affiliation(s)
- Lauren Lenz
- Myriad Genetics, Inc, 320 Wakara Way, Salt Lake City, UT, 84108, USA
| | - Chris Neff
- Myriad Genetics, Inc, 320 Wakara Way, Salt Lake City, UT, 84108, USA
| | - Cara Solimeno
- Myriad Genetics, Inc, 320 Wakara Way, Salt Lake City, UT, 84108, USA
| | - Elizabeth S Cogan
- Myriad Genetics, Inc, 320 Wakara Way, Salt Lake City, UT, 84108, USA
| | | | | | - Carla Falkson
- University of Rochester Medical Center, Rochester, NY, USA
| | | | - James M Ford
- Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | - Andrea L Richardson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Anna Maria Storniolo
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nadine M Tung
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Shaveta Vinayak
- University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, 15. AstraZeneca, Seattle, WA, USA
| | | | | | | | | | - Erica L Mayer
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Thomas P Slavin
- Myriad Genetics, Inc, 320 Wakara Way, Salt Lake City, UT, 84108, USA
| | - Alexander Gutin
- Myriad Genetics, Inc, 320 Wakara Way, Salt Lake City, UT, 84108, USA
| | | | | | - Vered Stearns
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jerry S Lanchbury
- Myriad Genetics, Inc, 320 Wakara Way, Salt Lake City, UT, 84108, USA
| | - Kirsten M Timms
- Myriad Genetics, Inc, 320 Wakara Way, Salt Lake City, UT, 84108, USA.
| |
Collapse
|
6
|
Davoudi F, Moradi A, Becker TM, Lock JG, Abbey B, Fontanarosa D, Haworth A, Clements J, Ecker RC, Batra J. Genomic and Phenotypic Biomarkers for Precision Medicine Guidance in Advanced Prostate Cancer. Curr Treat Options Oncol 2023; 24:1451-1471. [PMID: 37561382 PMCID: PMC10547634 DOI: 10.1007/s11864-023-01121-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2023] [Indexed: 08/11/2023]
Abstract
OPINION STATEMENT Prostate cancer (PCa) is the second most diagnosed malignant neoplasm and is one of the leading causes of cancer-related death in men worldwide. Despite significant advances in screening and treatment of PCa, given the heterogeneity of this disease, optimal personalized therapeutic strategies remain limited. However, emerging predictive and prognostic biomarkers based on individual patient profiles in combination with computer-assisted diagnostics have the potential to guide precision medicine, where patients may benefit from therapeutic approaches optimally suited to their disease. Also, the integration of genotypic and phenotypic diagnostic methods is supporting better informed treatment decisions. Focusing on advanced PCa, this review discusses polygenic risk scores for screening of PCa and common genomic aberrations in androgen receptor (AR), PTEN-PI3K-AKT, and DNA damage response (DDR) pathways, considering clinical implications for diagnosis, prognosis, and treatment prediction. Furthermore, we evaluate liquid biopsy, protein biomarkers such as serum testosterone levels, SLFN11 expression, total alkaline phosphatase (tALP), neutrophil-to-lymphocyte ratio (NLR), tissue biopsy, and advanced imaging tools, summarizing current phenotypic biomarkers and envisaging more effective utilization of diagnostic and prognostic biomarkers in advanced PCa. We conclude that prognostic and treatment predictive biomarker discovery can improve the management of patients, especially in metastatic stages of advanced PCa. This will result in decreased mortality and enhanced quality of life and help design a personalized treatment regimen.
Collapse
Affiliation(s)
- Fatemeh Davoudi
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afshin Moradi
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| | - Therese M. Becker
- Ingham Institute for Applied Medical Research, University of Western Sydney and University of New South Wales, Liverpool, 2170 Australia
| | - John G. Lock
- Ingham Institute for Applied Medical Research, University of Western Sydney and University of New South Wales, Liverpool, 2170 Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, 2052 Australia
| | - Brian Abbey
- Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Sciences, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC Australia
| | - Davide Fontanarosa
- School of Clinical Sciences, Queensland University of Technology, Gardens Point Campus, 2 George St, Brisbane, QLD 4000 Australia
- Centre for Biomedical Technologies (CBT), Queensland University of Technology, Brisbane, QLD 4000 Australia
| | - Annette Haworth
- Institute of Medical Physics, School of Physics, University of Sydney, Camperdown, NSW 2006 Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| | - Rupert C. Ecker
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
- TissueGnostics GmbH, EU 1020 Vienna, Austria
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| |
Collapse
|
7
|
Li W, Gao L, Yi X, Shi S, Huang J, Shi L, Zhou X, Wu L, Ying J. Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:962-975. [PMID: 36791952 PMCID: PMC10928375 DOI: 10.1016/j.gpb.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 12/23/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Defects in genes involved in the DNA damage response cause homologous recombination repair deficiency (HRD). HRD is found in a subgroup of cancer patients for several tumor types, and it has a clinical relevance to cancer prevention and therapies. Accumulating evidence has identified HRD as a biomarker for assessing the therapeutic response of tumor cells to poly(ADP-ribose) polymerase inhibitors and platinum-based chemotherapies. Nevertheless, the biology of HRD is complex, and its applications and the benefits of different HRD biomarker assays are controversial. This is primarily due to inconsistencies in HRD assessments and definitions (gene-level tests, genomic scars, mutational signatures, or a combination of these methods) and difficulties in assessing the contribution of each genomic event. Therefore, we aim to review the biological rationale and clinical evidence of HRD as a biomarker. This review provides a blueprint for the standardization and harmonization of HRD assessments.
Collapse
Affiliation(s)
- Wenbin Li
- Department of Pathology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lin Gao
- Geneplus-Shenzhen, Shenzhen 518000, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Yi
- Geneplus-Beijing, Beijing 102206, China
| | | | - Jie Huang
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| |
Collapse
|
8
|
Feng D, Wang J, Li D, Wu R, Wei W, Zhang C. Senescence-associated secretory phenotype constructed detrimental and beneficial subtypes and prognostic index for prostate cancer patients undergoing radical prostatectomy. Discov Oncol 2023; 14:155. [PMID: 37624511 PMCID: PMC10457268 DOI: 10.1007/s12672-023-00777-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/22/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Cellular senescence is growing in popularity in cancer. A dual function is played by the senescence-associated secretory phenotype (SASP) that senescent cells produce in the development of pro-inflammatory niches, tissue regeneration or destruction, senescence propagation, and malignant transformation. In this study, we conducted thorough bioinformatic analysis and meta-analysis to discover detrimental and beneficial subtypes and prognostic index for prostate cancer (PCa) patients using the experimentally confirmed SASP genes. METHODS We identified differentially expressed and prognosis-related SASP genes and used them to construct two molecular subtypes and risk score. Another two external cohorts were used to confirm the prognostic effect of the above subtypes and risk score and meta-analysis was further conducted. Additionally, functional analysis, tumor stemness and heterogeneity and tumor microenvironment were also evaluated. We completed analyses using software R 3.6.3 and its suitable packages. Meta-analysis was performed by software Stata 14.0. RESULTS Through multivariate Cox regression analysis and consensus clustering analysis, we used VGF, IGFBP3 and ANG to establish detrimental and beneficial subtypes in the TCGA cohort, which was validated through other two independent cohorts. Meta-analysis showed that detrimental SASP group had significantly higher risk of biochemical recurrence (BCR) than beneficial SASP group (HR: 2.48). Moreover, we also constructed and validated risk score based on these genes to better guide clinical practice. DNA repair, MYC target, oxidative phosphorylation, proteasome and ribosome were highly enriched in detrimental SASP group. Detrimental SASP group had significantly higher levels of B cells, CD8+ T cells, homologous recombination deficiency, loss of heterozygosity, microsatellite instability, purity, tumor mutation burden, mRNAsi, differentially methylated probes and epigenetically regulated RNA expression than beneficial SASP group. The top mutation genes between detrimental and beneficial SASP groups were SPOP, FOXA1, KMT2C, APC, BSN, DNAH17, MYH6, EPPK1, ZNF536 and ZC3H13 with statistical significance. CONCLUSIONS From perspective of SASP, we found detrimental and beneficial tumor subtypes which were closely associated with BCR-free survival for PCa patients, which might be important for the furture research in the field of PCa.
Collapse
Affiliation(s)
- Dechao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, People's Republic of China.
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dengxiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ruicheng Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wuran Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chi Zhang
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, People's Republic of China.
| |
Collapse
|
9
|
Yan S, Imam M. Progress and prospects in research and clinical practice of hormone receptor-positive, HER-2-negative breast cancer with BRCA1/2 mutations. Discov Oncol 2023; 14:110. [PMID: 37351713 PMCID: PMC10290022 DOI: 10.1007/s12672-023-00732-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023] Open
Abstract
Breast cancer (BC) is a heterogeneous disease that is the most common cancer in women worldwide. However, precise subtyping and corresponding treatments have improved patient outcomes. Hormone receptor (HR)-positive, human epidermal growth factor receptor type 2 (HER2)-negative (HR+/HER2-) BC with BRCA1 and/or BRCA2 mutations (BRCA1/2m) is a unique BC subset with dual drivers: homologous recombination deficiency and hormone receptor signaling. Wild-type BRCA1/2 suppresses estrogen receptor-mediated signaling. Loss-of-function mutations in BRCA1/2 release estrogen receptor suppression, leading to reduced sensitivity to endocrine therapy. Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis) exert antitumor effects against this subtype and can be used in combination with endocrine therapy. Although PARPis have been evaluated in metastatic triple-negative breast cancer, their efficacy against HR+/HER2- BC has not been clearly established. The present review summarizes recent advances and prospects in the progress of the HR+/HER2-/BRCA1/2m subgroup. As such, this article provides theoretical guidance for future research and promotes the use of PARPis for the treatment of HR+/HER2-/BRCA1/2m BC.
Collapse
Affiliation(s)
- Shunchao Yan
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110022, China.
| | - Murshid Imam
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110022, China
| |
Collapse
|
10
|
Clinical Utility of Genomic Tests Evaluating Homologous Recombination Repair Deficiency (HRD) for Treatment Decisions in Early and Metastatic Breast Cancer. Cancers (Basel) 2023; 15:cancers15041299. [PMID: 36831640 PMCID: PMC9954086 DOI: 10.3390/cancers15041299] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/17/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Breast cancer is the most frequently occurring cancer worldwide. With its increasing incidence, it is a major public health problem, with many therapeutic challenges such as precision medicine for personalized treatment. Thanks to next-generation sequencing (NGS), progress in biomedical technologies, and the use of bioinformatics, it is now possible to identify specific molecular alterations in tumor cells-such as homologous recombination deficiencies (HRD)-enabling us to consider using DNA-damaging agents such as platinum salts or PARP inhibitors. Different approaches currently exist to analyze impairment of the homologous recombination pathway, e.g., the search for specific mutations in homologous recombination repair (HRR) genes, such as BRCA1/2; the use of genomic scars or mutational signatures; or the development of functional tests. Nevertheless, the role and value of these different tests in breast cancer treatment decisions remains to be clarified. In this review, we summarize current knowledge on the clinical utility of genomic tests, evaluating HRR deficiency for treatment decisions in early and metastatic breast cancer.
Collapse
|
11
|
Wang X, Xu Y, Zhang Y, Wang S, Zhang X, Yi X, Zhang S, Wang J. HRD-MILN: Accurately estimate tumor homologous recombination deficiency status from targeted panel sequencing data. Front Genet 2022; 13:990244. [PMID: 36246633 PMCID: PMC9554509 DOI: 10.3389/fgene.2022.990244] [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: 07/09/2022] [Accepted: 09/09/2022] [Indexed: 11/15/2022] Open
Abstract
Homologous recombination deficiency (HRD) is a critical feature guiding drug and treatment selection, mainly for ovarian and breast cancers. As it cannot be directly observed, HRD status is estimated on a small set of genomic instability features from sequencing data. The existing methods often perform poorly when handling targeted panel sequencing data; however, the targeted panel is the most popular sequencing strategy in clinical practices. Thus, we proposed HRD-MILN to overcome the computational challenges from targeted panel sequencing. HRD-MILN incorporated a multi-instance learning framework to discover as many loss of heterozygosity (LOH) associated with HRD status to cluster as possible. Then the HRD score is obtained based on the association between the LOHs and the cluster in the sample to be estimated, and finally, the HRD status is estimated based on the score. In comparison experiments on targeted panel sequencing data, the Precision of HRD-MILN could achieve 87%, significantly improved from 63% reported by the existing methods, where the highest margin of improvement reached 14%. It also presented advantages on whole exome sequencing data. Based on our best knowledge, HRD-MILN is the first practical tool for estimating HRD status from targeted panel sequencing data and could benefit clinical applications.
Collapse
Affiliation(s)
- Xuwen Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Ying Xu
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Yinbin Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shenjie Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Xuanping Zhang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Jiayin Wang, ; Shuqun Zhang,
| | - Jiayin Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Jiayin Wang, ; Shuqun Zhang,
| |
Collapse
|
12
|
Jackson CG, Moore KN, Cantrell L, Erickson BK, Duska LR, Richardson DL, Landrum LM, Holman LL, Walker JL, Mannel RS, Moxley KM, Queimado L, Cohoon A, Ding K, Dockery LE. A phase II trial of bevacizumab and rucaparib in recurrent carcinoma of the cervix or endometrium. Gynecol Oncol 2022; 166:44-49. [PMID: 35491267 PMCID: PMC10428664 DOI: 10.1016/j.ygyno.2022.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 11/22/2022]
Abstract
OBJECTIVE The aim of this study was to examine the tolerability and efficacy of combination bevacizumab rucaparib therapy in patients with recurrent cervical or endometrial cancer. PATIENTS & METHODS Thirty-three patients with recurrent cervical or endometrial cancer were enrolled. Patients were required to have tumor progression after first line treatment for metastatic, or recurrent disease. Rucaparib was given at 600 mg BID twice daily for each 21-day cycle. Bevacizumab was given at 15 mg/kg on day 1 of each 21-day cycle. The primary endpoint was efficacy as determined by objective response rate or 6-month progression free survival. RESULTS Of the 33 patients enrolled, 28 were evaluable. Patients with endometrial cancer had a response rate of 17% while patients with cervical cancer had a response rate of 14%. Median progression free survival was 3.8 months (95% C·I 2.5 to 5.7 months), and median overall survival was 10.1 months (95% C·I 7.0 to 15.1 months). Patients with ARID1A mutations displayed a better response rate (33%) and 6-month progression free survival (PFS6) rate (67%) than the entire study population. Observed toxicity was similar to that of previous studies with bevacizumab and rucaparib. CONCLUSIONS The combination of bevacizumab with rucaparib did not show significantly increased anti-tumor activity in all patients with recurrent cervical or endometrial cancer. However, patients with ARID1A mutations had a higher response rate and PFS6 suggesting this subgroup may benefit from the combination of bevacizumab and rucaparib. Further study is needed to confirm this observation. No new safety signals were seen.
Collapse
Affiliation(s)
- C G Jackson
- Stephenson Cancer Center Section of Gynecologic Oncology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - K N Moore
- Stephenson Cancer Center Section of Gynecologic Oncology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - L Cantrell
- Division of Gynecologic Oncology, University of Virginia, Department of Obstetrics and Gynecology; Charlottesville, VA, USA
| | - B K Erickson
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Minnesota; Minneapolis, MN, USA
| | - L R Duska
- Division of Gynecologic Oncology, University of Virginia, Department of Obstetrics and Gynecology; Charlottesville, VA, USA
| | - D L Richardson
- Stephenson Cancer Center Section of Gynecologic Oncology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - L M Landrum
- Stephenson Cancer Center Section of Gynecologic Oncology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - L L Holman
- Stephenson Cancer Center Section of Gynecologic Oncology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - J L Walker
- Stephenson Cancer Center Section of Gynecologic Oncology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - R S Mannel
- Stephenson Cancer Center Section of Gynecologic Oncology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - K M Moxley
- Stephenson Cancer Center Section of Gynecologic Oncology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - L Queimado
- Department of Otolaryngology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - A Cohoon
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - K Ding
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center; Oklahoma City, OK, USA
| | - L E Dockery
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of North Carolina; Chapel Hill, NC, USA.
| |
Collapse
|
13
|
Lee JD, Ryu WJ, Han HJ, Kim TY, Kim MH, Sohn J. Molecular Characterization of BRCA1 c.5339T>C Missense Mutation in DNA Damage Response of Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14102405. [PMID: 35626017 PMCID: PMC9139203 DOI: 10.3390/cancers14102405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
BRCA1 L1780P BRCT domain mutation has been recognized as a pathogenic mutation in patients with breast cancer. However, the molecular significance of this mutation has not yet been studied in triple-negative breast cancer (TNBC) cells in vitro. We established MDA-MB 231, HCC1937, and HCC1395 TNBC cell lines expressing BRCA1 L1780P mutant. BRCA1 L1780P mutant TNBC cells showed increased migration and invasion capacity, as well as increased sensitivity to olaparib and carboplatin compared to BRCA1 wild-type cells. BRCA1 L1780P mutant TNBC cells showed decreased RAD51 expression and reduced nuclear RAD51 foci formation following carboplatin and olaparib treatment. The molecular interaction between p-ATM and BRCA1 was abrogated following introduction of BRCA1 L1780P mutant plasmid in TNBC cells, suggesting that the BRCA1 L1780P mutation disrupts the p-ATM-BRCA1 protein-protein interaction. We established an olaparib-resistant BRCA1 L1780P mutant TNBC cell line by chronic drug treatment. Olaparib-resistant cell lines showed upregulation of RAD51 expression upon olaparib treatment, and reduction in RAD51 expression in olaparib-resistant cells restored olaparib sensitivity. Collectively, these results suggest that the BRCA1 L1780P mutation impairs RAD51 recruitment by disrupting p-ATM-BRCA1 interaction, which is a crucial molecular factor in homologous recombination and olaparib sensitivity. Further therapeutic targeting of RAD51 in BRCA1 L1780P mutant breast cancer is warranted.
Collapse
Affiliation(s)
- Jeong Dong Lee
- Department of Human Biology and Genomics, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Won-Ji Ryu
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul 03722, Korea; (W.-J.R.); (H.J.H.); (T.Y.K.)
| | - Hyun Ju Han
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul 03722, Korea; (W.-J.R.); (H.J.H.); (T.Y.K.)
| | - Tae Yeong Kim
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul 03722, Korea; (W.-J.R.); (H.J.H.); (T.Y.K.)
| | - Min Hwan Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
- Correspondence: (M.H.K.); (J.S.); Tel.: +82-2-2228-8135 (M.H.K. & J.S.)
| | - Joohyuk Sohn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
- Correspondence: (M.H.K.); (J.S.); Tel.: +82-2-2228-8135 (M.H.K. & J.S.)
| |
Collapse
|
14
|
Conroy JM, Pabla S, Glenn ST, Seager RJ, Van Roey E, Gao S, Burgher B, Andreas J, Giamo V, Mallon M, Lee YH, DePietro P, Nesline M, Wang Y, Lenzo FL, Klein R, Zhang S. A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors. PLoS One 2021; 16:e0260089. [PMID: 34855780 PMCID: PMC8639101 DOI: 10.1371/journal.pone.0260089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
Timely and accurate identification of molecular alterations in solid tumors is essential for proper management of patients with advanced cancers. This has created a need for rapid, scalable comprehensive genomic profiling (CGP) systems that detect an increasing number of therapeutically-relevant variant types and molecular signatures. In this study, we assessed the analytical performance of the TruSight Oncology 500 High-Throughput assay for detection of somatic alterations from formalin-fixed paraffin-embedded tissue specimens. In parallel, we developed supporting software and automated sample preparation systems designed to process up to 70 clinical samples in a single NovaSeq 6000TM sequencing run with a turnaround time of <7 days from specimen receipt to report. The results demonstrate that the scalable assay accurately and reproducibly detects small variants, copy number alterations, microsatellite instability (MSI) and tumor mutational burden (TMB) from 40ng DNA, and multiple gene fusions, including known and unknown partners and splice variants from 20ng RNA. 717 tumor samples and reference materials with previously known alterations in 96 cancer-related genes were sequenced to evaluate assay performance. All variant classes were reliably detected at consistent and reportable variant allele percentages with >99% overall accuracy and precision. Our results demonstrate that the high-throughput CGP assay is a reliable method for accurate detection of molecular alterations in support of precision therapeutics in oncology. The supporting systems and scalable workflow allow for efficient interpretation and prompt reporting of hundreds of patient cancer genomes per week with excellent analytical performance.
Collapse
Affiliation(s)
- Jeffrey M. Conroy
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
- Research Support Services, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Sarabjot Pabla
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Sean T. Glenn
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
- Laboratory Operations, OmniSeq Inc., Buffalo, New York, United States of America
- HemePath Molecular, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - R. J. Seager
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Erik Van Roey
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Shuang Gao
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Blake Burgher
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Jonathan Andreas
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Vincent Giamo
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Melissa Mallon
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Yong Hee Lee
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Paul DePietro
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Mary Nesline
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Yirong Wang
- Information Technology, OmniSeq Inc., Buffalo, New York, United States of America
| | - Felicia L. Lenzo
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Roger Klein
- Medical Affairs, OmniSeq Inc., Buffalo, New York, United States of America
| | - Shengle Zhang
- Laboratory Operations, OmniSeq Inc., Buffalo, New York, United States of America
| |
Collapse
|
15
|
Fugger K, Hewitt G, West SC, Boulton SJ. Tackling PARP inhibitor resistance. Trends Cancer 2021; 7:1102-1118. [PMID: 34563478 DOI: 10.1016/j.trecan.2021.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022]
Abstract
Homologous recombination-deficient (HRD) tumours, including those harbouring mutations in the BRCA genes, are hypersensitive to treatment with inhibitors of poly(ADP-ribose) polymerase (PARPis). Despite high response rates, most HRD cancers ultimately develop resistance to PARPi treatment through reversion mutations or genetic/epigenetic alterations to DNA repair pathways. Counteracting these resistance pathways, thereby increasing the potency of PARPi therapy, represents a potential strategy to improve the treatment of HRD cancers. In this review, we discuss recent insights derived from genetic screens that have identified a number of novel genes that can be targeted to improve PARPi treatment of HRD cancers and may provide a means to overcome PARPi resistance.
Collapse
Affiliation(s)
- Kasper Fugger
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen C West
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Artios Pharma Ltd. B940, Babraham Research Campus, Cambridge, CB22 3FH, UK.
| |
Collapse
|
16
|
GSA: an independent development algorithm for calling copy number and detecting homologous recombination deficiency (HRD) from target capture sequencing. BMC Bioinformatics 2021; 22:562. [PMID: 34814825 PMCID: PMC8609767 DOI: 10.1186/s12859-021-04487-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/17/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The gain or loss of large chromosomal regions or even whole chromosomes is termed as genomic scarring and can be observed as copy number variations resulting from the failure of DNA damage repair. RESULTS In this study, a new algorithm called genomic scar analysis (GSA) has developed and validated to calculate homologous recombination deficiency (HRD) score. The two critical submodules were tree recursion (TR) segmentation and filtering, and the estimation and correction of the tumor purity and ploidy. Then, this study evaluated the rationality of segmentation and genotype identification by the GSA algorithm and compared with other two algorithms, PureCN and ASCAT, found that the segmentation result of GSA algorithm was more logical. In addition, the results indicated that the GSA algorithm had an excellent predictive effect on tumor purity and ploidy, if the tumor purity was more than 20%. Furtherly, this study evaluated the HRD scores and BRCA1/2 deficiency status of 195 clinical samples, and the results indicated that the accuracy was 0.98 (comparing with Affymetrix OncoScan™ assay) and the sensitivity was 95.2% (comparing with BRCA1/2 deficiency status), both were well-behaved. Finally, HRD scores and 16 genes mutations (TP53 and 15 HRR pathway genes) were analyzed in 17 cell lines, the results showed that there was higher frequency in HRR pathway genes in high HRD score samples. CONCLUSIONS This new algorithm, named as GSA, could effectively and accurately calculate the purity and ploidy of tumor samples through NGS data, and then reflect the degree of genomic instability and large-scale copy number variations of tumor samples.
Collapse
|
17
|
Giunta EF, Annaratone L, Bollito E, Porpiglia F, Cereda M, Banna GL, Mosca A, Marchiò C, Rescigno P. Molecular Characterization of Prostate Cancers in the Precision Medicine Era. Cancers (Basel) 2021; 13:4771. [PMID: 34638258 PMCID: PMC8507555 DOI: 10.3390/cancers13194771] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer (PCa) therapy has been recently revolutionized by the approval of new therapeutic agents in the metastatic setting. However, the optimal therapeutic strategy in such patients should be individualized in the light of prognostic and predictive molecular factors, which have been recently studied: androgen receptor (AR) alterations, PTEN-PI3K-AKT pathway deregulation, homologous recombination deficiency (HRD), mismatch repair deficiency (MMRd), and tumor microenvironment (TME) modifications. In this review, we highlighted the clinical impact of prognostic and predictive molecular factors in PCa patients' outcomes, identifying biologically distinct subtypes. We further analyzed the relevant methods to detect these factors, both on tissue, i.e., immunohistochemistry (IHC) and molecular tests, and blood, i.e., analysis of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). Moreover, we discussed the main pros and cons of such techniques, depicting their present and future roles in PCa management, throughout the precision medicine era.
Collapse
Affiliation(s)
- Emilio Francesco Giunta
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80131 Naples, Italy;
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (C.M.)
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Turin, Italy
| | - Enrico Bollito
- Department of Pathology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, 10043 Turin, Italy;
| | - Francesco Porpiglia
- Department of Urology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, 10043 Turin, Italy;
| | - Matteo Cereda
- Cancer Genomics and Bioinformatics Unit, IIGM-Italian Institute for Genomic Medicine, c/o IRCCS Candiolo, 10060 Turin, Italy;
- Candiolo Cancer Institute, FPO—IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
| | - Giuseppe Luigi Banna
- Department of Oncology, Portsmouth Hospitals University NHS Trust, Portsmouth PO2 8QD, UK;
| | - Alessandra Mosca
- Multidisciplinary Outpatient Oncology Clinic, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Turin, Italy;
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; (L.A.); (C.M.)
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Turin, Italy
| | - Pasquale Rescigno
- Interdisciplinary Group for Translational Research and Clinical Trials, Urological Cancers (GIRT-Uro), Candiolo Cancer Institute, FPO-IRCCS, Candiolo, 10060 Turin, Italy
| |
Collapse
|
18
|
Malka MM, Eberle J, Niedermayer K, Zlotos DP, Wiesmüller L. Dual PARP and RAD51 Inhibitory Drug Conjugates Show Synergistic and Selective Effects on Breast Cancer Cells. Biomolecules 2021; 11:biom11070981. [PMID: 34356606 PMCID: PMC8301877 DOI: 10.3390/biom11070981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/04/2023] Open
Abstract
The genetic principle of synthetic lethality has most successfully been exploited in therapies engaging Poly-ADP-ribose-polymerase (PARP) inhibitors to treat patients with homologous recombination (HR)-defective tumors. In this work, we went a step further following the idea of a local molecular cooperation and designed hybrid compounds M1–M3. The drug conjugates M1–M3 combine Olaparib, the first PARP inhibitor approved for clinical use, with Cpd 1, an inhibitor of RAD51 that blocks its HR functions and yet permits RAD51 nucleoprotein filament formation on single-stranded DNA. While in M2 and M3, the parental drugs are linked by -CO-(CH2)n-CO-spacers (n = 2 and 4, respectively), they are directly merged omitting the piperazine ring of Olaparib in M1. Monitoring anti-survival effects of M1–M3 in six breast cancer cell lines of different molecular subtypes showed that in each cell line, at least one of the drug conjugates decreased viability by one to two orders of magnitude compared with parental drugs. While triple-negative breast cancer (TNBC) cells with frequent BRCA1 pathway dysfunction were sensitive to spacer-linked hybrid compounds M1 and M2 regardless of their HR capacities, non-TNBC cells were responsive to the merged drug conjugate M1 only, suggesting different spatial requirements for dual inhibition in these two groups of cell lines. These results demonstrate that, depending on chemical linkage, dual PARP1-RAD51 inhibitory drugs can either sensitize non-TNBC and re-sensitize TNBC cells, or discriminate between these groups of cells.
Collapse
Affiliation(s)
- Matthews M. Malka
- Department of Pharmaceutical Chemistry, The German University in Cairo, New Cairo City, Main Entrance of Al Tagamoa Al Khames, Cairo 11835, Egypt;
| | - Julia Eberle
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstrasse 43, 89075 Ulm, Germany; (J.E.); (K.N.)
| | - Kathrin Niedermayer
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstrasse 43, 89075 Ulm, Germany; (J.E.); (K.N.)
| | - Darius P. Zlotos
- Department of Pharmaceutical Chemistry, The German University in Cairo, New Cairo City, Main Entrance of Al Tagamoa Al Khames, Cairo 11835, Egypt;
- Correspondence: (D.P.Z.); (L.W.)
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstrasse 43, 89075 Ulm, Germany; (J.E.); (K.N.)
- Correspondence: (D.P.Z.); (L.W.)
| |
Collapse
|
19
|
Chevrier S, Richard C, Collot T, Mananet H, Arnould L, Boidot R. An Algorithm Combining Patient Performance Status, Second Hit Analysis, PROVEAN and Dann Prediction Tools Could Foretell Sensitization to PARP Inhibitors in Digestive, Skin, Ovarian and Breast Cancers. Cancers (Basel) 2021; 13:cancers13133113. [PMID: 34206535 PMCID: PMC8268870 DOI: 10.3390/cancers13133113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary PARP inhibitors, a family of targeted cancer therapeutics, have been shown to be efficient in patients with some deficiencies in the homologous recombination machinery. However, a quick and reliable identification of patients who would benefit from such therapies remains a challenge. In particular, patients with tumors carrying variants of unknown significance (VUS) in homologous recombination genes do not currently benefit from PARP inhibitor treatments. In this study, we present an algorithm that may allow classification of these variants with regard to their impact on tumor responsiveness to PARP inhibitors. If validated on a larger patient sample, our algorithm would allow patients with tumors potentially responsive to PARP inhibitors to benefit from this therapy. Abstract PARP inhibitors yield interesting outcomes for patients with ovarian tumors harboring BRCA1 or BRCA2 mutation, but also with other tumors with homologous repair (HR) deficiency. About 40% of variants are variants of unknown significance (VUS), blocking the use of PARP inhibitors. In this study, we analyzed NGS data from 78 metastatic patients treated with PARP inhibitors. We tested NGS data and in silico predictions to classify VUS as potentially benign or deleterious. Among 41 patients treated with olaparib, three had tumors harboring benign and 26 pathogenic variants, while 12 had VUS. Progression-Free Survival (PFS) analysis showed that benign variants did not respond to olaparib whereas pathogenic variants were associated with a median PFS of 190 days. Surprisingly, median PFS of patients with VUS-carrying tumors suggested that some of them may be sensitive to PARP inhibitors. By testing different in silico predictions and variant allelic frequency, we obtained an algorithm predicting VUS sensitivity to PARP inhibitors for patients with a Performance Status below 3. Our work suggests that VUS in HR genes could be predicted as benign or deleterious, which may increase the number of patients eligible for PARP inhibitor treatment. Further studies in a larger sample are warranted to validate our prediction algorithm.
Collapse
Affiliation(s)
- Sandy Chevrier
- Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France; (S.C.); (C.R.); (L.A.)
| | - Corentin Richard
- Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France; (S.C.); (C.R.); (L.A.)
| | - Thomas Collot
- Department of Medical Oncology, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France;
| | - Hugo Mananet
- Platform of Transfer in Cancer Biology, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France;
| | - Laurent Arnould
- Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France; (S.C.); (C.R.); (L.A.)
| | - Romain Boidot
- Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France; (S.C.); (C.R.); (L.A.)
- UMR CNRS 6302, University of Burgundy, 21079 Dijon, France
- Correspondence: ; Tel.: +33-3-80-73-77-67; Fax: +33-3-80-73-77-82
| |
Collapse
|
20
|
Singh HM, Bailey P, Hübschmann D, Berger AK, Neoptolemos JP, Jäger D, Siveke J, Springfeld C. Poly(ADP-ribose) polymerase inhibition in pancreatic cancer. Genes Chromosomes Cancer 2021; 60:373-384. [PMID: 33341987 DOI: 10.1002/gcc.22932] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited treatment options. Recently, the poly(ADP-ribose) polymerase inhibitor (PARPi) olaparib has been approved for maintenance therapy after successful platinum-based chemotherapy in patients with germline mutations in BRCA1 and BRCA2. Approval was based on the POLO study that has shown a significant improvement in progression-free survival for patients with metastatic PDAC after at least 4 months of platinum-based chemotherapy. Hopefully, this first biomarker-directed targeted therapy for a relevant subgroup of pancreatic cancer patients is only the beginning of an era of personalized therapy for pancreatic cancer. The potential role for PARPi in improving survival in patients with pancreatic cancer containing somatic tumor mutations has yet to be established. Multiple studies investigating whether PARPi therapy might benefit a larger group of pancreatic cancer patients with homologous recombination repair deficiency and whether combinations with chemotherapy, immunotherapy, or small molecules can improve efficacy are currently underway. We here review the molecular basis for PARPi therapy in PDAC patients and recent developments in clinical studies.
Collapse
Affiliation(s)
- Hans Martin Singh
- Department of Medical Oncology, Heidelberg University Hospital, National Center for Tumor Diseases, Heidelberg, Germany
| | - Peter Bailey
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.,Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Hübschmann
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Institute for Stem cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Immunology, Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anne Katrin Berger
- Department of Medical Oncology, Heidelberg University Hospital, National Center for Tumor Diseases, Heidelberg, Germany
| | - John P Neoptolemos
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology, Heidelberg University Hospital, National Center for Tumor Diseases, Heidelberg, Germany
| | - Jens Siveke
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site University Hospital Essen) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Springfeld
- Department of Medical Oncology, Heidelberg University Hospital, National Center for Tumor Diseases, Heidelberg, Germany
| |
Collapse
|
21
|
Lerksuthirat T, Wikiniyadhanee R, Chitphuk S, Stitchantrakul W, Sampattavanich S, Jirawatnotai S, Jumpathong J, Dejsuphong D. DNA Repair Biosensor-Identified DNA Damage Activities of Endophyte Extracts from Garcinia cowa. Biomolecules 2020; 10:E1680. [PMID: 33339185 PMCID: PMC7765599 DOI: 10.3390/biom10121680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 12/03/2022] Open
Abstract
Recent developments in chemotherapy focus on target-specific mechanisms, which occur only in cancer cells and minimize the effects on normal cells. DNA damage and repair pathways are a promising target in the treatment of cancer. In order to identify novel compounds targeting DNA repair pathways, two key proteins, 53BP1 and RAD54L, were tagged with fluorescent proteins as indicators for two major double strand break (DSB) repair pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). The engineered biosensor cells exhibited the same DNA repair properties as the wild type. The biosensor cells were further used to investigate the DNA repair activities of natural biological compounds. An extract from Phyllosticta sp., the endophyte isolated from the medicinal plant Garcinia cowa Roxb. ex Choisy, was tested. The results showed that the crude extract induced DSB, as demonstrated by the increase in the DNA DSB marker γH2AX. The damaged DNA appeared to be repaired through NHEJ, as the 53BP1 focus formation in the treated fraction was higher than in the control group. In conclusion, DNA repair-based biosensors are useful for the preliminary screening of crude extracts and biological compounds for the identification of potential targeted therapeutic drugs.
Collapse
Affiliation(s)
- Tassanee Lerksuthirat
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (S.C.); (W.S.)
| | - Rakkreat Wikiniyadhanee
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Sermsiri Chitphuk
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (S.C.); (W.S.)
| | - Wasana Stitchantrakul
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.L.); (S.C.); (W.S.)
| | - Somponnat Sampattavanich
- Siriraj Center of Research for Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.J.)
| | - Siwanon Jirawatnotai
- Siriraj Center of Research for Excellence (SiCORE) for Systems Pharmacology, Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.J.)
| | - Juangjun Jumpathong
- Center of Excellent in Research for Agricultural Biotechnology and Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand
| | - Donniphat Dejsuphong
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| |
Collapse
|
22
|
Fan Y, Ying H, Wu X, Chen H, Hu Y, Zhang H, Wu L, Yang Y, Mao B, Zheng L. The mutational pattern of homologous recombination (HR)-associated genes and its relevance to the immunotherapeutic response in gastric cancer. Cancer Biol Med 2020; 17:1002-1013. [PMID: 33299649 PMCID: PMC7721103 DOI: 10.20892/j.issn.2095-3941.2020.0089] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/19/2020] [Indexed: 12/24/2022] Open
Abstract
Objective: Currently, there is an urgent need to identify immunotherapeutic biomarkers to increase the benefit of immune checkpoint inhibitors (ICIs) for patients with gastric cancer (GC). Homologous recombination deficiency (HRD) can modify the tumor immune microenvironment by increasing the presence of tumor-infiltrating lymphocytes and therefore might serve as a biomarker of immunotherapeutic response. We aimed to analyze the mutational pattern of HR-associated genes in Chinese patients with GC and its relevance to the tumor immune profile and clinical immunotherapeutic response. Methods: A panel of 543 cancer-associated genes was used to analyze genomic profiles in a cohort comprising 484 Chinese patients with GC. Correlations between HR gene mutations and tumor immunity or clinical outcomes were identified via bioinformatic analysis using 2 GC genomic datasets (TCGA and MSK-IMPACT). Results: Fifty-one of the 484 (10.54%) patients carried at least one somatic mutation in an HR gene; ATM (16/484, 3.31%) was among the most frequently mutated HR genes in the Chinese cohort. Mutations in HR genes were associated with elevated tumor mutational burden, enhanced immune activity, and microsatellite instability status. In the MSK-IMPACT cohort comprising 49 patients with stomach adenocarcinoma or gastroesophageal junction adenocarcinoma treated with ICIs, patients with HR-mut GC (n = 12) had significantly better overall survival than those with HR-wt GC (n = 37) (log-rank test, P < 0.05). Conclusions: Our data suggest that detection of somatic mutations in HR genes might aid in identifying patients who might benefit from immune checkpoint blockade therapy.
Collapse
Affiliation(s)
- Yue Fan
- Department of integrated Traditional Chinese Medicine and Western Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Haifeng Ying
- Department of Traditional Chinese Medicine, Ruijin Hospital, Shanghai Jiaotong University, Shanghai 200025, China
| | - Xueying Wu
- Genecast Precision Medicine Technology Institute, Beijing 100191, China
| | - Huan Chen
- Genecast Precision Medicine Technology Institute, Beijing 100191, China
| | - Ying Hu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Henghui Zhang
- Genecast Precision Medicine Technology Institute, Beijing 100191, China
| | - Lijia Wu
- Genecast Precision Medicine Technology Institute, Beijing 100191, China
| | - Ying Yang
- Genecast Precision Medicine Technology Institute, Beijing 100191, China
| | - Beibei Mao
- Genecast Precision Medicine Technology Institute, Beijing 100191, China
| | - Lan Zheng
- Department of Traditional Chinese Medicine, Ruijin Hospital, Shanghai Jiaotong University, Shanghai 200025, China
| |
Collapse
|
23
|
Hays E, Nettleton E, Carter C, Morales M, Vo L, Passo M, Vélez-Cruz R. The SWI/SNF ATPase BRG1 stimulates DNA end resection and homologous recombination by reducing nucleosome density at DNA double strand breaks and by promoting the recruitment of the CtIP nuclease. Cell Cycle 2020; 19:3096-3114. [PMID: 33044911 PMCID: PMC7714457 DOI: 10.1080/15384101.2020.1831256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA double strand breaks (DSBs) are among the most toxic DNA lesions and can be repaired accurately through homologous recombination (HR). HR requires processing of the DNA ends by nucleases (DNA end resection) in order to generate the required single-stranded DNA (ssDNA) regions. The SWI/SNF chromatin remodelers are 10–15 subunit complexes that contain one ATPase (BRG1 or BRM). Multiple subunits of these complexes have recently been identified as a novel family of tumor suppressors. These complexes are capable of remodeling chromatin by pushing nucleosomes along the DNA. More recent studies have identified these chromatin remodelers as important factors in DNA repair. Using the DR-U2OS reporter system, we show that the down regulation of BRG1 significantly reduces HR efficiency, while BRM has a minor effect. Inactivation of BRG1 impairs DSB repair and results in a defect in DNA end resection, as measured by the amount of BrdU-containing ssDNA generated after DNA damage. Inactivation of BRG1 also impairs the activation of the ATR kinase, reduces the levels of chromatin-bound RPA, and reduces the number of RPA and RAD51 foci after DNA damage. This defect in DNA end resection is explained by the defective recruitment of GFP-CtIP to laser-induced DSBs in the absence of BRG1. Importantly, we show that BRG1 reduces nucleosome density at DSBs. Finally, inactivation of BRG1 renders cells sensitive to anti-cancer drugs that induce DSBs. This study identifies BRG1 as an important factor for HR, which suggests that BRG1-mutated cancers have a DNA repair vulnerability that can be exploited therapeutically.
Collapse
Affiliation(s)
- Emily Hays
- Department of Biochemistry and Molecular Genetics, Midwestern University , Downers Grove, IL, USA.,College of Graduate Studies, Midwestern University , Downers Grove, IL, USA
| | - Elizabeth Nettleton
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Caitlin Carter
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Mariangel Morales
- College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Biomedical Sciences Program, Midwestern University , Downers Grove, IL, USA
| | - Lynn Vo
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Max Passo
- College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Biomedical Sciences Program, Midwestern University , Downers Grove, IL, USA
| | - Renier Vélez-Cruz
- Department of Biochemistry and Molecular Genetics, Midwestern University , Downers Grove, IL, USA.,College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Chicago College of Optometry, Midwestern University , Downers Grove, IL, USA
| |
Collapse
|
24
|
Guo L, Li Y, Zhao C, Peng J, Song K, Chen L, Zhang P, Ma H, Yuan C, Yan S, Fang Y, Kong B. RECQL4, Negatively Regulated by miR-10a-5p, Facilitates Cell Proliferation and Invasion via MAFB in Ovarian Cancer. Front Oncol 2020; 10:524128. [PMID: 33014878 PMCID: PMC7500455 DOI: 10.3389/fonc.2020.524128] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022] Open
Abstract
The high frequency of somatic copy number alterations, as opposed to point mutations, is considered a unique feature of ovarian cancer. Amplification-dependent overexpression of RecQ protein-like 4 (RECQL4), which participates in DNA replication and repair, mediates the development of various cancers, but its pathobiological and clinical roles are poorly understood. Here, using bioinformatics analysis, RECQL4 amplification was found to occur in 27% of ovarian cancer samples in the TCGA cohort. RECQL4 was found to be upregulated and associated with a poor prognosis based on the immunohistochemistry staining of ovarian cancer. Functionally, RECQL4 overexpression increased proliferation and invasion of ovarian cancer cells. RECQL4 silencing had the opposite effects. In addition, RECQL4 knockdown enhanced the sensitivity of ovarian cancer cells to cisplatin and PARP inhibitor (PARPi). Further mechanistic investigations revealed that MAFB was a downstream target of RECQL4. The oncogenic effect of RECQL4 was attenuated after MAFB knockdown. Moreover, RECQL4 overexpression was negatively regulated by the tumor suppressor miR-10a-5p. Collectively, these findings indicate that genomic amplification and low expression of miR-10a-5p contribute to RECQL4 overexpression in ovarian cancer. This is the first study to reveal the oncogenic functions and clinical significance of RECQL4 in ovarian cancer.
Collapse
Affiliation(s)
- Li Guo
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Obstetrics and Gynecology, Qingdao Municipal Hospital, Shandong University, Qingdao, China
| | - Yingwei Li
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chen Zhao
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiali Peng
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Long Chen
- Department of Obstetrics and Gynecology, Qingdao Municipal Hospital, Shandong University, Qingdao, China
| | - Ping Zhang
- Department of Obstetrics and Gynecology, Qingdao Municipal Hospital, Shandong University, Qingdao, China
| | - Hanlin Ma
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shi Yan
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yan Fang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| |
Collapse
|
25
|
Agiannitopoulos K, Papadopoulou E, Tsaousis GN, Pepe G, Kampouri S, Patsea E, Lypas G, Nasioulas G. Report of a germline double heterozygote in MSH2 and PALB2. Mol Genet Genomic Med 2020; 8:e1242. [PMID: 32853479 PMCID: PMC7549547 DOI: 10.1002/mgg3.1242] [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: 07/31/2019] [Revised: 03/17/2020] [Accepted: 03/20/2020] [Indexed: 12/22/2022] Open
Abstract
Background Carriers with pathogenic variants in MSH2 have increased risk to develop colorectal, endometrium, ovarian, and other types of cancer. The PALB2 is associated with breast, ovarian, pancreatic, and prostate cancer. We describe the case of a 42‐year‐old female diagnosed with endometrial cancer at the age of 42 years with a strong family history of colorectal cancer, which was referred to our private diagnostic laboratory for genetic testing. Methods In this study, we performed next‐generation sequencing (NGS) using an amplicon based 26 genes panel. The presence of multi‐exonic copy number variations (CNVs) was investigated by computational analysis and Multiplex Ligation‐dependent Probe Amplification (MLPA). Results A gross deletion of the genomic region encompassing exons 11–16 of the MSH2 and the loss‐of‐function variant c.757_758delCT, p.(Leu253Ilefs*3) in the PALB2 were identified in the proband. Conclusions Multigene analysis using NGS technology allows the identification of pathogenic variants in genes that would normally not be tested based on the patient diagnosis. In our case these results explained not only the personal and/or family history of cancer but also allowed the surveillance for prevention of other cancer types. Moreover, the detection of large genomic rearrangements should be routinely included in hereditary cancer testing.
Collapse
Affiliation(s)
| | | | | | | | | | - Eleni Patsea
- Department of Pathology, IASSO General Hospital, Athens, Greece
| | - George Lypas
- Department of Genetic Oncology/Medical Oncology, Hygeia Hospital, Athens, Greece
| | | |
Collapse
|
26
|
Santana dos Santos E, Lallemand F, Petitalot A, Caputo SM, Rouleau E. HRness in Breast and Ovarian Cancers. Int J Mol Sci 2020; 21:E3850. [PMID: 32481735 PMCID: PMC7312125 DOI: 10.3390/ijms21113850] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian and breast cancers are currently defined by the main pathways involved in the tumorigenesis. The majority are carcinomas, originating from epithelial cells that are in constant division and subjected to cyclical variations of the estrogen stimulus during the female hormonal cycle, therefore being vulnerable to DNA damage. A portion of breast and ovarian carcinomas arises in the context of DNA repair defects, in which genetic instability is the backdrop for cancer initiation and progression. For these tumors, DNA repair deficiency is now increasingly recognized as a target for therapeutics. In hereditary breast/ovarian cancers (HBOC), tumors with BRCA1/2 mutations present an impairment of DNA repair by homologous recombination (HR). For many years, BRCA1/2 mutations were only screened on germline DNA, but now they are also searched at the tumor level to personalize treatment. The reason of the inactivation of this pathway remains uncertain for most cases, even in the presence of a HR-deficient signature. Evidence indicates that identifying the mechanism of HR inactivation should improve both genetic counseling and therapeutic response, since they can be useful as new biomarkers of response.
Collapse
Affiliation(s)
- Elizabeth Santana dos Santos
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800 Villejuif, France;
- Department of Clinical Oncology, A.C. Camargo Cancer Center, São Paulo 01509-010, Brazil
| | - François Lallemand
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Sandrine M. Caputo
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800 Villejuif, France;
| |
Collapse
|
27
|
Guerreiro IM, Barros-Silva D, Lopes P, Cantante M, Cunha AL, Lobo J, Antunes L, Rodrigues A, Soares M, Henrique R, Jerónimo C. RAD51Bme Levels as a Potential Predictive Biomarker for PD-1 Blockade Response in Non-Small Cell Lung Cancer. J Clin Med 2020; 9:jcm9041000. [PMID: 32252414 PMCID: PMC7230458 DOI: 10.3390/jcm9041000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Lung cancer (LC) cells frequently express high levels of programmed death-ligand 1 (PD-L1). Although these levels grossly correlate with the likelihood of response to specific checkpoint inhibitors, the response prediction is rather imperfect, and more accurate predictive biomarkers are mandatory. We examined the methylation profile of RAD51B (RAD51Bme) as a candidate predictive biomarker for anti-PD-1 therapy efficacy in non-small cell lung cancer (NSCLC), correlating with patients’ outcome. PD-L1 immunoexpression and RAD51Bme levels were analysed in NSCLC samples obtained from patients not treated with anti-PD-1 (Untreated Cohort (#1)) and patients treated with PD-1 blockade (Treated Cohort (#2)). Of a total of 127 patients assessed, 58.3% depicted PD-L1 positivity (PD-L1+). RAD51Bme levels were significantly associated with PD-L1 immunoexpression. Patients with PD-1 blockade clinical benefit disclosed higher RAD51Bme levels (p = 0.0390) and significantly lower risk of disease progression (HR 0.37; 95% CI: 0.15–0.88; p = 0.025). Combining RAD51Bme+ with PD-L1+ improved the sensitivity of the test to predict immunotherapy response. PD-L1+ was also associated with lower risk of death (HR 0.35; 95% CI: 0.15–0.81; p = 0.014). Thus, RAD51Bme levels might be combined with validated predictive biomarker PD-L1 immunostaining to select patients who will most likely experience clinical benefit from PD-1 blockade. The predictive value of RAD51Bme should be confirmed in prospective studies.
Collapse
Affiliation(s)
- Inês Maria Guerreiro
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
- Correspondence: (I.M.G.); (C.J.); Tel.: +351-225-084-000 (I.M.G.); Fax: +351-225-084-001 (I.M.G.)
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
| | - Paula Lopes
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Mariana Cantante
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Ana Luísa Cunha
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Luís Antunes
- Cancer Epidemiology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
| | - Ana Rodrigues
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
| | - Marta Soares
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Correspondence: (I.M.G.); (C.J.); Tel.: +351-225-084-000 (I.M.G.); Fax: +351-225-084-001 (I.M.G.)
| |
Collapse
|
28
|
Identification of miR-210 and combination biomarkers as useful agents in early screening non-small cell lung cancer. Gene 2020; 729:144225. [DOI: 10.1016/j.gene.2019.144225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/07/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022]
|
29
|
YARS as an oncogenic protein that promotes gastric cancer progression through activating PI3K-Akt signaling. J Cancer Res Clin Oncol 2020; 146:329-342. [PMID: 31912229 PMCID: PMC6985085 DOI: 10.1007/s00432-019-03115-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Members of the aaRS (aminoacyl-tRNA synthetase) family are proteins controlling the aminoacylation process, in which YARS (tyrosyl-tRNA synthetase) catalyzes the binding of tyrosine to its cognate tRNA and plays an important role in basic biosynthesis. Several studies have demonstrated the association between YARS mutation and certain developmental abnormalities/diseases, yet YARS's linkage with cancer remains uncategorized. In this study, by combining in silico, in vitro, and in vivo studies, we explored the expressions and functions of YARS in gastric cancer (GC). METHODS We evaluated YARS's distribution in tumor and paired normal tissues/specimens of GC by referring to large cohort online datasets and patient-derived tissue specimens. YARS-related changes were assessed by phenotypical/molecular experiments and RNA-sequencing analysis in GC cell lines harboring YARS knockdown or overexpression. RESULTS Both the transcript and protein levels of YARS were evidently higher in gastric cancer tissues than in paired normal tissues. YARS knockdown induced repressed proliferation and invasiveness, as well as enhanced apoptosis in GC cell lines, while abnormally upregulating YARS expression promoted gastric cancer growth in vivo. We inferred based on RNA-sequencing that YARS modulates multiple cancerous signaling pathways and proved through cellular experiments that YARS promoted GC progression, as well as homologous recombination by activating PI3K-Akt signaling. CONCLUSIONS By revealing the existence of a YARS-PI3K-Akt signaling axis in gastric cancer, we discovered that tRNA synthetase YARS is a novel tumorigenic factor, characterized by its upregulation in tumor-derived specimens, as well as its functions in promoting gastric cancer progression.
Collapse
|
30
|
Li P, Xu Y, Zhang Q, Li Y, Jia W, Wang X, Xie Z, Liu J, Zhao D, Shao M, Chen S, Mo N, Jiang Z, Li L, Liu R, Huang W, Chang L, Chen S, Li H, Zuo W, Li J, Zhang R, Yang X. Evaluating the role of RAD52 and its interactors as novel potential molecular targets for hepatocellular carcinoma. Cancer Cell Int 2019; 19:279. [PMID: 31719794 PMCID: PMC6836504 DOI: 10.1186/s12935-019-0996-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
Background Radiation sensitive 52 (RAD52) is an important protein that mediates DNA repair in tumors. However, little is known about the impact of RAD52 on hepatocellular carcinoma (HCC). We investigated the expression of RAD52 and its values in HCC. Some proteins that might be coordinated with RAD52 in HCC were also analyzed. Methods Global RAD52 mRNA levels in HCC were assessed using The Cancer Genome Atlas (TCGA) database. RAD52 expression was analyzed in 70 HCC tissues and adjacent tissues by quantitative real-time PCR (qRT-PCR), Western blotting and immunohistochemistry. The effect of over-expressed RAD52 in Huh7 HCC cells was investigated. The String database was then used to perform enrichment and functional analysis of RAD52 and its interactome. Cytoscape software was used to create a protein–protein interaction network. Molecular interaction studies with RAD52 and its interactome were performed using the molecular docking tools in Hex8.0.0. Finally, these DNA repair proteins, which interact with RAD52, were also analyzed using the TCGA dataset and were detected by qRT-PCR. Based on the TCGA database, algorithms combining ROC between RAD52 and RAD52 interactors were used to diagnose HCC by binary logistic regression. Results In TCGA, upregulated RAD52 related to gender was obtained in HCC. The area under the receiver operating characteristic curve (AUC) of RAD52 was 0.704. The results of overall survival (OS) and recurrence-free survival (RFS) indicated no difference in the prognosis between patients with high and low RAD52 gene expression. We validated that RAD52 expression was increased at the mRNA and protein levels in Chinese HCC tissues compared with adjacent tissues. Higher RAD52 was associated with older age, without correlation with other clinicopathological factors. In vitro, over-expressed RAD52 significantly promoted the proliferation and migration of Huh7 cells. Furthermore, RAD52 interactors (radiation sensitive 51, RAD51; X-ray repair cross complementing 6, XRCC6; Cofilin, CFL1) were also increased in HCC and participated in some biological processes with RAD52. Protein structure analysis showed that RAD52–RAD51 had the firmest binding structure with the lowest E-total energy (− 1120.5 kcal/mol) among the RAD52–RAD51, RAD52–CFL1, and RAD52–XRCC6 complexes. An algorithm combining ROC between RAD52 and its interactome indicated a greater specificity and sensitivity for HCC screening. Conclusions Overall, our study suggested that RAD52 plays a vital role in HCC pathogenesis and serves as a potential molecular target for HCC diagnosis and treatment. This study’s findings regarding the multigene prediction and diagnosis of HCC are valuable.
Collapse
Affiliation(s)
- Ping Li
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China.,4College & Hospital of Stomatology Guangxi Medical University, Nanning, Guangxi China.,5Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi China
| | - YanZhen Xu
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China.,8Department of Pathophysiology, Guangxi Medical University, Nanning, Guangxi China
| | - Qinle Zhang
- Genetic and Metabolic Central Laboratory, The Maternal and Children Health Hospital of Guangxi, Guangxi, China
| | - Yu Li
- Medical Science Laboratory at Liuzhou Worker's Hospital, Liuzhou, Guangxi China
| | - Wenxian Jia
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China.,6College of Pharmacy, Guangxi Medical University, Nanning, Guangxi China
| | - Xiao Wang
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Zhibin Xie
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China
| | - Jiayi Liu
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China.,4College & Hospital of Stomatology Guangxi Medical University, Nanning, Guangxi China.,5Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi China
| | - Dong Zhao
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China
| | - Mengnan Shao
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China
| | - Suixia Chen
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China.,8Department of Pathophysiology, Guangxi Medical University, Nanning, Guangxi China
| | - Nanfang Mo
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Zhiwen Jiang
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Liuyan Li
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Run Liu
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Wanying Huang
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Li Chang
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Siyu Chen
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Hongtao Li
- 2Scientific Research Center, Guilin Medical University, Guilin, Guangxi China
| | - Wenpu Zuo
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | - Jiaquan Li
- 3Medical Scientific Research Center, Guangxi Medical University, Nanning, Guangxi China
| | | | - Xiaoli Yang
- 1Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, Guangxi China.,2Scientific Research Center, Guilin Medical University, Guilin, Guangxi China
| |
Collapse
|
31
|
A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity. Genes (Basel) 2019; 10:genes10100770. [PMID: 31575041 PMCID: PMC6826991 DOI: 10.3390/genes10100770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Knowledge about synthetic lethality can be applied to enhance the efficacy of anticancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug–gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct antitumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in the Saccharomyces cerevisiae genomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug–gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug–gene interaction specific to cytarabine was less enriched in gene ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-gene ontology (GO)-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast–human homologs with correlated differential gene expression and drug efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
Collapse
|
32
|
Liu L, Bai X, Wang J, Tang XR, Wu DH, Du SS, Du XJ, Zhang YW, Zhu HB, Fang Y, Guo ZQ, Zeng Q, Guo XJ, Liu Z, Dong ZY. Combination of TMB and CNA Stratifies Prognostic and Predictive Responses to Immunotherapy Across Metastatic Cancer. Clin Cancer Res 2019; 25:7413-7423. [PMID: 31515453 DOI: 10.1158/1078-0432.ccr-19-0558] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/17/2019] [Accepted: 09/05/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Although tumor mutation burden (TMB) has been well known to predict the response to immune checkpoint inhibitors (ICI), lack of randomized clinical trial data has restricted its clinical application. This study aimed to explore the significance and feasibility of biomarker combination based on TMB and copy-number alteration (CNA) for the prognosis of each tumor and prediction for ICI therapy in metastatic pan-cancer milieu. EXPERIMENTAL DESIGN Non-ICI-treated MSK pan-cancer cohort was used for prognosis analysis. Three independent immunotherapy cohorts, including non-small cell lung cancer (n = 240), skin cutaneous melanoma (n = 174), and mixed cancer (Dana-Farber, n = 98) patients from previous studies, were analyzed for efficacy of ICI therapy. RESULTS TMB and CNA showed optimized combination for the prognosis of most metastatic cancer types, and patients with TMBlowCNAlow showed better survival. In the predictive analysis, both TMB and CNA were independent predictive factors for ICI therapy. Remarkably, when TMB and CNA were jointly analyzed, those with TMBhighCNAlow showed favorable responses to ICI therapy. Meanwhile, TMBhighCNAlow as a new biomarker showed better prediction for ICI efficacy compared with either TMB-high or CNA-low alone. Furthermore, analysis of the non-ICI-treated MSK pan-cancer cohort supported that the joint stratification of TMB and CNA can be used to categorize tumors into distinct sensitivity to ICI therapy across pan-tumors. CONCLUSIONS The combination of TMB and CNA can jointly stratify multiple metastatic tumors into groups with different prognosis and heterogeneous clinical responses to ICI treatment. Patients with TMBhighCNAlow cancer can be an optimal subgroup for ICI therapy.
Collapse
Affiliation(s)
- Li Liu
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xue Bai
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xin-Ran Tang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - De-Hua Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sha-Sha Du
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiu-Ju Du
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yao-Wei Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hong-Bo Zhu
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuan Fang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ze-Qin Guo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qin Zeng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xue-Jun Guo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhu Liu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhong-Yi Dong
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| |
Collapse
|
33
|
Gourley C, Balmaña J, Ledermann JA, Serra V, Dent R, Loibl S, Pujade-Lauraine E, Boulton SJ. Moving From Poly (ADP-Ribose) Polymerase Inhibition to Targeting DNA Repair and DNA Damage Response in Cancer Therapy. J Clin Oncol 2019; 37:2257-2269. [PMID: 31050911 DOI: 10.1200/jco.18.02050] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The DNA damage response (DDR) pathway coordinates the identification, signaling, and repair of DNA damage caused by endogenous or exogenous factors and regulates cell-cycle progression with DNA repair to minimize DNA damage being permanently passed through cell division. Severe DNA damage that cannot be repaired may trigger apoptosis; as such, the DDR pathway is of crucial importance as a cancer target. Poly (ADP-ribose) polymerase (PARP) is the best-known element of the DDR, and several PARP inhibitors have been licensed. However, there are approximately 450 proteins involved in DDR, and a number of these other targets are being investigated in the laboratory and clinic. We review the most recent evidence for the clinical effect of PARP inhibition in breast and ovarian cancer and explore expansion into the first-line setting and into other tumor types. We critique the evidence for patient selection techniques and summarize what is known about mechanisms of PARP inhibitor resistance. We then discuss what is known about the preclinical rationale for targeting other members of the DDR pathway and the associated tumor cell genetics that may confer sensitivity to these agents. Examples include DNA damage sensors (MLH1), damage signaling molecules (ataxia-telangiectasia mutated; ataxia-telangiectasia mutated-related and Rad3-related; CHK1/2; DNA-dependent protein kinase, catalytic subunit; WEE1; CDC7), or effector proteins for repair (POLQ [also referred to as POLθ], RAD51, poly [ADP-ribose] glycohydrolase). Early-phase clinical trials targeting some of these molecules, either as a single agent or in combination, are discussed. Finally, we outline the challenges that must be addressed to maximize the therapeutic opportunity that targeting DDR provides.
Collapse
Affiliation(s)
- Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Judith Balmaña
- Vall d'Hebron University Hospital, Barcelona, Spain.,Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Violeta Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Rebecca Dent
- National Cancer Center and Duke - NUS Medical School, Singapore, Singapore
| | | | | | - Simon J Boulton
- The Francis Crick Institute, London, United Kingdom.,Artios Pharma, Cambridge, United Kingdom
| |
Collapse
|
34
|
Next Generation Sequencing (NGS): A Revolutionary Technology in Pharmacogenomics and Personalized Medicine in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1168:9-30. [DOI: 10.1007/978-3-030-24100-1_2] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
35
|
Complexity of genome sequencing and reporting: Next generation sequencing (NGS) technologies and implementation of precision medicine in real life. Crit Rev Oncol Hematol 2018; 133:171-182. [PMID: 30661654 DOI: 10.1016/j.critrevonc.2018.11.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/23/2018] [Indexed: 12/17/2022] Open
Abstract
The finalization of the Human Genome Project in 2003 paved the way for a deeper understanding of cancer, favouring a faster progression towards "personalized" medicine. Research in oncology has progressively focused on the sequencing of cancer genomes, to better understand the genetic basis of tumorigenesis and identify actionable alterations to guide cancer therapy. Thanks to the development of next-generation-sequencing (NGS) techniques, sequencing of tumoral DNA is today technically easier, faster and cheaper. Commercially available NGS panels enable the detection of single or global genomic alterations, namely gene mutation and mutagenic burden, both on germline and somatic DNA, potentially predicting the response or resistance to cancer treatments. Profiling of tumor DNA is nowadays a standard in cancer research and treatment. In this review we discuss the history, techniques and applications of NGS in cancer care, under a "personalized tailored therapy" perspective.
Collapse
|
36
|
Fei Z, Gu W, Xie R, Su H, Jiang Y. Artesunate enhances radiosensitivity of esophageal cancer cells by inhibiting the repair of DNA damage. J Pharmacol Sci 2018; 138:131-137. [PMID: 30337244 DOI: 10.1016/j.jphs.2018.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 08/16/2018] [Accepted: 09/20/2018] [Indexed: 01/24/2023] Open
Abstract
Radiotherapy plays an important therapeutic role in esophageal cancer (EC). However, acquired radioresistance impairs the efficacy of radiotherapy, often leading to treatment failure. Therefore, it is important to develop novel radiosensitizers to enhance the clinical treatment of EC. The purpose of this study was to investigate the role of artesunate (ART) on radiosensitivity of human EC cell line TE-1. We found that ART inhibited the proliferation of EC cells and enhanced the radiosensitivity of TE-1 cells (SER = 1.24). In vivo tumor growth of xenografts was inhibited markedly by irradiation (IR) combined with ART, with a tumor inhibition rate of 53.76% in IR + ART group vs. 41.13% in IR-alone group. Pretreatment with ART significantly prompted cell apoptosis and reversed the IR-induced G2/M arrest. ART treatment could aggravate DNA damage of EC cells and prolong the formation of γ-H2AX foci induced by IR. ART up-regulated P21 and down-regulated the expression of cyclin D1, RAD51, RAD54, Ku70 and Ku86 protein of irradiated TE-1 cells. These findings support that ART induce radiosensitivity of TE-1 cells in vitro and in vivo, and may prove to be a promising radiosensitizer for EC treatment.
Collapse
Affiliation(s)
- Zhenhua Fei
- Department of Oncology, The 1st Affiliated Hospital of Wenzhou Medical University, No.2 Fuxue Lane, Wenzhou, Zhejiang, 325000, PR China
| | - Wenyue Gu
- Department of Pathology, Yancheng Hospital Affiliated Southeast University, No.2 Xingdu Road, Yancheng, Jiangsu, 224000, PR China
| | - Raoying Xie
- Department of Oncology, The 1st Affiliated Hospital of Wenzhou Medical University, No.2 Fuxue Lane, Wenzhou, Zhejiang, 325000, PR China
| | - Huafang Su
- Department of Oncology, The 1st Affiliated Hospital of Wenzhou Medical University, No.2 Fuxue Lane, Wenzhou, Zhejiang, 325000, PR China
| | - Yiyan Jiang
- Department of Tumor Rehabilitation, The 1st Affiliated Hospital of Wenzhou Medical University, No.2 Fuxue Lane, Wenzhou, Zhejiang Province, 325000, China.
| |
Collapse
|
37
|
Wang R, Li Y, Chen Y, Wang L, Wu Q, Guo Y, Li Y, Liu J, Wang L. Inhibition of RAD54B suppresses proliferation and promotes apoptosis in hepatoma cells. Oncol Rep 2018; 40:1233-1242. [PMID: 29956808 PMCID: PMC6072389 DOI: 10.3892/or.2018.6522] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/15/2018] [Indexed: 01/20/2023] Open
Abstract
RAD54 homolog B is a central motor protein of homologous recombination (HR), which plays an important role in the development and evolution of human cancer. Recent studies have indicated that RAD54B is aberrantly expressed in a variety of cancers and exhibits numerous biological functions, including participating in the repair of DNA double strand breaks. However, the expression and function of RAD54B in liver cancer have not yet been reported. The aim of the present study was to investigate the expression of RAD54B and elucidate its role in liver cancer cell lines by inhibiting RAD54B using a lentivirus-mediated shRNA interference system. We also assessed the effect of RAD54B on cell proliferation, colony formation, cell cycle distribution and cell apoptosis in BEL-7404 and SMMC-7721 cell lines using shRAD54B or shCtrl transfection. Furthermore, we analyzed the relationship between the expression of RAD54B protein, as measured by immunohistochemical staining, and the prognosis of patients with hepatoma. We found that RAD54B was highly expressed in liver cancer cell lines compared with the normal hepatic cell line LO2. Similarly, positive expression of RAD54B, which is associated with poor prognosis, was also observed in 52/83 samples of liver cancer tissue. Additionally, RAD54B downregulation significantly inhibited cell proliferation and colony formation, while also inducing G1/S cell cycle arrest and apoptosis in BEL-7404 and SMMC-7721 cells. These results indicated that RAD54B has oncogenic properties, and may be a potential treatment target for liver cancer patients.
Collapse
Affiliation(s)
- Rui Wang
- Department of Oncology, Shanghai General Hospital of Nanjing Medical University, Shanghai 201620, P.R. China
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yawei Li
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yufo Chen
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Lei Wang
- Department of Oncology, Shanghai General Hospital of Nanjing Medical University, Shanghai 201620, P.R. China
| | - Qiong Wu
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yuanyuan Guo
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yumei Li
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Jing Liu
- Department of Medical Oncology, First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Liwei Wang
- Department of Oncology, Shanghai General Hospital of Nanjing Medical University, Shanghai 201620, P.R. China
| |
Collapse
|
38
|
Lieberman HB, Rai AJ, Friedman RA, Hopkins KM, Broustas CG. Prostate cancer: unmet clinical needs and RAD9 as a candidate biomarker for patient management. Transl Cancer Res 2018; 7:S651-S661. [PMID: 30079300 PMCID: PMC6071673 DOI: 10.21037/tcr.2018.01.21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Prostate cancer is a complex disease, with multiple subtypes and clinical presentations. Much progress has been made in recent years to understand the underlying genetic basis that drives prostate cancer. Such mechanistic information is useful for development of novel therapeutic targets, to identify biomarkers for early detection or to distinguish between aggressive and indolent disease, and to predict treatment outcome. Multiple tests have become available in recent years to address these clinical needs for prostate cancer. We describe several of these assays, summarizing test details, performance characteristics, and acknowledging their limitations. There is a pressing unmet need for novel biomarkers that can demonstrate improvement in these areas. We introduce one such candidate biomarker, RAD9, describe its functions in the DNA damage response, and detail why it can potentially fill this void. RAD9 has multiple roles in prostate carcinogenesis, making it potentially useful as a clinical tool for men with prostate cancer. RAD9 was originally identified as a radioresistance gene, and subsequent investigations revealed several key functions in the response of cells to DNA damage, including involvement in cell cycle checkpoint control, at least five DNA repair pathways, and apoptosis. Further studies indicated aberrant overexpression in approximately 45% of prostate tumors, with a strong correlation between RAD9 abundance and cancer stage. A causal relationship between RAD9 and prostate cancer was first demonstrated using a mouse model, where tumorigenicity of human prostate cancer cells after subcutaneous injection into nude mice was diminished when RNA interference was used to reduce the normally high levels of the protein. In addition to activity needed for the initial development of tumors, cell culture studies indicated roles for RAD9 in promoting prostate cancer progression by controlling cell migration and invasion through regulation of ITGB1 protein levels, and anoikis resistance by modulating AKT activation. Furthermore, RAD9 enhances the resistance of human prostate cancer cells to radiation in part by regulating ITGB1 protein abundance. RAD9 binds androgen receptor and inhibits androgen-induced androgen receptor's activity as a transcription factor. Moreover, RAD9 also acts as a gene-specific transcription factor, through binding p53 consensus sequences at target gene promoters, and this likely contributes to its oncogenic activity. Given these diverse and extensive activities, RAD9 plays important roles in the initiation and progression of prostate cancer and can potentially serve as a valuable biomarker useful in the management of patients with this disease.
Collapse
Affiliation(s)
- Howard B. Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Alex J. Rai
- Department of Pathology and Cell Biology and Special Chemistry Laboratories, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA
| | - Richard A. Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center and Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Kevin M. Hopkins
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Constantinos G. Broustas
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, NY, USA
| |
Collapse
|
39
|
Ovarian Cancers: Genetic Abnormalities, Tumor Heterogeneity and Progression, Clonal Evolution and Cancer Stem Cells. MEDICINES 2018; 5:medicines5010016. [PMID: 29389895 PMCID: PMC5874581 DOI: 10.3390/medicines5010016] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 02/07/2023]
Abstract
Four main histological subtypes of ovarian cancer exist: serous (the most frequent), endometrioid, mucinous and clear cell; in each subtype, low and high grade. The large majority of ovarian cancers are diagnosed as high-grade serous ovarian cancers (HGS-OvCas). TP53 is the most frequently mutated gene in HGS-OvCas; about 50% of these tumors displayed defective homologous recombination due to germline and somatic BRCA mutations, epigenetic inactivation of BRCA and abnormalities of DNA repair genes; somatic copy number alterations are frequent in these tumors and some of them are associated with prognosis; defective NOTCH, RAS/MEK, PI3K and FOXM1 pathway signaling is frequent. Other histological subtypes were characterized by a different mutational spectrum: LGS-OvCas have increased frequency of BRAF and RAS mutations; mucinous cancers have mutation in ARID1A, PIK3CA, PTEN, CTNNB1 and RAS. Intensive research was focused to characterize ovarian cancer stem cells, based on positivity for some markers, including CD133, CD44, CD117, CD24, EpCAM, LY6A, ALDH1. Ovarian cancer cells have an intrinsic plasticity, thus explaining that in a single tumor more than one cell subpopulation, may exhibit tumor-initiating capacity. The improvements in our understanding of the molecular and cellular basis of ovarian cancers should lead to more efficacious treatments.
Collapse
|