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Halperin R, Tirosh A. Mid-Treatment Response to 177-Lutetium Dotatate Predicts Overall Outcome in Patients With Advanced Neuroendocrine Tumors. JCO Oncol Pract 2024:OP2300789. [PMID: 38935916 DOI: 10.1200/op.23.00789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 06/29/2024] Open
Abstract
PURPOSE Patients with advanced, well-differentiated neuroendocrine tumors (WD-NETs) often require both peptide receptor radionuclide therapy (PRRT) and subsequent chemotherapy. However, no mid-PRRT predictors are available to identify patients who will not benefit from subsequent PRRT to limit their radiation exposure. Our aim is to characterize patients for whom subsequent PRRT is less efficacious on the basis of mid-PRRT evaluation. MATERIALS AND METHODS A retrospective study of patients with WD-NET who underwent ≥four PRRT cycles. Data gathered included demographics, tumor grade, stage, and response (partial response [PR], stable disease [SD], and progressive disease [PD]) on the basis of RECIST 1.1 criteria and 68Ga-dotatate positron emission tomography-computerized tomography pretreatment, after second and fourth treatment cycle, 6 months after fourth cycle, and at last follow-up. RESULTS Fifty-one patients (51.6% women; age at diagnosis 66.0 ± 1.65 years), with pancreatic NET (PNET; n = 24), small intestine NET (n = 13), or other NET (n = 14), received PRRT, resulting in PR (n = 21), SD (n = 23), and PD (n = 3). Of the patients reaching PR after PRRT, most reached PR after two treatments (70.4%), with only 11.8% PR occurring between subsequent cycles (P = .001). Furthermore, patients with PR at mid-treatment had higher PR rates after PRRT completion than those with SD (P = .007). Patients harboring PNET who achieved PR had a more pronounced reduction of tumor burden in additional cycles than patients who did not (25.6% v 1.5%; P = .03, respectively). On the multivariable model, adjusted for grade and primary site, PR at mid-treatment evaluation was associated with a 20.9 adjusted odds ratio for additional PR at PRRT completion (P = .002). CONCLUSION Mid-PRRT assessment predicts subsequent PRRT response in patients with WD-NET, especially those with PNET, informing personalized management and consideration of reduced bone marrow radiation exposure in high-risk patients.
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Affiliation(s)
- Reut Halperin
- ENTIRE-Endocrine Neoplasia Translational Research Center, Ramat Gan, Israel
- Division of Endocrinology, Metabolism and Diabetes, Sheba Medical Center, Ramat Gan, Israel
- Tel Aviv University Faculty of Medicine, Ramat Gan, Israel
| | - Amit Tirosh
- ENTIRE-Endocrine Neoplasia Translational Research Center, Ramat Gan, Israel
- Division of Endocrinology, Metabolism and Diabetes, Sheba Medical Center, Ramat Gan, Israel
- Tel Aviv University Faculty of Medicine, Ramat Gan, Israel
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Yang Q, Li X, Zhu W. Identification of a unique stress response state of T cells-related gene signature in patients with gastric cancer. Aging (Albany NY) 2024; 16:9709-9726. [PMID: 38848147 DOI: 10.18632/aging.205895] [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: 11/09/2023] [Accepted: 04/25/2024] [Indexed: 06/09/2024]
Abstract
Gastric cancer (GC), the third most lethal cancer worldwide, is often diagnosed at an advanced stage, leaving limited therapeutic options. Given the diverse outcomes among GC patients with similar AJCC/UICC-TNM characteristics, there is a pressing need for more reliable prognostic tools. Recent advances in targeted therapy and immunotherapy have underscored this necessity. In this context, our study focused on a novel stress response state of T cells, termed TSTR, identified across multiple cancers, which is associated with resistance to immunotherapy. We aimed to develop a predictive gene signature for the TSTR phenotype within the tumor microenvironment (TME) of GC patients. By categorizing GC patients into high and low TSTR groups based on the infiltration states of TME TSTR cells, we observed significant differences in clinical prognosis and characteristics between the groups. Through a multi-step bioinformatics approach, we established an eight-gene signature based on genes differentially expressed between these groups. We conducted functional validations for the signature gene PDGFRL in GC cells. This gene signature effectively stratifies GC patients into high and low-risk categories, demonstrating robustness in predicting clinical outcomes. Furthermore, these risk groups exhibited distinct immune profiles, somatic mutations, and drug susceptibilities, highlighting the potential of our gene signature to enhance personalized treatment strategies in clinical practice.
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Affiliation(s)
- Qin Yang
- Puai Medical College, Shaoyang University, The First Affiliated Hospital of Shaoyang University, Shaoyang, Hunan, China
| | - Xin Li
- Department of Immunology, School of Basic Medicine, Central South University, Changsha, Hunan, China
| | - Weiyuan Zhu
- Puai Medical College, Shaoyang University, The First Affiliated Hospital of Shaoyang University, Shaoyang, Hunan, China
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3
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Wang MM, Zhao Y, Liu J, Fan RR, Tang YQ, Guo ZY, Li T. The role of the cGAS-STING signaling pathway in viral infections, inflammatory and autoimmune diseases. Acta Pharmacol Sin 2024:10.1038/s41401-023-01185-5. [PMID: 38822084 DOI: 10.1038/s41401-023-01185-5] [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: 08/06/2023] [Accepted: 10/18/2023] [Indexed: 06/02/2024] Open
Abstract
Pattern recognition receptors are an essential part of the immune system, which detect pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) and help shape both innate and adaptive immune responses. When dsDNA is present, cyclic GMP-AMP Synthase (cGAS) produces a second messenger called cyclic GMP-AMP (cGAMP), which then triggers an adaptor protein called STING, and eventually activates the expression of type I interferon (IFN) and pro-inflammatory cytokines in immune cells. The cGAS-STING signaling pathway has been receiving a lot of attention lately as a key immune-surveillance mediator. In this review, we summarize the present circumstances of the cGAS-STING signaling pathway in viral infections and inflammatory diseases, as well as autoimmune diseases. Modulation of the cGAS-STING signaling pathway provides potential strategies for treating viral infections, inflammatory diseases, and autoimmune diseases.
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Affiliation(s)
- Ming-Ming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Yue Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Rong-Rong Fan
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden
| | - Yan-Qing Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Zheng-Yang Guo
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China
| | - Ting Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao, 999078, China.
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4
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Huang T, Sun F, Gao K, Wang Y, Zhu G, Chen F. The Role of Peripheral Inflammatory Markers and Coagulation Factors in Patients with Central Nervous System (CNS) Immune Disease and Glioma. World Neurosurg 2024:S1878-8750(24)00843-X. [PMID: 38763458 DOI: 10.1016/j.wneu.2024.05.080] [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: 04/17/2024] [Accepted: 05/14/2024] [Indexed: 05/21/2024]
Abstract
OBJECTIVE Gliomas are associated with high rates of disability and mortality, and currently, there is a lack of specific and sensitive biomarkers for diagnosis. The ideal biomarkers should be detected early through noninvasive methods. Our research aims to develop a rapid, convenient, noninvasive diagnostic method for gliomas, as well as for grading and differentiation. METHOD We retrospectively collected data from patients who underwent surgery for glioma, trigeminal neuralgia/hemifacial spasmschwannoma, and those diagnosed with multiple sclerosis at our institution from January 2018 to December 2020. Inflammatory markers and coagulation factor levels were collected on admission, and neutrophil count (NLR), (WBC count minus neutrophil count) / lymphocyte count, platelet count / lymphocyte count, lymphocyte count / monocyte count, and albumin count [g/L] + total lymphocyte count × 5 were calculated for patients. Analyze the significance of biomarkers in the diagnosis and grading of gliomas, the diagnosis of MS, and the differential diagnosis of them. RESULTS We evaluated 155 healthy individuals, 64 trigeminal neuralgia/hemifacial spasm patients, 47 MS patients, 316 schwannoma patients, and 814 with glioma patients. Compared with healthy controls and MS group, the preoperative levels of NLR, (WBC count minus neutrophil count) / lymphocyte count, D-dimer, Fibrinogen, Antithrobin, and Factor VIII of glioma patients were significantly higher in glioma patients and positively correlated with the grade of glioma. Conversely, 0020 lymphocyte count / Monocyte count and albumin count [g/L] + total lymphocyte count × 5 were significantly lower and negatively correlated with glioma grading. ROC curves confirmed that for the diagnosis of glioma, NLR showed a maximum area under the curve value of 0.8616 (0.8322-0.8910), followed by D-dimer and Antithrombin, with area under the curve values of 0.8205 (0.7601-0.8809) and 0.8455 (0.8153-0.8758), respectively. NLR and d-dimer also showed great sensitivity in the diagnosis of MS and differential diagnosis with gliomas. CONCLUSIONS Our study demonstrated that multiple inflammatory markers and coagulation factors could be utilized as biomarkers for the glioma diagnosis, grading, and differential diagnosis of MS. Furthermore, the combination of these markers exhibited high sensitivity and specificity.
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Affiliation(s)
- Tao Huang
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Fang Sun
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Kailun Gao
- Department of Anesthesiology, Xuzhou Central Hospital, Xu Zhou, China
| | - Yuan Wang
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Gang Zhu
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Fan Chen
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China.
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Wang M, Pan Z, Chu X, Yao X, Duan X, Wan J, Lou X, Li W, Yan Y, Chen L, An J, Qin Z. Chemotherapy-induced PTEN-L secretion promotes the selection of PTEN-deficient tumor cells. J Exp Clin Cancer Res 2024; 43:140. [PMID: 38730468 PMCID: PMC11088029 DOI: 10.1186/s13046-024-03059-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND PTEN loss has been identified in various tumor types and is linked to unfavorable clinical outcomes. In addition to PTEN mutation, multiple mechanisms contribute to PTEN loss during tumor development. However, the natural selection process of PTEN-deficient tumor cells remains unclear. Here, we aimed at further elucidating the role of PTEN-L in tumor progression. METHODS PTEN knockout cell lines were generated using CRISPR/Cas9 technology. Ni-NTA affinity column chromatography was employed for PTEN-L purification. Tumor cell metastasis was evaluated in murine models and observed using the IVIS Spectrum Imaging System. RNA-sequencing, western blotting, PCR, flow cytometry, and cell proliferation assays were employed to investigate tumor cell dormancy and related mechanisms. RESULTS The chemotherapeutic drugs, cisplatin, paclitaxel, and doxorubicin, induced tumor cells to secrete PTEN-long (PTEN-L), which shields PTEN-deficient tumor cells from chemotherapy-induced apoptosis better than it shields PTEN-intact cells. Further investigation revealed that PTEN-L treatment induced dormancy in PTEN-null tumor cells, characterized by an increase in p16 and p27 levels, cell-cycle arrest, reduced cell proliferation, and enhanced DNA repair. Furthermore, PTEN-L treatment selectively promoted the accumulation and growth of PTEN-null tumor cells in the lungs of C57BL/6J mice, while evading immune surveillance. Mechanistically, PTEN-L induced dormancy in PTEN-null tumor cells by activating the p38 signaling pathway. Addition of a p38 inhibitor effectively reversed dormancy and growth of PTEN-deficient tumor cells in the lungs. We also demonstrated that PTEN expression played a pivotal role in determining the outcome of PTEN-L-mediated antitumor therapy. CONCLUSIONS In summary, PTEN-L was identified as a potent inducer of dormancy in PTEN-deficient tumor cells, which increased their efficient selection within the tumor microenvironment.
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Affiliation(s)
- Ming Wang
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China.
| | - Zhenzhen Pan
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xu Chu
- The first affiliated hospital of Henan University of science and technology, Luo Yang, China
| | - Xiaohan Yao
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xixi Duan
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jiajia Wan
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xiaohan Lou
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Wenqing Li
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yan Yan
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Lin Chen
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Junfeng An
- Guangzhou DaAn Clinical Laboratory Center Co. Ltd, YunKang Group, Guangzhou, 510000, China
| | - Zhihai Qin
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, 450052, China.
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6
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Decollogny M, Rottenberg S. Persisting cancer cells are different from bacterial persisters. Trends Cancer 2024; 10:393-406. [PMID: 38429144 DOI: 10.1016/j.trecan.2024.02.002] [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: 10/20/2023] [Revised: 01/22/2024] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
The persistence of drug-sensitive tumors poses a significant challenge in cancer treatment. The concept of bacterial persisters, which are a subpopulation of bacteria that survive lethal antibiotic doses, is frequently used to compare to residual disease in cancer. Here, we explore drug tolerance of cancer cells and bacteria. We highlight the fact that bacteria, in contrast to cancer cells, have been selected for survival at the population level and may therefore possess contingency mechanisms that cancer cells lack. The precise mechanisms of drug-tolerant cancer cells and bacterial persisters are still being investigated. Undoubtedly, by understanding common features as well as differences, we, in the cancer field, can learn from microbiology to find strategies to eradicate persisting cancer cells.
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Affiliation(s)
- Morgane Decollogny
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Bern Center for Precision Medicine and Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Bern Center for Precision Medicine and Department for BioMedical Research, University of Bern, Bern, Switzerland.
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7
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Yalala S, Gondane A, Poulose N, Liang J, Mills IG, Itkonen HM. CDK9 inhibition activates innate immune response through viral mimicry. FASEB J 2024; 38:e23628. [PMID: 38661032 DOI: 10.1096/fj.202302375r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
Cancer cells frequently exhibit hyperactivation of transcription, which can lead to increased sensitivity to compounds targeting the transcriptional kinases, in particular CDK9. However, mechanistic details of CDK9 inhibition-induced cancer cell-selective anti-proliferative effects remain largely unknown. Here, we discover that CDK9 inhibition activates the innate immune response through viral mimicry in cancer cells. In MYC over-expressing prostate cancer cells, CDK9 inhibition leads to the gross accumulation of mis-spliced RNA. Double-stranded RNA (dsRNA)-activated kinase can recognize these mis-spliced RNAs, and we show that the activity of this kinase is required for the CDK9 inhibitor-induced anti-proliferative effects. Using time-resolved transcriptional profiling (SLAM-seq), targeted proteomics, and ChIP-seq, we show that, similar to viral infection, CDK9 inhibition significantly suppresses transcription of most genes but allows selective transcription and translation of cytokines related to the innate immune response. In particular, CDK9 inhibition activates NFκB-driven cytokine signaling at the transcriptional and secretome levels. The transcriptional signature induced by CDK9 inhibition identifies prostate cancers with a high level of genome instability. We propose that it is possible to induce similar effects in patients using CDK9 inhibition, which, we show, causes DNA damage in vitro. In the future, it is important to establish whether CDK9 inhibitors can potentiate the effects of immunotherapy against late-stage prostate cancer, a currently lethal disease.
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Affiliation(s)
- Shivani Yalala
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Aishwarya Gondane
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ninu Poulose
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jing Liang
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Harri M Itkonen
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Huang Y, Jiang W, Zhou R. DAMP sensing and sterile inflammation: intracellular, intercellular and inter-organ pathways. Nat Rev Immunol 2024:10.1038/s41577-024-01027-3. [PMID: 38684933 DOI: 10.1038/s41577-024-01027-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2024] [Indexed: 05/02/2024]
Abstract
Damage-associated molecular patterns (DAMPs) are endogenous molecules that are released from host cells as a result of cell death or damage. The release of DAMPs in tissues is associated with loss of tissue homeostasis. Sensing of DAMPs by innate immune receptors triggers inflammation, which can be beneficial in initiating the processes that restore tissue homeostasis but can also drive inflammatory diseases. In recent years, the sensing of intracellular DAMPs has received extensive attention in the field of sterile inflammation. However, emerging studies have shown that DAMPs that originate from neighbouring cells, and even from distal tissues or organs, also mediate sterile inflammatory responses. This multi-level sensing of DAMPs is crucial for intercellular, trans-tissue and trans-organ communication. Here, we summarize how DAMP-sensing receptors detect DAMPs from intracellular, intercellular or distal tissue and organ sources to mediate sterile inflammation. We also discuss the possibility of targeting DAMPs or their corresponding receptors to treat inflammatory diseases.
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Affiliation(s)
- Yi Huang
- Key Laboratory of Immune Response and Immunotherapy, Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
| | - Wei Jiang
- Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Rongbin Zhou
- Key Laboratory of Immune Response and Immunotherapy, Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China.
- Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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Bao S, Yi M, Xiang B, Chen P. Antitumor mechanisms and future clinical applications of the natural product triptolide. Cancer Cell Int 2024; 24:150. [PMID: 38678240 PMCID: PMC11055311 DOI: 10.1186/s12935-024-03336-y] [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: 11/15/2023] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
Triptolide (TPL) is a compound sourced from Tripterygium wilfordii Hook. F., a traditional Chinese medicinal herb recognized for its impressive anti-inflammatory, anti-angiogenic, immunosuppressive, and antitumor qualities. Notwithstanding its favorable attributes, the precise mechanism through which TPL influences tumor cells remains enigmatic. Its toxicity and limited water solubility significantly impede the clinical application of TPL. We offer a comprehensive overview of recent research endeavors aimed at unraveling the antitumor mechanism of TPL in this review. Additionally, we briefly discuss current strategies to effectively manage the challenges associated with TPL in future clinical applications. By compiling this information, we aim to enhance the understanding of the underlying mechanisms involved in TPL and identify potential avenues for further advancement in antitumor therapy.
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Affiliation(s)
- Shiwei Bao
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
- FuRong Laboratory, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Mei Yi
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China.
- FuRong Laboratory, Changsha, 410078, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
| | - Pan Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
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10
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Chen Z, Huang H, Huang H, Yu L, Weng H, Xiao J, Zou L, Zhang H, Liang C, Zhou H, Guo H, Wang Z, Li Z, Wu T, Zhang H, Wu H, Peng Z, Zhai L, Chen X, Liang Y, Hong H, Lin T. Genomic features reveal potential benefit of adding anti-PD-1 immunotherapy to treat non-upper aerodigestive tract natural killer/T-cell lymphoma. Leukemia 2024; 38:829-839. [PMID: 38378844 DOI: 10.1038/s41375-024-02171-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
Natural killer/T-cell lymphoma (NKTCL) is a highly heterogeneous disease with a poor prognosis. However, the genomic characteristics and proper treatment strategies for non-upper aerodigestive tract NKTCL (NUAT-NKTCL), a rare subtype of NKTCL, remain largely unexplored. In this study, 1589 patients newly diagnosed with NKTCL at 14 hospitals were assessed, 196 (12.3%) of whom had NUAT-NKTCL with adverse clinical characteristics and an inferior prognosis. By using whole-genome sequencing (WGS) and whole-exome sequencing (WES) data, we found strikingly different mutation profiles between upper aerodigestive tract (UAT)- and NUAT-NKTCL patients, with the latter group exhibiting significantly higher genomic instability. In the NUAT-NKTCL cohort, 128 patients received frontline P-GEMOX chemotherapy, 37 of whom also received anti-PD-1 immunotherapy. The application of anti-PD-1 significantly improved progression-free survival (3-year PFS rate 53.9% versus 17.0%, P = 0.009) and overall survival (3-year OS rate 63.7% versus 29.2%, P = 0.01) in the matched NUAT-NKTCL cohort. WES revealed frequent mutations involving immune regulation and genomic instability in immunochemotherapy responders. Our study showed distinct clinical characteristics and mutational profiles in NUAT-NKTCL compared with UAT patients and suggested adding anti-PD-1 immunotherapy in front-line treatment of NUAT-NKTCL. Further studies are needed to validate the efficacy and related biomarkers for immunochemotherapy proposed in this study.
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Affiliation(s)
- Zegeng Chen
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - He Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Huageng Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Le Yu
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Huawei Weng
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Jian Xiao
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China
| | - Liqun Zou
- Department of Medical Oncology of Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Huilai Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Chaoyong Liang
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Hui Zhou
- Hunan Cancer Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, China
| | - Hongqiang Guo
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450003, China
| | - Zhao Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zhiming Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Tao Wu
- The Affiliated Hospital of Guizhou Medical University, Guizhou Cancer Hospital, Guiyang, 550004, China
| | - Hongyu Zhang
- Department of Oncology, The Fifth Affiliated Hospital Sun Yat-Sen University, Zhuhai, 519000, China
| | - Huijing Wu
- Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Zhigang Peng
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Linzhu Zhai
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xinggui Chen
- Department of Medical Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Yang Liang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Huangming Hong
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China.
| | - Tongyu Lin
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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11
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Meng YW, Liu JY. Pathological and pharmacological functions of the metabolites of polyunsaturated fatty acids mediated by cyclooxygenases, lipoxygenases, and cytochrome P450s in cancers. Pharmacol Ther 2024; 256:108612. [PMID: 38369063 DOI: 10.1016/j.pharmthera.2024.108612] [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: 10/30/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
Oxylipins have garnered increasing attention because they were consistently shown to play pathological and/or pharmacological roles in the development of multiple cancers. Oxylipins are the metabolites of polyunsaturated fatty acids via both enzymatic and nonenzymatic pathways. The enzymes mediating the metabolism of PUFAs include but not limited to lipoxygenases (LOXs), cyclooxygenases (COXs), and cytochrome P450s (CYPs) pathways, as well as the down-stream enzymes. Here, we systematically summarized the pleiotropic effects of oxylipins in different cancers through pathological and pharmacological aspects, with specific reference to the enzyme-mediated oxylipins. We discussed the specific roles of oxylipins on cancer onset, growth, invasion, and metastasis, as well as the expression changes in the associated metabolic enzymes and the associated underlying mechanisms. In addition, we also discussed the clinical application and potential of oxylipins and related metabolic enzymes as the targets for cancer prevention and treatment. We found the specific function of most oxylipins in cancers, especially the underlying mechanisms and clinic applications, deserves and needs further investigation. We believe that research on oxylipins will provide not only more therapeutic targets for various cancers but also dietary guidance for both cancer patients and healthy humans.
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Affiliation(s)
- Yi-Wen Meng
- CNTTI of the Institute of Life Sciences & Department of Anesthesia of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China
| | - Jun-Yan Liu
- CNTTI of the Institute of Life Sciences & Department of Anesthesia of the Second Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China; Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing 400016, China; College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
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12
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Stergiopoulos GM, Iankov I, Galanis E. Personalizing Oncolytic Immunovirotherapy Approaches. Mol Diagn Ther 2024; 28:153-168. [PMID: 38150172 DOI: 10.1007/s40291-023-00689-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2023] [Indexed: 12/28/2023]
Abstract
Development of successful cancer therapeutics requires exploration of the differences in genetics, metabolism, and interactions with the immune system among malignant and normal cells. The clinical observation of spontaneous tumor regression following natural infection with microorganism has created the premise of their use as cancer therapeutics. Oncolytic viruses (OVs) originate from viruses with attenuated virulence in humans, well-characterized vaccine strains of known human pathogens, or engineered replication-deficient viral vectors. Their selectivity is based on receptor expression level and post entry restriction factors that favor replication in the tumor, while keeping the normal cells unharmed. Clinical trials have demonstrated a wide range of patient responses to virotherapy, with subgroups of patients significantly benefiting from OV administration. Tumor-specific gene signatures, including antiviral interferon-stimulated gene (ISG) expression profile, have demonstrated a strong correlation with tumor permissiveness to infection. Furthermore, the combination of OVs with immunotherapeutics, including anticancer vaccines and immune checkpoint inhibitors [ICIs, such as anti-PD-1/PD-L1 or anti-CTLA-4 and chimeric antigen receptor (CAR)-T or CAR-NK cells], could synergistically improve the therapeutic outcome. Creating response prediction algorithms represents an important step for the transition to individualized immunovirotherapy approaches in the clinic. Integrative predictors could include tumor mutational burden (TMB), inflammatory gene signature, phenotype of tumor-infiltrating lymphocytes, tumor microenvironment (TME), and immune checkpoint receptor expression on both immune and target cells. Additionally, the gut microbiota has recently been recognized as a systemic immunomodulatory factor and could further be used in the optimization of individualized immunovirotherapy algorithms.
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Affiliation(s)
| | - Ianko Iankov
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Evanthia Galanis
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
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13
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Rypens C, Van Berckelaer C, Berditchevski F, van Dam P, Van Laere S. Deciphering the molecular biology of inflammatory breast cancer through molecular characterization of patient samples and preclinical models. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 384:77-112. [PMID: 38637101 DOI: 10.1016/bs.ircmb.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Inflammatory breast cancer is an aggressive subtype of breast cancer with dismal patient prognosis and a unique clinical presentation. In the past two decades, molecular profiling technologies have been used in order to gain insight into the molecular biology of IBC and to search for possible targets for treatment. Although a gene signature that accurately discriminates between IBC and nIBC patient samples and preclinical models was identified, the overall genomic and transcriptomic differences are small and ambiguous, mainly due to the limited sample sizes of the evaluated patient series and the failure to correct for confounding effects of the molecular subtypes. Nevertheless, data collected over the past 20 years by independent research groups increasingly support the existence of several IBC-specific biological characteristics. In this review, these features are classified as established, emerging and conceptual hallmarks based on the level of evidence reported in the literature. In addition, a synoptic model is proposed that integrates all hallmarks and that can explain how cancer cell intrinsic mechanisms (i.e. NF-κB activation, genomic instability, MYC-addiction, TGF-β resistance, adaptive stress response, chromatin remodeling, epithelial-to-mesenchymal transition) can contribute to the establishment of the dynamic immune microenvironment associated with IBC. It stands to reason that future research projects are needed to further refine (parts of) this model and to investigate its clinical translatability.
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Affiliation(s)
- Charlotte Rypens
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium; CellCarta N V, Wilrijk, Belgium
| | - Christophe Van Berckelaer
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Peter van Dam
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium; Multidisciplinary Oncological Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, Edegem, Belgium
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium.
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14
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Chen M, Yu S, van der Sluis T, Zwager MC, Schröder CP, van der Vegt B, van Vugt MATM. cGAS-STING pathway expression correlates with genomic instability and immune cell infiltration in breast cancer. NPJ Breast Cancer 2024; 10:1. [PMID: 38167507 PMCID: PMC10761738 DOI: 10.1038/s41523-023-00609-z] [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: 05/03/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Genomic instability, as caused by oncogene-induced replication stress, can lead to the activation of inflammatory signaling, involving the cGAS-STING and JAK-STAT pathways. Inflammatory signaling has been associated with pro-tumorigenic features, but also with favorable response to treatment, including to immune checkpoint inhibition. In this study, we aim to explore relations between inflammatory signaling, markers of replication stress, and immune cell infiltration in breast cancer. Expression levels of cGAS-STING signaling components (STING, phospho-TBK1, and phospho-STAT1), replication stress markers (γH2AX and pRPA), replication stress-related proto-oncogenes (Cyclin E1 and c-Myc) and immune cell markers (CD20, CD4, and CD57) are determined immunohistochemically on primary breast cancer samples (n = 380). RNA-sequencing data from TCGA (n = 1082) and METABRIC (n = 1904) are used to calculate cGAS-STING scores. pTBK1, pSTAT1 expression and cGAS-STING pathway scores are all increased in triple-negative breast cancers compared to other subtypes. Expression of γH2AX, pRPA, Cyclin E1, c-Myc, and immune cell infiltration positively correlate with p-STAT1 expression (P < 0.001). Additionally, we observe significant positive associations between expression of pTBK1 and γH2AX, pRPA, c-Myc, and number of CD4+ cells and CD20+ cells. Also, cGAS-STING scores are correlated with genomic instability metrics, such as homologous recombination deficiency (P < 0.001) and tumor mutational burden (P < 0.01). Moreover, data from the I-SPY2 clinical trial (n = 71) confirms that higher cGAS-STING scores are observed in breast cancer patients who responded to immunotherapy combined with chemotherapy. In conclusion, the cGAS-STING pathway is highly expressed in TNBCs and is correlated with genomic instability and immune cell infiltration.
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Affiliation(s)
- Mengting Chen
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Shibo Yu
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tineke van der Sluis
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mieke C Zwager
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carolien P Schröder
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bert van der Vegt
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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15
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Manetsch P, Böhi F, Nowak K, Leslie Pedrioli DM, Hottiger MO. PARP7-mediated ADP-ribosylation of FRA1 promotes cancer cell growth by repressing IRF1- and IRF3-dependent apoptosis. Proc Natl Acad Sci U S A 2023; 120:e2309047120. [PMID: 38011562 DOI: 10.1073/pnas.2309047120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023] Open
Abstract
PARP7 was reported to promote tumor growth in a cell-autonomous manner and by repressing the antitumor immune response. Nevertheless, the molecular mechanism of how PARP7-mediated ADP-ribosylation exerts these effects in cancer cells remains elusive. Here, we identified PARP7 as a nuclear and cysteine-specific mono-ADP-ribosyltransferase that modifies targets critical for regulating transcription, including the AP-1 transcription factor FRA1. Loss of FRA1 ADP-ribosylation via PARP7 inhibition by RBN-2397 or mutation of the ADP-ribosylation site C97 increased FRA1 degradation by the proteasome via PSMC3. The reduction in FRA1 protein levels promoted IRF1- and IRF3-dependent cytokine as well as proapoptotic gene expression, culminating in CASP8-mediated apoptosis. Furthermore, high PARP7 expression was indicative of the PARP7 inhibitor response in FRA1-positive lung and breast cancer cells. Collectively, our findings highlight the connected roles of PARP7 and FRA1 and emphasize the clinical potential of PARP7 inhibitors for FRA1-driven cancers.
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Affiliation(s)
- Patrick Manetsch
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Flurina Böhi
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Cancer Biology Ph.D. Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Kathrin Nowak
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Deena M Leslie Pedrioli
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
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16
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Nemtsova MV, Kuznetsova EB, Bure IV. Chromosomal Instability in Gastric Cancer: Role in Tumor Development, Progression, and Therapy. Int J Mol Sci 2023; 24:16961. [PMID: 38069284 PMCID: PMC10707305 DOI: 10.3390/ijms242316961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
According to the Cancer Genome Atlas (TCGA), gastric cancers are classified into four molecular subtypes: Epstein-Barr virus-positive (EBV+), tumors with microsatellite instability (MSI), tumors with chromosomal instability (CIN), and genomically stable (GS) tumors. However, the gastric cancer (GC) with chromosomal instability remains insufficiently described and does not have effective markers for molecular and histological verification and diagnosis. The CIN subtype of GC is characterized by chromosomal instability, which is manifested by an increased frequency of aneuploidies and/or structural chromosomal rearrangements in tumor cells. Structural rearrangements in the CIN subtype of GC are not accidental and are commonly detected in chromosomal loci, being abnormal because of specific structural organization. The causes of CIN are still being discussed; however, according to recent data, aberrations in the TP53 gene may cause CIN development or worsen its phenotype. Clinically, patients with the CIN subtype of GC demonstrate poor survival, but receive the maximum benefit from adjuvant chemotherapy. In the review, we consider the molecular mechanisms and possible causes of chromosomal instability in GC, the common rearrangements of chromosomal loci and their impact on the development and clinical course of the disease, as well as the driver genes, their functions, and perspectives on their targeting in the CIN subtype of GC.
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Affiliation(s)
- Marina V. Nemtsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (E.B.K.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Ekaterina B. Kuznetsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (E.B.K.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Irina V. Bure
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (E.B.K.)
- Russian Medical Academy of Continuous Professional Education, 125993 Moscow, Russia
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17
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Zhou X, Sekino Y, Li HT, Fu G, Yang Z, Zhao S, Gujar H, Zu X, Weisenberger DJ, Gill IS, Tulpule V, D’souza A, Quinn DI, Han B, Liang G. SETD2 Deficiency Confers Sensitivity to Dual Inhibition of DNA Methylation and PARP in Kidney Cancer. Cancer Res 2023; 83:3813-3826. [PMID: 37695044 PMCID: PMC10843145 DOI: 10.1158/0008-5472.can-23-0401] [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: 02/07/2023] [Revised: 07/18/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
SETD2 deficiency alters the epigenetic landscape by causing depletion of H3K36me3 and plays an important role in diverse forms of cancer, most notably in aggressive and metastatic clear-cell renal cell carcinomas (ccRCC). Development of an effective treatment scheme targeting SETD2-compromised cancer is urgently needed. Considering that SETD2 is involved in DNA methylation and DNA repair, a combination treatment approach using DNA hypomethylating agents (HMA) and PARP inhibitors (PARPi) could have strong antitumor activity in SETD2-deficient kidney cancer. We tested the effects of the DNA HMA 5-aza-2'-dexoxydytidine (DAC), the PARPi talazoparib (BMN-673), and both in combination in human ccRCC models with or without SETD2 deficiency. The combination treatment of DAC and BMN-673 synergistically increased cytotoxicity in vitro in SETD2-deficient ccRCC cell lines but not in SETD2-proficient cell lines. DAC and BMN-673 led to apoptotic induction, increased DNA damage, insufficient DNA damage repair, and increased genomic instability. Furthermore, the combination treatment elevated immune responses, upregulated STING, and enhanced viral mimicry by activating transposable elements. Finally, the combination effectively suppressed the growth of SETD2-deficient ccRCC in in vivo mouse models. Together, these findings indicate that combining HMA and PARPi is a promising potential therapeutic strategy for treating SETD2-compromised ccRCC. SIGNIFICANCE SETD2 deficiency creates a vulnerable epigenetic status that is targetable using a DNA hypomethylating agent and PARP inhibitor combination to suppress renal cell carcinoma, identifying a precision medicine-based approach for SETD2-compromised cancers.
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Affiliation(s)
- Xinyi Zhou
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, Xiangya Hospital, Central South University, Hunan, Changsha 410008, China
| | - Yohei Sekino
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hong-Tao Li
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guanghou Fu
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Zhi Yang
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Shuqing Zhao
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Hemant Gujar
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Hunan, Changsha 410008, China
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Inderbir S. Gill
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Varsha Tulpule
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anishka D’souza
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David I Quinn
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bo Han
- Department of Surgery, Keck School of Medicine of USC, Los Angeles, California; Department of Surgery and Biomedical Engineering, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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18
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Zhong W, Chen H, Yang J, Huang C, Lin Y, Huang J. Inflammatory response-based prognostication and personalized therapy decisions in clear cell renal cell cancer to aid precision oncology. BMC Med Genomics 2023; 16:265. [PMID: 37885006 PMCID: PMC10601329 DOI: 10.1186/s12920-023-01687-5] [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: 03/01/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
OBJECTIVE The impact of inflammatory response on tumor development and therapeutic response is of significant importance in clear cell renal cell carcinoma (ccRCC). The customization of specialized prognostication approaches and the exploration of supplementary treatment options hold critical clinical implications in relation to the inflammatory response. METHODS In the present study, unsupervised clustering was implemented on TCGA-KIRC tumors using transcriptome profiles of inflammatory response genes, which was then validated in two ccRCC datasets (E-MATB-1980 and ICGC) and two immunotherapy datasets (IMvigor210 and Liu et al.) via SubMap and NTP algorithms. Combining co-expression and LASSO analyses, inflammatory response-based scoring system was defined, which was evaluated in pan-cancer. RESULTS Three reproducible inflammatory response subtypes (named IR1, IR2 and IR3) were determined and independently verified, each exhibiting distinct molecular, clinical, and immunological characteristics. Among these subtypes, IR2 had the best OS outcomes, followed by IR3 and IR1. In terms of anti-angiogenic agents, sunitinib may be appropriate for IR1 patients, while axitinib and pazopanib may be suitable for IR2 patients, and sorafenib for IR3 patients. Additionally, IR1 patients might benefit from anti-CTLA4 therapy. A scoring system called IRscore was defined for individual ccRCC patients. Patients with high IRscore presented a lower response rate to anti-PD-L1 therapy and worse prognostic outcomes. Pan-cancer analysis demonstrated the immunological features and prognostic relevance of the IRscore. CONCLUSION Altogether, characterization of inflammatory response subtypes and IRscore provides a roadmap for patient risk stratification and personalized treatment decisions, not only in ccRCC, but also in pan-cancer.
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Affiliation(s)
- Weimin Zhong
- Central laboratory, The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian Province, China
| | - Huijing Chen
- Central laboratory, The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian Province, China
| | - Jiayi Yang
- Central laboratory, The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian Province, China
| | - Chaoqun Huang
- Central laboratory, The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian Province, China
| | - Yao Lin
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China.
| | - Jiyi Huang
- Department of Nephrology, The Fifth Hospital of Xiamen, Xiamen, 361101, Fujian Province, People's Republic of China.
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19
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Sasaki N, Homme M, Kitajima S. Targeting the loss of cGAS/STING signaling in cancer. Cancer Sci 2023; 114:3806-3815. [PMID: 37475576 PMCID: PMC10551601 DOI: 10.1111/cas.15913] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/28/2023] [Accepted: 07/09/2023] [Indexed: 07/22/2023] Open
Abstract
The cGAS/STING pathway provides a key host defense mechanism by detecting the accumulation of cytoplasmic double-stranded DNA (dsDNA) and mediating innate and adaptive immune signaling. In addition to detecting pathogen-derived dsDNA, cGAS senses intrinsic dsDNA, such as those associated with defective cell cycle progression and mitophagy that has leaked from the nucleus or mitochondria, and subsequently evokes host immunity to eliminate pathogenic cells. In cancer cells, dysregulation of DNA repair and cell cycle caused at the DNA replication checkpoint and spindle assembly checkpoint results in aberrant cytoplasmic dsDNA accumulation, stimulating anti-tumor immunity. Therefore, the suppression of cGAS/STING signaling is beneficial for survival and frequently observed in cancer cells as a way to evade detection by the immune system, and is likely to be related to immune checkpoint blockade (ICB) resistance. Indeed, the mechanisms of ICB resistance overlap with those acquired in cancers during immunoediting to evade immune surveillance. This review highlights the current understanding of cGAS/STING suppression in cancer cells and discusses how to establish effective strategies to regenerate effective anti-tumor immunity through reactivation of the cGAS/STING pathway.
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Affiliation(s)
- Nobunari Sasaki
- Department of Cell BiologyCancer Institute, Japanese Foundation for Cancer ResearchTokyoJapan
| | - Mizuki Homme
- Department of Cell BiologyCancer Institute, Japanese Foundation for Cancer ResearchTokyoJapan
| | - Shunsuke Kitajima
- Department of Cell BiologyCancer Institute, Japanese Foundation for Cancer ResearchTokyoJapan
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20
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Zhang W, Xu M, Chen F, Su Y, Yu M, Xing L, Chang Y, Yan T. Targeting the JAK2-STAT3 pathway to inhibit cGAS-STING activation improves neuronal senescence after ischemic stroke. Exp Neurol 2023; 368:114474. [PMID: 37419174 DOI: 10.1016/j.expneurol.2023.114474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/12/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023]
Abstract
Neuroinflammation after cerebral ischemia is a key event in progressive brain injury after ischemic stroke. The JAK2/STAT3 pathway is pivotal for neuroinflammation; however, its role in brain senescence after ischemic stroke is unclear. Here, we report that inflammation is increased in the brains of C57BL/6 stroke mice. Treatment of ischemic stroke in adult mice with a JAK kinase inhibitor (AG490) alleviated neurobehavioral defects, reduced brain infarct volume, reduced expression of pro-inflammatory cytokines, and decreased activation of pro-inflammatory microglia. Moreover, AG490 treatment reduced oxidative DNA damage and cellular senescence in the brains of mice following ischemic stroke. Cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) were associated with inflammation and senescence. Furthermore, AG490 blocked cGAS/STING/NF-κBp65 expression. Overall, our results indicate that inhibition of JAK2/STAT3 can alleviate the negative neurological consequences of ischemic stroke, likely due to repression of cGAS/STING/NF-κB p65, leading to reduced neuroinflammation and neuronal senescence. Therefore, JAK2/STAT3 may represent a viable therapeutic target for preventing senescence after ischemic stroke.
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Affiliation(s)
- Wei Zhang
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post Neurotrauma, Neurorepair, and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Meijie Xu
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post Neurotrauma, Neurorepair, and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Fangyu Chen
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post Neurotrauma, Neurorepair, and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Yue Su
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post Neurotrauma, Neurorepair, and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Mingjing Yu
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post Neurotrauma, Neurorepair, and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Ling Xing
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post Neurotrauma, Neurorepair, and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Yifan Chang
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post Neurotrauma, Neurorepair, and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Tao Yan
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin Neurological Institute, Key Laboratory of Post Neurotrauma, Neurorepair, and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China.
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Zhao J, Yang Y, Pan Y, Zhou P, Wang J, Zheng Y, Zhang X, Zhai S, Zhang X, Li L, Yang D. Transcription Factor GLI1 Induces IL-6-Mediated Inflammatory Response and Facilitates the Progression of Adamantinomatous Craniopharyngioma. ACS Chem Neurosci 2023; 14:3347-3356. [PMID: 37691264 DOI: 10.1021/acschemneuro.3c00031] [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] [Indexed: 09/12/2023] Open
Abstract
Adamantinomatous craniopharyngioma (ACP) is a neuroendocrine tumor whose pathogenesis remains unclear. This study investigated the role of glioma-associated oncogene family zinc finger 1 (GLI1), a transcription factor in the sonic hedgehog (SHH) signaling pathway, in ACP. We discovered that GLI1 regulates the expression of IL-6, thereby triggering inflammatory responses in ACP and influencing the tumor's progression. Analyzing the Gene Expression Omnibus (GEO) database chip GSE68015, we found that GLI1 is overexpressed in ACP, correlating positively with the spite of ACP and inflammation markers. Knockdown of GLI1 significantly inhibited the levels of tumor necrosis factor α, interleukin-6 (IL-6), and IL-1β in ACP cells, as well as cell proliferation and migration. We further identified a binding site between GLI1 and the promoter region of IL-6, demonstrating that GLI1 can enhance the expression of IL-6. These findings were verified in vivo, where activation of the SHH pathway significantly promoted GLI1 and IL-6 expressions in nude mice, inducing inflammation and tumor growth. Conversely, GLI1 knockdown markedly suppressed these processes. Our study uncovers a potential molecular mechanism for the occurrence of inflammatory responses and tumor progression in ACP.
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Affiliation(s)
- Jingyi Zhao
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Yongqiang Yang
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Yuanyuan Pan
- Institute of Radiation Therapy and Tumor Critical Care of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Pengcheng Zhou
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Juan Wang
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Yingjuan Zheng
- Institute of Radiation Therapy and Tumor Critical Care of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Xiangxian Zhang
- Henan Key Laboratory of Molecular Radiotherapy, Zhengzhou 450052, P.R. China
| | - Suna Zhai
- Henan Key Laboratory of Molecular Radiotherapy, Zhengzhou 450052, P.R. China
| | - Xiqian Zhang
- Institute of Radiation Therapy and Tumor Critical Care of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Liming Li
- Comprehensive Hyperthermia Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Daoke Yang
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
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Sokač M, Kjær A, Dyrskjøt L, Haibe-Kains B, JWL Aerts H, Birkbak NJ. Spatial transformation of multi-omics data unlocks novel insights into cancer biology. eLife 2023; 12:RP87133. [PMID: 37669321 PMCID: PMC10479962 DOI: 10.7554/elife.87133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023] Open
Abstract
The application of next-generation sequencing (NGS) has transformed cancer research. As costs have decreased, NGS has increasingly been applied to generate multiple layers of molecular data from the same samples, covering genomics, transcriptomics, and methylomics. Integrating these types of multi-omics data in a combined analysis is now becoming a common issue with no obvious solution, often handled on an ad hoc basis, with multi-omics data arriving in a tabular format and analyzed using computationally intensive statistical methods. These methods particularly ignore the spatial orientation of the genome and often apply stringent p-value corrections that likely result in the loss of true positive associations. Here, we present GENIUS (GEnome traNsformatIon and spatial representation of mUltiomicS data), a framework for integrating multi-omics data using deep learning models developed for advanced image analysis. The GENIUS framework is able to transform multi-omics data into images with genes displayed as spatially connected pixels and successfully extract relevant information with respect to the desired output. We demonstrate the utility of GENIUS by applying the framework to multi-omics datasets from the Cancer Genome Atlas. Our results are focused on predicting the development of metastatic cancer from primary tumors, and demonstrate how through model inference, we are able to extract the genes which are driving the model prediction and are likely associated with metastatic disease progression. We anticipate our framework to be a starting point and strong proof of concept for multi-omics data transformation and analysis without the need for statistical correction.
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Affiliation(s)
- Mateo Sokač
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
- Bioinformatics Research Center, Aarhus UniversityAarhusDenmark
| | - Asbjørn Kjær
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
- Bioinformatics Research Center, Aarhus UniversityAarhusDenmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Temerty Faculty of Medicine, University of TorontoTorontoCanada
| | - Hugo JWL Aerts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical SchoolBostonUnited States
- Departments of Radiation Oncology and Radiology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical SchoolBostonUnited States
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht UniversityMaastrichtNetherlands
| | - Nicolai J Birkbak
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
- Bioinformatics Research Center, Aarhus UniversityAarhusDenmark
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23
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Shao C, Ren Y, Zhou H, Chen C, Dettman EJ, Lee LC, Cristescu R, Gozman A, Jin F, Zhou W. Association Between Homologous Recombination Repair Biomarkers and Survival in Patients With Solid Tumors. JCO Precis Oncol 2023; 7:e2300195. [PMID: 37972338 DOI: 10.1200/po.23.00195] [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: 04/21/2023] [Revised: 08/16/2023] [Accepted: 09/06/2023] [Indexed: 11/19/2023] Open
Abstract
PURPOSE Mutations in BRCA1 and/or BRCA2 (BRCAm), other homologous recombination repair genes (HRRm), and homologous recombination deficiency (HRD) lead to an accumulation of genomic alterations that can drive tumorigenesis. The prognostic impact of these HRR pathway defects on overall survival (OS) in patients not receiving poly (ADP-ribose) polymerase inhibitors (PARPi) or immunotherapy is unclear. We evaluated the association of HRR biomarkers with OS in patients with advanced solid tumors receiving therapy excluding PARPi and immunotherapy. METHODS Deidentified data were collected through December 31, 2020, from a real-world clinicogenomic database (CGDB) with data originating from approximately 280 cancer clinics in the United States. Patients age 18 years and older with an advanced/metastatic diagnosis between 2018 and 2019 for 1 of 15 solid tumors and available data in the CGDB were included. The primary analysis evaluated the association between HRR pathway biomarkers and OS, using start of second-line therapy as the index date (to reduce immortal time bias). RESULTS A total of 9,457 patients had available data for BRCA/HRR and 5,792 for HRD status; 4,890 (51.7%) were women and mean (SD) age was 65.9 (11.5) years. For the primary analysis, adjusted hazard ratios for OS were BRCAm (n = 156) versus BRCA wild-type (wt; n = 3,131; 0.83 [95% CI, 0.60 to 1.17]); for HRRm (n = 467) versus HRRwt (n = 282; 0.95 [95% CI, 0.79 to 1.14]); and for HRD-positive (n = 447) versus -negative (n = 1,687; 1.22 [95% CI, 1.02 to 1.47]). Results were similar using start of first-line and start of third-line therapy as index dates. CONCLUSION This large, real-world study found no association between OS and either BRCA or HRR status but identified a possible linkage between HRD positivity and shorter median OS in patients with advanced solid tumors who did not receive PARPi or immunotherapy.
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Benada J, Bulanova D, Azzoni V, Petrosius V, Ghazanfar S, Wennerberg K, Sørensen C. Synthetic lethal interaction between WEE1 and PKMYT1 is a target for multiple low-dose treatment of high-grade serous ovarian carcinoma. NAR Cancer 2023; 5:zcad029. [PMID: 37325550 PMCID: PMC10262308 DOI: 10.1093/narcan/zcad029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Ovarian cancer is driven by genetic alterations that necessitate protective DNA damage and replication stress responses through cell cycle control and genome maintenance. This creates specific vulnerabilities that may be exploited therapeutically. WEE1 kinase is a key cell cycle control kinase, and it has emerged as a promising cancer therapy target. However, adverse effects have limited its clinical progress, especially when tested in combination with chemotherapies. A strong genetic interaction between WEE1 and PKMYT1 led us to hypothesize that a multiple low-dose approach utilizing joint WEE1 and PKMYT1 inhibition would allow exploitation of the synthetic lethality. We found that the combination of WEE1 and PKMYT1 inhibition exhibited synergistic effects in eradicating ovarian cancer cells and organoid models at a low dose. The WEE1 and PKMYT1 inhibition synergistically promoted CDK activation. Furthermore, the combined treatment exacerbated DNA replication stress and replication catastrophe, leading to increase of the genomic instability and inflammatory STAT1 signalling activation. These findings suggest a new multiple low-dose approach to harness the potency of WEE1 inhibition through the synthetic lethal interaction with PKMYT1 that may contribute to the development of new treatments for ovarian cancer.
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Affiliation(s)
- Jan Benada
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Daria Bulanova
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Violette Azzoni
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Valdemaras Petrosius
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224, 2800 Kgs Lyngby, Denmark
| | - Saba Ghazanfar
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Krister Wennerberg
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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25
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Wardlaw CP, Petrini JH. ISG15: A link between innate immune signaling, DNA replication, and genome stability. Bioessays 2023; 45:e2300042. [PMID: 37147792 PMCID: PMC10473822 DOI: 10.1002/bies.202300042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/07/2023]
Abstract
Interferon stimulated gene 15 (ISG15) encodes a ubiquitin-like protein that is highly induced upon activation of interferon signaling and cytoplasmic DNA sensing pathways. As part of the innate immune system ISG15 acts to inhibit viral replication and particle release via the covalent conjugation to both viral and host proteins. Unlike ubiquitin, unconjugated ISG15 also functions as an intracellular and extra-cellular signaling molecule to modulate the immune response. Several recent studies have shown ISG15 to also function in a diverse array of cellular processes and pathways outside of the innate immune response. This review explores the role of ISG15 in maintaining genome stability, particularly during DNA replication, and how this relates to cancer biology. It puts forth the hypothesis that ISG15, along with DNA sensors, function within a DNA replication fork surveillance pathway to help maintain genome stability.
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Affiliation(s)
| | - John H.J. Petrini
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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26
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Göder A, Quinlan A, Rainey MD, Bennett D, Shamavu D, Corso J, Santocanale C. PTBP1 enforces ATR-CHK1 signaling determining the potency of CDC7 inhibitors. iScience 2023; 26:106951. [PMID: 37378325 PMCID: PMC10291475 DOI: 10.1016/j.isci.2023.106951] [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: 01/24/2023] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
CDC7 kinase is crucial for DNA replication initiation and fork processing. CDC7 inhibition mildly activates the ATR pathway, which further limits origin firing; however, to date the relationship between CDC7 and ATR remains controversial. We show that CDC7 and ATR inhibitors are either synergistic or antagonistic depending on the degree of inhibition of each individual kinase. We find that Polypyrimidine Tract Binding Protein 1 (PTBP1) is important for ATR activity in response to CDC7 inhibition and genotoxic agents. Compromised PTBP1 expression makes cells defective in RPA recruitment, genomically unstable, and resistant to CDC7 inhibitors. PTBP1 deficiency affects the expression and splicing of many genes indicating a multifactorial impact on drug response. We find that an exon skipping event in RAD51AP1 contributes to checkpoint deficiency in PTBP1-deficient cells. These results identify PTBP1 as a key factor in replication stress response and define how ATR activity modulates the activity of CDC7 inhibitors.
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Affiliation(s)
- Anja Göder
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Aisling Quinlan
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Michael D. Rainey
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Declan Bennett
- School of Mathematical & Statistical Sciences, University of Galway, Galway H91TK33, Ireland
| | - Daniel Shamavu
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Jacqueline Corso
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Corrado Santocanale
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
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27
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Li P, Wang W, Wang S, Cao G, Pan T, Huang Y, Wan H, Zhang W, Huang Y, Jin H, Wang Z. PTPRC promoted CD8+ T cell mediated tumor immunity and drug sensitivity in breast cancer: based on pan-cancer analysis and artificial intelligence modeling of immunogenic cell death-based drug sensitivity stratification. Front Immunol 2023; 14:1145481. [PMID: 37388747 PMCID: PMC10302730 DOI: 10.3389/fimmu.2023.1145481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023] Open
Abstract
Background Immunogenic cell death (ICD) is a result of immune cell infiltration (ICI)-mediated cell death, which is also a novel acknowledgment to regulate cellular stressor-mediated cell death, including drug therapy and radiotherapy. Methods In this study, TCGA and GEO data cohorts were put into artificial intelligence (AI) to identify ICD subtypes, and in vitro experiments were performed. Results Gene expression, prognosis, tumor immunity, and drug sensitivity showed significance among ICD subgroups, Besides, a 14-gene-based AI model was able to represent the genome-based drug sensitivity prediction, which was further verified in clinical trials. Network analysis revealed that PTPRC was the pivotal gene in regulating drug sensitivity by regulating CD8+ T cell infiltration. Through in vitro experiments, intracellular down-regulation of PTPRC enhanced paclitaxel tolerance in triple breast cancer (TNBC) cell lines. Meanwhile, the expression level of PTPRC was positively correlated with CD8+ T cell infiltration. Furthermore, the down-regulation of PTPRC increased the level of TNBC-derived PD-L1 and IL2. Discussion ICD-based subtype clustering of pan-cancer was helpful to evaluate chemotherapy sensitivity and immune cell infiltration, and PTPRC was a potential target to against drug resistance of breast cancer.
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Affiliation(s)
- Pengping Li
- Department of Thyroid & Breast Surgery, The First People’s Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang, China
| | - Wei Wang
- Department of Oncology, The Second Affiliated Hospital of Bengbu Medical College, Anhui, China
| | - Shaowen Wang
- Neuromedicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Guodong Cao
- The Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Tonghe Pan
- The Department of Ningbo Eye Hospital, Affiliated to Wenzhou Medical University, Ningbo, Zhejiang, China
| | - Yuqing Huang
- Department of Thyroid & Breast Surgery, The First People’s Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang, China
| | - Hong Wan
- The Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Anhui Public Health Clinical Center, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Weijun Zhang
- Department of Thyroid & Breast Surgery, The First People’s Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang, China
| | - Yate Huang
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Haigang Jin
- Department of Thyroid & Breast Surgery, The First People’s Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang, China
| | - Zhenyu Wang
- Department of Thyroid & Breast Surgery, The First People’s Hospital of Xiaoshan District, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang, China
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28
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Randolph ME, Afifi M, Gorthi A, Weil R, Wilky BA, Weinreb J, Ciero P, ter Hoeve N, van Diest PJ, Raman V, Bishop AJR, Loeb DM. RNA Helicase DDX3 Regulates RAD51 Localization and DNA Damage Repair in Ewing Sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.10.544474. [PMID: 37333164 PMCID: PMC10274875 DOI: 10.1101/2023.06.10.544474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
We previously demonstrated that RNA helicase DDX3X (DDX3) can be a therapeutic target in Ewing sarcoma (EWS), but its role in EWS biology remains unclear. The present work demonstrates that DDX3 plays a unique role in DNA damage repair (DDR). We show that DDX3 interacts with several proteins involved in homologous recombination, including RAD51, RECQL1, RPA32, and XRCC2. In particular, DDX3 colocalizes with RAD51 and RNA:DNA hybrid structures in the cytoplasm of EWS cells. Inhibition of DDX3 RNA helicase activity increases cytoplasmic RNA:DNA hybrids, sequestering RAD51 in the cytoplasm, which impairs nuclear translocation of RAD51 to sites of double-stranded DNA breaks thus increasing sensitivity of EWS to radiation treatment, both in vitro and in vivo. This discovery lays the foundation for exploring new therapeutic approaches directed at manipulating DDR protein localization in solid tumors.
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Affiliation(s)
- Matthew E. Randolph
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Marwa Afifi
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Aparna Gorthi
- Greehey Children’s Cancer Research Institute and Department of Cell Systems & Anatomy, UT Health San Antonio, San Antonio, TX
| | - Rachel Weil
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Breelyn A. Wilky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Joshua Weinreb
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Paul Ciero
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Natalie ter Hoeve
- Department of Pathology, University Medical Centre Utrecht, The Netherlands
| | - Paul J. van Diest
- Department of Pathology, University Medical Centre Utrecht, The Netherlands
| | - Venu Raman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
- Department of Radiology, Johns Hopkins University, Baltimore, MD
- Department of Pharmacology, Johns Hopkins University, Baltimore, MD
| | - Alexander J. R. Bishop
- Greehey Children’s Cancer Research Institute and Department of Cell Systems & Anatomy, UT Health San Antonio, San Antonio, TX
| | - David M. Loeb
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
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29
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Fonseca-Montaño MA, Vázquez-Santillán KI, Hidalgo-Miranda A. The current advances of lncRNAs in breast cancer immunobiology research. Front Immunol 2023; 14:1194300. [PMID: 37342324 PMCID: PMC10277570 DOI: 10.3389/fimmu.2023.1194300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy and the leading cause of cancer-related death in women worldwide. Breast cancer development and progression are mainly associated with tumor-intrinsic alterations in diverse genes and signaling pathways and with tumor-extrinsic dysregulations linked to the tumor immune microenvironment. Significantly, abnormal expression of lncRNAs affects the tumor immune microenvironment characteristics and modulates the behavior of different cancer types, including breast cancer. In this review, we provide the current advances about the role of lncRNAs as tumor-intrinsic and tumor-extrinsic modulators of the antitumoral immune response and the immune microenvironment in breast cancer, as well as lncRNAs which are potential biomarkers of tumor immune microenvironment and clinicopathological characteristics in patients, suggesting that lncRNAs are potential targets for immunotherapy in breast cancer.
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Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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30
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Gao K, Lian W, Zhao R, Huang W, Xiong J. The joint role of methylation and immune-related lncRNAs in ovarian cancer: Defining molecular subtypes and developing prognostic signature. Transl Oncol 2023; 34:101704. [PMID: 37257331 DOI: 10.1016/j.tranon.2023.101704] [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: 03/10/2023] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023] Open
Abstract
INTRODUCTION Complex outcome of ovarian cancer (OC) stems from the tumor immune microenvironment (TIME) influenced by genetic and epigenetic factors. This study aimed to comprehensively explored the subclasses of OC through lncRNAs related to both N6-methyladenosine (m6A)/N1-methyladenosine (m1A)/N7-methylguanosine (m7G)/5-methylcytosine (m5C) in terms of epigenetic variability and immune molecules and develop a new set of risk predictive systems. MATERIAL AND METHODS The lncRNA data of OC were collected from TCGA. Spearman correlation analysis on lncRNA data of OC with immune-related gene expression and with m6A/m5C/m1A/m7G were respectively conducted. The m6A/m5C/m1A/m7G-related m6A/m5C/m1A/m7G related immune lncRNA subtypes were identified on the basis of the prognostic lncRNAs. Heterogeneity among subtypes was evaluated by tumor mutation analysis, tumor microenvironment (TME) component analysis, response to immune checkpoint blocked (ICB) and chemotherapeutic drugs. A risk predictive system was developed based on the results of Cox regression analysis and random survival forest analysis of the differences between each specific cluster and other clusters. RESULTS Three m6A/m5C/m1A/m7G-related immune lncRNA subtypes of OC showing distinct differences in prognosis, mutation pattern, TIME components, immunotherapy and chemotherapy response were identified. A set of risk predictive system consisting of 10 lncRNA for OC was developed, according to which the risk score of samples in each OC dataset was calculated and risk type was defined. CONCLUSIONS This study classified three m6A/m5C/m1A/m7G-related immune lncRNA subtypes with distinct heterogeneous mutation patterns, TME components, ICB therapy and immune response, and provided a set of risk predictive system consisted of 10 lncRNA for OC.
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Affiliation(s)
- Kefei Gao
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Wenqin Lian
- Department of Burns and Plastic & Wound Repair Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361100, China
| | - Rui Zhao
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Weiming Huang
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China.
| | - Jian Xiong
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China.
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31
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Stenmark Tullberg A, Sjöström M, Niméus E, Killander F, Chang SL, Feng FY, Speers CW, Pierce LJ, Kovács A, Lundstedt D, Holmberg E, Karlsson P. Integrating Tumor-Intrinsic and Immunologic Factors to Identify Immunogenic Breast Cancers from a Low-Risk Cohort: Results from the Randomized SweBCG91RT Trial. Clin Cancer Res 2023; 29:1783-1793. [PMID: 37071498 PMCID: PMC10150244 DOI: 10.1158/1078-0432.ccr-22-2746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/18/2022] [Accepted: 01/20/2023] [Indexed: 04/19/2023]
Abstract
PURPOSE The local immune infiltrate's influence on tumor progression may be closely linked to tumor-intrinsic factors. The study aimed to investigate whether integrating immunologic and tumor-intrinsic factors can identify patients from a low-risk cohort who may be candidates for radiotherapy (RT) de-escalation. EXPERIMENTAL DESIGN The SweBCG91RT trial included 1,178 patients with stage I to IIA breast cancer, randomized to breast-conserving surgery with or without adjuvant RT, and followed for a median of 15.2 years. We trained two models designed to capture immunologic activity and immunomodulatory tumor-intrinsic qualities, respectively. We then analyzed if combining these two variables could further stratify tumors, allowing for identifying a subgroup where RT de-escalation is feasible, despite clinical indicators of a high risk of ipsilateral breast tumor recurrence (IBTR). RESULTS The prognostic effect of the immunologic model could be predicted by the tumor-intrinsic model (Pinteraction = 0.01). By integrating measurements of the immunologic- and tumor-intrinsic models, patients who benefited from an active immune infiltrate could be identified. These patients benefited from standard RT (HR, 0.28; 95% CI, 0.09-0.85; P = 0.025) and had a 5.4% 10-year incidence of IBTR after irradiation despite high-risk genomic indicators and a low frequency of systemic therapy. In contrast, high-risk tumors without an immune infiltrate had a high 10-year incidence of IBTR despite RT treatment (19.5%; 95% CI, 12.2-30.3). CONCLUSIONS Integrating tumor-intrinsic and immunologic factors may identify immunogenic tumors in early-stage breast cancer populations dominated by ER-positive tumors. Patients who benefit from an activated immune infiltrate may be candidates for RT de-escalation.
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Affiliation(s)
- Axel Stenmark Tullberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Martin Sjöström
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Emma Niméus
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Lund, Sweden
| | - Fredrika Killander
- Department of Clinical Sciences Lund, Oncology/Pathology and Surgery, Lund University, Lund, Sweden
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | | | - Felix Y. Feng
- University of California San Francisco, San Francisco, California
| | | | - Lori J. Pierce
- University of Michigan Medical School, Ann Arbor, Michigan
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Dan Lundstedt
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Erik Holmberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
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Liu N, Liu G, Ma Q, Li X. Chromosome instability-associated prognostic signature and cluster investigation for cutaneous melanoma cases. IET Syst Biol 2023. [PMID: 37186446 DOI: 10.1049/syb2.12064] [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: 11/06/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Chromosomal instability (CIN) is closely associated to the early detection of several clinical tumours. In this study, the authors first established a novel prognostic model of melanoma using the hub genes of CIN, based on the datasets of The cancer genome atlas-skin cutaneous melanoma (TCGA-SKCM) and GSE65904 cohorts. Based on the risk scores of our model, the disease-specific survival (DSS) prognosis was worse in the high-risk group. Combining risk score, stage, age, ulceration, and clark factors, a Nomogram was generated to predict 1, 3, 5-year survival rates, which indicated a good clinical validity. Our finding also showed a correlation between high/low risk and tumour infiltration levels of 'activated CD8 T cells' and 'effector memory CD8 T cells'. Moreover, the authors first performed a CIN-based tumour clustering analysis using TCGA-SKCM cases, and identified two melanoma clusters, which exhibit the distinct DSS prognosis and the tumour-infiltrating levels of CD8 T cells. Taken together, a promising CIN-related prognostic signature and clustering for melanoma cases were first established in our study.
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Affiliation(s)
- Ning Liu
- Department of Plastic and Burns Surgery, Tianjin First Center Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Guangjing Liu
- Department of Plastic and Burns Surgery, Tianjin First Center Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Qian Ma
- Department of Plastic and Burns Surgery, Tianjin First Center Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Xiaobing Li
- Department of Plastic and Burns Surgery, Tianjin First Center Hospital, School of Medicine, Nankai University, Tianjin, China
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Li Y, Wang X, Hou X, Ma X. Could Inhibiting the DNA Damage Repair Checkpoint Rescue Immune-Checkpoint-Inhibitor-Resistant Endometrial Cancer? J Clin Med 2023; 12:jcm12083014. [PMID: 37109350 PMCID: PMC10144486 DOI: 10.3390/jcm12083014] [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: 02/17/2023] [Revised: 03/23/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Endometrial cancer (EC) is increasingly undermining female health worldwide, with poor survival rates for advanced or recurrent/metastatic diseases. The application of immune checkpoint inhibitors (ICIs) has opened a window of opportunity for patients with first-line therapy failure. However, there is a subset of patients with endometrial cancer who remain insensitive to immunotherapy alone. Therefore, it is necessary to develop new therapeutic agents and further explore reliable combinational strategies to optimize the efficacy of immunotherapy. DNA damage repair (DDR) inhibitors as novel targeted drugs are able to generate genomic toxicity and induce cell death in solid tumors, including EC. Recently, growing evidence has demonstrated the DDR pathway modulates innate and adaptive immunity in tumors. In this review, we concentrate on the exploration of the intrinsic correlation between DDR pathways, especially the ATM-CHK2-P53 pathway and the ATR-CHK1-WEE1 pathway, and oncologic immune response, as well as the feasibility of adding DDR inhibitors to ICIs for the treatment of patients with advanced or recurrent/metastatic EC. We hope that this review will offer some beneficial references to the investigation of immunotherapy and provide a reasonable basis for "double-checkpoint inhibition" in EC.
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Affiliation(s)
- Yinuo Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangyu Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Hou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiangyi Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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Agborbesong E, Zhou JX, Li LX, Harris PC, Calvet JP, Li X. Prdx5 regulates DNA damage response through autophagy-dependent Sirt2-p53 axis. Hum Mol Genet 2023; 32:567-579. [PMID: 36067023 PMCID: PMC9896474 DOI: 10.1093/hmg/ddac218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/15/2022] [Accepted: 08/26/2022] [Indexed: 02/07/2023] Open
Abstract
DNA damage response (DDR) is an important signaling-transduction network that promotes the repair of DNA lesions which can induce and/or support diseases. However, the mechanisms involved in its regulation are not fully understood. Recent studies suggest that the peroxiredoxin 5 (Prdx5) enzyme, which detoxifies reactive oxygen species, is associated to genomic instability and signal transduction. Its role in the regulation of DDR, however, is not well characterized. In this study, we demonstrate a role of Prdx5 in the regulation of the DDR signaling pathway. Knockdown of Prdx5 resulted in DNA damage manifested by the induction of phosphorylated histone H2AX (γ-H2AX) and p53-binding protein 1 (53BP1). We show that Prdx5 regulates DDR through (1) polo-like kinase 1 (Plk1) mediated phosphorylation of ataxia telangiectasia mutated (ATM) kinase to further trigger downstream mediators Chek1 and Chek2; (2) the increase of the acetylation of p53 at lysine 382, stabilizing p53 in the nucleus and enhancing transcription and (3) the induction of autophagy, which regulates the recycling of molecules involved in DDR. We identified Sirt2 as a novel deacetylase of p53 at lysine 382, and Sirt2 regulated the acetylation status of p53 at lysine 382 in a Prdx5-dependent manner. Furthermore, we found that exogenous expression of Prdx5 decreased DNA damage and the activation of ATM in Pkd1 mutant renal epithelial cells, suggesting that Prdx5 may play a protective role from DNA damage in cystic renal epithelial cells. This study identified a novel mechanism of Prdx5 in the regulation of DDR through the ATM/p53/Sirt2 signaling cascade.
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Affiliation(s)
- Ewud Agborbesong
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Julie X Zhou
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Linda X Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Peter C Harris
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - James P Calvet
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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Bloom EA, Peters PN, Whitaker R, Russell S, Albright B, Cummings S, Timms KM, Slavin T, Probst B, Strickland KC, Previs RA. Association of Genomic Instability Score, Tumor Mutational Burden, and Tumor-Infiltrating Lymphocytes as Biomarkers in Uterine Serous Carcinoma. Cancers (Basel) 2023; 15:528. [PMID: 36672477 PMCID: PMC9856872 DOI: 10.3390/cancers15020528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/22/2022] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Background: Uterine serous carcinomas represent 10% of uterine carcinomas but account for nearly 40% of deaths from the disease. Improved molecular characterization of these tumors is instrumental in guiding targeted treatment and improving outcomes. This study assessed the genomic instability score (GIS), tumor mutational burden (TMB), and tumor-infiltrating lymphocytes (TILs) in patients with USC. Methods: A retrospective cohort study evaluated patients with USC following staging surgery. The GIS and TMB were determined from archived specimens. We evaluated the tumoral expression of CD3, CD4, CD8, FOXP3, and CD68 using immunohistochemistry. T-tests were used to assess associations of TILs with the GIS. Results: We evaluated 53 patients with USC. The median GIS was 31 (range: 0−52) and a higher GIS was not associated with progression-free (PFS) or overall survival (OS). The median TMB was 1.35 mt/Mb; patients with TMB > 1.35 mt/Mb had improved PFS and OS (p = 0.005; p = 0.002, respectively). Tumors with increased CD3+ and CD4+ immune cells had a higher mean GIS (p = 0.013, p = 0.002). Conclusions: TMB > 1.35 mt/Mb was associated with improved survival in USC patients, whereas the GIS was not. Lower TMB thresholds may provide prognostic value for less immunogenic tumors such as USC. In this limited cohort, we observed that increased TIL populations were correlated with a higher GIS.
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Affiliation(s)
- Elizabeth A. Bloom
- Duke University School of Medicine, Duke University, Durham, NC 27710, USA
| | - Pamela N. Peters
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Regina Whitaker
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shonagh Russell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Benjamin Albright
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shelly Cummings
- Myriad Genetics Laboratories, Inc., Salt Lake City, UT 84108, USA
| | - Kirsten M. Timms
- Myriad Genetics Laboratories, Inc., Salt Lake City, UT 84108, USA
| | - Thomas Slavin
- Myriad Genetics Laboratories, Inc., Salt Lake City, UT 84108, USA
| | - Braden Probst
- Myriad Genetics Laboratories, Inc., Salt Lake City, UT 84108, USA
| | | | - Rebecca A. Previs
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University School of Medicine, Durham, NC 27710, USA
- Labcorp Oncology, Durham, NC 27560, USA
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Xun Z, Wang Y, Long J, Li Y, Yang X, Sun H, Zhao H. Development and validation of a genomic instability-related lncRNA prognostic model for hepatocellular carcinoma. Front Genet 2023; 13:1034979. [PMID: 36712850 PMCID: PMC9877230 DOI: 10.3389/fgene.2022.1034979] [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: 09/02/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Genomic instability is a characteristic of tumors, and recent studies have shown that it is related to a poor prognosis of multiple cancers. Long non-coding RNAs (lncRNAs) have become a research hotspot in recent years, and many unknown biological functions are being explored. For example, some lncRNAs play a critical role in the initiation and progression of multiple cancer types by modulating genomic instability. However, the role of genomic instability-related lncRNAs in liver cancer remains unclear. Therefore, we screened genomic instability-related lncRNAs by combining somatic mutation data and RNA-Seq data in The Cancer Genome Atlas (TCGA) database. We established a genomic instability-related lncRNA model (GLncM) involving ZFPM2-AS1 and MIR210HG to predict the hepatocellular carcinoma (HCC) prognosis and further explore the clinical significance of these lncRNAs, and the robustness of the model was validated in the verification set. Thereafter, we calculated the immune score for each patient and explored the relationship between genome instability and the immune microenvironment. The analysis indicated that this model was better than the immune microenvironment in predicting the prognosis of HCC patients, suggesting that the GLncM may be an effective indicator of HCC prognosis and providing a new direction and strategy for estimating the prognosis of HCC patients.
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Xu X, Wu Y, Jia G, Zhu Q, Li D, Xie K. A signature based on glycosyltransferase genes provides a promising tool for the prediction of prognosis and immunotherapy responsiveness in ovarian cancer. J Ovarian Res 2023; 16:5. [PMID: 36611197 PMCID: PMC9826597 DOI: 10.1186/s13048-022-01088-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is the most fatal gynaecological malignancy and has a poor prognosis. Glycosylation, the biosynthetic process that depends on specific glycosyltransferases (GTs), has recently attracted increasing importance due to the vital role it plays in cancer. In this study, we aimed to determine whether OC patients could be stratified by glycosyltransferase gene profiles to better predict the prognosis and efficiency of immune checkpoint blockade therapies (ICBs). METHODS We retrieved transcriptome data across 420 OC and 88 normal tissue samples using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, respectively. An external validation dataset containing 185 OC samples was downloaded from the Gene Expression Omnibus (GEO) database. Knockdown and pathway prediction of B4GALT5 were conducted to investigate the function and mechanism of B4GALT5 in OC proliferation, migration and invasion. RESULTS A total of 50 differentially expressed GT genes were identified between OC and normal ovarian tissues. Two clusters were stratified by operating consensus clustering, but no significant prognostic value was observed. By applying the least absolute shrinkage and selection operator (LASSO) Cox regression method, a 6-gene signature was built that classified OC patients in the TCGA cohort into a low- or high-risk group. Patients with high scores had a worse prognosis than those with low scores. This risk signature was further validated in an external GEO dataset. Furthermore, the risk score was an independent risk predictor, and a nomogram was created to improve the accuracy of prognostic classification. Notably, the low-risk OC patients exhibited a higher degree of antitumor immune cell infiltration and a superior response to ICBs. B4GALT5, one of six hub genes, was identified as a regulator of proliferation, migration and invasion in OC. CONCLUSION Taken together, we established a reliable GT-gene-based signature to predict prognosis, immune status and identify OC patients who would benefit from ICBs. GT genes might be a promising biomarker for OC progression and a potential therapeutic target for OC.
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Affiliation(s)
- Xuyao Xu
- grid.459791.70000 0004 1757 7869Department of Gynecology, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing, 210004 China
| | - Yue Wu
- grid.459791.70000 0004 1757 7869Department of Gynecology, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing, 210004 China
| | - Genmei Jia
- grid.459791.70000 0004 1757 7869Department of Women Health Care, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing, 210004 China
| | - Qiaoying Zhu
- grid.459791.70000 0004 1757 7869Department of Gynecology, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing, 210004 China
| | - Dake Li
- grid.459791.70000 0004 1757 7869Department of Gynecology, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing, 210004 China
| | - Kaipeng Xie
- grid.459791.70000 0004 1757 7869Department of Women Health Care, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing, 210004 China ,grid.459791.70000 0004 1757 7869Department of Public Health, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing, 210004 China
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Abstract
High-fidelity DNA replication is critical for the faithful transmission of genetic information to daughter cells. Following genotoxic stress, specialized DNA damage tolerance pathways are activated to ensure replication fork progression. These pathways include translesion DNA synthesis, template switching and repriming. In this Review, we describe how DNA damage tolerance pathways impact genome stability, their connection with tumorigenesis and their effects on cancer therapy response. We discuss recent findings that single-strand DNA gap accumulation impacts chemoresponse and explore a growing body of evidence that suggests that different DNA damage tolerance factors, including translesion synthesis polymerases, template switching proteins and enzymes affecting single-stranded DNA gaps, represent useful cancer targets. We further outline how the consequences of DNA damage tolerance mechanisms could inform the discovery of new biomarkers to refine cancer therapies.
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Affiliation(s)
- Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
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Sorokin M, Rabushko E, Rozenberg JM, Mohammad T, Seryakov A, Sekacheva M, Buzdin A. Clinically relevant fusion oncogenes: detection and practical implications. Ther Adv Med Oncol 2022; 14:17588359221144108. [PMID: 36601633 PMCID: PMC9806411 DOI: 10.1177/17588359221144108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/22/2022] [Indexed: 12/28/2022] Open
Abstract
Mechanistically, chimeric genes result from DNA rearrangements and include parts of preexisting normal genes combined at the genomic junction site. Some rearranged genes encode pathological proteins with altered molecular functions. Those which can aberrantly promote carcinogenesis are called fusion oncogenes. Their formation is not a rare event in human cancers, and many of them were documented in numerous study reports and in specific databases. They may have various molecular peculiarities like increased stability of an oncogenic part, self-activation of tyrosine kinase receptor moiety, and altered transcriptional regulation activities. Currently, tens of low molecular mass inhibitors are approved in cancers as the drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins, that is, including ALK, ABL, EGFR, FGFR1-3, NTRK1-3, MET, RET, ROS1 moieties. Therein, the presence of the respective RTK fusion in the cancer genome is the diagnostic biomarker for drug prescription. However, identification of such fusion oncogenes is challenging as the breakpoint may arise in multiple sites within the gene, and the exact fusion partner is generally unknown. There is no gold standard method for RTK fusion detection, and many alternative experimental techniques are employed nowadays to solve this issue. Among them, RNA-seq-based methods offer an advantage of unbiased high-throughput analysis of only transcribed RTK fusion genes, and of simultaneous finding both fusion partners in a single RNA-seq read. Here we focus on current knowledge of biology and clinical aspects of RTK fusion genes, related databases, and laboratory detection methods.
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Affiliation(s)
| | - Elizaveta Rabushko
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia,I.M. Sechenov First Moscow State Medical
University, Moscow, Russia
| | | | - Tharaa Mohammad
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia
| | | | - Marina Sekacheva
- I.M. Sechenov First Moscow State Medical
University, Moscow, Russia
| | - Anton Buzdin
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia,I.M. Sechenov First Moscow State Medical
University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic
Chemistry, Moscow, Russia,PathoBiology Group, European Organization for
Research and Treatment of Cancer (EORTC), Brussels, Belgium
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Pan-Cancer Analysis of the Prognostic and Immunotherapeutic Value of MITD1. Cells 2022; 11:cells11203308. [PMID: 36291174 PMCID: PMC9600621 DOI: 10.3390/cells11203308] [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: 07/30/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Microtubule-interacting and trafficking domain containing 1 (MITD1) is associated with abscission during cytokinesis. However, systematic investigation into its role in cancer is lacking. Therefore, we explored the pan-cancer role of MITD1 using multiple databases. Expression and clinical survival, immunological, and enrichment analyses were performed using R packages and online tools. For breast cancer, single-cell level analysis, immunochemistry, and in vitro experiments were performed to explore the mechanism of MITD1. A nomogram was established to predict the prognosis of patients with breast cancer and evaluate the immunotherapy biomarker based on two datasets. In some cancers, high MITD1 expression was associated with a more favorable prognosis. For instance, it inhibited tumor cell proliferation and migration in breast cancer. MITD1 may regulate cancer development by altering the tumor microenvironment, and MITD1 expression may predict the response to immune checkpoint blockade, platinum, and poly ADP-ribose polymerase inhibitor therapies. Our nomogram was used to determine the prognosis of patients with breast cancer. MITD1 can also predict the response to immunotherapy. Our first pan-cancer study of MITD1 has shown that it plays different roles in cancer development and therapy. In breast cancer, MITD1 inhibited cell proliferation and migration and serves as a new biomarker.
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Shi C, Qin K, Lin A, Jiang A, Cheng Q, Liu Z, Zhang J, Luo P. The role of DNA damage repair (DDR) system in response to immune checkpoint inhibitor (ICI) therapy. J Exp Clin Cancer Res 2022; 41:268. [PMID: 36071479 PMCID: PMC9450390 DOI: 10.1186/s13046-022-02469-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
As our understanding of the mechanisms of cancer treatment has increased, a growing number of studies demonstrate pathways through which DNA damage repair (DDR) affects the immune system. At the same time, the varied response of patients to immune checkpoint blockade (ICB) therapy has prompted the discovery of various predictive biomarkers and the study of combination therapy. Here, our investigation explores the interactions involved in combination therapy, accompanied by a review that summarizes currently identified and promising predictors of response to immune checkpoint inhibitors (ICIs) that are useful for classifying oncology patients. In addition, this work, which discusses immunogenicity and several components of the tumor immune microenvironment, serves to illustrate the mechanism by which higher response rates and improved efficacy of DDR inhibitors (DDRi) in combination with ICIs are achieved.
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Ding Q, Hou Z, Zhao Z, Chen Y, Zhao L, Xiang Y. Identification of the prognostic signature based on genomic instability-related alternative splicing in colorectal cancer and its regulatory network. Front Bioeng Biotechnol 2022; 10:841034. [PMID: 35923577 PMCID: PMC9340224 DOI: 10.3389/fbioe.2022.841034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/27/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Colorectal cancer (CRC) is a heterogeneous disease with many somatic mutations defining its genomic instability. Alternative Splicing (AS) events, are essential for maintaining genomic instability. However, the role of genomic instability-related AS events in CRC has not been investigated. Methods: From The Cancer Genome Atlas (TCGA) program, we obtained the splicing profiles, the single nucleotide polymorphism, transcriptomics, and clinical information of CRC. Combining somatic mutation and AS events data, a genomic instability-related AS signature was constructed for CRC. Mutations analyses, clinical stratification analyses, and multivariate Cox regression analyses evaluated this signature in training set. Subsequently, we validated the sensitivity and specificity of this prognostic signature using a test set and the entire TCGA dataset. We constructed a nomogram for the prognosis prediction of CRC patients. Differentially infiltrating immune cells were screened by using CIBERSORT. Inmmunophenoscore (IPS) analysis was used to evaluate the response of immunotherapy. The AS events-related splicing factors (SF) were analyzed by Pearson’s correlation. The effects of SF regulating the prognostic AS events in proliferation and migration were validated in Caco2 cells. Results: A prognostic signature consisting of seven AS events (PDHA1-88633-ES, KIAA1522-1632-AP, TATDN1-85088-ES, PRMT1-51042-ES, VEZT-23786-ES, AIG1-77972-AT, and PHF11-25891-AP) was constructed. Patients in the high-risk score group showed a higher somatic mutation. The genomic instability risk score was an independent variable associated with overall survival (OS), with a hazard ratio of a risk score of 1.537. The area under the curve of receiver operator characteristic curve of the genomic instability risk score in predicting the OS of CRC patients was 0.733. Furthermore, a nomogram was established and could be used clinically to stratify patients to predict prognosis. Patients defined as high-risk by this signature showed a lower proportion of eosinophils than the low-risk group. Patients with low risk were more sensitive to anti-CTLA4 immunotherapy. Additionally, HSPA1A and FAM50B were two SF regulating the OS-related AS. Downregulation of HSPA1A and FAM50B inhibited the proliferation and migration of Caco2 cells. Conclusion: We constructed an ideal prognostic signature reflecting the genomic instability and OS of CRC patients. HSPA1A and FAM50B were verified as two important SF regulating the OS-related AS.
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Affiliation(s)
- Qiuying Ding
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Zhengping Hou
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Zhibo Zhao
- The Department of Hepatobiliary Surgery of the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yao Chen
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Yao Chen, ; Lei Zhao, ; Yue Xiang,
| | - Lei Zhao
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Yao Chen, ; Lei Zhao, ; Yue Xiang,
| | - Yue Xiang
- Centre for Lipid Research, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Yao Chen, ; Lei Zhao, ; Yue Xiang,
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The Role of Inflammatory Cytokines in the Pathogenesis of Colorectal Carcinoma—Recent Findings and Review. Biomedicines 2022; 10:biomedicines10071670. [PMID: 35884974 PMCID: PMC9312930 DOI: 10.3390/biomedicines10071670] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
The inflammatory process plays a significant role in the development of colon cancer (CRC). Intestinal cytokine networks are critical mediators of tissue homeostasis and inflammation but also impact carcinogenesis at all stages of the disease. Recent studies suggest that inflammation is of greater importance in the serrated pathway than in the adenoma-carcinoma pathway. Interleukins have gained the most attention due to their potential role in CRC pathogenesis and promising results of clinical trials. Malignant transformation is associated with the pro-tumorigenic and anti-tumorigenic cytokines. The harmony between proinflammatory and anti-inflammatory factors is crucial to maintaining homeostasis. Immune cells in the tumor microenvironment modulate immune sensitivity and facilitate cancer escape from immune surveillance. Therefore, clarifying the role of underlying cytokine pathways and the effects of their modulation may be an important step to improve the effectiveness of cancer immunotherapy.
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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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Zhu J, Huang Q, Liu S, Peng X, Xue J, Feng T, Huang W, Chen Z, Lai K, Ji Y, Wang M, Yuan R. Construction of a Novel LncRNA Signature Related to Genomic Instability to Predict the Prognosis and Immune Activity of Patients With Hepatocellular Carcinoma. Front Immunol 2022; 13:856186. [PMID: 35479067 PMCID: PMC9037030 DOI: 10.3389/fimmu.2022.856186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 01/10/2023] Open
Abstract
Background Genomic instability (GI) plays a crucial role in the development of various cancers including hepatocellular carcinoma. Hence, it is meaningful for us to use long non-coding RNAs related to genomic instability to construct a prognostic signature for patients with HCC. Methods Combining the lncRNA expression profiles and somatic mutation profiles in The Cancer Genome Atlas database, we identified GI-related lncRNAs (GILncRNAs) and obtained the prognosis-related GILncRNAs through univariate regression analysis. These lncRNAs obtained risk coefficients through multivariate regression analysis for constructing GI-associated lncRNA signature (GILncSig). ROC curves were used to evaluate signature performance. The International Cancer Genomics Consortium (ICGC) cohort, and in vitro experiments were used for signature external validation. Immunotherapy efficacy, tumor microenvironments, the half-maximal inhibitory concentration (IC50), and immune infiltration were compared between the high- and low-risk groups with TIDE, ESTIMATE, pRRophetic, and ssGSEA program. Results Five GILncRNAs were used to construct a GILncSig. It was confirmed that the GILncSig has good prognostic evaluation performance for patients with HCC by drawing a time-dependent ROC curve. Patients were divided into high- and low-risk groups according to the GILncSig risk score. The prognosis of the low-risk group was significantly better than that of the high-risk group. Independent prognostic analysis showed that the GILncSig could independently predict the prognosis of patients with HCC. In addition, the GILncSig was correlated with the mutation rate of the HCC genome, indicating that it has the potential to measure the degree of genome instability. In GILncSig, LUCAT1 with the highest risk factor was further validated as a risk factor for HCC in vitro. The ESTIMATE analysis showed a significant difference in stromal scores and ESTIMATE scores between the two groups. Multiple immune checkpoints had higher expression levels in the high-risk group. The ssGSEA results showed higher levels of tumor-antagonizing immune cells in the low-risk group compared with the high-risk group. Finally, the GILncSig score was associated with chemotherapeutic drug sensitivity and immunotherapy efficacy of patients with HCC. Conclusion Our research indicates that GILncSig can be used for prognostic evaluation of patients with HCC and provide new insights for clinical decision-making and potential therapeutic strategies.
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Affiliation(s)
- Jinfeng Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qian Huang
- Department of General Practice, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Sicheng Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xingyu Peng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ju Xue
- Department of Pathology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Tangbin Feng
- Department of Surgery, II, Duchang County Hospital of Traditional Chinese Medicine, Jiujiang, China
| | - Wulang Huang
- Department of General Surgery, Affiliated Hospital of Jinggangshan University, Jian, China
| | - Zhimeng Chen
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kuiyuan Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yufei Ji
- The Second Clinical Medical College of Nanchang University, Nanchang, China
| | - Miaomiao Wang
- Queen Mary College of Nanchang University, Nanchang, China
| | - Rongfa Yuan
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Wang Q, Du J, Hua S, Zhao K. TREX1 Plays Multiple Roles in Human Diseases. Cell Immunol 2022; 375:104527. [DOI: 10.1016/j.cellimm.2022.104527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/12/2022] [Accepted: 04/10/2022] [Indexed: 11/15/2022]
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Barchi JJ. Glycoconjugate Nanoparticle-Based Systems in Cancer Immunotherapy: Novel Designs and Recent Updates. Front Immunol 2022; 13:852147. [PMID: 35432351 PMCID: PMC9006936 DOI: 10.3389/fimmu.2022.852147] [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: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 11/15/2022] Open
Abstract
For many years, cell-surface glycans (in particular, Tumor-Associated Carbohydrate Antigens, TACAs) have been the target of both passive and active anticancer immunotherapeutic design. Recent advances in immunotherapy as a treatment for a variety of malignancies has revolutionized anti-tumor treatment regimens. Checkpoint inhibitors, Chimeric Antigen Receptor T-cells, Oncolytic virus therapy, monoclonal antibodies and vaccines have been developed and many approvals have led to remarkable outcomes in a subset of patients. However, many of these therapies are very selective for specific patient populations and hence the search for improved therapeutics and refinement of techniques for delivery are ongoing and fervent research areas. Most of these agents are directed at protein/peptide epitopes, but glycans-based targets are gaining in popularity, and a handful of approved immunotherapies owe their activity to oligosaccharide targets. In addition, nanotechnology and nanoparticle-derived systems can help improve the delivery of these agents to specific organs and cell types based on tumor-selective approaches. This review will first outline some of the historical beginnings of this research area and subsequently concentrate on the last 5 years of work. Based on the progress in therapeutic design, predictions can be made as to what the future holds for increasing the percentage of positive patient outcomes for optimized systems.
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Affiliation(s)
- Joseph J. Barchi
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
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Immunosuppressive Signaling Pathways as Targeted Cancer Therapies. Biomedicines 2022. [DOI: 10.3390/biomedicines10030682
expr 829797163 + 949875436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Immune response has been shown to play an important role in defining patient prognosis and response to cancer treatment. Tumor-induced immunosuppression encouraged the recent development of new chemotherapeutic agents that assists in the augmentation of immune responses. Molecular mechanisms that tumors use to evade immunosurveillance are attributed to their ability to alter antigen processing/presentation pathways and the tumor microenvironment. Cancer cells take advantage of normal molecular and immunoregulatory machinery to survive and thrive. Cancer cells constantly adjust their genetic makeup using several mechanisms such as nucleotide excision repair as well as microsatellite and chromosomal instability, thus giving rise to new variants with reduced immunogenicity and the ability to continue to grow without restrictions. This review will focus on the central molecular signaling pathways involved in immunosuppressive cells and briefly discuss how cancer cells evade immunosurveillance by manipulating antigen processing cells and related proteins. Secondly, the review will discuss how these pathways can be utilized for the implementation of precision medicine and deciphering drug resistance.
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Immunosuppressive Signaling Pathways as Targeted Cancer Therapies. Biomedicines 2022; 10:biomedicines10030682. [PMID: 35327484 PMCID: PMC8945019 DOI: 10.3390/biomedicines10030682] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 12/23/2022] Open
Abstract
Immune response has been shown to play an important role in defining patient prognosis and response to cancer treatment. Tumor-induced immunosuppression encouraged the recent development of new chemotherapeutic agents that assists in the augmentation of immune responses. Molecular mechanisms that tumors use to evade immunosurveillance are attributed to their ability to alter antigen processing/presentation pathways and the tumor microenvironment. Cancer cells take advantage of normal molecular and immunoregulatory machinery to survive and thrive. Cancer cells constantly adjust their genetic makeup using several mechanisms such as nucleotide excision repair as well as microsatellite and chromosomal instability, thus giving rise to new variants with reduced immunogenicity and the ability to continue to grow without restrictions. This review will focus on the central molecular signaling pathways involved in immunosuppressive cells and briefly discuss how cancer cells evade immunosurveillance by manipulating antigen processing cells and related proteins. Secondly, the review will discuss how these pathways can be utilized for the implementation of precision medicine and deciphering drug resistance.
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