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Gao A, Wang X, Wang J, Zhong D, Zhang L. Homologous recombination deficiency status predicts response to immunotherapy-based treatment in non-small cell lung cancer patients. Thorac Cancer 2024; 15:1842-1853. [PMID: 39081050 PMCID: PMC11367659 DOI: 10.1111/1759-7714.15408] [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: 03/05/2024] [Revised: 06/11/2024] [Accepted: 07/04/2024] [Indexed: 09/03/2024] Open
Abstract
BACKGROUND Homologous recombination deficiency (HRD) is a biomarker that predicts response to ovarian cancer treatment with poly (ADP-ribose) polymerase (PARP) inhibitors or breast cancer treatment with first-line platinum-based chemotherapy. However, there are few studies on the prognosis of lung cancer patients treated with immune checkpoint inhibitor (ICI) therapy using HRD as a biomarker. METHODS We studied the relationship between HRD status and the effectiveness of first-line ICI-based therapy in EGFR/ALK wild-type metastatic non-small cell lung cancer patients (NSCLC) patients. RESULTS This study included 22 treatment naïve NSCLC patients. The HRD score ranged from -26.37 to 92.34, with an average of 24.57. Based on analysis of the progression-free survival (PFS) data from the included NSCLC patients, threshold traversal was carried out. HRD (+) was defined as an HRD score of 31 or higher. Kaplan-Meier PFS survival analysis showed prolonged median PFS (mPFS) in NSCLC patients with HRD (+) versus HRD (-) (N/A vs. 7.0 ms, log-rank p = 0.029; HR 0.20, 95% CI: 0.04-0.96, likelihood-ratio p = 0.03). In patients with PD-L1 TPS ≥50% and HRD score ≥31 (co-status high), the mPFS was temporarily not reached during the follow-up period. In patients with PD-L1 TPS <1% and HRD score <31, the mPFS was 3 ms. Cox regression analysis showed that the hazard ratio of the co-status was 0.14 (95% CI: 0.04-0.54), which was a good prognostic factor, and the prognostic effect of co-status was better than that of HRD score alone. CONCLUSION The HRD status can be identified as an independent significance in NSCLC patients treated with first-line ICI-based therapy.
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Affiliation(s)
- Ai Gao
- Department of Medical OncologyTianjin Medical University General HospitalTianjinChina
| | - Xin Wang
- Department of Medical OncologyTianjin Medical University General HospitalTianjinChina
| | - Jing Wang
- Department of Medical OncologyTianjin Medical University General HospitalTianjinChina
| | - Diansheng Zhong
- Department of Medical OncologyTianjin Medical University General HospitalTianjinChina
| | - Linlin Zhang
- Department of Medical OncologyTianjin Medical University General HospitalTianjinChina
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Lou Y, Chen Y, Guo K, Li B, Zheng S. Emerging biomarkers for immunotherapy response in biliary tract cancers: a comprehensive review of immune checkpoint inhibitor strategies. Biomark Med 2024:1-13. [PMID: 39143949 DOI: 10.1080/17520363.2024.2385297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/14/2024] [Indexed: 08/16/2024] Open
Abstract
Biliary tract cancers (BTCs) have rising incidence and mortality rates. Chemotherapy's limited efficacy has led to exploring new treatments like immunotherapy. which offers modest benefits. Moreover, the identification of reliable predictive biomarkers for immune checkpoint therapy in BTCs remains elusive, hindering personalized treatment strategies. This review provides an overview of the current landscape of emerging biomarkers for immunotherapy response in BTCs. We discuss the incremental benefits of combination therapy and the evolving role of immunotherapy in managing advanced BTC. Additionally, we highlight the need for robust predictive biomarkers to optimize treatment outcomes and foster a more individualized approach to patient care. We aim to identify promising research avenues and strategies to enhance therapeutic efficacy and patient survival in BTCs.
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Affiliation(s)
- Yidan Lou
- Zhejiang University School of Medicine, Hangzhou, 310006, China
- Department of Oncology, Hangzhou First People's Hospital, Hangzhou, 310006, China
| | - Yijing Chen
- Zhejiang University School of Medicine, Hangzhou, 310006, China
- Department of Oncology, Hangzhou First People's Hospital, Hangzhou, 310006, China
| | - Kaibo Guo
- Department of Oncology, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Key Laboratory of Clinical Cancer Pharmacology & Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Westlake University, Hangzhou, 310006, China
| | - Binbin Li
- Department of Oncology, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Department of Oncology, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310006, China
| | - Song Zheng
- Zhejiang University School of Medicine, Hangzhou, 310006, China
- Department of Oncology, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Key Laboratory of Clinical Cancer Pharmacology & Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Westlake University, Hangzhou, 310006, China
- Department of Oncology, The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310006, China
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Ding JH, Xiao Y, Yang F, Song XQ, Xu Y, Ding XH, Ding R, Shao ZM, Di GH, Jiang YZ. Guanosine diphosphate-mannose suppresses homologous recombination repair and potentiates antitumor immunity in triple-negative breast cancer. Sci Transl Med 2024; 16:eadg7740. [PMID: 38170790 DOI: 10.1126/scitranslmed.adg7740] [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: 01/22/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with poor prognosis. TNBCs with high homologous recombination deficiency (HRD) scores benefit from DNA-damaging agents, including platinum drugs and poly(ADP-ribose) polymerase (PARP) inhibitors, whereas those with low HRD scores still lack therapeutic options. Therefore, we sought to exploit metabolic alterations to induce HRD and sensitize DNA-damaging agents in TNBCs with low HRD scores. We systematically analyzed TNBC metabolomics and identified a metabolite, guanosine diphosphate (GDP)-mannose (GDP-M), that impeded homologous recombination repair (HRR). Mechanistically, the low expression of the upstream enzyme GDP-mannose-pyrophosphorylase-A (GMPPA) led to the endogenous up-regulation of GDP-M in TNBC. The accumulation of GDP-M in tumor cells further reduced the interaction between breast cancer susceptibility gene 2 (BRCA2) and ubiquitin-specific peptidase 21 (USP21), which promoted the ubiquitin-mediated degradation of BRCA2 to inhibit HRR. Therapeutically, we illustrated that the supplementation of GDP-M sensitized DNA-damaging agents to impair tumor growth in both in vitro (cancer cell line and patient-derived organoid) and in vivo (xenograft in immunodeficient mouse) models. Moreover, the combination of GDP-M with DNA-damaging agents activated STING-dependent antitumor immunity in immunocompetent syngeneic mouse models. Therefore, GDP-M supplementation combined with PARP inhibition augmented the efficacy of anti-PD-1 antibodies. Together, these findings suggest that GDP-M is a crucial HRD-related metabolite and propose a promising therapeutic strategy for TNBCs with low HRD scores using the combination of GDP-M, PARP inhibitors, and anti-PD-1 immunotherapy.
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Affiliation(s)
- Jia-Han Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201203, P. R. China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Fan Yang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Xiao-Qing Song
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Ying Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Xiao-Hong Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Rui Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
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Bachmann C. New Achievements from Molecular Biology and Treatment Options for Refractory/Relapsed Ovarian Cancer-A Systematic Review. Cancers (Basel) 2023; 15:5356. [PMID: 38001616 PMCID: PMC10669965 DOI: 10.3390/cancers15225356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Ovarian cancer (OC) has a high rate of mortality and is the fifth most common cause of death in females all over the world. The etiology is still unclear. Numerous factors such as smoking, obesity, and unhealthy diet may affect the risk of OC. Having a family history of breast and OC is one of the main risks for developing OC. Mutations of BRCA1/2 are associated with OC risk as well. The histopathological classification of OC reveals the four most common types: serous, clear cell, endometrioid, and mucinous; these are epithelial OC types, and other types are rare. Furthermore, OC can be subdivided into types I and II. Type I tumors are most probably caused by atypical proliferative tumors. Type II tumors include high-grade carcinoma of the serous type, carcinosarcoma, and carcinoma, which are not differentiated and generally originate from tubal intraepithelial carcinoma of the serous type. Typically, type I tumors are present in early stages, usually with good prognosis. Type II tumors are classified as high-grade tumors and are most often diagnosed at advanced FIGO stages with poor prognosis. High-grade serous OC accounts for 90% of serous OC. Tumor heterogeneity aggravates OC treatment. The standard care for primary epithelial ovarian cancer (EOC) is cytoreductive surgery followed by platinum-based chemotherapy. Neoadjuvant chemotherapy can be used in certain cases followed by cytoreductive surgery. The main prognostic factor is complete tumor resection. However, about 70% of patients relapse. Resistance to chemotherapeutic agents remains a major challenge in EOC treatment, in which many different factors are involved. In recent years, the examination of molecular parameters and their prognostic impact has become increasingly relevant in EOC, and furthermore, the use of immunotherapy has expanded the therapeutic range. As the clinical need is greatest for relapsed patients, this systematic review will focus on recent advances in molecular biology with prognostic and predictive markers and treatment options for recurrent/refractory OC. Inclusion criteria for the review: potential prospective or predictive biomarkers in preclinical or clinical use in relapsed and refractory OC, prognostic impact, clinical and preclinical trials, and immunotherapy. Exclusion criteria for the review: primary OC, no full text or abstract available, not the topic mentioned above, and text not available in English. Risk of bias: the included studies were evaluated descriptively for the topics mentioned above, and data were not compared with each other. The objective is to highlight the molecular mechanisms of the most promising targeted agents under clinical investigation to demonstrate their potential relevance in recurrent/refractory OC.
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Affiliation(s)
- Cornelia Bachmann
- Department of Womens' Health, University Tübingen, 72070 Tübingen, Germany
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Xu JZ, Xia QD, Sun JX, Liu CQ, Lu JL, Xu MY, An Y, Xun Y, Liu Z, Hu J, Li C, Wang SG. Establishment of a novel indicator of pyroptosis regulated gene transcription level and its application in pan-cancer. Sci Rep 2023; 13:17911. [PMID: 37863886 PMCID: PMC10589244 DOI: 10.1038/s41598-023-44700-8] [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: 04/18/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Pyroptosis is a type of programmed cell death and plays a dual role in distinct cancers. It is elusive to evaluate the activation level of pyroptosis and to appraise the involvement of pyroptosis in the occurrence and development of diverse tumors. Accordingly, we herein established an indicator to evaluate pyroptosis related gene transcription levels based on the expression level of genes involved in pyroptosis and tried to elaborated on the association between pyroptosis and tumors across diverse tumor types. We found that pyroptosis related gene transcription levels could predict the prognosis of patients, which could act as either a favorable or a dreadful factor in diverse cancers. According to signaling pathway analyses we observed that pyroptosis played a significant role in immune regulation and tumorigenesis and had strong links with other forms of cell death. We also performed analysis on the crosstalk between pyroptosis and immune status and further investigated the predictive potential of pyroptosis level for the efficacy of immunotherapy. Lastly, we manifested that pyroptosis status could serve as a biomarker to the efficacy of chemotherapy across various cancers. In summary, this study established a quantitative indicator to evaluate pyroptosis related gene transcription levels, systematically explored the role of pyroptosis in pan-cancer. These results could provide potential research directions targeting pyroptosis, and highlighted that pyroptosis may be used to develop a novel strategy for the treatment of cancer.
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Affiliation(s)
- Jin-Zhou Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi-Dong Xia
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Xuan Sun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen-Qian Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun-Lin Lu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng-Yao Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ye An
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Xun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cong Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Luo K, Qian Z, Jiang Y, Lv D, Zhu K, Shao J, Hu Y, Lv C, Huang Q, Gao Y, Jin S, Shang D. Characterization of the metabolic alteration-modulated tumor microenvironment mediated by TP53 mutation and hypoxia. Comput Biol Med 2023; 163:107078. [PMID: 37356294 DOI: 10.1016/j.compbiomed.2023.107078] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/08/2023] [Accepted: 05/27/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND TP53 mutation and hypoxia play an essential role in cancer progression. However, the metabolic reprogramming and tumor microenvironment (TME) heterogeneity mediated by them are still not fully understood. METHODS The multi-omics data of 32 cancer types and immunotherapy cohorts were acquired to comprehensively characterize the metabolic reprogramming pattern and the TME across cancer types and explore immunotherapy candidates. An assessment model for metabolic reprogramming was established by integration of multiple machine learning methods, including lasso regression, neural network, elastic network, and survival support vector machine (SVM). Pharmacogenomics analysis and in vitro assay were conducted to identify potential therapeutic drugs. RESULTS First, we identified metabolic subtype A (hypoxia-TP53 mutation subtype) and metabolic subtype B (non-hypoxia-TP53 wildtype subtype) in hepatocellular carcinoma (HCC) and showed that metabolic subtype A had an "immune inflamed" microenvironment. Next, we established an assessment model for metabolic reprogramming, which was more effective compared to the traditional prognostic indicators. Then, we identified a potential targeting drug, teniposide. Finally, we performed the pan-cancer analysis to illustrate the role of metabolic reprogramming in cancer and found that the metabolic alteration (MA) score was positively correlated with tumor mutational burden (TMB), neoantigen load, and homologous recombination deficiency (HRD) across cancer types. Meanwhile, we demonstrated that metabolic reprogramming mediated a potential immunotherapy-sensitive microenvironment in bladder cancer and validated it in an immunotherapy cohort. CONCLUSION Metabolic alteration mediated by hypoxia and TP53 mutation is associated with TME modulation and tumor progression across cancer types. In this study, we analyzed the role of metabolic alteration in cancer and propose a predictive model for cancer prognosis and immunotherapy responsiveness. We also explored a potential therapeutic drug, teniposide.
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Affiliation(s)
- Kunpeng Luo
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and lmaging Artificial Intelligence, Hengyang Medical School, University of South China Hengyang, Hunan, 421001, China; School of Computer, University of South China, Hengyang, Hunan, 421001, China; Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Zhipeng Qian
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and lmaging Artificial Intelligence, Hengyang Medical School, University of South China Hengyang, Hunan, 421001, China; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yanan Jiang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, 150081, China; Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang, 150081, China
| | - Dongxu Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Kaibin Zhu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Harbin, Heilongjiang, 150081, China
| | - Jing Shao
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Ying Hu
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Chengqian Lv
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Qianqian Huang
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yang Gao
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Shizhu Jin
- Department of Gastroenterology and Hepatology, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Desi Shang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and lmaging Artificial Intelligence, Hengyang Medical School, University of South China Hengyang, Hunan, 421001, China; School of Computer, University of South China, Hengyang, Hunan, 421001, China; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
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Yaromina A, Koi L, Schuitmaker L, van der Wiel AMMA, Dubois LJ, Krause M, Lambin P. Overcoming radioresistance with the hypoxia-activated prodrug CP-506: A pre-clinical study of local tumour control probability. Radiother Oncol 2023; 186:109738. [PMID: 37315579 DOI: 10.1016/j.radonc.2023.109738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND PURPOSE Tumour hypoxia is an established radioresistance factor. A novel hypoxia-activated prodrug CP-506 has been proven to selectively target hypoxic tumour cells and to cause anti-tumour activity. The current study investigates whether CP-506 improves outcome of radiotherapy in vivo. MATERIALS AND METHODS Mice bearing FaDu and UT-SCC-5 xenografts were randomized to receive 5 daily injections of CP-506/vehicle followed by single dose (SD) irradiation. In addition, CP-506 was combined once per week with fractionated irradiation (30 fractions/6 weeks). Animals were followed-up to score all recurrences. In parallel, tumours were harvested to evaluate pimonidazole hypoxia, DNA damage (γH2AX), expression of oxidoreductases. RESULTS CP-506 treatment significantly increased local control rate after SD in FaDu, 62% vs. 27% (p = 0.024). In UT-SCC-5, this effect was not curative and only marginally significant. CP-506 induced significant DNA damage in FaDu (p = 0.009) but not in UT- SCC-5. Hypoxic volume (HV) was significantly smaller (p = 0.038) after pretreatment with CP-506 as compared to vehicle in FaDu but not in less responsive UT-SCC-5. Adding CP-506 to fractionated radiotherapy in FaDu did not result in significant benefit. CONCLUSION The results support the use of CP-506 in combination with radiation in particular using hypofractionation schedules in hypoxic tumours. The magnitude of effect depends on the tumour model, therefore it is expected that applying appropriate patient stratification strategy will further enhance the benefit of CP-506 treatment for cancer patients. A phase I-IIA clinical trial of CP-506 in monotherapy or in combination with carboplatin or a checkpoint inhibitor has been approved (NCT04954599).
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Affiliation(s)
- Ala Yaromina
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands.
| | - Lydia Koi
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, and Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiooncology-OncoRay, Dresden, Germany
| | - Lesley Schuitmaker
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands
| | | | - Ludwig Jerome Dubois
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands
| | - Mechthild Krause
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, and Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiooncology-OncoRay, Dresden, Germany; German Cancer Consortium (DKTK), partner site Dresden, German Cancer Research Center, Heidelberg, National Center for Tumour Diseases (NCT), partner site Dresden, German Cancer Consortium (DKTK), core center Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philippe Lambin
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, the Netherlands
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Yang Y, Li J, Jing C, Zhai Y, Bai Z, Yang Y, Deng W. Inhibition of neuroactive ligand-receptor interaction pathway can enhance immunotherapy response in colon cancer: an in silico study. Expert Rev Anticancer Ther 2023; 23:1205-1215. [PMID: 37555253 DOI: 10.1080/14737140.2023.2245567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND The potential mechanism underlying the association between Homologous recombination deficiency (HRD) and immunotherapy in colon cancer has not been investigated. METHODS The exon sequencing data and transcriptome data of 456 colon adenocarcinoma (COAD) patients were obtained from the TCGA database. Pathway activity score was calculated by GSVA methods and engaged in further survival analysis. The prognostic value of the candidate pathways was validated in an external GEO cohort and an immunotherapy cohort. RESULTS Patients with high HRD were associated with poor prognosis, lower tumor mutation burden and microsatellite instability, higher fraction genome alteration, and less sensitivity to immunotherapy in COAD. And then, the neuroactive ligand-receptor interaction pathway was over-activated in high-HRD tumors and associated with immunosuppression in colon cancer with high HRD. Besides, the pathway was associated with prognosis and immunotherapy response in COAD. Moreover, genes in this pathway such as LTB4R2 can be used as a novel target for therapy development in colon cancer. CONCLUSION Our study not only revealed the potential mechanism of HRD and the function of the neuroactive ligand-receptor interaction pathway in colon cancer but also provided new clues for the improvement of immunotherapy response in colon cancer.
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Affiliation(s)
- Yun Yang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jun Li
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Chao Jing
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yuhao Zhai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhigang Bai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Yingchi Yang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Wei Deng
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing, China
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9
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He P, Ma Y, Wu Y, Zhou Q, Du H. Exploring PANoptosis in breast cancer based on scRNA-seq and bulk-seq. Front Endocrinol (Lausanne) 2023; 14:1164930. [PMID: 37455906 PMCID: PMC10338225 DOI: 10.3389/fendo.2023.1164930] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Background PANoptosis, a cell death pathway involving pyroptosis, apoptosis, and necroptosis, is pivotal in the development of malignancy. However, in the field of breast cancer, the interaction between PANoptosis and tumor cells has not been thoroughly explored. Methods We downloaded breast cancer data and GSE176078 single-cell sequencing dataset from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases to obtain PANoptosis-associated genes. To construct prognostic models, COX and LASSO regression was used to identify PANoptosis-associated genes with prognostic value. Finally, immune infiltration analysis and differential analysis of biological functions were performed. Results Risk grouping was performed according to the prognostic model constructed by COX regression and LASSO regression. The low-risk group showed a better prognosis (P < 0.05) and possessed higher levels of immune infiltration and expression of immune checkpoint-related genes. In addition, the lower the risk score, the higher the degree of microsatellite instability (MSI). Meanwhile, radixin (RDX), the gene with the highest hazard ratio (HR) value among PANoptosis prognosis-related genes, was explicitly expressed in artery Iendothelial cells (ECs) and was widely involved in signaling pathways such as immune response and cell proliferation, possessing rich biological functions. Conclusion We demonstrated the potential of PANoptosis-based molecular clustering and prognostic features in predicting the survival of breast cancer patients. Furthermore, this study has led to a deeper understanding of the role of PANoptosis in breast cancer and has the potential to provide new directions for immunotherapy of breast cancer.
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Affiliation(s)
- Puxing He
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Yan ‘an University, Yan’an, Shaanxi, China
| | - Yixuan Ma
- School of Basic Medicine, Yan 'an University, Yan’an, Shaanxi, China
| | - Yaolu Wu
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Yan ‘an University, Yan’an, Shaanxi, China
| | - Qing Zhou
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Yan ‘an University, Yan’an, Shaanxi, China
| | - Huan Du
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Yan ‘an University, Yan’an, Shaanxi, China
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10
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Zhang X, G. Dapar ML, Zhang X, Chen Y. A pan-cancer analysis of the oncogenic role of YKT6 in human tumors. Medicine (Baltimore) 2023; 102:e33546. [PMID: 37058019 PMCID: PMC10101269 DOI: 10.1097/md.0000000000033546] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/27/2023] [Indexed: 04/15/2023] Open
Abstract
YKT6, as a Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein with vesicle trafficking, plays an essential role in the development and progression of tumor. However, the gene of YKT6 has not been fully assessed in pan-cancer studies. We aim to investigate the gene of YKT6 across 33 different types of tumor by using the Cancer Genome Atlas, Gene Expression Omnibus database, and other several kinds of bioinformatic tools. YKT6 is significantly up-regulated in most tumors, and we found that overexpression of YKT6 is positively associated with poor prognosis of overall survival and poor disease-free survival prognosis in several tumors, such as Adrenocortical carcinoma, Bladder Urothelial Carcinoma, Head and Neck squamous cell carcinoma. We also detected distinct associations exist between YKT6 and tumor mutational burden or microsatellite instability with tumors. YKT6 expression was positively related to cancer-associated fibroblasts for TCGA tumors of colon adenocarcinoma and LGG. Furthermore, we discovered a significantly positively correlation between YKT6 expression and endothelial cell in tumors of colon adenocarcinoma, HNSC-HPV+, OV, READ and THCA. While a negative relationship was obtained between YKT6 expression and endothelial cell in KIRC. Moreover, "Syntaxin binding," "SNARE complex," "vesicle fusion" and "DNA replication" are involved in the influence of YKT6 on tumor pathogenesis. Our pan-cancer analysis offers a deep comprehending the gene of YKT6 in tumoeigenesis from viewpoint of clinical tumor samples.
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Affiliation(s)
- Xuezhong Zhang
- Department of Biology, College of Arts and Sciences, Central Mindanao University, Musuan, Philippines
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, China
| | - Mark Lloyd G. Dapar
- Department of Biology, College of Arts and Sciences, Central Mindanao University, Musuan, Philippines
- Center for Biodiversity Research and Extension in Mindanao, Central Mindanao University, Musuan, Philippines
- Microtechnique and Systematics Laboratory, Natural Science Research Center, Musuan, Philippines
| | - Xin Zhang
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, China
| | - Yingjun Chen
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, China
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Winkelmann R, Bankov K, Döring C, Cinatl J, Grothe S, Rothweiler F, Michaelis M, Schmitt C, Wild PJ, Demes M, Cinatl J, Vallo S. Increased HRD score in cisplatin resistant penile cancer cells. BMC Cancer 2022; 22:1352. [PMID: 36564761 PMCID: PMC9789628 DOI: 10.1186/s12885-022-10432-7] [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: 09/16/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND/INTRODUCTION Penile cancer is a rare disease in demand for new therapeutic options. Frequently used combination chemotherapy with 5 fluorouracil (5-FU) and cisplatin (CDDP) in patients with metastatic penile cancer mostly results in the development of acquired drug resistance. Availability of cell culture models with acquired resistance against standard therapy could help to understand molecular mechanisms underlying chemotherapy resistance and to identify candidate treatments for an efficient second line therapy. METHODS We generated a cell line from a humanpapilloma virus (HPV) negative penile squamous cell carcinoma (UKF-PEC-1). This cell line was subject to chronic exposure to chemotherapy with CDDP and / or 5-FU to induce acquired resistance in the newly established chemo-resistant sublines (PEC-1rCDDP2500, adapted to 2500 ng/ml CDDP; UKF-PEC-1r5-FU500, adapted to 500 ng/ml 5- FU; UKF-PEC1rCDDP2500/r5-FU500, adapted to 2500 ng/ml CDDP and 500 ng/ml 5 -FU). Afterwards cell line pellets were formalin-fixed, paraffin embedded and subject to sequencing as well as testing for homologous recombination deficiency (HRD). Additionally, exemplary immunohistochemical stainings for p53 and gammaH2AX were applied for verification purposes. Finally, UKF-PEC-1rCDDP2500, UKF-PEC-1r5-FU500, UKF-PEC1rCDDP2500/r5-FU500, and UKF-PEC-3 (an alternative penis cancer cell line) were tested for sensitivity to paclitaxel, docetaxel, olaparib, and rucaparib. RESULTS AND CONCLUSIONS The chemo-resistant sublines differed in their mutational landscapes. UKF-PEC-1rCDDP2500 was characterized by an increased HRD score, which is supposed to be associated with increased PARP inhibitor and immune checkpoint inhibitor sensitivity in cancer. However, UKF-PEC-1rCDDP2500 did not display sensitivity to PARP inhibitors.
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Affiliation(s)
- Ria Winkelmann
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Katrin Bankov
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Claudia Döring
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | | | - Sebastian Grothe
- Dr. Petra Joh Forschungshaus, Frankfurt Am Main, Germany ,grid.411088.40000 0004 0578 8220Institute of Medical Virology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Florian Rothweiler
- Dr. Petra Joh Forschungshaus, Frankfurt Am Main, Germany ,grid.411088.40000 0004 0578 8220Institute of Medical Virology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Martin Michaelis
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Christina Schmitt
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Peter J. Wild
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany ,grid.417999.b0000 0000 9260 4223Frankfurt Institute for Advanced Studies (FIAS), Frankfurt Am Main, Germany
| | - Melanie Demes
- grid.411088.40000 0004 0578 8220Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Jindrich Cinatl
- Dr. Petra Joh Forschungshaus, Frankfurt Am Main, Germany ,grid.411088.40000 0004 0578 8220Institute of Medical Virology, University Hospital Frankfurt, Frankfurt Am Main, Germany
| | - Stefan Vallo
- grid.411088.40000 0004 0578 8220Institute of Medical Virology, University Hospital Frankfurt, Frankfurt Am Main, Germany ,grid.411088.40000 0004 0578 8220Department of Urology, University Hospital Frankfurt, Frankfurt Am Main, Germany ,Urologie an der Zeil, Frankfurt Am Main, Germany
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12
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Biomarkers and translational research approaches in breast cancer—an update. MEMO - MAGAZINE OF EUROPEAN MEDICAL ONCOLOGY 2022. [DOI: 10.1007/s12254-022-00855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SummaryDiagnosis and decision-making in the treatment of breast cancer patients is vastly dependent on the exploration of biomarkers. Estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 are long-standing biomarkers, which determine the breast cancer subtype. In current practice, gene expression analyses further define the molecular breast cancer subtype and give additional information on disease characteristics. Prognostic biomarkers provide information regarding recurrence risk and survival. Predictive biomarkers, such as programmed cell death ligand 1 expression, are tools for identifying patients who can benefit from specific therapy regimens in order to choose the best treatment option for the patient. While some biomarkers are affordable and readily available, others remain technically complex to access. Translational research builds the bridge from discovering novel biomarkers in preclinical studies to testing their application utility in the clinical setting. Integrating translational studies into clinical trials is therefore essential to find novel and reliable biomarkers for an optimal personalized treatment approach for patients with breast cancer.
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13
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Zhang G, Zhang K, Zhao Y, Yang Q, Lv X. A novel stemness-hypoxia-related signature for prognostic stratification and immunotherapy response in hepatocellular carcinoma. BMC Cancer 2022; 22:1103. [DOI: 10.1186/s12885-022-10195-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The specific differentiation potential, unlimited proliferation, and self-renewal capacity of cancer stem cells (CSCs) are closely related to the occurrence, recurrence, and drug resistance of hepatocellular carcinoma (HCC), as well as hypoxia. Therefore, an in-depth analysis of the relationship between HCC stemness, oxygenation status, and the effectiveness of immunotherapy is necessary to improve the poor prognosis of HCC patients.
Methods
The weighted gene co-expression network analysis (WGCNA) was utilized to find hypoxia-related genes, and the stemness index (mRNAsi) was evaluated using the one-class logistic regression (OCLR) technique. Based on stemness-hypoxia-related genes (SHRGs), population subgroup categorization using NMF cluster analysis was carried out. The relationship between SHRGs and survival outcomes was determined using univariate Cox regression. The LASSO-Cox regression strategy was performed to investigate the quality and establish the classifier associated with prognosis. The main effect of risk scores on the tumor microenvironment (TME) and its response to immune checkpoint drugs was also examined. Finally, qRT-PCR was performed to explore the expression and prognostic value of the signature in clinical samples.
Results
After identifying tumor stemness- and hypoxia-related genes through a series of bioinformatics analyses, we constructed a prognostic stratification model based on these SHRGs, which can be effectively applied to the prognostic classification of HCC patients and the prediction of immune checkpoint inhibitors (ICIs) efficacy. Independent validation of the model in the ICGC cohort yielded good results. In addition, we also constructed hypoxic cell models in Herp3B and Huh7 cells to verify the expression of genes in the prognostic model and found that C7, CLEC1B, and CXCL6 were not only related to the tumor stemness but also related to hypoxia. Finally, we found that the constructed signature had a good prognostic value in the clinical sample.
Conclusions
We constructed and validated a stemness-hypoxia-related prognostic signature that can be used to predict the efficacy of ICIs therapy. We also verified that C7, CLEC1B, and CXCL6 are indeed associated with stemness and hypoxia through a hypoxic cell model, which may provide new ideas for individualized immunotherapy.
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van der Wiel AMA, Schuitmaker L, Cong Y, Theys J, Van Hoeck A, Vens C, Lambin P, Yaromina A, Dubois LJ. Homologous Recombination Deficiency Scar: Mutations and Beyond-Implications for Precision Oncology. Cancers (Basel) 2022; 14:cancers14174157. [PMID: 36077694 PMCID: PMC9454578 DOI: 10.3390/cancers14174157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/05/2023] Open
Abstract
Homologous recombination deficiency (HRD) is a prevalent in approximately 17% of tumors and is associated with enhanced sensitivity to anticancer therapies inducing double-strand DNA breaks. Accurate detection of HRD would therefore allow improved patient selection and outcome of conventional and targeted anticancer therapies. However, current clinical assessment of HRD mainly relies on determining germline BRCA1/2 mutational status and is insufficient for adequate patient stratification as mechanisms of HRD occurrence extend beyond functional BRCA1/2 loss. HRD, regardless of BRCA1/2 status, is associated with specific forms of genomic and mutational signatures termed HRD scar. Detection of this HRD scar might therefore be a more reliable biomarker for HRD. This review discusses and compares different methods of assessing HRD and HRD scar, their advances into the clinic, and their potential implications for precision oncology.
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Affiliation(s)
- Alexander M. A. van der Wiel
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Lesley Schuitmaker
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ying Cong
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Jan Theys
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Arne Van Hoeck
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Conchita Vens
- Institute of Cancer Science, University of Glasgow, Glasgow G61 1BD, Scotland, UK
- Department of Radiation Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Philippe Lambin
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ala Yaromina
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ludwig J. Dubois
- The M-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands
- Correspondence:
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15
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A Pan-Cancer Analysis of UBE2S in Tumorigenesis, Prognosis, Pathway, Immune Infiltration and Evasion, and Therapy Response from an Immune-Oncology Perspective. JOURNAL OF ONCOLOGY 2022; 2022:3982539. [PMID: 35578600 PMCID: PMC9107357 DOI: 10.1155/2022/3982539] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 11/18/2022]
Abstract
Background Ubiquitin conjugating enzyme E2S (UBE2S), a member of the ubiquitin-conjugating enzyme family, is known to play a pivotal role in tumorigenesis and progression in some tumor types. However, whether UBE2S plays an irreplaceable role in the immune-oncology context of tumorigenesis, prognosis, pathogenesis, immune regulation, and therapeutic response through certain common molecular mechanisms remains to be defined. The present pan-cancer study was intended to decipher the landscape of UBE2S in pathologic, immunological, and therapeutic aspects across various cancers. Methods Data used for UBE2S analysis were obtained from TCGA database. The pan-cancer analysis was mainly focused on the expression patterns, prognostic values, mutation landscapes, biological pathways, tumor microenvironment remodeling, and therapeutic resistance of UBE2S using multiple databases including cBioPortal, Cancer Cell Line Encyclopedia (CCLE) database, Tumor Immune Estimation Resource (TIMER), and Gene Expression Profiling Interactive Analysis (GEPIA). External experimental validation was conducted to delineate the association of UBE2S with tumor phenotypes through assays of proliferation, colony formation, and migration. Data processing, statistical analysis, and plotting were performed using R software and GraphPad Prism software. Results UBE2S was aberrantly expressed in almost all human cancers, and elevated UBE2S expression was unfavorably associated with the clinical pathological stage and prognosis. DNA methylation and RNA modification were significantly correlated with the UBE2S expression level. The results of enrichment analysis revealed that UBE2S positively regulated MYC, G2M cell cycle, and DNA repair pathways and negatively regulated adipogenesis, fatty acid metabolism, and heme metabolism. In addition, UBE2S exhibited a significantly positive correlation with myeloid-derived suppressor cell MDSC and Th2 subsets in almost all tumors analyzed. UBE2S could confer immune evasion via coexpressed immunoinhibitors and T cell exhaustion. Notably, a higher UBE2S expression indicated a higher level of stemness, TMB, MSI, and MMR deficiency and DNA methyltransferases, as well as chemotherapeutic resistance in various cancers. Notably, in vitro functional validation showed that UBE2S knockdown attenuated the phenotypes of proliferation, clonogenicity, and migration in hepatocellular carcinoma cells. Conclusions Our study provided meaningful clues to support UBE2S as an immune-oncogenic molecule and shed light on potential applications of UBE2S in cancer detection, prognostic prediction, and therapeutic response assessment.
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16
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A high homologous recombination deficiency score is associated with poor survival and a non-inflamed tumor microenvironment in head and neck squamous cell carcinoma patients. Oral Oncol 2022; 128:105860. [DOI: 10.1016/j.oraloncology.2022.105860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/19/2022] [Accepted: 04/05/2022] [Indexed: 11/20/2022]
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17
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Seligson ND, Tang J, Jin DX, Bennett MP, Elvin JA, Graim K, Hays JL, Millis SZ, Miles WO, Chen JL. Drivers of genomic loss of heterozygosity in leiomyosarcoma are distinct from carcinomas. NPJ Precis Oncol 2022; 6:29. [PMID: 35468996 PMCID: PMC9038792 DOI: 10.1038/s41698-022-00271-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022] Open
Abstract
Leiomyosarcoma (LMS) is a rare, aggressive, mesenchymal tumor. Subsets of LMS have been identified to harbor genomic alterations associated with homologous recombination deficiency (HRD); particularly alterations in BRCA2. Whereas genomic loss of heterozygosity (gLOH) has been used as a surrogate marker of HRD in other solid tumors, the prognostic or clinical value of gLOH in LMS (gLOH-LMS) remains poorly defined. We explore the genomic drivers associated with gLOH-LMS and their clinical import. Although the distribution of gLOH-LMS scores are similar to that of carcinomas, outside of BRCA2, there was no overlap with previously published gLOH-associated genes from studies in carcinomas. We note that early stage tumors with elevated gLOH demonstrated a longer disease-free interval following resection in LMS patients. Taken together, and despite similarities to carcinomas in gLOH distribution and clinical import, gLOH-LMS are driven by different genomic signals. Additional studies will be required to isolate and confirm the unique differences in biological factors driving these differences.
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Affiliation(s)
- Nathan D Seligson
- Department of Pharmacotherapy and Translational Research, The University of Florida, Jacksonville, FL, USA.,Department of Pharmacogenomics and Translational Research, Nemours Children's Specialty Care, Jacksonville, FL, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Joy Tang
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Monica P Bennett
- Department of Pharmacotherapy and Translational Research, The University of Florida, Jacksonville, FL, USA
| | | | - Kiley Graim
- Department of Computer and Information Science and Engineering, The University of Florida, Gainesville, FL, USA
| | - John L Hays
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH, USA
| | | | - Wayne O Miles
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - James L Chen
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA. .,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
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18
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Targeting DNA Damage Response and Immune Checkpoint for Anticancer Therapy. Int J Mol Sci 2022; 23:ijms23063238. [PMID: 35328658 PMCID: PMC8952261 DOI: 10.3390/ijms23063238] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 01/27/2023] Open
Abstract
Deficiency in DNA damage response (DDR) genes leads to impaired DNA repair functions that will induce genomic instability and facilitate cancer development. However, alterations of DDR genes can serve as biomarkers for the selection of suitable patients to receive specific therapeutics, such as immune checkpoint blockade (ICB) therapy. In addition, certain altered DDR genes can be ideal therapeutic targets through adapting the mechanism of synthetic lethality. Recent studies indicate that targeting DDR can improve cancer immunotherapy by modulating the immune response mediated by cGAS-STING-interferon signaling. Investigations of the interplay of DDR-targeting and ICB therapies provide more effective treatment options for cancer patients. This review introduces the mechanisms of DDR and discusses their crucial roles in cancer therapy based on the concepts of synthetic lethality and ICB. The contemporary clinical trials of DDR-targeting and ICB therapies in breast, colorectal, and pancreatic cancers are included.
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19
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Wang Y, Fan J, Chen T, Xu L, Liu P, Xiao L, Wu T, Zhou Q, Zheng Q, Liu C, Chan FL, Wu D. A novel ferroptosis-related gene prognostic index for prognosis and response to immunotherapy in patients with prostate cancer. Front Endocrinol (Lausanne) 2022; 13:975623. [PMID: 36034466 PMCID: PMC9399637 DOI: 10.3389/fendo.2022.975623] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/13/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) is among the leading causes of cancer death worldwide. Ferroptosis refers to an iron-dependent form of regulated cell death and is involved in prostate tumorigenesis. A few ferroptosis-related gene signatures have been developed to predict the prognosis for PCa patients. However, previous signatures were typically established based on biochemical recurrence-free survival, which has proven not to be a good surrogate for overall survival (OS). This study aimed to construct a novel ferroptosis-related gene prognostic index (FRGPI) to predict disease-free survival (DFS) and response to immunotherapy for PCa patients after radical prostatectomy. METHODS Gene expression and clinicopathological data on PCa patients were obtained from the TCGA database. Ferroptosis-related hub genes associated with DFS of PCa patients were identified by an in-depth bioinformatics analysis using a novel and comprehensive algorithm based on functional enrichment, consensus clustering, weighted gene co-expression network analysis (WGCNA), and protein-protein interaction (PPI) network construction. The FRGPI was established on the basis of the genes selected using multivariate cox regression analysis and further validated in two additional PCa cohorts. Next, the clinicopathological, molecular, and immune profiles were characterized and compared between FRGPI-high and FRGPI-low subgroups. Finally, the predictive role of the FRGPI in response to immunotherapy was estimated using a metastatic urothelial cancer cohort treated with an anti-PD-L1 agent. RESULTS The FRGPI was constructed based on four genes (E2F1, CDC20, TYMS, and NUP85), and FRGPI-high patients had worse DFS than FRGPI-low patients. Multivariate cox regression analysis revealed that FRGPI could act as an independent prognostic factor for PCa patients after radical prostatectomy. A prognostic nomogram comprising the FRGPI and other clinicopathological parameters was established to predict the DFS for PCa patients quantitatively. In addition, comprehensive results demonstrated that high FRGPI scores showed a significantly positive correlation with worse clinicopathological features, higher mutation counts, increased frequency of copy number variations (CNVs), higher homologous recombination deficiency (HRD) and immune scores, higher mRNAsi, and more importantly, enhanced sensitivity to immunotherapy. CONCLUSIONS FRGPI is not only a promising and robust prognostic biomarker, but also a potential indicator of immunotherapeutic outcomes for PCa patients after radical prostatectomy.
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Affiliation(s)
- Yuliang Wang
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, China
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiaqi Fan
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Shenzhen, China
| | - Tao Chen
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Lele Xu
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Pengyu Liu
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Lijia Xiao
- Department of Clinical Laboratory Medicine Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Tao Wu
- Department of Urology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Qingchun Zhou
- Department of Urology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Qingyou Zheng
- Department of Urology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Chunxiao Liu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Chunxiao Liu, ; Franky Leung Chan, ; Dinglan Wu,
| | - Franky Leung Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- *Correspondence: Chunxiao Liu, ; Franky Leung Chan, ; Dinglan Wu,
| | - Dinglan Wu
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Shenzhen, China
- *Correspondence: Chunxiao Liu, ; Franky Leung Chan, ; Dinglan Wu,
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