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Kipcak A, Sezan S, Karpat O, Kaya E, Baylan S, Sariyar E, Yandim C, Karagonlar ZF. Suppression of CTC1 inhibits hepatocellular carcinoma cell growth and enhances RHPS4 cytotoxicity. Mol Biol Rep 2024; 51:799. [PMID: 39001931 DOI: 10.1007/s11033-024-09756-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/25/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Although DNA repair mechanisms function to maintain genomic integrity, in cancer cells these mechanisms may negatively affect treatment efficiency. The strategy of targeting cancer cells via inhibiting DNA damage repair has been successfully used in breast and ovarian cancer using PARP inhibitors. Unfortunately, such strategies have not yet yielded results in liver cancer. Hepatocellular carcinoma (HCC), the most common type of liver cancer, is a treatment-resistant malignancy. Despite the development of guided therapies, treatment regimens for advanced HCC patients still fall short of the current need and significant problems such as cancer relapse with resistance still exist. In this paper, we targeted telomeric replication protein CTC1, which is responsible for telomere maintenance. METHODS CTC expression was analyzed using tumor and matched-tissue RNA-sequencing data from TCGA and GTEx. In HCC cell lines, q-RT-PCR and Western blotting were used to detect CTC1 expression. The knock-down of CTC1 was achieved using lentiviral plasmids. The effects of CTC1 silencing on HCC cells were analyzed by flow cytometry, MTT, spheroid and colony formation assays. RESULTS CTC1 is significantly downregulated in HCC tumor samples. However, CTC1 protein levels were higher in sorafenib-resistant cell lines compared to the parental groups. CTC1 inhibition reduced cell proliferation in sorafenib-resistant HCC cell lines and diminished their spheroid and colony forming capacities. Moreover, these cells were more sensitive to single and combined drug treatment with G4 stabilizer RHPS4 and sorafenib. CONCLUSION Our results suggest that targeting CTC1 might be a viable option for combinational therapies designed for sorafenib resistant HCC patients.
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Affiliation(s)
- Arda Kipcak
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
- Department of Psychology, University of Virginia, Charlottesville, VA, USA
| | - Sila Sezan
- Division of Bioengineering, Graduate School, İzmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Ozum Karpat
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Ezgi Kaya
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Sude Baylan
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Ece Sariyar
- Division of Bioengineering, Graduate School, İzmir University of Economics, Sakarya Cad, İzmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Izmir, Turkey
| | - Cihangir Yandim
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey
| | - Zeynep Firtina Karagonlar
- Department of Genetics and Bioengineering, Izmir University of Economics, Sakarya Cad, İzmir, Turkey.
- Division of Bioengineering, Graduate School, İzmir University of Economics, Sakarya Cad, İzmir, Turkey.
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Lehrich BM, Zhang J, Monga SP, Dhanasekaran R. Battle of the biopsies: Role of tissue and liquid biopsy in hepatocellular carcinoma. J Hepatol 2024; 80:515-530. [PMID: 38104635 PMCID: PMC10923008 DOI: 10.1016/j.jhep.2023.11.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/27/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
The diagnosis and management of hepatocellular carcinoma (HCC) have improved significantly in recent years. With the introduction of immunotherapy-based combination therapy, there has been a notable expansion in treatment options for patients with unresectable HCC. Simultaneously, innovative molecular tests for early detection and management of HCC are emerging. This progress prompts a key question: as liquid biopsy techniques rise in prominence, will they replace traditional tissue biopsies, or will both techniques remain relevant? Given the ongoing challenges of early HCC detection, including issues with ultrasound sensitivity, accessibility, and patient adherence to surveillance, the evolution of diagnostic techniques is more relevant than ever. Furthermore, the accurate stratification of HCC is limited by the absence of reliable biomarkers which can predict response to therapies. While the advantages of molecular diagnostics are evident, their potential has not yet been fully harnessed, largely because tissue biopsies are not routinely performed for HCC. Liquid biopsies, analysing components such as circulating tumour cells, DNA, and extracellular vesicles, provide a promising alternative, though they are still associated with challenges related to sensitivity, cost, and accessibility. The early results from multi-analyte liquid biopsy panels are promising and suggest they could play a transformative role in HCC detection and management; however, comprehensive clinical validation is still ongoing. In this review, we explore the challenges and potential of both tissue and liquid biopsy, highlighting that these diagnostic methods, while distinct in their approaches, are set to jointly reshape the future of HCC management.
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Affiliation(s)
- Brandon M Lehrich
- Department of Pathology and Pittsburgh Liver Institute, University of Pittsburgh, School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Josephine Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Staford, CA, 94303, USA
| | - Satdarshan P Monga
- Department of Pathology and Pittsburgh Liver Institute, University of Pittsburgh, School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.
| | - Renumathy Dhanasekaran
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Staford, CA, 94303, USA.
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Zhang R, Li Q, Yu X, Hou Y, Yan L, Gao Y, Ji L, Zhang X, Fang M, Huang L, Yu Z, Gao Y, Li M. Integrating bulk and single-cell RNA sequencing data to establish necroptosis-related lncRNA risk model and analyze the immune microenvironment in hepatocellular carcinoma. Heliyon 2023; 9:e22083. [PMID: 38034714 PMCID: PMC10685373 DOI: 10.1016/j.heliyon.2023.e22083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023] Open
Abstract
Background The increasing evidence suggests that necroptosis mediates many behaviors of tumors, as well as the regulation of the tumor microenvironment. Long non-coding RNAs (lncRNAs) are involved in a variety of regulatory processes during tumor development and are significantly associated with patient prognosis. It suggests that necroptosis-related lncRNAs (NRlncRNAs) may serve as biomarkers for the prognosis of hepatocellular carcinoma (HCC). Methods lncRNA expression profiles of HCC were obtained from TCGA database. LncRNAs associated with necroptosis were extracted using correlation analysis. Prognostic models were constructed based on least absolute shrinkage and selection operator algorithm (LASSO) and multivariate Cox regression analysis. The differences of tumor microenvironment between high-risk and low-risk groups were further analyzed. Single-cell RNA sequencing data of HCC was performed to assess the enrichment of necroptosis-related genes in immune cell subsets. Finally, real-time RT-PCR was used to detect the prognosis-related lncRNAs expression in different HCC cell lines. Results We constructed a prognostic signature based on 8 NRlncRNAs, which also showed good predictive accuracy. The model showed that the prognosis of patients with high-risk score was significantly worse than that of patients with low-risk score (P < 0.05). Combined with the clinical characteristics and risk score of HCC, Nomogram was drawn for reference in clinical practice. In addition, immune cell infiltration analysis and single cell RNA sequencing analysis showed that a low level of immune infiltration was observed in patients at high risk and that there was a significant correlation between NRlncRNAs and macrophages. The results of RT-qPCR also showed that 8 necroptosis-related lncRNAs were highly expressed in HCC cell lines and human liver cancer tissues. Conclusion This prognostic signature based on the necroptosis-related lncRNAs may provide meaningful clinical insights for the prognosis and immunotherapy responses in patients with HCC.
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Affiliation(s)
- Rongjie Zhang
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Qian Li
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Xiaoxiao Yu
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Yiwen Hou
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Liang Yan
- General Surgery Department of Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Yating Gao
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Longshan Ji
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Xin Zhang
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Miao Fang
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Lingying Huang
- Department of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Zhuo Yu
- Department of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
| | - Yueqiu Gao
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
- Institute of Infectious Diseases of Integrated Traditional Chinese and Western Medicine, China
| | - Man Li
- Laboratory of cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, China
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Lin HS, Pang WP, Yuan H, Kong YZ, Long FL, Zhang RZ, Yang L, Fang QL, Pan AP, Fan XH, Li MF. Molecular subtypes based on DNA sensors predict prognosis and tumor immunophenotype in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:6798-6821. [PMID: 37451838 PMCID: PMC10415551 DOI: 10.18632/aging.204870] [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: 12/27/2022] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
DNA sensors play crucial roles in inflammation and have been indicated to be involved in antitumor or tumorigenesis, while it is still unclear whether DNA sensors have potential roles in the prognosis and immunotherapy of hepatocellular carcinoma (HCC). Herein, The Cancer Genome Atlas and Gene Expression Omnibus databases were used to analyze RNA sequencing data and clinical information. A total of 14 DNA sensors were collected and performed consensus clustering to determine their molecular mechanisms in HCC. Two distinct molecular subtypes (Clusters C1 and C2) were identified and were associated with different overall survival (OS). Immune subtype analysis revealed that C1 was mainly characterized by inflammation, while C2 was characterized by lymphocyte depletion. Immune scoring and immunomodulatory function analysis confirmed the different immune microenvironment of C1 and C2. Notably, significant differences in "Hot Tumor" Immunophenotype were observed between the two subtypes. Moreover, the prognostic model based on DNA sensors is capable of effectively predicting the OS of HCC patients. Besides, the chemotherapeutic drug analysis showed the different sensitivity of two subtypes. Taken together, our study shows that the proposed DNA sensors were a reliable signature to predict the prognosis and immunotherapy response with potential application in the clinical decision and treatment of HCC.
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Affiliation(s)
- Hong-Sheng Lin
- Department of Microbiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Wen-Peng Pang
- Department of Microbiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Hao Yuan
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Yin-Zhi Kong
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Fu-Li Long
- Department of Hepatology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Rong-Zhen Zhang
- Department of Hepatology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Li Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Qiao-Ling Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Ai-Ping Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
| | - Xiao-Hui Fan
- Department of Microbiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Ming-Fen Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning 530023, China
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Ji JH, Ha SY, Lee D, Sankar K, Koltsova EK, Abou-Alfa GK, Yang JD. Predictive Biomarkers for Immune-Checkpoint Inhibitor Treatment Response in Patients with Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:7640. [PMID: 37108802 PMCID: PMC10144688 DOI: 10.3390/ijms24087640] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has one of the highest mortality rates among solid cancers. Late diagnosis and a lack of efficacious treatment options contribute to the dismal prognosis of HCC. Immune checkpoint inhibitor (ICI)-based immunotherapy has presented a new milestone in the treatment of cancer. Immunotherapy has yielded remarkable treatment responses in a range of cancer types including HCC. Based on the therapeutic effect of ICI alone (programmed cell death (PD)-1/programmed death-ligand1 (PD-L)1 antibody), investigators have developed combined ICI therapies including ICI + ICI, ICI + tyrosine kinase inhibitor (TKI), and ICI + locoregional treatment or novel immunotherapy. Although these regimens have demonstrated increasing treatment efficacy with the addition of novel drugs, the development of biomarkers to predict toxicity and treatment response in patients receiving ICI is in urgent need. PD-L1 expression in tumor cells received the most attention in early studies among various predictive biomarkers. However, PD-L1 expression alone has limited utility as a predictive biomarker in HCC. Accordingly, subsequent studies have evaluated the utility of tumor mutational burden (TMB), gene signatures, and multiplex immunohistochemistry (IHC) as predictive biomarkers. In this review, we aim to discuss the current state of immunotherapy for HCC, the results of the predictive biomarker studies, and future direction.
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Affiliation(s)
- Jun Ho Ji
- Division of Hematology and Oncology, Department of Internal Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon 51353, Republic of Korea
- Karsh Division of Gastroenterology and Hepatology, Comprehensive Transplant Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sang Yun Ha
- Karsh Division of Gastroenterology and Hepatology, Comprehensive Transplant Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 03181, Republic of Korea
| | - Danbi Lee
- Karsh Division of Gastroenterology and Hepatology, Comprehensive Transplant Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Kamya Sankar
- Division of Medical Oncology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ekaterina K. Koltsova
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ghassan K. Abou-Alfa
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weil Cornell Medicine, Cornell University, New York, NY 14853, USA
| | - Ju Dong Yang
- Karsh Division of Gastroenterology and Hepatology, Comprehensive Transplant Center, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Maimaiti A, Liu Y, Abulaiti A, Wang X, Feng Z, Wang J, Mijiti M, Turhon M, Alimu N, Wang Y, Liang W, Jiang L, Pei Y. Genomic Profiling of Lower-Grade Gliomas Subtype with Distinct Molecular and Clinicopathologic Characteristics via Altered DNA-Damage Repair Features. J Mol Neurosci 2023; 73:269-286. [PMID: 37067735 DOI: 10.1007/s12031-023-02116-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: 12/26/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023]
Abstract
Lower WHO grade II and III gliomas (LGGs) exhibit significant genetic and transcriptional heterogeneity, and the heterogeneity of DNA damage repair (DDR) and its relationship to tumor biology, transcriptome, and tumor microenvironment (TME) remains poorly understood. In this study, we conducted multi-omics data integration to investigate DDR alterations in LGG. Based on clinical parameters and molecular characteristics, LGG patients were categorized into distinct DDR subtypes, namely, DDR-activated and DDR-suppressed subtypes. We compared gene mutation, immune spectrum, and immune cell infiltration between the two subtypes. DDR scores were generated to classify LGG patients based on DDR subtype features, and the results were validated using a multi-layer data cohort. We found that DDR activation was associated with poorer overall survival and that clinicopathological features of advanced age and higher grade were more common in the DDR-activated subtype. DDR-suppressed subtypes exhibited more frequent mutations in IDH1. In addition, we observed significant upregulation of activated immune cells in the DDR-activated subgroup, which suggests that immune cell infiltration significantly influences tumor progression and immunotherapeutic responses. Furthermore, we constructed a DDR signature for LGG using six DDR genes, which allowed for the division of patients into low- and high-risk groups. Quantitative real-time PCR results showed that CDK1, CDK2, TYMS, SMC4, and WEE1 were significantly upregulated in LGG samples compared to normal brain tissue samples. Overall, our study sheds light on DDR heterogeneity in LGG and provides insight into the molecular pathways of DDR involved in LGG development.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Yanwen Liu
- Department of Medical Laboratory, Xinjiang Production and Construction Corps Hospital, 830002, Urumqi, Xinjiang, China
| | - Aimitaji Abulaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Xixian Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Zhaohai Feng
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Jiaming Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Maimaitili Mijiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Mirzat Turhon
- Department of Neurointerventional Surgery, Beijing Neurosurgical Institute, Capital Medical University, 100070, Beijing, China
- Department of Neurointerventional Surgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
| | - Nilipaer Alimu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Wenbao Liang
- Department of Neurosurgery, The Fourth Affiliated Hospital of Xinjiang Medical University, No. 116, Huanghe Road, Shaibak District, 830000, Urumqi, Xinjiang, China.
| | - Lei Jiang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China.
| | - Yinan Pei
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China.
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Zhao Y, Xiao Y, Hu Z, Wang J, Xu Z, Mo Y, Qi G, Chen K, Wu W, Ma W. Bibliometric analysis of single-cell sequencing researches on immune cells and their application of DNA damage repair in cancer immunotherapy. Front Oncol 2023; 13:1067305. [PMID: 36776314 PMCID: PMC9909395 DOI: 10.3389/fonc.2023.1067305] [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: 10/11/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
INTRODUCTION In recent decades, single-cell sequencing technology has developed rapidly and used widely in various fields of life sciences, especially for the detection of immune cells. A bibliometric analysis of single-cell sequencing research work on immune cells published during the 2011-2021 period should provide new insight on the use of single-cell sequencing. METHODS We screened 1,460 publications on single-cell sequencing on immune cells according to the publication date, article type, language, and country. REULTS The United States published the first and largest number of articles, while China's research started relatively late, but ranked second in the number of publications. T cells were the most commonly studied immune cells by single-cell sequencing, followed by mononuclear macrophages. Cancer biology was the most common field of immune cell research by single-cell sequencing. Single-cell sequencing studies using γδ T cells were mainly in the fields of cancer biology and cell development, and focused over time from cell surface receptor to cell function. Through in-depth analysis of the articles on single-cell sequencing of T cells in the oncology field, our analysis found that immunotherapy and tumor microenvironment were the most popular research directions in recent years. DISCUSSION The combination of DNA damage repair and immunotherapy seems to provide a new strategy for cancer therapy.
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Affiliation(s)
- Yu Zhao
- Department of Hematology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Yuanxun Xiao
- Department of Burn & Plastic Surgery, Yuebei People’s Hospital Affiliated to Shantou University Medical College, Shaoguan, Guangdong, China
| | - Zhengbo Hu
- Department of Orthopaedics, Yuebei People’s Hospital Affiliated to Shantou University Medical College, Shaoguan, Guangdong, China
| | - Ji Wang
- Department of Spine Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhiguang Xu
- Department of Spine Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yizhang Mo
- Department of Spine Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guojun Qi
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, Guangdong, China
| | - Kebing Chen
- Department of Spine Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- *Correspondence: Kebing Chen, ; Wu Wu, ; Weiying Ma,
| | - Wu Wu
- Orthopedics Rehabilitation Department, Guangdong Work Injury Rehabilitation Center, Guangzhou, Guangdong, China
- *Correspondence: Kebing Chen, ; Wu Wu, ; Weiying Ma,
| | - Weiying Ma
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- *Correspondence: Kebing Chen, ; Wu Wu, ; Weiying Ma,
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Li L, Zou BJ, Zhao JZ, Liang JB, She ZY, Zhou WY, Lin SX, Tian L, Luo WJ, He FZ. A novel DNA damage repair-related signature for predicting prognositc and treatment response in non-small lung cancer. Front Oncol 2022; 12:961274. [PMID: 36408135 PMCID: PMC9673481 DOI: 10.3389/fonc.2022.961274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/14/2022] [Indexed: 10/06/2023] Open
Abstract
DNA damage repair (DDR) is essential for maintaining genome integrity and modulating cancer risk, progression, and therapeutic response. DDR defects are common among non-small lung cancer (NSCLC), resulting in new challenge and promise for NSCLC treatment. Thus, a thorough understanding of the molecular characteristics of DDR in NSCLC is helpful for NSCLC treatment and management. Here, we systematically analyzed the relationship between DDR alterations and NSCLC prognosis, and successfully established and validated a six-DDR gene prognostic model via LASSO Cox regression analysis based on the expression of prognostic related DDR genes, CDC25C, NEIL3, H2AFX, NBN, XRCC5, RAD1. According to this model, NSCLC patients were classified into high-risk subtype and low-risk subtype, each of which has significant differences between the two subtypes in clinical features, molecular features, immune cell components, gene mutations, DDR pathway activation status and clinical outcomes. The high-risk patients was characterized with worse prognosis, lower proportion and number of DDR mutations, unique immune profile and responsive to immunetherapy. And the low-risk patients tend to have superior survival, while being less responsive to immunotherapy and more sensitive to treatment with DNA-damaging chemotherapy drugs. Overall, this molecular classification based on DDR expression profile enables hierarchical management of patients and personalized clinical treatment, and provides potential therapeutic targets for NSCLC.
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Affiliation(s)
- Ling Li
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Bao-jia Zou
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Juan-zhi Zhao
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jia-bi Liang
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zi-yue She
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wen-ying Zhou
- Department of Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Si-xiao Lin
- Department of Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Lin Tian
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wen-ji Luo
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Fa-zhong He
- Department of Quality Control, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, Guangdong, China
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Testa U, Pelosi E, Castelli G. Clinical value of identifying genes that inhibit hepatocellular carcinomas. Expert Rev Mol Diagn 2022; 22:1009-1035. [PMID: 36459631 DOI: 10.1080/14737159.2022.2154658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
INTRODUCTION Primary liver cancer is a major health problem being the sixth most frequent cancer in the world and the fourth most frequent cause of cancer-related death in the world. The most common histological type of liver cancer is hepatocellular carcinoma (HCC, 75-80%). AREAS COVERED Based on primary literature, this review provides an updated analysis of studies of genetic characterization of HCC at the level of gene mutation profiling, copy number alterations and gene expression, with definition of molecular subgroups and identification of some molecular biomarkers and therapeutic targets. EXPERT OPINION A detailed and comprehensive study of the genetic abnormalities characterizing different HCC subsets represents a fundamental tool for a better understanding of the disease heterogeneity and for the identification of subgroups of patients responding or resistant to targeted treatments and for the discovery of new therapeutic targets. It is expected that a comprehensive characterization of these tumors may provide a fundamental contribution to improve the survival of a subset of HCC patients. Immunotherapy represents a new fundamental strategy for the treatment of HCC.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore Di Sanità, ROME, ITALY
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore Di Sanità, ROME, ITALY
| | - Germana Castelli
- Department of Oncology, Istituto Superiore Di Sanità, ROME, ITALY
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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: 25] [Impact Index Per Article: 12.5] [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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11
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Li Y, Zhang K, Peng L, Chen L, Gao H, Chen H. Multiple Perspectives Reveal the Role of DNA Damage Repair Genes in the Molecular Classification and Prognosis of Pancreatic Adenocarcinoma. Int J Mol Sci 2022; 23:ijms231810231. [PMID: 36142142 PMCID: PMC9499455 DOI: 10.3390/ijms231810231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is a highly heterogeneous and immunosuppressive cancer. This study investigated the diversity of DNA damage repair (DDR) and immune microenvironment in PAAD by transcriptomic and genomic analysis. Patients with PAAD were divided into two DDR-based subtypes with distinct prognosis and molecular characteristics. The differential expression genes were mostly enriched in DDR and immune-related pathways. In order to distinguish high- and low-risk groups clinically, a DDR- and immune-based 5-gene prognostic signature (termed DPRS) was established. Patients in the high-risk group had inferior prognosis, a low level of immune checkpoint gene expression and low sensitivity to DDR-associated inhibitors. Furthermore, single-cell sequencing was used to observe the performance of the DDR-based signature in a high dimension, and immunohistochemistry was used to verify the relationship between the genes we identified and the prognosis of patients with PAAD. In conclusion, the DDR heterogeneity of PAAD was demonstrated, and a novel DDR- and immune-based risk-scoring model was constructed, which indicated the feasibility of DPRS in predicting prognosis and drug response in PAAD patients.
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Affiliation(s)
- Yujie Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ke Zhang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Linjia Peng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lianyu Chen
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huifeng Gao
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hao Chen
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Correspondence: ; Tel.: +86-18017312356
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12
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Smith MA, Van Alsten SC, Walens A, Damrauer JS, Maduekwe UN, Broaddus RR, Love MI, Troester MA, Hoadley KA. DNA Damage Repair Classifier Defines Distinct Groups in Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:cancers14174282. [PMID: 36077818 PMCID: PMC9454479 DOI: 10.3390/cancers14174282] [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: 08/05/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary DNA repair pathways have been implicated in hepatocellular carcinoma outcomes. We found that hepatocellular carcinomas (HCC) could be separated into two groups (high and low) based on the overall expression of genes involved in DNA repair. Among the low repair group, there were three subgroups, one of which shared features of the high repair group. Given the important role of liver in metabolism and detoxification and its regenerative capacity, proliferation and DNA damage responses are critical in subdividing major biological categories of liver tumors. High repair samples showed more proliferative and regenerative signatures and had poorer outcomes versus the low repair that were more associated with the genes involved in normal liver biology. These biological groups suggest that dysregulation in endogenous liver processes promotes a pro-tumorigenic microenvironment that may facilitate tumor progression or identify tumors that require more substantial clinical intervention. Abstract DNA repair pathways have been associated with variability in hepatocellular carcinoma (HCC) clinical outcomes, but the mechanism through which DNA repair varies as a function of liver regeneration and other HCC characteristics is poorly understood. We curated a panel of 199 genes representing 15 DNA repair pathways to identify DNA repair expression classes and evaluate their associations with liver features and clinicopathologic variables in The Cancer Genome Atlas (TCGA) HCC study. We identified two groups in HCC, defined by low or high expression across all DNA repair pathways. The low-repair group had lower grade and retained the expression of classical liver markers, whereas the high-repair group had more clinically aggressive features, increased p53 mutant-like gene expression, and high liver regenerative gene expression. These pronounced features overshadowed the variation in the low-repair subset, but when considered separately, the low-repair samples included three subgroups: L1, L2, and L3. L3 had high DNA repair expression with worse progression-free (HR 1.24, 95% CI 0.81–1.91) and overall (HR 1.63, 95% CI 0.98–2.71) survival. High-repair outcomes were also significantly worse compared with the L1 and L2 groups. HCCs vary in DNA repair expression, and a subset of tumors with high regeneration profoundly disrupts liver biology and poor prognosis.
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Affiliation(s)
- Markia A. Smith
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah C. Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrea Walens
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeffrey S. Damrauer
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ugwuji N. Maduekwe
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Russell R. Broaddus
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa A. Troester
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Katherine A. Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
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Yang J, Chen Z, Gong Z, Li Q, Ding H, Cui Y, Tang L, Li S, Wan L, Li Y, Ju S, Ding C, Zhao J. Immune Landscape and Classification in Lung Adenocarcinoma Based on a Novel Cell Cycle Checkpoints Related Signature for Predicting Prognosis and Therapeutic Response. Front Genet 2022; 13:908104. [PMID: 35646074 PMCID: PMC9130860 DOI: 10.3389/fgene.2022.908104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most common malignancies with the highest mortality globally, and it has a poor prognosis. Cell cycle checkpoints play a central role in the entire system of monitoring cell cycle processes, by regulating the signalling pathway of the cell cycle. Cell cycle checkpoints related genes (CCCRGs) have potential utility in predicting survival, and response to immunotherapies and chemotherapies. To examine this, based on CCCRGs, we identified two lung adenocarcinoma subtypes, called cluster1 and cluster2, by consensus clustering. Enrichment analysis revealed significant discrepancies between the two subtypes in gene sets associated with cell cycle activation and tumor progression. In addition, based on Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression, we have developed and validated a cell cycle checkpoints-related risk signature to predict prognosis, tumour immune microenvironment: (TIME), immunotherapy and chemotherapy responses for lung adenocarcinoma patients. Results from calibration plot, decision curve analysis (DCA), and time-dependent receiver operating characteristic curve (ROC) revealed that combining age, gender, pathological stages, and risk score in lung adenocarcinoma patients allowed for a more accurate and predictive nomogram. The area under curve for lung adenocarcinoma patients with 1-, 3-, 5-, and 10-year overall survival was: 0.74, 0.73, 0.75, and 0.81, respectively. Taken together, our proposed 4-CCCRG signature can serve as a clinically useful indicator to help predict patients outcomes, and could provide important guidance for immunotherapies and chemotherapies decision for lung adenocarcinoma patients.
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Affiliation(s)
- Jian Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhike Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zetian Gong
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qifan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hao Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lijuan Tang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shiqin Li
- Department of Urinary Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Wan
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou, China
| | - Yu Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Sheng Ju
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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