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Peng B, Shen F, Chen Z, Yu Y, Liu R, Zhang Y, Long G, Hu G, Liu Y. Transposable Element Is Predictive of Chemotherapy- and Immunotherapy-Related Overall Survival in Glioma. Biomedicines 2025; 13:1177. [PMID: 40427005 DOI: 10.3390/biomedicines13051177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2025] [Revised: 04/27/2025] [Accepted: 05/08/2025] [Indexed: 05/29/2025] Open
Abstract
Background: Glioma is the most common type of malignant brain tumor. Temozolomide (TMZ) is a limited systematic treatment option for glioma, including low-grade glioma (LGG) and glioblastoma (GBM). However, not all patients benefit from TMZ and some develop resistance to it. MGMT methylation has been used to identify patients who may benefit from TMZ, but it is not effective in all cases. Objectives: There is an urgent need for new biomarkers to predict the survival of patients who receive TMZ. Methods: We utilized a recently developed method called REdiscoverTE to precisely measure the expression of transposable elements (TE). We performed Cox regression analysis to assess the predictive ability for prognosis and conducted a series of correlation studies to uncover potential mechanisms. Results: We identified three TEs, LTR81B, LTR27B, and MER39B, that were strongly predictive of longer survival in glioma patients receiving chemotherapy. We discovered that the expression of these TEs was positively associated with immune cells that enhance the immune system and negatively associated with immune cells suppressing the immune response, as well as molecules that control immune checkpoints. These three TEs were also found to predict better survival in patients receiving immunotherapy. Conclusions: In conclusion, we demonstrate that the expression of TEs can serve as a novel biomarker for the overall survival of glioma patients who receive TMZ chemotherapy or immunotherapy.
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Affiliation(s)
- Bi Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Fan Shen
- Nursing Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ziqi Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yongkai Yu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Rundong Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yiling Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guoxian Long
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guangyuan Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuanhui Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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Xie W, Zhang Y, Xu J, Sun F, Zhu J, Que Y, Huang J, Zhen Z, Lu S, Wang J, Zhang Y. Characteristics, treatments, and outcomes of adolescents and adults with neuroblastoma: a retrospective study in China. Ther Adv Med Oncol 2025; 17:17588359251337494. [PMID: 40351327 PMCID: PMC12064894 DOI: 10.1177/17588359251337494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Accepted: 04/08/2025] [Indexed: 05/14/2025] Open
Abstract
Background Neuroblastoma (NB) is rare in adolescents and adults, resulting in limited availability of data. Objectives We comprehensively investigated the characteristics, treatments, and outcomes of adolescent and adult patients with NB, aiming to provide a more in-depth insight into this disease. Design A retrospective, single-center study. Methods We retrieved and analyzed the medical data of patients with NB aged 10 years or older at diagnosis who were treated at Sun Yat-sen University Cancer Center between June 2005 and January 2024. Results Sixty-five patients (30 males and 35 females) were enrolled, with a median age of 20 years (interquartile range, 14-26 years), including 27 patients aged 10-18 years and 38 patients aged >18 years. Most patients were classified as M-stage disease (n = 40, 61.5%), high-risk (n = 42, 64.6%), and poorly differentiated NB (n = 27, 41.5%). Additionally, 3 (6.7%) patients had MYCN amplification, and 5 (25%) had ALK mutations. The genomic landscape revealed that mutations in the cell cycle and DNA repair pathways are related to chemotherapy sensitivity. After induction therapy, 34 (52.3%) patients achieved complete response (CR). The 5-year progression-free survival (PFS) and overall survival (OS) rates were 33.1% ± 6.9% and 55.1% ± 7.6%, respectively. Patients who achieved CR after induction therapy had superior PFS (p = 0.009), with 5-year PFS rates of 44.0% ± 10.6% compared to 18.5% ± 8.5% in non-CR patients. Conclusion Adolescent and adult patients with NB exhibit distinct characteristics, less chemotherapy sensitivity, and poorer outcomes compared to pediatric patients. Achieving CR after induction therapy is associated with better outcomes. Further investigation for new therapies is required.
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Affiliation(s)
- Weiji Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Yu Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Jiaqian Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Feifei Sun
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Jia Zhu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Yi Que
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Junting Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Zijun Zhen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Suying Lu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Yuexiu District, Guangzhou City, Guangdong 510060, P.R. China
| | - Juan Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Yuexiu District, Guangzhou City, Guangdong 510060, P.R. China
| | - Yizhuo Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Yuexiu District, Guangzhou City, Guangdong 510060, P.R. China
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Haider S, Brough R, Madera S, Iacovacci J, Gulati A, Wicks A, Alexander J, Pettitt SJ, Tutt ANJ, Lord CJ. The transcriptomic architecture of common cancers reflects synthetic lethal interactions. Nat Genet 2025; 57:522-529. [PMID: 40033056 PMCID: PMC11906352 DOI: 10.1038/s41588-025-02108-2] [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: 04/18/2024] [Accepted: 01/28/2025] [Indexed: 03/05/2025]
Abstract
To maintain cell fitness, deleterious genetic alterations are buffered by compensatory changes in additional genes. In cancer, buffering processes could be targeted by synthetic lethality. However, despite the large-scale identification of synthetic lethal effects in preclinical models, evidence that these operate clinically is limited. This impedes the application of synthetic lethal approaches. By integrating molecular profiling data from >9,000 cancers with synthetic lethal screens, we show that transcriptomic buffering of tumor suppressor gene (TSG) loss by hyperexpression of synthetic lethal partners is a common phenomenon, extending to multiple TSGs and histotypes. Transcriptomic buffering is also notable in cancers that phenocopy TSG loss, such as BRCAness cancers, where expression of BRCA1/2 synthetic lethal genes correlates with clinical outcome. Synthetic lethal genes that exhibit transcriptomic buffering also represent more robust synthetic lethal effects. These observations have implications for understanding how tumor cells tolerate TSG loss, in part explain transcriptomic architectures in cancer and provide insight into target selection.
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Affiliation(s)
- Syed Haider
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK.
| | - Rachel Brough
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Santiago Madera
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Jacopo Iacovacci
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Aditi Gulati
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Andrew Wicks
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - John Alexander
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK
| | - Stephen J Pettitt
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK.
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
| | - Andrew N J Tutt
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK.
| | - Christopher J Lord
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, London, UK.
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
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Li Q, Zhang Y, Luo S, Zhang Z, Oberg AL, Kozono DE, Lu H, Sarkaria JN, Ma L, Wang L. Identify Non-mutational p53 Functional Deficiency in Human Cancers. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae064. [PMID: 39325855 PMCID: PMC11702981 DOI: 10.1093/gpbjnl/qzae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 07/23/2024] [Accepted: 08/21/2024] [Indexed: 09/28/2024]
Abstract
An accurate assessment of p53's functional statuses is critical for cancer genomic medicine. However, there is a significant challenge in identifying tumors with non-mutational p53 inactivation which is not detectable through DNA sequencing. These undetected cases are often misclassified as p53-normal, leading to inaccurate prognosis and downstream association analyses. To address this issue, we built the support vector machine (SVM) models to systematically reassess p53's functional statuses in TP53 wild-type (TP53WT) tumors from multiple The Cancer Genome Atlas (TCGA) cohorts. Cross-validation demonstrated the good performance of the SVM models with a mean area under the receiver operating characteristic curve (AUROC) of 0.9822, precision of 0.9747, and recall of 0.9784. Our study revealed that a significant proportion (87%-99%) of TP53WT tumors actually had compromised p53 function. Additional analyses uncovered that these genetically intact but functionally impaired (termed as predictively reduced function of p53 or TP53WT-pRF) tumors exhibited genomic and pathophysiologic features akin to TP53-mutant tumors: heightened genomic instability and elevated levels of hypoxia. Clinically, patients with TP53WT-pRF tumors experienced significantly shortened overall survival or progression-free survival compared to those with predictively normal function of p53 (TP53WT-pN) tumors, and these patients also displayed increased sensitivity to platinum-based chemotherapy and radiation therapy.
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Affiliation(s)
- Qianpeng Li
- National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zhang
- National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sicheng Luo
- National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhang Zhang
- National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ann L Oberg
- Division of Computational Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - David E Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Lina Ma
- National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liguo Wang
- Division of Computational Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota Rochester, Rochester, MN 55904, USA
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Frye CC, Tennant L, Yeager A, Azimzadeh P, Bhardwaj P, Xu Y, Liu J, Othoum G, Maher CA, Chernock R, Goedegebuure SP, Gillanders W, Olson JA, Brown TC. Overexpression of human DNA polymerase theta is a biomarker of aggressive and DNA repair-deficient papillary thyroid cancers. Surgery 2024; 176:1380-1387. [PMID: 38897886 DOI: 10.1016/j.surg.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 04/19/2024] [Accepted: 05/05/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND DNA polymerase theta (POLQ) is an enzyme that repairs double-strand DNA breaks. POLQ is overexpressed in several cancer types, and increased expression is associated with a poor prognosis. Ablating POLQ function in vitro increases drug sensitivity to agents that cause double-strand DNA breaks, including chemotherapies and ionizing radiation. POLQ's role in thyroid cancer remains poorly understood. METHODS Expression of POLQ and other genes of interest were analyzed in 513 papillary thyroid cancers (505 primary tumors and 8 metastatic lesions) and 59 normal thyroid samples available in the Cancer Genome Atlas. The Cancer Genome Atlas RNA and DNA sequencing data were queried with the Xena platform. The Recombination Proficiency Score was calculated to assess DNA repair efficiency. Other signaling events associated with thyroid tumorigenesis and clinical outcomes were analyzed. Univariate and multivariate analyses were performed. Treatment with the POLQ inhibitors ART558 and Novobiocin tested the effect of POLQ inhibition on in vitro thyroid cancer growth. RESULTS POLQ expression was increased in papillary thyroid cancers compared to normal thyroid tissue (P < .05). POLQ expression levels were inversely correlated with Recombination Proficiency Score levels (P < .05). POLQ expression was highest in tall cell papillary thyroid cancers and in metastases. Higher POLQ expression was also associated with dedifferentiation, BRAF signaling, and shorter progression-free intervals (P < .05). Treatment with POLQ inhibitors decreased in vitro thyroid cancer growth (P < .05). CONCLUSION These findings suggest that increased POLQ expression could serve as a valuable clinical marker and a potential therapeutic target in the treatment of thyroid cancer.
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Affiliation(s)
- C Corbin Frye
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO.
| | - Lena Tennant
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Ashley Yeager
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Pedram Azimzadeh
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Priya Bhardwaj
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Yifei Xu
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO
| | - Jingxia Liu
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO
| | - Ghofran Othoum
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Christopher A Maher
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Rebecca Chernock
- Department of Pathology and Immunology, Division of Anatomic and Molecular Pathology, Washington University School of Medicine, Saint Louis, MO
| | - S Peter Goedegebuure
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - William Gillanders
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - John A Olson
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
| | - Taylor C Brown
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, Saint Louis, MO
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Yadav P, Jain R, Yadav RK. Emerging roles of cancer-associated histone mutations in genomic instabilities. Front Cell Dev Biol 2024; 12:1455572. [PMID: 39439908 PMCID: PMC11494296 DOI: 10.3389/fcell.2024.1455572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 09/10/2024] [Indexed: 10/25/2024] Open
Abstract
Epigenetic mechanisms often fuel the quick evolution of cancer cells from normal cells. Mutations or aberrant expressions in the enzymes of DNA methylation, histone post-translational modifications, and chromatin remodellers have been extensively investigated in cancer pathogenesis; however, cancer-associated histone mutants have gained momentum in recent decades. Next-generation sequencing of cancer cells has identified somatic recurrent mutations in all the histones (H3, H4, H2A, H2B, and H1) with different frequencies for various tumour types. Importantly, the well-characterised H3K27M, H3G34R/V, and H3K36M mutations are termed as oncohistone mutants because of their wide roles, from defects in cellular differentiation, transcriptional dysregulation, and perturbed epigenomic profiles to genomic instabilities. Mechanistically, these histone mutants impart their effects on histone modifications and/or on irregular distributions of chromatin complexes. Recent studies have identified the crucial roles of the H3K27M and H3G34R/V mutants in the DNA damage response pathway, but their impacts on chemotherapy and tumour progression remain elusive. In this review, we summarise the recent developments in their functions toward genomic instabilities and tumour progression. Finally, we discuss how such a mechanistic understanding can be harnessed toward the potential treatment of tumours harbouring the H3K27M, H3G34R/V, and H3K36M mutations.
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Bogani G, Monk BJ, Powell MA, Westin SN, Slomovitz B, Moore KN, Eskander RN, Raspagliesi F, Barretina-Ginesta MP, Colombo N, Mirza MR. Adding immunotherapy to first-line treatment of advanced and metastatic endometrial cancer. Ann Oncol 2024; 35:414-428. [PMID: 38431043 DOI: 10.1016/j.annonc.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Immunotherapy has transformed the endometrial cancer treatment landscape, particularly for those exhibiting mismatch repair deficiency [MMRd/microsatellite instability-hypermutated (MSI-H)]. A growing body of evidence supports the integration of immunotherapy with chemotherapy as a first-line treatment strategy. Recently, findings from ongoing trials such as RUBY (NCT03981796), NRG-GY018 (NCT03914612), AtTEnd (NCT03603184), and DUO-E (NCT04269200) have been disclosed. MATERIALS AND METHODS This paper constitutes a review and meta-analysis of phase III trials investigating the role of immunotherapy in the first-line setting for advanced or recurrent endometrial cancer. RESULTS The pooled data from 2320 patients across these trials substantiate the adoption of chemotherapy alongside immunotherapy, revealing a significant improvement in progression-free survival compared to chemotherapy alone [hazard ratio (HR) 0.70, 95% confidence interval (CI) 0.62-0.79] across all patient groups. Progression-free survival benefits are more pronounced in MMRd/MSI-H tumors (n = 563; HR 0.33, 95% CI 0.23-0.43). This benefit, albeit less robust, persists in the MMR-proficient/microsatellite stable group (n = 1757; HR 0.74, 95% CI 0.60-0.91). Pooled data further indicate that chemotherapy plus immunotherapy enhances overall survival compared to chemotherapy alone in all patients (HR 0.75, 95% CI 0.63-0.89). However, overall survival data maturity remains low. CONCLUSIONS The incorporation of immunotherapy into the initial treatment for advanced and metastatic endometrial cancer brings about a substantial improvement in oncologic outcomes, especially within the MMRd/MSI-H subset. This specific subgroup is currently a focal point of investigation for evaluating the potential of chemotherapy-free regimens. Ongoing exploratory analyses aim to identify non-responding patients eligible for inclusion in clinical trials.
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Affiliation(s)
- G Bogani
- Gynecological Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy.
| | - B J Monk
- GOG Foundation, Florida Cancer Specialists and Research Institute, West Palm Beach
| | - M A Powell
- Division of Gynecologic Oncology, Washington University School of Medicine, St. Louis
| | - S N Westin
- University of Texas MD Anderson Cancer Center, Houston
| | - B Slomovitz
- Division of Gynecologic Oncology, Mount Sinai Medical Center, Miami Beach
| | - K N Moore
- Stephenson Cancer Center at the University of Oklahoma Medical Center, Oklahoma
| | - R N Eskander
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, Rebecca and John Moores Cancer Center, La Jolla, USA
| | - F Raspagliesi
- Gynecological Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - M-P Barretina-Ginesta
- Medical Oncology, Catalan Institute of Oncology, Hospital Universitari Dr. Josep Trueta, Girona; Precision Oncology Group (OncoGIR-Pro), Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona; Department of Medical Sciences, Girona University, Girona, Spain
| | - N Colombo
- Gynecologic Oncology Program, European Institute of Oncology IRCCS, Milan; Department of Medicine and Surgery, University of Milan-Bicocca, Milan, Italy
| | - M R Mirza
- Nordic Society of Gynecological Oncology and Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
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Sebastian NT, Webb A, Shilo K, Robb R, Xu-Welliver M, Haglund K, Brownstein J, DeNicola GM, Shen C, Williams TM. A PI3K gene expression signature predicts for recurrence in early-stage non-small cell lung cancer treated with stereotactic body radiation therapy. Cancer 2023; 129:3971-3977. [PMID: 37560930 DOI: 10.1002/cncr.34983] [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: 04/14/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
INTRODUCTION Increasingly, early-stage non-small cell lung cancer (NSCLC) is treated with stereotactic body radiation therapy (SBRT). Although treatment is generally effective, a small subset of tumors will recur because of radioresistance. Preclinical studies suggested PI3K-AKT-mTOR activation mediates radioresistance. This study sought to validate this finding in tumor samples from patients who underwent SBRT for NSCLC. METHODS Patients with T1-3N0 NSCLC treated with SBRT at our institution were included. Total RNA of formalin-fixed paraffin-embedded tumor biopsy specimens (pretherapy) was isolated and analyzed using the Clariom D assay. Risk scores from a PI3K activity signature and four published NSCLC signatures were generated and dichotomized by the median. Kaplan-Meier curves and Cox regressions were used to analyze their association with recurrence and overall survival (OS). The PI3K signature was also tested in a data set of resected NSCLC for additional validation. RESULTS A total of 92 patients were included, with a median follow-up of 18.3 months for living patients. There was no association of any of the four published gene expression signatures with recurrence or OS. However, high PI3K risk score was associated with higher local recurrence (hazard ratio [HR], 11.72; 95% CI, 1.40-98.0; p = .023) and worse disease-free survival (DFS) (HR, 3.98; 95% CI, 1.57-10.09; p = .0035), but not OS (p = .49), regional recurrence (p = .15), or distant recurrence (p = .85). In the resected NSCLC data set (n = 361), high PI3K risk score was associated with decreased OS (log-rank p = .013) but not DFS (p = 0.54). CONCLUSIONS This study validates that higher PI3K activity, measured by gene expression, is associated with local recurrence and worse DFS in early-stage NSCLC patients treated with SBRT. This may be useful in prognostication and/or tailoring treatment, and merits further validation.
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Affiliation(s)
- Nikhil T Sebastian
- Department of Radiation Oncology, Emory University, Atlanta, Georgia, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Konstantin Shilo
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Ryan Robb
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Meng Xu-Welliver
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Karl Haglund
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Jeremy Brownstein
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Gina M DeNicola
- Department of Metabolism and Physiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Changxian Shen
- Department of Radiation Oncology, City of Hope, Duarte, California, USA
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Sahgal P, Patil DT, Bala P, Sztupinszki ZM, Tisza V, Spisak S, Luong AG, Huffman B, Prosz A, Singh H, Lazaro JB, Szallasi Z, Cleary JM, Sethi NS. Replicative stress in gastroesophageal cancer is associated with chromosomal instability and sensitivity to DNA damage response inhibitors. iScience 2023; 26:108169. [PMID: 37965133 PMCID: PMC10641495 DOI: 10.1016/j.isci.2023.108169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/01/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
Gastroesophageal adenocarcinoma (GEA) is an aggressive malignancy with chromosomal instability (CIN). To understand adaptive responses enabling DNA damage response (DDR) and CIN, we analyzed matched normal, premalignant, and malignant gastric lesions from human specimens and a carcinogen-induced mouse model, observing activation of replication stress, DDR, and p21 in neoplastic progression. In GEA cell lines, expression of DDR markers correlated with ploidy abnormalities, such as number of high-level focal amplifications and whole-genome duplication (WGD). Integrating TP53 status, ploidy abnormalities, and DDR markers into a compositive score helped predict GEA cell lines with enhanced sensitivity to Chk1/2 and Wee1 inhibition, either alone or combined with irinotecan (SN38). We demonstrate that Chk1/2 or Wee1 inhibition combined with SN38/irinotecan shows greater anti-tumor activity in human gastric cancer organoids and an in vivo xenograft mouse model. These findings indicate that specific DDR biomarkers and ploidy abnormalities may predict premalignant progression and response to DDR pathway inhibitors.
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Affiliation(s)
- Pranshu Sahgal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Deepa T. Patil
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
| | - Zsofia M. Sztupinszki
- Danish Cancer Institute, 2100 Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - Anna G. Luong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brandon Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Aurel Prosz
- Danish Cancer Institute, 2100 Copenhagen, Denmark
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zoltan Szallasi
- Danish Cancer Institute, 2100 Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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10
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Tovey H, Sipos O, Parker JS, Hoadley KA, Quist J, Kernaghan S, Kilburn L, Salgado R, Loi S, Kennedy RD, Roxanis I, Gazinska P, Pinder SE, Bliss J, Perou CM, Haider S, Grigoriadis A, Tutt A, Cheang MCU. Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727). Clin Cancer Res 2023; 29:3691-3705. [PMID: 37574209 PMCID: PMC10502473 DOI: 10.1158/1078-0432.ccr-23-0370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/23/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023]
Abstract
PURPOSE The TNT trial (NCT00532727) showed no evidence of carboplatin superiority over docetaxel in metastatic triple-negative breast cancer (mTNBC), but carboplatin benefit was observed in the germline BRCA1/2 mutation subgroup. Broader response-predictive biomarkers are needed. We explored the predictive ability of DNA damage response (DDR) and immune markers. EXPERIMENTAL DESIGN Tumor-infiltrating lymphocytes were evaluated for 222 of 376 patients. Primary tumors (PT) from 186 TNT participants (13 matched recurrences) were profiled using total RNA sequencing. Four transcriptional DDR-related and 25 immune-related signatures were evaluated. We assessed their association with objective response rate (ORR) and progression-free survival (PFS). Conditional inference forest clustering was applied to integrate multimodal data. The biology of subgroups was characterized by 693 gene expression modules and other markers. RESULTS Transcriptional DDR-related biomarkers were not predictive of ORR to either treatment overall. Changes from PT to recurrence were demonstrated; in chemotherapy-naïve patients, transcriptional DDR markers separated carboplatin responders from nonresponders (P values = 0.017; 0.046). High immune infiltration was associated with docetaxel ORR (interaction P values < 0.05). Six subgroups were identified; the immune-enriched cluster had preferential docetaxel response [62.5% (D) vs. 29.4% (C); P = 0.016]. The immune-depleted cluster had preferential carboplatin response [8.0% (D) vs. 40.0% (C); P = 0.011]. DDR-related subgroups were too small to assess ORR. CONCLUSIONS High immune features predict docetaxel response, and high DDR signature scores predict carboplatin response in treatment-naïve mTNBC. Integrating multimodal DDR and immune-related markers identifies subgroups with differential treatment sensitivity. Treatment options for patients with immune-low and DDR-proficient tumors remains an outstanding need. Caution is needed using PT-derived transcriptional signatures to direct treatment in mTNBC, particularly DDR-related markers following prior chemotherapy.
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Affiliation(s)
- Holly Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Orsolya Sipos
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Joel S. Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Katherine A. Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jelmar Quist
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Sarah Kernaghan
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Lucy Kilburn
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Sherene Loi
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Ioannis Roxanis
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patrycja Gazinska
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
- Biobank Research Group, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Sarah E. Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Judith Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Charles M. Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Syed Haider
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Anita Grigoriadis
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Andrew Tutt
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Maggie Chon U. Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
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11
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Chelariu-Raicu A, Trillsch F, Burges A, Czogalla B, Hester A, Wuerstlein R, Harbeck N, Mahner S. PARP inhibitors: risk factors for toxicity and matching patients to the proper poly (ADP-ribose) polymerase inhibitor (PARPi) therapy. Int J Gynecol Cancer 2023; 33:812-822. [PMID: 36707086 DOI: 10.1136/ijgc-2022-003990] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The past 5 years have seen several fundamental advances in ovarian cancer, with important new insights towards novel therapeutic opportunities within the DNA repair pathway. With the incorporation of poly (ADP-ribose) polymerase inhibitors (PARPi) into maintenance treatment regimens, the management of short- and long-term adverse events are key clinical priorities. Currently, three different PARPi are clinically beneficial and have been approved for primary and recurrent ovarian cancer: olaparib, niraparib, and rucaparib. The duration of treatment with PARPi in patients with ovarian cancer varies; patients can receive treatment for up to 2 or 3 years in first-line setting, or continue treatment until unacceptable toxicity or progression occurs in recurrent disease. Despite their similar mechanisms of action, these three inhibitors have specific toxicity profiles, which may lead to dose interruptions or discontinuation of treatment. This review summarizes the current indications for PARPi, including their role in recurrent and first-line maintenance treatment for advanced ovarian cancer. We also outline dose modifications leading to treatment disruption and potential changes in quality of life after prolonged treatment. Finally, we highlight the patient groups most likely to benefit from each of the three different PARPi.
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Affiliation(s)
- Anca Chelariu-Raicu
- Department of Obstetrics and Gynecology, Breast Center, Gynecologic Cancer Center and CCC Munich, Ludwig Maximilians University Munich, Munich, Bayern, Germany
- German Cancer Consortium (DKTK), partner site Munich, German Cancer Research Center, Munich, Germany
| | - Fabian Trillsch
- Department of Obstetrics and Gynecology, Breast Center, Gynecologic Cancer Center and CCC Munich, Ludwig Maximilians University Munich, Munich, Bayern, Germany
| | - Alexander Burges
- Department of Obstetrics and Gynecology, Breast Center, Gynecologic Cancer Center and CCC Munich, Ludwig Maximilians University Munich, Munich, Bayern, Germany
| | - Bastian Czogalla
- Department of Obstetrics and Gynecology, Breast Center, Gynecologic Cancer Center and CCC Munich, Ludwig Maximilians University Munich, Munich, Bayern, Germany
| | - Anna Hester
- Department of Obstetrics and Gynecology, Breast Center, Gynecologic Cancer Center and CCC Munich, Ludwig Maximilians University Munich, Munich, Bayern, Germany
| | - Rahel Wuerstlein
- Department of Obstetrics and Gynecology, Breast Center, Gynecologic Cancer Center and CCC Munich, Ludwig Maximilians University Munich, Munich, Bayern, Germany
| | - Nadia Harbeck
- Department of Obstetrics and Gynecology, Breast Center, Gynecologic Cancer Center and CCC Munich, Ludwig Maximilians University Munich, Munich, Bayern, Germany
| | - Sven Mahner
- Department of Obstetrics and Gynecology, Breast Center, Gynecologic Cancer Center and CCC Munich, Ludwig Maximilians University Munich, Munich, Bayern, Germany
- German Cancer Consortium (DKTK), partner site Munich, German Cancer Research Center, Munich, Germany
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12
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Sahgal P, Patil DT, Sztupinszki ZM, Tisza V, Spisak S, Huffman B, Prosz A, Singh H, Lazaro JB, Szallasi Z, Cleary JM, Sethi NS. Replicative stress in gastroesophageal adenocarcinoma is associated with chromosomal instability and sensitivity to DNA damage response inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534412. [PMID: 37034740 PMCID: PMC10081209 DOI: 10.1101/2023.03.27.534412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Gastroesophageal adenocarcinoma (GEA) is an aggressive, often lethal, malignancy that displays marked chromosomal instability (CIN). To understand adaptive responses that enable CIN, we analyzed paired normal, premalignant, and malignant gastric lesions from human specimens and a carcinogen-induced mouse model, observing activation of replication stress, DNA damage response (DDR), and cell cycle regulator p21 in neoplastic progression. In GEA cell lines, expression of DDR markers correlated with ploidy abnormalities, including high-level focal amplifications and whole-genome duplication (WGD). Moreover, high expression of DNA damage marker H2AX correlated with CIN, WGD, and inferior patient survival. By developing and implementing a composite diagnostic score that incorporates TP53 mutation status, ploidy abnormalities, and H2AX expression, among other genomic information, we can identify GEA cell lines with enhanced sensitivity to DDR pathway inhibitors targeting Chk1/2 and Wee1. Anti-tumor properties were further augmented in combination with irinotecan (SN38) but not gemcitabine chemotherapy. These results implicate specific DDR biomarkers and ploidy abnormalities as diagnostic proxy that may predict premalignant progression and response to DDR pathway inhibitors.
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Affiliation(s)
- Pranshu Sahgal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, 02142, USA
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Deepa T. Patil
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
| | | | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Brandon Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aurel Prosz
- Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Zoltan Szallasi
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, 02142, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Lead Contact
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13
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Fan Z, Yu B, Pan T, Li F, Li J, Hou J, Liu W, Su L, Zhu Z, Yan C, Liu B. DKK1 as a robust predictor for adjuvant platinum chemotherapy benefit in resectable pStage II-III gastric cancer. Transl Oncol 2022; 27:101577. [PMID: 36332599 PMCID: PMC9636483 DOI: 10.1016/j.tranon.2022.101577] [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: 08/24/2022] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Adjuvant chemotherapy (ACT) with 5-FU alone or 5-FU plus platinum after curative surgery improves the prognosis of pStage II-III gastric cancer (GC). However, only a subset of patients benefits from adjuvant platinum. To avoid the side effects of platinum, it is significant to accurately screen the patients who would benefit maximally with this treatment. The present study aimed to assess the value of DKK1 in predicting the benefit of adjuvant platinum chemotherapy in patients with pStage II -III GC. METHODS Platinum sensitivity-related genes were screened by bioinformatics. DKK1 expression in 380 GC specimens was detected by immunohistochemistry (IHC) staining, and the correlation with adjuvant platinum-specific benefits were analyzed. RESULTS DKK1 was screened as the most significant platinum sensitivity-related gene. In patients with DKK1high GC, the estimated absolute 5-year overall survival (OS) benefits from adjuvant platinum for pStage II-III, II, IIIA, IIIB, and IIIC were 25.5%, 17.3%, 36.4%, 29.2% and 31.1%, respectively, and the estimated absolute 5-year disease-free survival (DFS) benefits in the corresponding stages were 27.4%, 17.5%, 36.7%, 29.7% and 31.5%, respectively. These benefits were significantly higher than those in the same TNM stage without adjusting for DKK1 status. The performance of DKK1 was independent of the TNM stage and other clinicopathological variables. Similar results were obtained in the TCGA and ACRG cohorts. Furthermore, nomograms were constructed to predict the survival benefits in DKK1 subgroups. CONCLUSIONS The stratification strategy based on DKK1 status is more precise than the TNM staging system for the selection of pStage II-III GC patients suitable for platinum-containing ACT.
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Affiliation(s)
- Zhiyuan Fan
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China,Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Beiqin Yu
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tao Pan
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fangyuan Li
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jianfang Li
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Junyi Hou
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wentao Liu
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Liping Su
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhenggang Zhu
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chao Yan
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China,Corresponding authors.
| | - Bingya Liu
- Department of General Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China,Corresponding authors.
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14
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Morris BB, Smith JP, Zhang Q, Jiang Z, Hampton OA, Churchman ML, Arnold SM, Owen DH, Gray JE, Dillon PM, Soliman HH, Stover DG, Colman H, Chakravarti A, Shain KH, Silva AS, Villano JL, Vogelbaum MA, Borges VF, Akerley WL, Gentzler RD, Hall RD, Matsen CB, Ulrich CM, Post AR, Nix DA, Singer EA, Larner JM, Stukenberg PT, Jones DR, Mayo MW. Replicative Instability Drives Cancer Progression. Biomolecules 2022; 12:1570. [PMID: 36358918 PMCID: PMC9688014 DOI: 10.3390/biom12111570] [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: 08/16/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 01/07/2023] Open
Abstract
In the past decade, defective DNA repair has been increasingly linked with cancer progression. Human tumors with markers of defective DNA repair and increased replication stress exhibit genomic instability and poor survival rates across tumor types. Seminal studies have demonstrated that genomic instability develops following inactivation of BRCA1, BRCA2, or BRCA-related genes. However, it is recognized that many tumors exhibit genomic instability but lack BRCA inactivation. We sought to identify a pan-cancer mechanism that underpins genomic instability and cancer progression in BRCA-wildtype tumors. Methods: Using multi-omics data from two independent consortia, we analyzed data from dozens of tumor types to identify patient cohorts characterized by poor outcomes, genomic instability, and wildtype BRCA genes. We developed several novel metrics to identify the genetic underpinnings of genomic instability in tumors with wildtype BRCA. Associated clinical data was mined to analyze patient responses to standard of care therapies and potential differences in metastatic dissemination. Results: Systematic analysis of the DNA repair landscape revealed that defective single-strand break repair, translesion synthesis, and non-homologous end-joining effectors drive genomic instability in tumors with wildtype BRCA and BRCA-related genes. Importantly, we find that loss of these effectors promotes replication stress, therapy resistance, and increased primary carcinoma to brain metastasis. Conclusions: Our results have defined a new pan-cancer class of tumors characterized by replicative instability (RIN). RIN is defined by the accumulation of intra-chromosomal, gene-level gain and loss events at replication stress sensitive (RSS) genome sites. We find that RIN accelerates cancer progression by driving copy number alterations and transcriptional program rewiring that promote tumor evolution. Clinically, we find that RIN drives therapy resistance and distant metastases across multiple tumor types.
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Affiliation(s)
- Benjamin B. Morris
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jason P. Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | | | | | | | | | - Susanne M. Arnold
- Division of Medical Oncology, Department of Internal Medicine, Markey Cancer Center, Lexington, KY 40536, USA
| | - Dwight H. Owen
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Jhanelle E. Gray
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Patrick M. Dillon
- Division of Hematology/Oncology, Department of Internal Medicine, University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Hatem H. Soliman
- Department of Breast Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Daniel G. Stover
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Howard Colman
- Huntsman Cancer Institute and Department of Neurosurgery, University of Utah, Salt Lake City, UT 84112, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Kenneth H. Shain
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Ariosto S. Silva
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - John L. Villano
- Division of Medical Oncology, Department of Internal Medicine, Markey Cancer Center, Lexington, KY 40536, USA
| | | | - Virginia F. Borges
- Division of Medical Oncology, University of Colorado Comprehensive Cancer Center, Aurora, CO 80045, USA
| | - Wallace L. Akerley
- Department of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Ryan D. Gentzler
- Division of Hematology/Oncology, Department of Internal Medicine, University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Richard D. Hall
- Division of Hematology/Oncology, Department of Internal Medicine, University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Cindy B. Matsen
- Department of Surgery, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - C. M. Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew R. Post
- Department of Biomedical Informatics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - David A. Nix
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Eric A. Singer
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - James M. Larner
- Department of Radiation Oncology, University of Virginia Comprehensive Cancer Center, Charlottesville, VA 22908, USA
| | - Peter Todd Stukenberg
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - David R. Jones
- Department of Thoracic Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Marty W. Mayo
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
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15
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Budke B, Zhong A, Sullivan K, Park C, Gittin DI, Kountz TS, Connell PP. Noncanonical NF-κB factor p100/p52 regulates homologous recombination and modulates sensitivity to DNA-damaging therapy. Nucleic Acids Res 2022; 50:6251-6263. [PMID: 35689636 PMCID: PMC9226503 DOI: 10.1093/nar/gkac491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 11/14/2022] Open
Abstract
Homologous recombination (HR) serves multiple roles in DNA repair that are essential for maintaining genomic stability, including double-strand DNA break (DSB) repair. The central HR protein, RAD51, is frequently overexpressed in human malignancies, thereby elevating HR proficiency and promoting resistance to DNA-damaging therapies. Here, we find that the non-canonical NF-κB factors p100/52, but not RelB, control the expression of RAD51 in various human cancer subtypes. While p100/p52 depletion inhibits HR function in human tumor cells, it does not significantly influence the proficiency of non-homologous end joining, the other key mechanism of DSB repair. Clonogenic survival assays were performed using a pair DLD-1 cell lines that differ only in their expression of the key HR protein BRCA2. Targeted silencing of p100/p52 sensitizes the HR-competent cells to camptothecin, while sensitization is absent in HR-deficient control cells. These results suggest that p100/p52-dependent signaling specifically controls HR activity in cancer cells. Since non-canonical NF-κB signaling is known to be activated after various forms of genomic crisis, compensatory HR upregulation may represent a natural consequence of DNA damage. We propose that p100/p52-dependent signaling represents a promising oncologic target in combination with DNA-damaging treatments.
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Affiliation(s)
- Brian Budke
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
| | - Alison Zhong
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
| | - Katherine Sullivan
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
| | - Chanyoung Park
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
| | - David I Gittin
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
| | - Timothy S Kountz
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
| | - Philip P Connell
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
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16
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Liu D, Benzaquen J, Morris LGT, Ilié M, Hofman P. Mutations in KMT2C, BCOR and KDM5C Predict Response to Immune Checkpoint Blockade Therapy in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14112816. [PMID: 35681795 PMCID: PMC9179442 DOI: 10.3390/cancers14112816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Efficient biomarkers are urgently needed to predict response to immune checkpoint blockade (ICB) therapy for non-small cell lung cancer (NSCLC), particularly NSCLC with low tumor mutational burden (TMB). Here, we show that mutations of three chromatin remodeling-related genes, including KMT2C, BCOR and KDM5C, are associated with the ICB response in NSCLC, including NSCLC with low TMB level. Furthermore, this association is further improved by a combined use of KMT2C/BCOR/KDM5C mutations with TMB or PD-L1 expression. These data suggest that KMT2C/BCOR/KDM5C mutation status has the potential to serve as a predictive biomarker for ICB therapy in NSCLC. Abstract Efficient predictive biomarkers are urgently needed to identify non-small cell lung cancer (NSCLC) patients who could benefit from immune checkpoint blockade (ICB) therapy. Since chromatin remodeling is required for DNA repair process, we asked whether mutations in chromatin remodeling genes could increase tumor mutational burden (TMB) and predict response to ICB therapy in NSCLC. Analysis of seven ICB-treated NSCLC cohorts revealed that mutations of three chromatin remodeling-related genes, including KMT2C, BCOR and KDM5C, were significantly associated with ICB response, and combined mutations of these three genes further enhance this association. NSCLC patients with KMT2C/BCOR/KDM5C mutations had comparable clinical outcomes to TMB-high patients in terms of objective response rate, durable clinical benefit and overall survival. Although KMT2C/BCOR/KDM5C mutations were positively correlated with TMB levels in NSCLC, the association of this mutation with better ICB response was independent of tumor TMB and programmed death-ligand 1 (PD-L1) level, and combination of KMT2C/BCOR/KDM5C mutations with TMB or PD-L1 further improve the prediction of ICB response in NSCLC patients. Cancer Genome Atlas (TCGA) pan-cancer analysis suggested that the association of KMT2C/BCOR/KDM5C mutations with ICB response observed here might not result from DNA repair defects. In conclusion, our data indicate that KMT2C/BCOR/KDM5C mutation has the potential to serve as a predictive biomarker, alone or combined with PD-L1 expression or TMB, for ICB therapy in NSCLC.
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Affiliation(s)
- Dingxie Liu
- Bluewater Biotech LLC, New Providence, NJ 07974, USA
- Correspondence: (D.L.); (P.H.)
| | - Jonathan Benzaquen
- Department of Pneumology, Pasteur Hospital, FHU OncoAge, 06000 Nice, France; (J.B.); (M.I.)
| | - Luc G. T. Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Marius Ilié
- Department of Pneumology, Pasteur Hospital, FHU OncoAge, 06000 Nice, France; (J.B.); (M.I.)
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, CHU Nice, FHU OncoAge, University Côte d’Azur, 06100 Nice, France
- Team 4, IRCAN, UMR 7284/U10181, FHU OncoAge, University Côte d’Azur, 06107 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), CHU of Nice, FHU OncoAge, University Côte d’Azur, 06100 Nice, France
- Correspondence: (D.L.); (P.H.)
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17
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Schrank TP, Prince AC, Sathe T, Wang X, Liu X, Alzhanov DT, Burtness B, Baldwin AS, Yarbrough WG, Issaeva N. NF-κB over-activation portends improved outcomes in HPV-associated head and neck cancer. Oncotarget 2022; 13:707-722. [PMID: 35634245 PMCID: PMC9131933 DOI: 10.18632/oncotarget.28232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022] Open
Abstract
Evolving understanding of head and neck squamous cell carcinoma (HNSCC) is leading to more specific diagnostic disease classifications. Among HNSCC caused by the human papilloma virus (HPV), tumors harboring defects in TRAF3 or CYLD are associated with improved clinical outcomes and maintenance of episomal HPV. TRAF3 and CYLD are negative regulators of NF-κB and inactivating mutations of either leads to NF-κB overactivity. Here, we developed and validated a gene expression classifier separating HPV+ HNSCCs based on NF-κB activity. As expected, the novel classifier is strongly enriched in NF-κB targets leading us to name it the NF-κB Activity Classifier (NAC). High NF-κB activity correlated with improved survival in two independent cohorts. Using NAC, tumors with high NF-κB activity but lacking defects in TRAF3 or CYLD were identified; thus, while TRAF3 or CYLD gene defects identify the majority of tumors with NF-κB activation, unknown mechanisms leading to NF-kB activity also exist. The NAC correctly classified the functional consequences of two novel CYLD missense mutations. Using a reporter assay, we tested these CYLD mutations revealing that their activity to inhibit NF-kB was equivalent to the wild-type protein. Future applications of the NF-κB Activity Classifier may be to identify HPV+ HNSCC patients with better or worse survival with implications for treatment strategies.
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Affiliation(s)
- Travis P. Schrank
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
- These authors contributed equally to this work
| | - Andrew C. Prince
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
- These authors contributed equally to this work
| | - Tejas Sathe
- Department of Surgery, Otolaryngology, Yale, New Haven, CT 06519, USA
- Current address: Department of Surgery, Columbia University, New York, NY 10032, USA
| | - Xiaowei Wang
- Department of Pharmacology and Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
- Bioinformatics Core, University of Illinois Cancer Center, Chicago, IL 60612, USA
| | - Xinyi Liu
- Department of Pharmacology and Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
- Bioinformatics Core, University of Illinois Cancer Center, Chicago, IL 60612, USA
| | - Damir T. Alzhanov
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
| | - Barbara Burtness
- Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Albert S. Baldwin
- Department of Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Wendell G. Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
- Lineberger Cancer Center, UNC, Chapel Hill, NC 27599, USA
- Department of Pathology and Laboratory Medicine, UNC, Chapel Hill, NC 27599, USA
- Senior authors
| | - Natalia Issaeva
- Department of Otolaryngology/Head and Neck Surgery, UNC, Chapel Hill, NC 27599, USA
- Lineberger Cancer Center, UNC, Chapel Hill, NC 27599, USA
- Department of Pathology and Laboratory Medicine, UNC, Chapel Hill, NC 27599, USA
- Senior authors
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18
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Li P, Chen C, Li J, Yang L, Wang Y, Dong Z, Mi J, Zhang Y, Wang J, Wang H, Rodriguez R, Tian J, Wang Z. Homologous Recombination Related Signatures Predict Prognosis and Immunotherapy Response in Metastatic Urothelial Carcinoma. Front Genet 2022; 13:875128. [PMID: 35559013 PMCID: PMC9086193 DOI: 10.3389/fgene.2022.875128] [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: 02/14/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: This study used homologous recombination (HR) related signatures to develop a clinical prediction model for screening immune checkpoint inhibitors (ICIs) advantaged populations and identify hub genes in advanced metastatic urothelial carcinoma. Methods: The single-sample gene enrichment analysis and weighted gene co-expression network analysis were applied to identify modules associated with immune response and HR in IMvigor210 cohort samples. The principal component analysis was utilized to determine the differences in HR-related module gene signature scores across different tissue subtypes and clinical variables. Risk prediction models and nomograms were developed using differential gene expression analysis associated with HR scores, least absolute shrinkage and selection operator, and multivariate proportional hazards model regression. Additionally, hub genes were identified by analyzing the contribution of HR-related genes to principal components and overall survival analysis. Finally, clinical features from GSE133624, GSE13507, the TCGA, and other data sets were analyzed to validate the relationship between hub genes and tumor growth and mutation. Results: The HR score was significantly higher in the complete/partial response group than in the stable/progressive disease group. The majority of genes associated with HR were discovered to be involved in the cell cycle and others. Genomically unstable, high tumor level, and high immune level samples all exhibited significantly higher HR score than other sample categories, and higher HR scores were related to improved survival following ICIs treatment. The risk scores for AUNIP, SEPT, FAM72D, CAMKV, CXCL9, and FOXN4 were identified, and the training and verification groups had markedly different survival times. The risk score, tumor neoantigen burden, mismatch repair, and cell cycle regulation were discovered to be independent predictors of survival time following immunotherapy. Patients with a high level of expression of hub genes such as EME1, RAD51AP1, and RAD54L had a greater chance of surviving following immunotherapy. These genes are expressed at significantly higher levels in tumors, high-grade cancer, and invasive cancer than other categories, and are associated with TP53 and RB1 mutations. Conclusion: HR-related genes are upregulated in genomically unstable samples, the survival time of mUC patients after treatment with ICIs can be predicted using a normogram model based on HR signature.
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Affiliation(s)
- Pan Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Chaohu Chen
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Jianpeng Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Li Yang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Yuhan Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Zhilong Dong
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Jun Mi
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Yunxin Zhang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Juan Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China
| | - Hanzhang Wang
- Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ronald Rodriguez
- Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Junqiang Tian
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
| | - Zhiping Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-Urology, Lanzhou, China
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19
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Takamatsu S, Brown JB, Yamaguchi K, Hamanishi J, Yamanoi K, Takaya H, Kaneyasu T, Mori S, Mandai M, Matsumura N. Utility of Homologous Recombination Deficiency Biomarkers Across Cancer Types. JCO Precis Oncol 2022; 6:e2200085. [PMID: 35613413 PMCID: PMC9200383 DOI: 10.1200/po.22.00085] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Homologous recombination DNA repair deficiency (HRD) is associated with sensitivity to platinum and poly (ADP-ribose) polymerase inhibitors in certain cancer types, including breast, ovarian, pancreatic, and prostate. In these cancers, BRCA1/2 alterations and genomic scar signatures are useful indicators for assessing HRD. However, alterations in other homologous recombination repair (HRR)-related genes and their clinical significance in other cancer types have not been adequately and systematically investigated. A comprehensive pan-cancer analysis on the clinical significance of homologous recombination deficiency![]()
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Affiliation(s)
- Shiro Takamatsu
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - J B Brown
- Life Science Informatics Research Unit, Department of Molecular Biosciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Yamaguchi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junzo Hamanishi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Yamanoi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisamitsu Takaya
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Tomoko Kaneyasu
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Mori
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Noriomi Matsumura
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
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20
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Lou S, Wang Y, Zhang J, Yin X, Zhang Y, Wang Y, Xue Y. Patient-Level DNA Damage Repair Pathway Profiles and Anti-Tumor Immunity for Gastric Cancer. Front Immunol 2022; 12:806324. [PMID: 35082793 PMCID: PMC8785952 DOI: 10.3389/fimmu.2021.806324] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/20/2021] [Indexed: 12/25/2022] Open
Abstract
DNA damage repair (DDR) comprises the detection and correction of alterations in the chemical structure of DNA. The dysfunction of the DDR process has been determined to have important implications for tumor carcinogenesis, malignancy progression, treatment resistance, and prognosis assessment. However, the role of the DDR process in gastric cancer (GC) remains to be fully understood. Thus, a total of 2,019 GC samples from our hospital (Harbin Medical University Cancer Hospital in china) and 12 public data sets were included in our study. In this study, single-sample gene set enrichment analysis (ssGSEA) was used to generate the DDR pathway activity profiles of 8 DDR sub-pathways and identify a DDR pathway signature by combining the DDR sub-pathway gene sets. The DDR pathway profiling’s impacts on the clinical outcomes, biological functions, genetic variants, immune heterogeneity, and treatment responses were analyzed through multidimensional genomics and clinical data. The results demonstrate that the DDR pathway profiling was clearly distinguished between tumor and normal tissues. The DDR pathway profiling reveals patient-level variations, which may contribute to explaining the high heterogeneity of human GC for the biological features and treatment outcomes. Thus, tumors with low DDR signature scores were independently correlated with shorter overall survival time and significantly associated with mesenchymal, invasion, and metastasis phenotypes. The statistical model integrating this DDR pathway signature with other clinical predictors outperforms each predictor alone for predicting overall survival in discrimination, calibration, and net clinical benefit. Moreover, low DDR signature scores were tightly associated with genome stability, characterized by low tumor mutational burden (TMB) and low fractions of genome alteration. Furthermore, this study confirms that patients with low DDR pathway signature scores might not benefit from adjuvant chemotherapy and a monoclonal antibody directed against programmed cell death-1 ligand 1 (anti-PD1) therapy. These findings highlighted that the DDR pathway profiling confers important implications for patients with GC and provides insights into the specific clinical and molecular features underlying the DDR process, which may help to facilitate clinical management.
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Affiliation(s)
- Shenghan Lou
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yufei Wang
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jian Zhang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xin Yin
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yao Zhang
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yimin Wang
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yingwei Xue
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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21
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Zuo K, Yuan X, Liang X, Sun X, Liu S, Connell PP, Li X, Yang W. qRT-PCR-based DNA homologous recombination-associated 4-gene score predicts pathologic complete response to platinum-based neoadjuvant chemotherapy in triple-negative breast cancer. Breast Cancer Res Treat 2021; 191:335-344. [PMID: 34797456 DOI: 10.1007/s10549-021-06442-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 11/02/2021] [Indexed: 12/31/2022]
Abstract
PURPOSE Cumulative evidence suggests that the addition of platinum agents as neoadjuvant chemotherapy (NACT) could improve the pathologic complete response (pCR) rate in triple-negative breast cancer (TNBC). We aimed to develop a DNA homologous recombination (HR)-associated gene expression score to predict tumor sensitivity to platinum-based NACT in TNBC. METHODS A retrospective cohort of 127 patients who were diagnosed with TNBC and received platinum-based NACT in Fudan University Shanghai Cancer Center from 2012 to 2017 was included in this study. Using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), the expression levels of eight HR-associated genes were analyzed from formalin-fixed paraffin-embedded core-needle biopsy samples obtained before NACT. A random forest model was built to estimate the weight of each gene expression level and clinicopathological factors. The training set was used to modulate parameters and select the best model. The performance of the final model was evaluated in the validation set. RESULTS A 4-gene (BRCA1, XRCC5, PARP1, and RAD51) scoring system was developed. TNBC patients with a higher score had a nearly fourfold likelihood of achieving pCR to platinum-based NACT compared with patients with a lower score [odds ratio (OR) = 3.878; P < 0.001]. At the cutoff value of - 2.644, the 4-gene scoring system showed high sensitivity in predicting pCR in the breast (93.0%) and pCR in the breast/axilla (91.8%), while at the cutoff value of - 1.969, the 4-gene score showed high specificity for pCR in the breast (85.7%) and pCR in the breast/axilla (80.8%). CONCLUSION The qRT-PCR-based 4-gene score has the potential to predict pCR to platinum-based NACT in TNBC.
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Affiliation(s)
- Ke Zuo
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Rd., Shanghai, 200032, China
| | | | - Xizi Liang
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Rd., Shanghai, 200032, China
| | - Xiangjie Sun
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Rd., Shanghai, 200032, China
| | - Shujin Liu
- Shuwen Biotech Company Ltd, Deqing, Zhejiang, China
| | - Philip P Connell
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, 60647, USA
| | - Xingmin Li
- Shuwen Biotech Company Ltd, Deqing, Zhejiang, China.
| | - Wentao Yang
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Rd., Shanghai, 200032, China.
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22
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Barenboim M, Kovac M, Ameline B, Jones DTW, Witt O, Bielack S, Burdach S, Baumhoer D, Nathrath M. DNA methylation-based classifier and gene expression signatures detect BRCAness in osteosarcoma. PLoS Comput Biol 2021; 17:e1009562. [PMID: 34762643 PMCID: PMC8584788 DOI: 10.1371/journal.pcbi.1009562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
Although osteosarcoma (OS) is a rare cancer, it is the most common primary malignant bone tumor in children and adolescents. BRCAness is a phenotypical trait in tumors with a defect in homologous recombination repair, resembling tumors with inactivation of BRCA1/2, rendering these tumors sensitive to poly (ADP)-ribose polymerase inhibitors (PARPi). Recently, OS was shown to exhibit molecular features of BRCAness. Our goal was to develop a method complementing existing genomic methods to aid clinical decision making on administering PARPi in OS patients. OS samples with DNA-methylation data were divided to BRCAness-positive and negative groups based on the degree of their genomic instability (n = 41). Methylation probes were ranked according to decreasing variance difference between two groups. The top 2000 probes were selected for training and cross-validation of the random forest algorithm. Two-thirds of available OS RNA-Seq samples (n = 17) from the top and bottom of the sample list ranked according to genome instability score were subjected to differential expression and, subsequently, to gene set enrichment analysis (GSEA). The combined accuracy of trained random forest was 85% and the average area under the ROC curve (AUC) was 0.95. There were 449 upregulated and 1,079 downregulated genes in the BRCAness-positive group (fdr < 0.05). GSEA of upregulated genes detected enrichment of DNA replication and mismatch repair and homologous recombination signatures (FWER < 0.05). Validation of the BRCAness classifier with an independent OS set (n = 20) collected later in the course of study showed AUC of 0.87 with an accuracy of 90%. GSEA signatures computed for this test set were matching the ones observed in the training set enrichment analysis. In conclusion, we developed a new classifier based on DNA-methylation patterns that detects BRCAness in OS samples with high accuracy. GSEA identified genome instability signatures. Machine-learning and gene expression approaches add new epigenomic and transcriptomic aspects to already established genomic methods for evaluation of BRCAness in osteosarcoma and can be extended to cancers characterized by genome instability. Osteosarcoma (OS) is the most common primary malignant tumor of bone in children and young adults with poor prognosis for patients with refractory or metastatic disease. A common feature, so-called BRCAness, exists in multiple cancers including OS and is characterized by homologous recombination deficiency. Tumors exhibiting BRCAness have been shown to respond to therapy with PARP inhibitors. Currently, BRCAness is mostly assessed by the genomic instability score. This method based on the DNA sequencing requires normal tissue DNA as control and is vulnerable to subjective interpretation of "genomic scarring" events. In this study, we implemented a classifier based on DNA methylation patterns. It is capable of detecting BRCAness in OS samples and does not require control tissue DNA. Therefore, it has the potential to support clinical decision making on administering PARPi in OS patients. We further corroborated the presence of BRCAness in OS by detecting homologous recombination signatures through gene expression analysis.
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Affiliation(s)
- Maxim Barenboim
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- * E-mail: (MB); (MN)
| | - Michal Kovac
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Baptiste Ameline
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
| | - David T. W. Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- University Hospital Heidelberg, Hematology and Immunology at the Department of Pediatric Oncology, Heidelberg, Germany
| | - Stefan Bielack
- Klinikum Stuttgart–Olgahospital, Stuttgart Cancer Center, Pediatrics 5 (Oncology, Hematology, Immunology), Stuttgart, Germany
| | - Stefan Burdach
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- CCC München—Comprehensive Cancer Center, DKTK German Cancer Consortium, Munich, Germany
| | - Daniel Baumhoer
- University Hospital Basel and University of Basel, Bone Tumour Reference Centre at the Institute of Pathology, Basel, Switzerland
| | - Michaela Nathrath
- Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Klinikum Kassel, Department of Pediatric Oncology, Kassel, Germany
- * E-mail: (MB); (MN)
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23
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Beyond the Double-Strand Breaks: The Role of DNA Repair Proteins in Cancer Stem-Cell Regulation. Cancers (Basel) 2021; 13:cancers13194818. [PMID: 34638302 PMCID: PMC8508278 DOI: 10.3390/cancers13194818] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cancer stem cells (CSCs) are a tumor cell population maintaining tumor growth and promoting tumor relapse if not wholly eradicated during treatment. CSCs are often equipped with molecular mechanisms making them resistant to conventional anti-cancer therapies whose curative potential depends on DNA damage-induced cell death. An elevated expression of some key DNA repair proteins is one of such defense mechanisms. However, new research reveals that the role of critical DNA repair proteins is extending far beyond the DNA repair mechanisms. This review discusses the diverse biological functions of DNA repair proteins in CSC maintenance and the adaptation to replication and oxidative stress, anti-cancer immune response, epigenetic reprogramming, and intracellular signaling mechanisms. It also provides an overview of their potential therapeutic targeting. Abstract Cancer stem cells (CSCs) are pluripotent and highly tumorigenic cells that can re-populate a tumor and cause relapses even after initially successful therapy. As with tissue stem cells, CSCs possess enhanced DNA repair mechanisms. An active DNA damage response alleviates the increased oxidative and replicative stress and leads to therapy resistance. On the other hand, mutations in DNA repair genes cause genomic instability, therefore driving tumor evolution and developing highly aggressive CSC phenotypes. However, the role of DNA repair proteins in CSCs extends beyond the level of DNA damage. In recent years, more and more studies have reported the unexpected role of DNA repair proteins in the regulation of transcription, CSC signaling pathways, intracellular levels of reactive oxygen species (ROS), and epithelial–mesenchymal transition (EMT). Moreover, DNA damage signaling plays an essential role in the immune response towards tumor cells. Due to its high importance for the CSC phenotype and treatment resistance, the DNA damage response is a promising target for individualized therapies. Furthermore, understanding the dependence of CSC on DNA repair pathways can be therapeutically exploited to induce synthetic lethality and sensitize CSCs to anti-cancer therapies. This review discusses the different roles of DNA repair proteins in CSC maintenance and their potential as therapeutic targets.
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Takamatsu S, Brown J, Yamaguchi K, Hamanishi J, Yamanoi K, Takaya H, Kaneyasu T, Mori S, Mandai M, Matsumura N. Utility of Homologous Recombination Deficiency Biomarkers Across Cancer Types. JCO Precis Oncol 2021; 5:PO.21.00141. [PMID: 34423229 PMCID: PMC8373547 DOI: 10.1200/po.21.00141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/07/2021] [Accepted: 07/06/2021] [Indexed: 12/24/2022] Open
Abstract
Homologous recombination DNA repair deficiency (HRD) is associated with sensitivity to platinum and poly (ADP-ribose) polymerase inhibitors in certain cancer types, including breast, ovarian, pancreatic, and prostate. In these cancers, BRCA1/2 alterations and genomic scar signatures are useful indicators for assessing HRD. However, alterations in other homologous recombination repair (HRR)-related genes and their clinical significance in other cancer types have not been adequately and systematically investigated. METHODS We obtained data sets of all solid tumors in The Cancer Genome Atlas and Cancer Cell Line Encyclopedia, and comprehensively analyzed HRR pathway gene alterations, their loss-of-heterozygosity status, and per-sample genomic scar scores, that is, the HRD score and mutational signature 3 ratio, DNA methylation profiles, gene expression profiles, somatic TP53 mutations, sex, and clinical or in vitro response to chemical exposure. RESULTS Biallelic alterations in HRR genes other than BRCA1/2 were also associated with elevated genomic scar scores. The association between HRR-related gene alterations and genomic scar scores differed significantly by sex and the presence of somatic TP53 mutations. HRD tumors determined by a combination of indices also showed HRD features in gene expression analysis and exhibited significantly higher sensitivity to DNA-damaging agents than non-HRD cases in both clinical samples and cell lines. CONCLUSION This study provides evidence for the usefulness of HRD analysis in all cancer types, improves chemotherapy decision making and its efficacy in clinical settings, and represents a substantial advancement in precision oncology.A comprehensive pan-cancer analysis on the clinical significance of homologous recombination deficiency.
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Affiliation(s)
- Shiro Takamatsu
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - J.B. Brown
- Life Science Informatics Research Unit, Department of Molecular Biosciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Yamaguchi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junzo Hamanishi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Yamanoi
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisamitsu Takaya
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Tomoko Kaneyasu
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Mori
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Noriomi Matsumura
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
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Meehan J, Gray M, Martínez-Pérez C, Kay C, McLaren D, Turnbull AK. Tissue- and Liquid-Based Biomarkers in Prostate Cancer Precision Medicine. J Pers Med 2021; 11:jpm11070664. [PMID: 34357131 PMCID: PMC8306523 DOI: 10.3390/jpm11070664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/24/2022] Open
Abstract
Worldwide, prostate cancer (PC) is the second-most-frequently diagnosed male cancer and the fifth-most-common cause of all cancer-related deaths. Suspicion of PC in a patient is largely based upon clinical signs and the use of prostate-specific antigen (PSA) levels. Although PSA levels have been criticised for a lack of specificity, leading to PC over-diagnosis, it is still the most commonly used biomarker in PC management. Unfortunately, PC is extremely heterogeneous, and it can be difficult to stratify patients whose tumours are unlikely to progress from those that are aggressive and require treatment intensification. Although PC-specific biomarker research has previously focused on disease diagnosis, there is an unmet clinical need for novel prognostic, predictive and treatment response biomarkers that can be used to provide a precision medicine approach to PC management. In particular, the identification of biomarkers at the time of screening/diagnosis that can provide an indication of disease aggressiveness is perhaps the greatest current unmet clinical need in PC management. Largely through advances in genomic and proteomic techniques, exciting pre-clinical and clinical research is continuing to identify potential tissue, blood and urine-based PC-specific biomarkers that may in the future supplement or replace current standard practices. In this review, we describe how PC-specific biomarker research is progressing, including the evolution of PSA-based tests and those novel assays that have gained clinical approval. We also describe alternative diagnostic biomarkers to PSA, in addition to biomarkers that can predict PC aggressiveness and biomarkers that can predict response to certain therapies. We believe that novel biomarker research has the potential to make significant improvements to the clinical management of this disease in the near future.
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Affiliation(s)
- James Meehan
- Translational Oncology Research Group, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.M.-P.); (C.K.); (A.K.T.)
- Correspondence:
| | - Mark Gray
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK;
| | - Carlos Martínez-Pérez
- Translational Oncology Research Group, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.M.-P.); (C.K.); (A.K.T.)
- Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Charlene Kay
- Translational Oncology Research Group, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.M.-P.); (C.K.); (A.K.T.)
- Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Duncan McLaren
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Edinburgh EH4 2XU, UK;
| | - Arran K. Turnbull
- Translational Oncology Research Group, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.M.-P.); (C.K.); (A.K.T.)
- Breast Cancer Now Edinburgh Research Team, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
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Koh SB, Ross K, Isakoff SJ, Melkonjan N, He L, Matissek KJ, Schultz A, Mayer EL, Traina TA, Carey LA, Rugo HS, Liu MC, Stearns V, Langenbucher A, Saladi SV, Ramaswamy S, Lawrence MS, Ellisen LW. RASAL2 Confers Collateral MEK/EGFR Dependency in Chemoresistant Triple-Negative Breast Cancer. Clin Cancer Res 2021; 27:4883-4897. [PMID: 34168046 DOI: 10.1158/1078-0432.ccr-21-0714] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/30/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022]
Abstract
PURPOSE While chemotherapy remains the standard treatment for triple-negative breast cancer (TNBC), identifying and managing chemoresistant tumors has proven elusive. We sought to discover hallmarks and therapeutically actionable features of refractory TNBC through molecular analysis of primary chemoresistant TNBC specimens. EXPERIMENTAL DESIGN We performed transcriptional profiling of tumors from a phase II clinical trial of platinum chemotherapy for advanced TNBC (TBCRC-009), revealing a gene expression signature that identified de novo chemorefractory tumors. We then employed pharmacogenomic data mining, proteomic and other molecular studies to define the therapeutic vulnerabilities of these tumors. RESULTS We reveal the RAS-GTPase-activating protein (RAS-GAP) RASAL2 as an upregulated factor that mediates chemotherapy resistance but also an exquisite collateral sensitivity to combination MAP kinase kinase (MEK1/2) and EGFR inhibitors in TNBC. Mechanistically, RASAL2 GAP activity is required to confer kinase inhibitor sensitivity, as RASAL2-high TNBCs sustain basal RAS activity through suppression of negative feedback regulators SPRY1/2, together with EGFR upregulation. Consequently, RASAL2 expression results in failed feedback compensation upon co-inhibition of MEK1/2 and EGFR that induces synergistic apoptosis in vitro and in vivo. In patients with TNBC, high RASAL2 levels predict clinical chemotherapy response and long-term outcomes, and are associated via direct transcriptional regulation with activated oncogenic Yes-Associated Protein (YAP). Accordingly, chemorefractory patient-derived TNBC models exhibit YAP activation, high RASAL2 expression, and tumor regression in response to MEK/EGFR inhibitor combinations despite well-tolerated intermittent dosing. CONCLUSIONS These findings identify RASAL2 as a mediator of TNBC chemoresistance that rewires MAPK feedback and cross-talk to confer profound collateral sensitivity to combination MEK1/2 and EGFR inhibitors.
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Affiliation(s)
- Siang-Boon Koh
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Kenneth Ross
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard University, Cambridge, Massachusetts
| | - Steven J Isakoff
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Nsan Melkonjan
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Lei He
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Karina J Matissek
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Andrew Schultz
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Erica L Mayer
- Harvard Medical School, Boston, Massachusetts.,Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Lisa A Carey
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hope S Rugo
- University of California San Francisco, San Francisco, California
| | - Minetta C Liu
- Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia
| | - Vered Stearns
- Johns Hopkins University and Sidney Kimmel Cancer Center, Baltimore, Maryland
| | - Adam Langenbucher
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Srinivas Vinod Saladi
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard University, Cambridge, Massachusetts.,Ludwig Center at Harvard, Harvard University, Boston, Massachusetts
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard University, Cambridge, Massachusetts
| | - Leif W Ellisen
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. .,Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Harvard, Harvard University, Boston, Massachusetts
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Oct4 confers stemness and radioresistance to head and neck squamous cell carcinoma by regulating the homologous recombination factors PSMC3IP and RAD54L. Oncogene 2021; 40:4214-4228. [PMID: 34079088 PMCID: PMC8211562 DOI: 10.1038/s41388-021-01842-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/29/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is often being diagnosed at an advanced stage, conferring a poor prognosis. The probability of local tumor control after radiotherapy depends on the eradication of cancer stem cells (CSCs) with activated DNA repair. This study provides evidence that the CSC-related transcription factor Oct4 contributes to HNSCC radioresistance by regulating DNA damage response and the CSC phenotype. Knockdown of Oct4 A isoform reduced self-renewal capacity in HNSCC and led to partial tumor cell radiosensitization caused by transcriptional downregulation of the cell cycle checkpoint kinases CHK1 and WEE1 and homologous recombination (HR) repair genes PSMC3IP and RAD54L. Besides, PARP inhibition with Olaparib selectively radiosensitized Oct4 A knockout, but not wild-type HNSCC cells. This finding links Oct4 A to the HR-mediated DNA repair mechanisms. In turn, knockdown of PSMC3IP and RAD54L reduced the HNSCC self-renewal capacity and clonogenic cell survival after irradiation, suggesting the interplay between DNA repair and the CSC phenotype. Similar to the effect of Oct4 knockdown, overexpression of Oct4 also resulted in significant HNSCC radiosensitization and increased DNA damage, suggesting that Oct4-dependent regulation of DNA repair depends on its fine-tuned expression. In line with this observation, HNSCC patients with high and low nuclear Oct4 expression at the invasive tumor front exhibited better loco-regional tumor control after postoperative radio(chemo)therapy compared to the intermediate expression subgroup. Thus, we found that the Oct4-driven transcriptional program plays a critical role in regulating HNSCC radioresistance, and a combination of radiotherapy with PARP inhibitors may induce synthetic lethality in Oct4-deregulated tumors.
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Adenocarcinoma of the Prostate: Future Directions for Translational Science. Prostate Cancer 2021. [DOI: 10.36255/exonpublications.prostatecancer.translationalscience.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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Delbart W, Ghanem GE, Karfis I, Flamen P, Wimana Z. Investigating intrinsic radiosensitivity biomarkers to peptide receptor radionuclide therapy with [ 177Lu]Lu-DOTATATE in a panel of cancer cell lines. Nucl Med Biol 2021; 96-97:68-79. [PMID: 33839677 DOI: 10.1016/j.nucmedbio.2021.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/02/2021] [Accepted: 03/20/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION [177Lu]Lu-DOTATATE is an effective systemic targeted radionuclide therapy for somatostatin receptor (SSTR) positive metastatic or inoperable neuroendocrine tumours (NET). However, for a given injected activity, tumour responses are variable. Our aim was to investigate whether SSTR expression/functionality and known characteristics of intrinsic radiosensitivity, namely proliferation rate, glucose metabolism, cell cycle phase, DNA repair and antioxidant defences were predictors of sensitivity to [177Lu]Lu-DOTATATE in SSTR expressing human cancer cell lines. METHODS In six human cancer cell lines and under basal condition, SSTR expression was assessed by qRT-PCR and immunocytochemistry. Its functionality was evaluated by binding/uptake assays with [68Ga]Ga- and [177Lu]Lu-DOTATATE. The radiosensitivity parameters were evaluated as follows: proliferation rate (cell counting), glucose metabolism ([18F]FDG uptake), antioxidant defences (qRT-PCR, colorimetric assay, flow cytometry), DNA repair (qRT-PCR) and cell cycle (flow cytometry). Effect of [177Lu]Lu-DOTATATE on cell viability was assessed 3, 7 and 10 days after 4 h incubation with [177Lu]Lu-DOTATATE using crystal violet. RESULTS Based on cell survival at day 10, cell lines were classified into two groups of sensitivity to [177Lu]Lu-DOTATATE. One group with <20% of survival decrease (-14 to -1%) and one group with >20% of survival decrease (-22 to -33%) compared to the untreated control cell lines. The latter had significantly lower total antioxidant capacity, glutathione (GSH) levels and glucose metabolism (p < 0.05) compared to the first group. SSTR (p = 0.64), proliferation rate (p = 0.74), cell cycle phase (p = 0.55), DNA repair (p > 0.22), combined catalase and GSH peroxidase expression (p = 0.42) and superoxide dismutase (SOD) activity (p = 0.41) were not significantly different between the two groups. CONCLUSION Antioxidant defences may be major determinants in [177Lu]Lu-DOTATATE radiosensitivity.
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Affiliation(s)
- Wendy Delbart
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium; Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.
| | - Ghanem E Ghanem
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium; Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.
| | - Ioannis Karfis
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.
| | - Patrick Flamen
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.
| | - Zéna Wimana
- Nuclear Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium; Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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Moutafi M, Economopoulou P, Rimm D, Psyrri A. PARP inhibitors in head and neck cancer: Molecular mechanisms, preclinical and clinical data. Oral Oncol 2021; 117:105292. [PMID: 33862558 DOI: 10.1016/j.oraloncology.2021.105292] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/13/2022]
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) have revolutionized the treatment landscape in several cancers. PARPi increase DNA damage particularly in tumors with underlying defects in DNA repair. In addition to PARPi-induced DNA damage, PARPi enhance immune priming and induce adaptive upregulation of programmed death ligand 1 (PD-L1) expression. Patients with head and neck squamous cell carcinoma (HNSCC) are characterized by aberrant DNA repair pathways, including nucleotide excision repair (NER), base excision repair (BER) and DNA double-strand breaks (DSBs) repair and these deregulated repair mechanisms are implicated in both the pathogenesis of the disease and the outcome of therapy. Cisplatin represents the cornerstone of treatment of HNSCC and cisplatin resistance impedes successful treatment outcomes. To this end, research strategies that are testing modulation of cisplatin sensitivity by PARPi are of particular interest. Moreover, given the immune modulating effects of PARPi and the recent approval of Programmed Cell Death- 1 (PD-1) checkpoint inhibitors in HNSCC, the design of trials combining PARPi and PD-1 checkpoint inhibitors represent a rational research strategy. In this review, we summarize data supporting the integration of PARP inhibitors into HNSCC therapeutic strategy.
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Affiliation(s)
- Myrto Moutafi
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Panagiota Economopoulou
- Section of Medical Oncology, 2(nd) Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - David Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Amanda Psyrri
- Section of Medical Oncology, 2(nd) Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
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Wang HC, Chan LP, Wu CC, Chang SJ, Moi SH, Luo CW, Pan MR. Silencing DNA Polymerase β Induces Aneuploidy as a Biomarker of Poor Prognosis in Oral Squamous Cell Cancer. Int J Mol Sci 2021; 22:ijms22052402. [PMID: 33673690 PMCID: PMC7957714 DOI: 10.3390/ijms22052402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Most patients with oral squamous cell cancer (OSCC) have a locally advanced stage at diagnosis. The treatment strategies are diverse, including surgery, radiotherapy and chemotherapy. Despite multimodality treatment, the response rate is unsatisfactory. DNA repair and genetic instability are highly associated with carcinogenesis and treatment outcomes in oral squamous cell cancer, affecting cell growth and proliferation. Therefore, focusing on DNA repair and genetic instability interactions could be a potential target for improving the outcomes of OSCC patients. DNA polymerase-β (POLB) is an important enzyme in base excision repair and contributes to gene instability, leading to tumorigenesis and cancer metastasis. The aim of our study was to confirm POLB regulates the growth of OSCC cells through modulation of cell cycle and chromosomal instability. We analyzed a tissue array from 133 OSCC patients and discovered that low POLB expression was associated with advanced tumor stage and poor overall survival. In multivariate Cox proportional hazards regression analysis, low POLB expression and advanced lymph node status were significantly associated with poor survival. By performing in vitro studies on model cell lines, we demonstrated that POLB silencing regulated cell cycles, exacerbated mitotic abnormalities and enhanced cell proliferation. After POLB depletion, OSCC cells showed chromosomal instability and aneuploidy. Thus, POLB is an important maintainer of karyotypic stability in OSCC cells.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Leong-Perng Chan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Otolaryngology-Head and Neck Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Otorhinolaryngology-Head and Neck Surgery, Kaohsiung Municipal Ta-Tung Hospital and Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shu-Jyuan Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Sin-Hua Moi
- Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, No.1, Sec. 1, Syuecheng Rd., Dashu District, Kaohsiung 84001, Taiwan;
| | - Chi-Wen Luo
- Department of Surgery, Division of Breast Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan;
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-7-3121101-5092-34; Fax: +886-7-3218309
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Morris BB, Wages NA, Grant PA, Stukenberg PT, Gentzler RD, Hall RD, Akerley WL, Varghese TK, Arnold SM, Williams TM, Coppola V, Jones DR, Auble DT, Mayo MW. MYBL2-Driven Transcriptional Programs Link Replication Stress and Error-prone DNA Repair With Genomic Instability in Lung Adenocarcinoma. Front Oncol 2021; 10:585551. [PMID: 33489883 PMCID: PMC7821388 DOI: 10.3389/fonc.2020.585551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/16/2020] [Indexed: 12/21/2022] Open
Abstract
It has long been recognized that defects in cell cycle checkpoint and DNA repair pathways give rise to genomic instability, tumor heterogeneity, and metastasis. Despite this knowledge, the transcription factor-mediated gene expression programs that enable survival and proliferation in the face of enormous replication stress and DNA damage have remained elusive. Using robust omics data from two independent studies, we provide evidence that a large cohort of lung adenocarcinomas exhibit significant genome instability and overexpress the DNA damage responsive transcription factor MYB proto-oncogene like 2 (MYBL2). Across two studies, elevated MYBL2 expression was a robust marker of poor overall survival and disease-free survival outcomes, regardless of disease stage. Clinically, elevated MYBL2 expression identified patients with aggressive early onset disease, increased lymph node involvement, and increased incidence of distant metastases. Analysis of genomic sequencing data demonstrated that MYBL2 High lung adenocarcinomas had elevated somatic mutation burden, widespread chromosomal alterations, and alterations in single-strand DNA break repair pathways. In this study, we provide evidence that impaired single-strand break repair, combined with a loss of cell cycle regulators TP53 and RB1, give rise to MYBL2-mediated transcriptional programs. Omics data supports a model wherein tumors with significant genomic instability upregulate MYBL2 to drive genes that control replication stress responses, promote error-prone DNA repair, and antagonize faithful homologous recombination repair. Our study supports the use of checkpoint kinase 1 (CHK1) pharmacological inhibitors, in targeted MYBL2 High patient cohorts, as a future therapy to improve lung adenocarcinoma patient outcomes.
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Affiliation(s)
- Benjamin B. Morris
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Department of Pathology, University of Virginia, Charlottesville, VA, United States
| | - Nolan A. Wages
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Patrick A. Grant
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL, United States
| | - P. Todd Stukenberg
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Ryan D. Gentzler
- Division of Medical Oncology, Department of Internal Medicine, Hematology/Oncology, University of Virginia Health System, Charlottesville, VA, United States
| | - Richard D. Hall
- Division of Medical Oncology, Department of Internal Medicine, Hematology/Oncology, University of Virginia Health System, Charlottesville, VA, United States
| | - Wallace L. Akerley
- Department of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, Salt Lake City, UT, United States
| | - Thomas K. Varghese
- Division of Thoracic Surgery, Department of Surgery, University of Utah, Salt Lake City, UT, United States
| | - Susanne M. Arnold
- Department of Internal Medicine, Division of Medical Oncology, Markey Cancer Center, Lexington, KY, United States
| | - Terence M. Williams
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - David R. Jones
- Department of Thoracic Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, United States
| | - David T. Auble
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Marty W. Mayo
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, United States
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Chen B, Lai J, Dai D, Chen R, Liao N, Gao G, Tang H. PARPBP is a prognostic marker and confers anthracycline resistance to breast cancer. Ther Adv Med Oncol 2020; 12:1758835920974212. [PMID: 33281951 PMCID: PMC7692344 DOI: 10.1177/1758835920974212] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/23/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND PARPBP (PARP1 binding protein) is an important suppressor of homologous recombination during DNA repair, but the expression and function of PARPBP in breast cancer remain unclear. METHODS PARPBP expression was analyzed in breast cancer patient samples and public datasets for its correlation with clinical outcome. The function of PARPBP in breast cancer cell proliferation and anthracycline treatment response were studied both in vitro and in vivo. RESULTS PARPBP was upregulated significantly at both mRNA and protein levels in breast cancer tissues compared with normal breast tissues. PARPBP high expression group had poorer overall survival (OS) than the PARPBP low expression group. Knockdown of PARPBP suppressed breast cancer cell proliferation and colony formation while overexpression of PARPBP did the opposite. We found that transcription factor forkhead box M1 (FOXM1) could activate PARPBP expression by directly binding to the promoter of PARPBP. In addition, high expression of PARPBP related with anthracycline resistance in breast cancer. Depletion of PARPBP increased breast cancer cell apoptosis and DNA damage caused by epirubicin. Moreover, tumor xenograft experiments further demonstrated that PARPBP was involved in breast cancer anthracycline resistance. CONCLUSION Taken together, our results highlight that PARPBP is a prognostic marker and confers anthracycline resistance on breast cancer.
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Affiliation(s)
- Bo Chen
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China
| | - Jianguo Lai
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Danian Dai
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Rong Chen
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China
| | - Guanfeng Gao
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hailin Tang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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Targeting Rad51 as a strategy for the treatment of melanoma cells resistant to MAPK pathway inhibition. Cell Death Dis 2020; 11:581. [PMID: 32719412 PMCID: PMC7385107 DOI: 10.1038/s41419-020-2702-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 11/09/2022]
Abstract
Rad51 is an essential factor of the homologous recombination DNA repair pathway and therefore plays an important role in maintaining genomic stability. We show that RAD51 and other homologous recombination repair genes are overexpressed in metastatic melanoma cell lines and in melanoma patient samples, which correlates with reduced survival of melanoma patients. In addition, Rad51 expression in melanoma cells was regulated on a transcriptional level by the MAPK signaling pathway with Elk1 as the main downstream transcriptional effector. Most strikingly, melanoma cells which developed resistance towards MAPK inhibitors could be efficiently targeted by Rad51 inhibitors similar to their sensitive counterparts, leading to DNA damage, G2/M arrest and apoptosis. Furthermore, the treatment of MAPK inhibitor resistant cells with Rad51 inhibitors enhances the susceptibility of these cells for MAPK inhibitor treatment in vitro and in vivo. These data indicate that Rad51 plays a critical role in the survival of metastatic melanoma cells and is a promising target for the therapy of melanoma irrespective of its MAPK inhibitor resistance status.
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Wanigasooriya K, Tyler R, Barros-Silva JD, Sinha Y, Ismail T, Beggs AD. Radiosensitising Cancer Using Phosphatidylinositol-3-Kinase (PI3K), Protein Kinase B (AKT) or Mammalian Target of Rapamycin (mTOR) Inhibitors. Cancers (Basel) 2020; 12:E1278. [PMID: 32443649 PMCID: PMC7281073 DOI: 10.3390/cancers12051278] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Radiotherapy is routinely used as a neoadjuvant, adjuvant or palliative treatment in various cancers. There is significant variation in clinical response to radiotherapy with or without traditional chemotherapy. Patients with a good response to radiotherapy demonstrate better clinical outcomes universally across different cancers. The PI3K/AKT/mTOR pathway upregulation has been linked to radiotherapy resistance. We reviewed the current literature exploring the role of inhibiting targets along this pathway, in enhancing radiotherapy response. We identified several studies using in vitro cancer cell lines, in vivo tumour xenografts and a few Phase I/II clinical trials. Most of the current evidence in this area comes from glioblastoma multiforme, non-small cell lung cancer, head and neck cancer, colorectal cancer, and prostate cancer. The biological basis for radiosensitivity following pathway inhibition was through inhibited DNA double strand break repair, inhibited cell proliferation, enhanced apoptosis and autophagy as well as tumour microenvironment changes. Dual PI3K/mTOR inhibition consistently demonstrated radiosensitisation of all types of cancer cells. Single pathway component inhibitors and other inhibitor combinations yielded variable outcomes especially within early clinical trials. There is ample evidence from preclinical studies to suggest that direct pharmacological inhibition of the PI3K/AKT/mTOR pathway components can radiosensitise different types of cancer cells. We recommend that future in vitro and in vivo research in this field should focus on dual PI3K/mTOR inhibitors. Early clinical trials are needed to assess the feasibility and efficacy of these dual inhibitors in combination with radiotherapy in brain, lung, head and neck, breast, prostate and rectal cancer patients.
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Affiliation(s)
- Kasun Wanigasooriya
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (J.D.B.-S.); (Y.S.); (A.D.B.)
- The New Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham B15 2TH, UK; (R.T.); (T.I.)
| | - Robert Tyler
- The New Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham B15 2TH, UK; (R.T.); (T.I.)
| | - Joao D. Barros-Silva
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (J.D.B.-S.); (Y.S.); (A.D.B.)
| | - Yashashwi Sinha
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (J.D.B.-S.); (Y.S.); (A.D.B.)
- The New Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham B15 2TH, UK; (R.T.); (T.I.)
| | - Tariq Ismail
- The New Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham B15 2TH, UK; (R.T.); (T.I.)
| | - Andrew D. Beggs
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (J.D.B.-S.); (Y.S.); (A.D.B.)
- The New Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham B15 2TH, UK; (R.T.); (T.I.)
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Gralewska P, Gajek A, Marczak A, Rogalska A. Participation of the ATR/CHK1 pathway in replicative stress targeted therapy of high-grade ovarian cancer. J Hematol Oncol 2020; 13:39. [PMID: 32316968 PMCID: PMC7175546 DOI: 10.1186/s13045-020-00874-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer is one of the most lethal gynecologic malignancies reported throughout the world. The initial, standard-of-care, adjuvant chemotherapy in epithelial ovarian cancer is usually a platinum drug, such as cisplatin or carboplatin, combined with a taxane. However, despite surgical removal of the tumor and initial high response rates to first-line chemotherapy, around 80% of women will develop cancer recurrence. Effective strategies, including chemotherapy and new research models, are necessary to improve the prognosis. The replication stress response (RSR) is characteristic of the development of tumors, including ovarian cancer. Hence, RSR pathway and DNA repair proteins have emerged as a new area for anticancer drug development. Although clinical trials have shown poly (ADP-ribose) polymerase inhibitors (PARPi) response rates of around 40% in women who carry a mutation in the BRCA1/2 genes, PARPi is responsible for tumor suppression, but not for complete tumor regression. Recent reports suggest that cells with impaired homologous recombination (HR) activities due to mutations in TP53 gene or specific DNA repair proteins are specifically sensitive to ataxia telangiectasia and Rad3-related protein (ATR) inhibitors. Replication stress activates DNA repair checkpoint proteins (ATR, CHK1), which prevent further DNA damage. This review describes the use of DNA repair checkpoint inhibitors as single agents and strategies combining these inhibitors with DNA-damaging compounds for ovarian cancer therapy, as well as the new platforms used for optimizing ovarian cancer therapy.
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Affiliation(s)
- Patrycja Gralewska
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Arkadiusz Gajek
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Agnieszka Marczak
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Aneta Rogalska
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, Institute of Biophysics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
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Prediction of Poor Response to Neoadjuvant Chemoradiation in Patients With Rectal Cancer Using a DNA Repair Deregulation Score: Picking the Losers Instead of the Winners. Dis Colon Rectum 2020; 63:300-309. [PMID: 31842156 DOI: 10.1097/dcr.0000000000001564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Patients with rectal cancer may undergo neoadjuvant chemoradiation even in early stages in an attempt to achieve complete clinical response and undergo organ preservation. However, prediction of tumor response is unavailable. In this setting, accurate identification of poor responders could spare patients with early stage disease from potentially unnecessary chemoradiation. OBJECTIVE This study focused on development/test of a score based on DNA repair gene expression to predict response to neoadjuvant chemoradiation in patients with rectal cancer. DESIGN Pretreatment biopsy samples from patients with rectal cancer undergoing neoadjuvant chemoradiation were collected and underwent gene expression analysis using RNA-Seq (test cohort). A score was constructed using 8 differentially expressed DNA repair genes between good (complete clinical) and poor responders (incomplete clinical) to treatment. The score was validated in 2 independent cohorts of patients undergoing similar treatment strategies and using quantitative polymerase chain reaction and microarray gene expression data. SETTINGS This was a retrospective analysis of gene expression data from 3 independent institutions. PATIENTS Patients with rectal cancer undergoing neoadjuvant chemoradiation (50.4-54.0 Gy and 5-fluorouracil-based chemotherapy) were eligible. Patients with complete clinical response, complete pathological response, or ≤10% residual cancer cells were considered good responders. Patients with >10% residual cancer cells were considered poor responders. The test cohort included 25 patients (16 poor responders). Validation cohort 1 included 28 patients (18 poor responders), and validation cohort 2 included 46 patients (22 poor responders). MAIN OUTCOMES MEASURES Response was correlated with the DNA repair score calculated using the expression levels of 8 DNA repair genes. DNA repair score sensitivity, specificity, and positive and negative predictive values were determined in test and validation cohorts. RESULTS Poor responders had significantly lower DNA repair scores when compared with good responders across all 3 cohorts, regardless of the gene expression platform used. A low score correctly predicted poor response in 93%, 90%, and 71% in test, validation 1, and validation 2 cohorts. LIMITATIONS This study was limited by its small sample size, different gene expression platforms, and treatment regimens across different cohorts used. CONCLUSIONS A DNA repair gene score may predict patients likely to have poor response to chemoradiation. This score may be a relevant tool to be investigated in future studies focused on chemoradiation used in the context of organ preservation. See Video Abstract at http://links.lww.com/DCR/B104. PREDICCIÓN DE RESPUESTA DEFICIENTE A LA RADIO-QUIMIOTERAPIA NEOADYUVANTE EN PACIENTES CON CÁNCER RECTAL UTILIZANDO UNA PUNTUACIÓN DE DESREGULACIÓN DE REPARACIÓN DE ADN: ESCOGER LOS PERDEDORES EN LUGAR DE LOS GANADORES: Los pacientes con cáncer rectal pueden someterse a radio-quimioterapia neoadyuvante incluso en estadios tempranos en el intento por lograr una respuesta clínica completa y permitir una preservación de órgano. Sin embargo, aun no existen herramientas disponible para la prediccion de la respuesta tumoral al tratamiento. En este contexto, la identificación precisa de los tumores con mala respuesta al tratamiento podría evitar que los pacientes con enfermedad en estadio temprano sean sometidos a radio-quimioterapia potencialmente innecesaria.Desarrollo / testeo de una puntuación basada en la expresión genes reparadores del ADN para predecir la respuesta a la nCRT en pacientes con cáncer rectal.Se recogieron muestras de biopsia de pre-tratamiento de pacientes con cáncer rectal sometidos a radio-quimioterapia neoadyuvante y se les realizó un análisis de expresión génica utilizando RNAseq (cohorte de prueba). Se construyó una puntuación utilizando 8 genes de reparación de ADN expresados diferencialmente entre buenos (respuesta clinica completa) y pobres respondedores (respuesta clinica incompleta) al tratamiento. La puntuación se validó en 2 cohortes independientes de pacientes sometidos a estrategias de tratamiento similares y utilizando qPCR y datos de expresión de genes en chips ADN (biotecnología -microarrays).Análisis retrospectivo de los datos de expresión génica de 3 instituciones independientes.Fueron incluidos aquellos pacientes con cáncer rectal sometidos a radio-quimioterapia neoadyuvante (50,4-54 Gy y quimioterapia basada en 5FU). Los pacientes con respuesta clínica completa, respuesta patológica completa o ≤10% de células cancerosas residuales se consideraron buenos respondedores. Los pacientes con> 10% de células cancerosas residuales se consideraron de respuesta deficiente. La cohorte de prueba incluyó a 25 pacientes (16 respondedores pobres). La cohorte de validación n. ° 1 incluyó a 28 pacientes (18 respondedores pobres) y la cohorte de validación n. ° 2 incluyó a 46 pacientes (22 respondedores pobres).La respuesta se correlacionó con la puntuación de reparación de ADN calculada utilizando los niveles de expresión de 8 genes de reparación de ADN. La sensibilidad del puntaje de reparación del ADN, la especificidad, los valores predictivos positivos y negativos se determinaron en las cohortes de prueba y validación.Los malos respondedores tuvieron puntuaciones de reparación de ADN significativamente más bajas en comparación con los buenos respondedores en las 3 cohortes, independientemente de la plataforma de expresión génica utilizada. Una puntuación baja predijo correctamente una respuesta pobre en el 93%, 90% y 71% en las cohortes de prueba, validación n. ° 1 y validación n. ° 2, respectivamente.Pequeño tamaño de la muestra, diferentes plataformas de expresión génica y regímenes de tratamiento en diferentes cohortes utilizadas.La puntuacion basada en genes de reparación del ADN puede predecir los pacientes con respuesta pobre a la radio-quimioterapia. Esta puntuación puede ser una herramienta relevante para investigar en futuros estudios centrados en la radio-quimioterapia utilizada en el contexto de la preservación de órganos. Consulte Video Resumen en http://links.lww.com/DCR/B104. (Traducción-Dr. Xavier Delgadillo and Dr. Laura Melina Fernandez).
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Zhou J, Li X, Zhang M, Gong J, Li Q, Shan B, Wang T, Zhang L, Zheng T, Li X. The aberrant expression of rhythm genes affects the genome instability and regulates the cancer immunity in pan-cancer. Cancer Med 2020; 9:1818-1829. [PMID: 31927791 PMCID: PMC7050078 DOI: 10.1002/cam4.2834] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 12/27/2019] [Indexed: 12/17/2022] Open
Abstract
Although emerging studies showed that certain rhythm genes regulate cancer progression, the expression and roles of the vast majority of rhythm genes in human cancer are largely unknown, and the hallmarks of cancer regulated by rhythm genes have not been detected. In this study, we detected the expression changes of rhythm genes in pan-cancer and found that almost all rhythm genes mutated in all cancer types, and their expression level was significantly altered partially due to abnormal methylation, and several rhythm genes regulate the expression of other rhythm genes in various cancer types. Furthermore, we revealed that rhythm genes are significantly enriched in genome instability and the expression of certain rhythm genes is correlated with the tumor mutation burden, microsatellite instability, and the expression of DNA damage repair genes in most of the detected cancer types. Moreover, rhythm genes are associated with the infiltration of immune cells and the efficiency of immune blockade therapy. This study provides a comprehensive understanding of the roles of rhythm genes in cancer immunity, which may provide a novel method for the diagnosis and treatment of cancer.
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Affiliation(s)
- Jian Zhou
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Xinhui Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Ji'nan Gong
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Qi Li
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Baocong Shan
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Tianzhen Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Lei Zhang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Tongsen Zheng
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, China
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Willers H, Keane FK, Kamran SC. Toward a New Framework for Clinical Radiation Biology. Hematol Oncol Clin North Am 2019; 33:929-945. [PMID: 31668212 DOI: 10.1016/j.hoc.2019.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Radiation biology has entered the era of precision oncology, and this article reviews time-tested factors that determine the effects of fractionated radiation therapy in a wide variety of tumor types and normal tissues: the association of tumor control with radiation dose, the importance of fractionation and overall treatment time, and the role of tumor hypoxia. Therapeutic gain can only be achieved if the increased tumor toxicity produced by biological treatment modifications is balanced against injury to early-responding and late-responding normal tissues. Developments in precision oncology and immuno-oncology will allow an emphasis on treatment individualization and predictive biomarker development.
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Affiliation(s)
- Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA.
| | - Florence K Keane
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA. https://twitter.com/KatieKeaneMD
| | - Sophia C Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA. https://twitter.com/sophia_kamran
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40
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Essers PBM, van der Heijden M, Verhagen CVM, Ploeg EM, de Roest RH, Leemans CR, Brakenhoff RH, van den Brekel MWM, Bartelink H, Verheij M, Vens C. Drug Sensitivity Prediction Models Reveal a Link between DNA Repair Defects and Poor Prognosis in HNSCC. Cancer Res 2019; 79:5597-5611. [PMID: 31515237 DOI: 10.1158/0008-5472.can-18-3388] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/16/2019] [Accepted: 09/05/2019] [Indexed: 11/16/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is characterized by the frequent manifestation of DNA crosslink repair defects. We established novel expression-based DNA repair defect markers to determine the clinical impact of such repair defects. Using hypersensitivity to the DNA crosslinking agents, mitomycin C and olaparib, as proxies for functional DNA repair defects in a panel of 25 HNSCC cell lines, we applied machine learning to define gene expression models that predict repair defects. The expression profiles established predicted hypersensitivity to DNA-damaging agents and were associated with mutations in crosslink repair genes, as well as downregulation of DNA damage response and repair genes, in two independent datasets. The prognostic value of the repair defect prediction profiles was assessed in two retrospective cohorts with a total of 180 patients with advanced HPV-negative HNSCC, who were treated with cisplatin-based chemoradiotherapy. DNA repair defects, as predicted by the profiles, were associated with poor outcome in both patient cohorts. The poor prognosis association was particularly strong in normoxic tumor samples and was linked to an increased risk of distant metastasis. In vitro, only crosslink repair-defective HNSCC cell lines are highly migratory and invasive. This phenotype could also be induced in cells by inhibiting rad51 in repair competent and reduced by DNA-PK inhibition. In conclusion, DNA crosslink repair prediction expression profiles reveal a poor prognosis association in HNSCC. SIGNIFICANCE: This study uses innovative machine learning-based approaches to derive models that predict the effect of DNA repair defects on treatment outcome in HNSCC.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/21/5597/F1.large.jpg.
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Affiliation(s)
- Paul B M Essers
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Martijn van der Heijden
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Caroline V M Verhagen
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Emily M Ploeg
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Reinout H de Roest
- Department of Otolaryngology/Head and Neck Surgery, VUmc Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - C René Leemans
- Department of Otolaryngology/Head and Neck Surgery, VUmc Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Ruud H Brakenhoff
- Department of Otolaryngology/Head and Neck Surgery, VUmc Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Michiel W M van den Brekel
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Harry Bartelink
- Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marcel Verheij
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Conchita Vens
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
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Kiratipaiboon C, Stueckle TA, Ghosh R, Rojanasakul LW, Chen YC, Dinu CZ, Rojanasakul Y. Acquisition of Cancer Stem Cell-like Properties in Human Small Airway Epithelial Cells after a Long-term Exposure to Carbon Nanomaterials. ENVIRONMENTAL SCIENCE. NANO 2019; 6:2152-2170. [PMID: 31372228 PMCID: PMC6675031 DOI: 10.1039/c9en00183b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cancer stem cells (CSCs) are a key driver of tumor formation and metastasis, but how they are affected by nanomaterials is largely unknown. The present study investigated the effects of different carbon-based nanomaterials (CNMs) on neoplastic and CSC-like transformation of human small airway epithelial cells and determined the underlying mechanisms. Using a physiologically relevant exposure model (long-term/low-dose) with system validation using a human carcinogen, asbestos, we demonstrated that single-walled carbon nanotubes, multi-walled carbon nanotubes, ultrafine carbon black, and crocidolite asbestos induced particle-specific anchorage-independent colony formation, DNA-strand break, and p53 downregulation, indicating genotoxicity and carcinogenic potential of CNMs. The chronic CNM-exposed cells exhibited CSC-like properties as indicated by 3D spheroid formation, anoikis resistance, and CSC markers expression. Mechanistic studies revealed specific self-renewal and epithelial-mesenchymal transition (EMT)-related transcription factors that are involved in the cellular transformation process. Pathway analysis of gene signaling networks supports the role of SOX2 and SNAI1 signaling in CNM-mediated transformation. These findings support the potential carcinogenicity of high aspect ratio CNMs and identified molecular targets and signaling pathways that may contribute to the disease development.
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Affiliation(s)
- Chayanin Kiratipaiboon
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia, 26506, United States
| | - Todd A Stueckle
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, 26505, United States
| | - Rajib Ghosh
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia, 26506, United States
| | - Liying W Rojanasakul
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, 26505, United States
| | - Yi Charlie Chen
- College of Science, Technology and Mathematics, Alderson Broaddus University, Philippi, West Virginia, 26416, United States
| | - Cerasela Zoica Dinu
- Department of Chemical Engineering, West Virginia University, Morgantown, West Virginia, 26506, United States
| | - Yon Rojanasakul
- Department of Pharmaceutical Sciences and WVU Cancer Institute, West Virginia University, Morgantown, West Virginia, 26506, United States
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Nicolae CM, O'Connor MJ, Schleicher EM, Song C, Gowda R, Robertson G, Dovat S, Moldovan GL. PARI (PARPBP) suppresses replication stress-induced myeloid differentiation in leukemia cells. Oncogene 2019; 38:5530-5540. [PMID: 30967629 DOI: 10.1038/s41388-019-0810-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/22/2019] [Accepted: 03/19/2019] [Indexed: 01/06/2023]
Abstract
Hyperproliferative cancer cells face increased replication stress, which can result in accumulation of DNA damage. As DNA damage can arrest proliferation, and, in the case of myeloid leukemia, induce differentiation of cancer cells, understanding the mechanisms that regulate the replication stress response is paramount. Here, we show that PARI, a replisome protein involved in regulating DNA repair and replication stress, suppresses differentiation of myeloid leukemia cells. We show that PARI is overexpressed in myeloid leukemia cells, and its knockdown reduces leukemia cell proliferation in vitro and in vivo in xenograft mouse models. PARI depletion enhances replication stress and DNA-damage accumulation, coupled with increased myeloid differentiation. Mechanistically, we show that PARI inhibits activation of the NF-κB pathway, which can initiate p21-mediated differentiation and proliferation arrest. Finally, we show that PARI expression negatively correlates with expression of differentiation markers in clinical myeloid leukemia samples, suggesting that targeting PARI may restore differentiation ability of leukemia cells and antagonize their proliferation.
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Affiliation(s)
- Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Michael J O'Connor
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Chunhua Song
- Department of Pediatrics, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Raghavendra Gowda
- Department of Pharmacology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Gavin Robertson
- Department of Pharmacology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Sinisa Dovat
- Department of Pediatrics, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
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43
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Thompson TC, Liu B, Li L. N-MYC regulation of DNA damage response in neuroendocrine prostate cancer: mechanistic insight and novel combination therapy approaches. Oncoscience 2018; 5:273-275. [PMID: 30652111 PMCID: PMC6326739 DOI: 10.18632/oncoscience.462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Timothy C Thompson
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Bo Liu
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Likun Li
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
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Hu LB, Chen Y, Meng XD, Yu P, He X, Li J. Nucleotide Excision Repair Factor XPC Ameliorates Prognosis by Increasing the Susceptibility of Human Colorectal Cancer to Chemotherapy and Ionizing Radiation. Front Oncol 2018; 8:290. [PMID: 30109214 PMCID: PMC6079218 DOI: 10.3389/fonc.2018.00290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 07/10/2018] [Indexed: 01/20/2023] Open
Abstract
Nucleotide excision repair (NER) is a DNA damage repair mechanism in mammals, but the relationship between NER and human colorectal cancer (HRC) progression has not been clarified yet. In this study, the expression of the NER genes XPA, XPC, XPF, XPG, ERCC1, and XPD was measured in normal and cancerous human colorectal tissue. Among them, only the XPC gene expression was significantly increased in colorectal cancer tissue. To establish the role of XPC in colorectal cancer, small interference RNA (siRNA) targeting XPC was used to knockdown the expression of XPC in HRC cell lines. In addition, an expression vector plasmid containing the XPC cDNA was constructed and stably transfected into HRC cell lines to overexpress the XPC gene. Interestingly, MTT and apoptosis assay demonstrated that XPC gene overexpression significantly increased the susceptibility of HRC cell lines to cisplatin and X-ray radiation. In order to study the relationship between XPC expression and the progression of HRC, XPC expression was measured in 167 patients with colorectal cancer. The results showed that patients with high XPC expression had longer survival time. Cox regression analysis showed that high XPC expression might be a potential predictive factor for colorectal cancer. In conclusion, XPC plays a key role in the susceptibility of colorectal cancer to chemotherapy and ionizing radiation and is associated with a good patients' prognosis.
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Affiliation(s)
- Liang-Bo Hu
- Department of Radiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Yin Chen
- Department of General Surgery, The People's Liberation Army 324 Hospital, Chongqing, China
| | - Xiao-Dong Meng
- Department of Urology, Bethune International Peace Hospital, Shijiazhuang, China
| | - Pan Yu
- Department of Burn and Plastic Surgery, Jinling Hospital, Nanjing, China
| | - Xu He
- Department of General Surgery, The People's Liberation Army 324 Hospital, Chongqing, China
| | - Jie Li
- Department of Nephrology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
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45
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Toward A variable RBE for proton beam therapy. Radiother Oncol 2018; 128:68-75. [PMID: 29910006 DOI: 10.1016/j.radonc.2018.05.019] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/09/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022]
Abstract
In the clinic, proton beam therapy (PBT) is based on the use of a generic relative biological effectiveness (RBE) of 1.1 compared to photons in human cancers and normal tissues. However, the experimental basis for this RBE lacks any significant number of representative tumor models and clinically relevant endpoints for dose-limiting organs at risk. It is now increasingly appreciated that much of the variations of treatment responses in cancers are due to inter-tumoral genomic heterogeneity. Indeed, recently it has been shown that defects in certain DNA repair pathways, which are found in subsets of many cancers, are associated with a RBE increase in vitro. However, there currently exist little in vivo or clinical data that confirm the existence of similarly increased RBE values in human cancers. Furthermore, evidence for variable RBE values for normal tissue toxicity has been sparse and conflicting to date. If we could predict variable RBE values in patients, we would be able to optimally use and personalize PBT. For example, predictive tumor biomarkers may facilitate selection of patients with proton-sensitive cancers previously ineligible for PBT. Dose de-escalation may be possible to reduce normal tissue toxicity, especially in pediatric patients. Knowledge of increased tumor RBE may allow us to develop biologically optimized therapies to enhance local control while RBE biomarkers for normal tissues could lead to a better understanding and prevention of unusual PBT-associated toxicity. Here, we will review experimental data on the repair of proton damage to DNA that impact both RBE values and biophysical modeling to predict RBE variations. Experimental approaches for studying proton sensitivity in vitro and in vivo will be reviewed as well and recent clinical findings discussed. Ultimately, therapeutically exploiting the understudied biological advantages of protons and developing approaches to limit treatment toxicity should fundamentally impact the clinical use of PBT.
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46
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Kamran SC, Mouw KW. Applying Precision Oncology Principles in Radiation Oncology. JCO Precis Oncol 2018; 2:PO.18.00034. [PMID: 32914000 PMCID: PMC7446508 DOI: 10.1200/po.18.00034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Radiation therapy is a critical component in the curative management of many solid tumor types, and advances in radiation delivery techniques during the past decade have led to improved disease control and quality of life for patients. During the same period, remarkable advances have also been made in understanding the genomic landscape of tumors; however, treatment decisions in radiation oncology continue to depend primarily on clinical and histopathologic characteristics rather than on the genetic features of the tumor or the patient. With the development of novel genomic techniques and their increasing use in clinical practice, radiation oncology is uniquely positioned to leverage these advances to identify novel biomarkers that could inform radiation dose, field, and the use of concurrent systemic agents. Here, we summarize efforts to use genomic techniques to guide radiation decisions, and we highlight some of the current opportunities and challenges that exist in attempting to apply precision oncology principles in radiation oncology.
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Affiliation(s)
- Sophia C. Kamran
- Sophia C. Kamran and Kent W. Mouw, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School; and Sophia C. Kamran, Harvard Radiation Oncology Program, Boston, MA
| | - Kent W. Mouw
- Sophia C. Kamran and Kent W. Mouw, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School; and Sophia C. Kamran, Harvard Radiation Oncology Program, Boston, MA
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47
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Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep 2018; 23:239-254.e6. [PMID: 29617664 PMCID: PMC5961503 DOI: 10.1016/j.celrep.2018.03.076] [Citation(s) in RCA: 760] [Impact Index Per Article: 108.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 12/20/2022] Open
Abstract
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53 and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3 in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53 mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.
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Affiliation(s)
| | - Linghua Wang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509, USA; Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | | | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Feng
- TESARO Inc., Waltham, MA 02451, USA
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase Miller
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Haoran Chen
- Department of Electrical and Computer Engineering, 3128 TAMU, Texas A&M University, College Station, TX 77843, USA
| | - Pora Kim
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Matthew H Bailey
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA 94115, USA; Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Denise Wolf
- University of California, San Francisco, San Francisco, CA 94115, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer, Houston, TX 77030, USA
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA; Department of Genetics, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Raymond J Monnat
- Departments of Pathology & Genome Sciences, University of Washington, Seattle, WA 98195-7705, USA.
| | | | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA; Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
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48
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Kirsch DG, Diehn M, Kesarwala AH, Maity A, Morgan MA, Schwarz JK, Bristow R, Demaria S, Eke I, Griffin RJ, Haas-Kogan D, Higgins GS, Kimmelman AC, Kimple RJ, Lombaert IM, Ma L, Marples B, Pajonk F, Park CC, Schaue D, Tran PT, Willers H, Wouters BG, Bernhard EJ. The Future of Radiobiology. J Natl Cancer Inst 2018; 110:329-340. [PMID: 29126306 PMCID: PMC5928778 DOI: 10.1093/jnci/djx231] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/19/2017] [Accepted: 10/06/2017] [Indexed: 12/23/2022] Open
Abstract
Innovation and progress in radiation oncology depend on discovery and insights realized through research in radiation biology. Radiobiology research has led to fundamental scientific insights, from the discovery of stem/progenitor cells to the definition of signal transduction pathways activated by ionizing radiation that are now recognized as integral to the DNA damage response (DDR). Radiobiological discoveries are guiding clinical trials that test radiation therapy combined with inhibitors of the DDR kinases DNA-dependent protein kinase (DNA-PK), ataxia telangiectasia mutated (ATM), ataxia telangiectasia related (ATR), and immune or cell cycle checkpoint inhibitors. To maintain scientific and clinical relevance, the field of radiation biology must overcome challenges in research workforce, training, and funding. The National Cancer Institute convened a workshop to discuss the role of radiobiology research and radiation biologists in the future scientific enterprise. Here, we review the discussions of current radiation oncology research approaches and areas of scientific focus considered important for rapid progress in radiation sciences and the continued contribution of radiobiology to radiation oncology and the broader biomedical research community.
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Affiliation(s)
- David G Kirsch
- Department of Radiation Oncology and Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC
| | - Max Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA
| | | | - Amit Maity
- Department of Radiation Oncology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - Julie K Schwarz
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Robert Bristow
- Department of Radiation Oncology, Princess Margaret Cancer Center, Toronto, ON, Canada
| | - Sandra Demaria
- Department of Radiation Oncology and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Iris Eke
- Radiation Oncology Branch, National Institutes of Health, Bethesda, MD
| | - Robert J Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Daphne Haas-Kogan
- Department of Radiation Oncology, Harvard Medical School, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston Children's Hospital, Boston, MA
| | - Geoff S Higgins
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Alec C Kimmelman
- Perlmutter Cancer Center and Department of Radiation Oncology, New York University Langone Medical Center, New York, NY
| | - Randall J Kimple
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Isabelle M Lombaert
- Department of Biologic and Materials Sciences, Biointerfaces Institute, School of Dentistry, University of Michigan, Ann Arbor, MI
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Brian Marples
- Department of Radiation Oncology, University of Miami, Miami, FL
| | - Frank Pajonk
- Department of Radiation Oncology, University of California, Los Angeles, CA
| | - Catherine C Park
- David Geffen School of Medicine, University of California, Los Angeles, CA
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Dörthe Schaue
- Division of Molecular and Cellular Oncology, University of California, Los Angeles, CA
| | - Phuoc T. Tran
- Department of Radiation Oncology and Molecular Radiation Sciences, Oncology and Urology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Brad G. Wouters
- Department of Radiation Oncology (RB), Princess Margaret Cancer Center
| | - Eric J Bernhard
- Radiation Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD
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49
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Peng G, Mills GB. Surviving Ovarian Cancer: An Affair between Defective DNA Repair and RB1. Clin Cancer Res 2017; 24:508-510. [PMID: 29191971 DOI: 10.1158/1078-0432.ccr-17-3022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/09/2017] [Accepted: 11/27/2017] [Indexed: 01/09/2023]
Abstract
Detailed clinical and molecular evaluation of large cohorts of exceptional survivors provides an unprecedented opportunity to identify mechanisms underlying long-term survival that can drive future therapeutic approaches and biomarker development. Exceptional survivors of high-grade serous ovarian cancer demonstrate concurrent disruption of homologous recombination DNA repair and retinoblastoma protein. Clin Cancer Res; 24(3); 508-10. ©2017 AACRSee related article by Garsed et al., p. 569.
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Affiliation(s)
- Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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50
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Choe KN, Moldovan GL. Forging Ahead through Darkness: PCNA, Still the Principal Conductor at the Replication Fork. Mol Cell 2017; 65:380-392. [PMID: 28157503 DOI: 10.1016/j.molcel.2016.12.020] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/28/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) lies at the center of the faithful duplication of eukaryotic genomes. With its distinctive doughnut-shaped molecular structure, PCNA was originally studied for its role in stimulating DNA polymerases. However, we now know that PCNA does much more than promote processive DNA synthesis. Because of the complexity of the events involved, cellular DNA replication poses major threats to genomic integrity. Whatever predicament lies ahead for the replication fork, PCNA is there to orchestrate the events necessary to handle it. Through its many protein interactions and various post-translational modifications, PCNA has far-reaching impacts on a myriad of cellular functions.
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Affiliation(s)
- Katherine N Choe
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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