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Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F. Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. CELL GENOMICS 2024; 4:100444. [PMID: 38190106 PMCID: PMC10794784 DOI: 10.1016/j.xgen.2023.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/12/2023] [Accepted: 10/24/2023] [Indexed: 01/09/2024]
Abstract
Immune checkpoint blockade (ICB) therapy targeting cytotoxic T-lymphocyte-associated protein 4, programmed death 1, and programmed death ligand 1 has shown durable remission and clinical success across different cancer types. However, patient outcomes vary among disease indications. Studies have identified prognostic biomarkers associated with immunotherapy response and patient outcomes derived from diverse data types, including next-generation bulk and single-cell DNA, RNA, T cell and B cell receptor sequencing data, liquid biopsies, and clinical imaging. Owing to inter- and intra-tumor heterogeneity and the immune system's complexity, these biomarkers have diverse efficacy in clinical trials of ICB. Here, we review the genetic and genomic signatures and image features of ICB studies for pan-cancer applications and specific indications. We discuss the advantages and disadvantages of computational approaches for predicting immunotherapy effectiveness and patient outcomes. We also elucidate the challenges of immunotherapy prognostication and the discovery of novel immunotherapy targets.
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Affiliation(s)
- Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA
| | - Catherine J Wu
- Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02138, USA; The Ludwig Center at Harvard, Boston, MA 02115, USA.
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Piao XM, Byun YJ, Zheng CM, Song SJ, Kang HW, Kim WT, Yun SJ. A New Treatment Landscape for RCC: Association of the Human Microbiome with Improved Outcomes in RCC. Cancers (Basel) 2023; 15:cancers15030935. [PMID: 36765892 PMCID: PMC9913391 DOI: 10.3390/cancers15030935] [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: 01/09/2023] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Microbes play different roles in metabolism, local or systemic inflammation, and immunity, and the human microbiome in tumor microenvironment (TME) is important for modulating the response to immunotherapy in cancer patients. Renal cell carcinoma (RCC) is an immunogenic tumor, and immunotherapy is the backbone of its treatment. Correlations between the microbiome and responsiveness to immune checkpoint inhibitors have been reported. This review summarizes the recent therapeutic strategies for RCC and the effects of TME on the systemic therapy of RCC. The current understanding and advances in microbiome research and the relationship between the microbiome and the response to immunotherapy for RCC are also discussed. Improving our understanding of the role of the microbiome in RCC treatment will facilitate the development of microbiome targeting therapies to modify the tumor microbiome and improve treatment outcomes.
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Affiliation(s)
- Xuan-Mei Piao
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Young Joon Byun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Chuang-Ming Zheng
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sun Jin Song
- Department of Emergency, Chungbuk National University Hospital, Cheongju 28644, Republic of Korea
| | - Ho Won Kang
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
- Department of Urology, Chungbuk National University Hospital, Cheongju 28644, Republic of Korea
| | - Won Tae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
- Department of Urology, Chungbuk National University Hospital, Cheongju 28644, Republic of Korea
| | - Seok Joong Yun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
- Department of Urology, Chungbuk National University Hospital, Cheongju 28644, Republic of Korea
- Correspondence: ; Tel.: +82-43-269-6142
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Yuan H, Gui R, Wang Z, Fang F, Zhao H. Gut microbiota: A novel and potential target for radioimmunotherapy in colorectal cancer. Front Immunol 2023; 14:1128774. [PMID: 36798129 PMCID: PMC9927011 DOI: 10.3389/fimmu.2023.1128774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers, with a high mortality rate, and is a major burden on human health worldwide. Gut microbiota regulate human immunity and metabolism through producing numerous metabolites, which act as signaling molecules and substrates for metabolic reactions in various biological processes. The importance of host-gut microbiota interactions in immunometabolic mechanisms in CRC is increasingly recognized, and interest in modulating the microbiota to improve patient's response to therapy has been raising. However, the specific mechanisms by which gut microbiota interact with immunotherapy and radiotherapy remain incongruent. Here we review recent advances and discuss the feasibility of gut microbiota as a regulatory target to enhance the immunogenicity of CRC, improve the radiosensitivity of colorectal tumor cells and ameliorate complications such as radiotoxicity. Currently, great breakthroughs in the treatment of non-small cell lung cancer and others have been achieved by radioimmunotherapy, but radioimmunotherapy alone has not been effective in CRC patients. By summarizing the recent preclinical and clinical evidence and considering regulatory roles played by microflora in the gut, such as anti-tumor immunity, we discuss the potential of targeting gut microbiota to enhance the efficacy of radioimmunotherapy in CRC and expect this review can provide references and fresh ideas for the clinical application of this novel strategy.
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Affiliation(s)
- Hanghang Yuan
- Department of Nuclear Medicine, The First Hospital of Jilin University, Changchun, China,National Health Commission (NHC) Key laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Ruirui Gui
- Department of Nuclear Medicine, The First Hospital of Jilin University, Changchun, China,National Health Commission (NHC) Key laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Zhicheng Wang
- National Health Commission (NHC) Key laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Fang Fang
- National Health Commission (NHC) Key laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China,*Correspondence: Fang Fang, ; Hongguang Zhao,
| | - Hongguang Zhao
- Department of Nuclear Medicine, The First Hospital of Jilin University, Changchun, China,*Correspondence: Fang Fang, ; Hongguang Zhao,
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Yu J, Yin Y, Yu Y, Cheng M, Zhang S, Jiang S, Dong M. Effect of concomitant antibiotics use on patient outcomes and adverse effects in patients treated with ICIs. Immunopharmacol Immunotoxicol 2022; 45:386-394. [DOI: 10.1080/08923973.2022.2145966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Jiuhang Yu
- College of Pharmacy, Jiamusi University, Jiamusi, China
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yichuang Yin
- College of Pharmacy, Jiamusi University, Jiamusi, China
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yang Yu
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mengfei Cheng
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuo Zhang
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuai Jiang
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mei Dong
- College of Pharmacy, Jiamusi University, Jiamusi, China
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, China
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Deluce J, Maleki Vareki S, Fernandes R. The role of gut microbiome in immune modulation in metastatic renal cell carcinoma. Ther Adv Med Oncol 2022; 14:17588359221122714. [PMID: 36105887 PMCID: PMC9465582 DOI: 10.1177/17588359221122714] [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: 02/16/2022] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Treatment of metastatic renal cell carcinomas (mRCC) has drastically improved
since the advent of immunotherapy with immune checkpoint inhibitors (ICIs), with
a significant proportion of patients achieving durable responses. While this has
revolutionized treatment and improved outcomes for mRCC patients, a large subset
of patients still does not respond to treatment with ICIs. Moreover, ICIs can
induce various immune-related adverse events, limiting their use in many
patients. Therefore, there is a need to identify the predictive biomarkers of
both efficacy and toxicity associated with ICIs, which would allow for a more
personalized approach and help with clinical decision-making. This review aims
to explore the role of the gut microbiome in RCC to overcome primary resistance
and predict response to treatment with ICIs. First, current therapeutic
strategies and mechanisms of action of ICI therapies for RCC treatment will be
reviewed. With the technological development of shotgun whole-genome sequencing,
the gut microbiome has emerged as an exciting field of research within oncology.
Thus, the role of the microbiome and its bidirectional interaction with ICIs and
other drugs will be explored, with a particular focus on the microbiome profile
in RCC. Lastly, the rationale for future clinical interventions to overcome
resistance to ICIs using fecal microbiota transplantation in patients with RCC
will be presented.
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Affiliation(s)
- Jasna Deluce
- Division of Medical Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Saman Maleki Vareki
- Division of Experimental Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, CanadaDepartment of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London Regional Cancer Program, Room A4-130A, Cancer Research Laboratory Program, London, ON N6A 3K7, Canada.Cancer Research Laboratory Program, Lawson Health Research Institute, London, ON, Canada
| | - Ricardo Fernandes
- Division of Medical Oncology, Department of Oncology, Schulich School of Medicine & Dentistry, Western University, 800 Commissioners Road East, Room A3-940, London ON N6A 5W9, Canada.Cancer Research Laboratory Program, Lawson Health Research Institute, London, ON, Canada
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Zhang W, Zhang J, Liu T, Xing J, Zhang H, Wang D, Tang D. Bidirectional effects of intestinal microbiota and antibiotics: a new strategy for colorectal cancer treatment and prevention. J Cancer Res Clin Oncol 2022; 148:2387-2404. [PMID: 35661254 DOI: 10.1007/s00432-022-04081-3] [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] [Received: 03/09/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Colorectal cancer (CRC) is the third most common cancer worldwide, and its incidence and mortality rates are increasing every year. The intestinal microbiota has been called the "neglected organ" and there is growing evidence that the intestinal microbiota and its metabolites can be used in combination with immunotherapy, radiotherapy and chemotherapy to greatly enhance the treatment of colorectal cancer and to address some of the side effects and adverse effects of these therapies. Antibiotics have great potential to eliminate harmful microbiota, control infection, and reduce colorectal cancer side effects. However, the use of antibiotics has been a highly controversial issue, and numerous retrospective studies have shown that the use of antibiotics affects the effectiveness of treatment (especially immunotherapy). Understanding the bi-directional role of the gut microbiota and antibiotics will further enhance our research into the diagnosis and treatment of cancer. METHODS We searched the "PubMed" database and selected the following keywords "intestinal microbiota, antibiotics, treatment, prevention, colorectal cancer". In this review, we discuss the role of the intestinal microbiota in immunotherapy, radiotherapy, chemotherapy, diagnosis, and prevention of CRC. We also conclude that the intestinal microbiota and antibiotics work together to promote the treatment of CRC through a bidirectional effect. RESULTS We found that the intestinal microbiota plays a key role in promoting immunotherapy, chemotherapy, radiotherapy, diagnosis and prevention of CRC. In addition, gut microbiota and antibiotic interactions could be a new strategy for CRC treatment. CONCLUSION The bi-directional role of the intestinal microbiota and antibiotics plays a key role in the prevention, diagnosis, and treatment of colorectal cancer.
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Affiliation(s)
- Wenjie Zhang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Jie Zhang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Tian Liu
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Juan Xing
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Huan Zhang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Daorong Wang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Northern Jiangsu Province Hospital, Yangzhou University, Yangzhou, 225001, China
| | - Dong Tang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Northern Jiangsu Province Hospital, Yangzhou University, Yangzhou, 225001, China.
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Li Y, Wang S, Lin M, Hou C, Li C, Li G. Analysis of interactions of immune checkpoint inhibitors with antibiotics in cancer therapy. Front Med 2022; 16:307-321. [PMID: 35648368 DOI: 10.1007/s11684-022-0927-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/24/2022] [Indexed: 11/04/2022]
Abstract
The discovery of immune checkpoint inhibitors, such as PD-1/PD-L1 and CTLA-4, has played an important role in the development of cancer immunotherapy. However, immune-related adverse events often occur because of the enhanced immune response enabled by these agents. Antibiotics are widely applied in clinical treatment, and they are inevitably used in combination with immune checkpoint inhibitors. Clinical practice has revealed that antibiotics can weaken the therapeutic response to immune checkpoint inhibitors. Studies have shown that the gut microbiota is essential for the interaction between immune checkpoint inhibitors and antibiotics, although the exact mechanisms remain unclear. This review focuses on the interactions between immune checkpoint inhibitors and antibiotics, with an in-depth discussion about the mechanisms and therapeutic potential of modulating gut microbiota, as well as other new combination strategies.
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Affiliation(s)
- Yingying Li
- Pharmacy Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shiyuan Wang
- Pharmacy Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Mengmeng Lin
- Pharmacy Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chunying Hou
- Pharmacy Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chunyu Li
- Pharmacy Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Guohui Li
- Pharmacy Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Gul Mohammad A, Li D, He R, Lei X, Mao L, Zhang B, Zhong X, Yin Z, Cao W, Zhang W, Hei R, Zheng Q, Zhang Y. Integrated analyses of an RNA binding protein-based signature related to tumor immune microenvironment and candidate drugs in osteosarcoma. Am J Transl Res 2022; 14:2501-2526. [PMID: 35559393 PMCID: PMC9091083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE Osteosarcoma is the most frequent primary bone malignancy, associated with frequent recurrence and lung metastasis. RNA-binding proteins (RBPs) are pivotal in regulating several aspects of cancer biology. Nonetheless, interaction between RBPs and the osteosarcoma immune microenvironment is poorly understood. We investigated whether RBPs can predict prognosis and immunotherapy response in osteosarcoma patients. METHODS We constructed an RBP-related prognostic signature (RRPS) by univariate coupled with multivariate analyses and verified the independent prognostic efficacy of the signature. Single-sample Gene Set Enrichment Analysis (ssGSEA) along with ESTIMATE analysis were carried out to investigate the variations in immune characteristics between subgroups with various RRPS-scores. Furthermore, we investigatedpossible small molecule drugs using the connectivity map database and validated the expression of hub RBPs by qRT-PCR. RESULTS The RRPS, consisting of seven hub RBPs, was an independent prognostic factor compared to traditional clinical features. The RRPS could distinguish immune functions, immune score, stromal score, tumor purity and tumor infiltration by immune cells in different osteosarcoma subjects. Additionally, patients with high RRPS-scores had lower expression of immune checkpoint genes than patients with low RRPS-scores. We finally identified six small molecule drugs that may improve prognosis in osteosarcoma patients and substantiated notable differences in the contents of these RBPs. CONCLUSION We evaluated the prognostic value and clinical application of an RBPs-based prognostic signature and identified promising biomarkers to predict immune cell infiltration and immunotherapy response in osteosarcoma.
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Affiliation(s)
- Abdulraheem Gul Mohammad
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Dapeng Li
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Rong He
- Cancer Institute, The Affiliated People’s Hospital of Jiangsu UniversityZhenjiang 212000, Jiangsu, China
| | - Xuan Lei
- Department of Burn and Plastic Surgery, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Lianghao Mao
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Bing Zhang
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Xinyu Zhong
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Zhengyu Yin
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Wenbing Cao
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Wenchao Zhang
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Ruoxuan Hei
- Department of Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu UniversityZhenjiang 212000, Jiangsu, China
| | - Qiping Zheng
- Department of Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu UniversityZhenjiang 212000, Jiangsu, China
- Shenzhen Academy of Peptide Targeting Technology at Pingshan, and Shenzhen Tyercan Bio-Pharm Co., Ltd.Shenzhen 518118, Guangdong, China
| | - Yiming Zhang
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
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