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Lu KQ, Li ZL, Zhang Q, Yin Q, Zhang YL, Ni WJ, Jiang LZ, He W, Wang B. CDK12 is a potential biomarker for diagnosis, prognosis and immunomodulation in pan-cancer. Sci Rep 2024; 14:6574. [PMID: 38503865 PMCID: PMC10951204 DOI: 10.1038/s41598-024-56831-7] [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: 08/07/2023] [Accepted: 03/12/2024] [Indexed: 03/21/2024] Open
Abstract
Cell cycle-dependent protein kinase 12 (CDK12) plays a key role in a variety of carcinogenesis processes and represents a promising therapeutic target for cancer treatment. However, to date, there have been no systematic studies addressing its diagnostic, prognostic and immunological value across cancers. Here, we found that CDK12 was significantly upregulated in various types of cancers, and it expression increased with progression in ten cancer types, including breast cancer, cholangiocarcinoma and colon adenocarcinoma. Moreover, the ROC curves indicated that CDK12 showed diagnostic value in eight cancer types. High CDK12 expression was associated with poor prognosis in eight types of cancer, including low-grade glioma, mesothelioma, melanoma and pancreatic cancer. Furthermore, we conducted immunoassays to explore the exact mechanisms underlying CDK12-induced carcinogenesis, which revealed that increased expression of CDK12 allowed tumours to evade immune surveillance and upregulate immune checkpoint genes. Additionally, mutational studies have shown that amplification and missense mutations are the predominant mutational events affecting CDK12 across cancers. These findings establish CDK12 as a significant biological indicator of cancer diagnosis, prognosis, and immunotherapeutic targeting. Early surveillance and employment of CDK12 inhibitors, along with concomitant immunotherapy interventions, may enhance the clinical outcomes of cancer patients.
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Affiliation(s)
- Ke-Qi Lu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Qian Zhang
- Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qing Yin
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Yi-Lin Zhang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Wei-Jie Ni
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - LiangYun-Zi Jiang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Wei He
- Department of Gastroenterology, Jiangsu Province Geriatric Institute, and Jiangsu Province Official Hospital, Geriatric Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Bin Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China.
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2
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Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach. Clin Cancer Res 2024; 30:849-864. [PMID: 37703185 PMCID: PMC10870121 DOI: 10.1158/1078-0432.ccr-23-0873] [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: 03/21/2023] [Revised: 03/26/2023] [Accepted: 08/08/2023] [Indexed: 09/15/2023]
Abstract
PURPOSE Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, multiple models are needed to fully elucidate key aspects of disease biology and to recapitulate clinically relevant phenotypes. EXPERIMENTAL DESIGN Matched patient samples, patient-derived xenografts (PDX), and PDX-derived cell lines were comprehensively evaluated using whole-genome sequencing and RNA sequencing. The in vivo metastatic phenotype of the PDX-derived cell lines was characterized in both an intravenous and an orthotopic murine model. As a proof-of-concept study, we tested the preclinical effectiveness of a cyclin-dependent kinase inhibitor on the growth of metastatic tumors in an orthotopic amputation model. RESULTS PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication in a subset of cell lines. The cell lines were heterogeneous in their metastatic capacity, and heterogeneous tissue tropism was observed in both intravenous and orthotopic models. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden. CONCLUSIONS The variation in metastasis predilection sites between osteosarcoma PDX-derived cell lines demonstrates their ability to recapitulate the spectrum of the disease observed in patients. We describe here a panel of new osteosarcoma PDX-derived cell lines that we believe will be of wide use to the osteosarcoma research community.
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Affiliation(s)
- Courtney R. Schott
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Amanda L. Koehne
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Leanne C. Sayles
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Elizabeth P. Young
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Cuyler Luck
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
| | - Katherine Yu
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
| | - Alex G. Lee
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Marcus R. Breese
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Stanley G. Leung
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Hang Xu
- Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Avanthi Tayi Shah
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Heng-Yi Liu
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Aviv Spillinger
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Inge H. Behroozfard
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Kieren D. Marini
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Phuong T. Dinh
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - María V. Pons Ventura
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Emma N. Vanderboon
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Florette K. Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Soo-Jin Cho
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Raffi S. Avedian
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - David G. Mohler
- Department of Orthopedic Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Melissa Zimel
- Department of Orthopedic Surgery, University of California San Francisco, San Francisco, California
| | - Rosanna Wustrack
- Department of Orthopedic Surgery, University of California San Francisco, San Francisco, California
| | - Christina Curtis
- Departments of Genetics and Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Marina Sirota
- Department of Pediatrics, University of California San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California
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3
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Pontius WD, Hong ES, Faber ZJ, Gray J, Peacock CD, Bayles I, Lovrenert K, Chin DH, Gryder BE, Bartels CF, Scacheri PC. Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis. Nat Commun 2023; 14:7209. [PMID: 37938582 PMCID: PMC10632377 DOI: 10.1038/s41467-023-42656-x] [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: 11/09/2022] [Accepted: 10/17/2023] [Indexed: 11/09/2023] Open
Abstract
The metastasis-invasion cascade describes the series of steps required for a cancer cell to successfully spread from its primary tumor and ultimately grow within a secondary organ. Despite metastasis being a dynamic, multistep process, most omics studies to date have focused on comparing primary tumors to the metastatic deposits that define end-stage disease. This static approach means we lack information about the genomic and epigenomic changes that occur during the majority of tumor progression. One particularly understudied phase of tumor progression is metastatic colonization, during which cells must adapt to the new microenvironment of the secondary organ. Through temporal profiling of chromatin accessibility and gene expression in vivo, we identify dynamic changes in the epigenome that occur as osteosarcoma tumors form and grow within the lung microenvironment. Furthermore, we show through paired in vivo and in vitro CRISPR drop-out screens and pharmacological validation that the upstream transcription factors represent a class of metastasis-specific dependency genes. While current models depict lung colonization as a discrete step within the metastatic cascade, our study shows it is a defined trajectory through multiple epigenetic states, revealing new therapeutic opportunities undetectable with standard approaches.
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Affiliation(s)
- W Dean Pontius
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA.
| | - Ellen S Hong
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zachary J Faber
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeremy Gray
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Craig D Peacock
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ian Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Katreya Lovrenert
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Diana H Chin
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Berkley E Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Amgen Research, Discovery Biomarkers, Thousand Oaks, CA, USA.
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4
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Liu S, Wu J, Lu X, Guo C, Zheng Q, Wang Y, Hu Q, Bian S, Luo L, Cheng Q, Liu Z, Dai W. Targeting CDK12 obviates the malignant phenotypes of colorectal cancer through the Wnt/β-catenin signaling pathway. Exp Cell Res 2023; 428:113613. [PMID: 37100369 DOI: 10.1016/j.yexcr.2023.113613] [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: 12/22/2022] [Revised: 04/06/2023] [Accepted: 04/22/2023] [Indexed: 04/28/2023]
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related mortality and lies third in terms of morbidity due to the limited number of effective druggable targets. Since cancer stem cells (CSCs) are considered to be one of the roots of tumorigenesis, outgrowth and metastasis, targeting CSCs may be a promising strategy to reverse the malignant phenotypes of CRC. Cyclin-dependent kinase 12 (CDK12) has been reported to be involved in the self-renewal of CSCs in various cancers, rendering it an attractive potential target against CSCs to consequently limit the malignant phenotypes in CRC. In the present study, we aimed to investigate whether CDK12 can be a potential therapeutic target for patients with CRC and clarify its underlying mechanism. We found that CDK12, but not CDK13 is required for CRC survival. CDK12 was found to drive tumor initiation according to the colitis-associated colorectal cancer mouse model. In addition, CDK12 promoted CRC outgrowth and hepatic metastasis in the subcutaneous allograft and liver metastasis mouse models, respectively. In particular, CDK12 was able to induce the self-renewal of CRC CSCs. Mechanistically, the activation of Wnt/β-catenin signaling mediated by CDK12 was implicated in stemness regulation and malignant phenotype maintenance. These findings indicate that CDK12 is a candidate druggable target in CRC. Therefore, the CDK12 inhibitor SR-4835 warrants clinical trial testing in patients with CRC.
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Affiliation(s)
- Shenglan Liu
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Junhong Wu
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Xiaolu Lu
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Caiyao Guo
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, 341000, China
| | - Qisheng Zheng
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Yu Wang
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, 341000, China
| | - Qiao Hu
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Shuigen Bian
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Li Luo
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Qilai Cheng
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
| | - Zhiping Liu
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, China.
| | - Wei Dai
- School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China.
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5
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Schott CR, Koehne AL, Sayles LC, Young EP, Luck C, Yu K, Lee AG, Breese MR, Leung SG, Xu H, Shah AT, Liu HY, Spillinger A, Behroozfard IH, Marini KD, Dinh PT, Pons Ventura MAV, Vanderboon EN, Hazard FK, Cho SJ, Avedian RS, Mohler DG, Zimel M, Wustrack R, Curtis C, Sirota M, Sweet-Cordero EA. Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524562. [PMID: 36711882 PMCID: PMC9882347 DOI: 10.1101/2023.01.19.524562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Models to study metastatic disease in rare cancers are needed to advance preclinical therapeutics and to gain insight into disease biology, especially for highly aggressive cancers with a propensity for metastatic spread. Osteosarcoma is a rare cancer with a complex genomic landscape in which outcomes for patients with metastatic disease are poor. As osteosarcoma genomes are highly heterogeneous, a large panel of models is needed to fully elucidate key aspects of disease biology and to recapitulate clinically-relevant phenotypes. We describe the development and characterization of osteosarcoma patient-derived xenografts (PDXs) and a panel of PDX-derived cell lines. Matched patient samples, PDXs, and PDX-derived cell lines were comprehensively evaluated using whole genome sequencing and RNA sequencing. PDXs and PDX-derived cell lines largely maintained the expression profiles of the patient from which they were derived despite the emergence of whole-genome duplication (WGD) in a subset of cell lines. These cell line models were heterogeneous in their metastatic capacity and their tissue tropism as observed in both intravenous and orthotopic models. As proof-of-concept study, we used one of these models to test the preclinical effectiveness of a CDK inhibitor on the growth of metastatic tumors in an orthotopic amputation model. Single-agent dinaciclib was effective at dramatically reducing the metastatic burden in this model.
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6
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Du X, Wei H, Zhang B, Wang B, Li Z, Pang LK, Zhao R, Yao W. Molecular mechanisms of osteosarcoma metastasis and possible treatment opportunities. Front Oncol 2023; 13:1117867. [PMID: 37197432 PMCID: PMC10183593 DOI: 10.3389/fonc.2023.1117867] [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: 12/07/2022] [Accepted: 04/18/2023] [Indexed: 05/19/2023] Open
Abstract
In osteosarcoma patients, metastasis of the primary cancer is the leading cause of death. At present, management options to prevent metastasis are limited and non-curative. In this study, we review the current state of knowledge on the molecular mechanisms of metastasis and discuss promising new therapies to combat osteosarcoma metastasis. Genomic and epigenomic changes, metabolic reprogramming, transcription factors, dysregulation of physiologic pathways, and alterations to the tumor microenvironment are some of the changes reportedly involved in the regulation of osteosarcoma metastasis. Key factors within the tumor microenvironment include infiltrating lymphocytes, macrophages, cancer-associated fibroblasts, platelets, and extracellular components such as vesicles, proteins, and other secreted molecules. We conclude by discussing potential osteosarcoma-limiting agents and their clinical studies.
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Affiliation(s)
- Xinhui Du
- Bone Soft Tissue Department, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Key Laboratory for Digital Assessment of Spinal-Pelvic Tumor and Surgical Aid Tools Design (Zhengzhou), Zhengzhou, Henan, China
- Key Laboratory for Perioperative Digital Assessment of Bone Tumors (Henan), Zhengzhou, Henan, China
- *Correspondence: Xinhui Du,
| | - Hua Wei
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Boya Zhang
- Bone Soft Tissue Department, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Key Laboratory for Digital Assessment of Spinal-Pelvic Tumor and Surgical Aid Tools Design (Zhengzhou), Zhengzhou, Henan, China
- Key Laboratory for Perioperative Digital Assessment of Bone Tumors (Henan), Zhengzhou, Henan, China
| | - Bangmin Wang
- Bone Soft Tissue Department, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Key Laboratory for Digital Assessment of Spinal-Pelvic Tumor and Surgical Aid Tools Design (Zhengzhou), Zhengzhou, Henan, China
- Key Laboratory for Perioperative Digital Assessment of Bone Tumors (Henan), Zhengzhou, Henan, China
| | - Zhehuang Li
- Bone Soft Tissue Department, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Key Laboratory for Digital Assessment of Spinal-Pelvic Tumor and Surgical Aid Tools Design (Zhengzhou), Zhengzhou, Henan, China
- Key Laboratory for Perioperative Digital Assessment of Bone Tumors (Henan), Zhengzhou, Henan, China
| | - Lon Kai Pang
- Baylor College of Medicine, Houston, TX, United States
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Weitao Yao
- Bone Soft Tissue Department, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- Key Laboratory for Digital Assessment of Spinal-Pelvic Tumor and Surgical Aid Tools Design (Zhengzhou), Zhengzhou, Henan, China
- Key Laboratory for Perioperative Digital Assessment of Bone Tumors (Henan), Zhengzhou, Henan, China
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7
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Wu W, Yu S, Yu X. Transcription-associated cyclin-dependent kinase 12 (CDK12) as a potential target for cancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188842. [PMID: 36460141 DOI: 10.1016/j.bbcan.2022.188842] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12), a transcription-related cyclin dependent kinase (CDK), plays a momentous part in multitudinous biological functions, such as replication, transcription initiation to elongation and termination, precursor mRNA (pre-mRNA) splicing, intron polyadenylation (IPA), and translation. CDK12 can act as a tumour suppressor or oncogene in disparate cellular environments, and its dysregulation likely provokes tumorigenesis. A comprehensive understanding of CDK12 will tremendously facilitate the exploitation of novel tactics for the treatment and precaution of cancer. Currently, CDK12 inhibitors are nonspecific and nonselective, which profoundly hinders the pharmacological target validation and drug exploitation process. Herein, we summarize the newly comprehension of the biological functions of CDK12 with a focus on recently emerged advancements of CDK12-associated therapeutic approaches in cancers.
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Affiliation(s)
- Wence Wu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengji Yu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiying Yu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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8
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Beird HC, Bielack SS, Flanagan AM, Gill J, Heymann D, Janeway KA, Livingston JA, Roberts RD, Strauss SJ, Gorlick R. Osteosarcoma. Nat Rev Dis Primers 2022; 8:77. [PMID: 36481668 DOI: 10.1038/s41572-022-00409-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Osteosarcoma is the most common primary malignant tumour of the bone. Osteosarcoma incidence is bimodal, peaking at 18 and 60 years of age, and is slightly more common in males. The key pathophysiological mechanism involves several possible genetic drivers of disease linked to bone formation, causing malignant progression and metastasis. While there have been significant improvements in the outcome of patients with localized disease, with event-free survival outcomes exceeding 60%, in patients with metastatic disease, event-free survival outcomes remain poor at less than 30%. The suspicion of osteosarcoma based on radiographs still requires pathological evaluation of a bone biopsy specimen for definitive diagnosis and CT imaging of the chest should be performed to identify lung nodules. So far, population-based screening and surveillance strategies have not been implemented due to the rarity of osteosarcoma and the lack of reliable markers. Current screening focuses only on groups at high risk such as patients with genetic cancer predisposition syndromes. Management of osteosarcoma requires a multidisciplinary team of paediatric and medical oncologists, orthopaedic and general surgeons, pathologists, radiologists and specialist nurses. Survivors of osteosarcoma require specialized medical follow-up, as curative treatment consisting of chemotherapy and surgery has long-term adverse effects, which also affect the quality of life of patients. The development of osteosarcoma model systems and related research as well as the evaluation of new treatment approaches are ongoing to improve disease outcomes, especially for patients with metastases.
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Affiliation(s)
- Hannah C Beird
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Stefan S Bielack
- Pediatric Oncology, Hematology, Immunology, Klinikum Stuttgart - Olgahospital, Stuttgart Cancer Center, Stuttgart, Germany
| | - Adrienne M Flanagan
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Jonathan Gill
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dominique Heymann
- Nantes Université, CNRS, UMR6286, US2B, Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | - Katherine A Janeway
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - J Andrew Livingston
- Department of Sarcoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan D Roberts
- Center for Childhood Cancer, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Sandra J Strauss
- University College London Hospitals NHS Foundation Trust, University College London, London, UK
| | - Richard Gorlick
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA. .,Department of Sarcoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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9
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Precision oncology using ex vivo technology: a step towards individualised cancer care? Expert Rev Mol Med 2022; 24:e39. [PMID: 36184897 PMCID: PMC9884776 DOI: 10.1017/erm.2022.32] [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] [Indexed: 01/11/2023]
Abstract
Despite advances in cancer genomics and the increased use of genomic medicine, metastatic cancer is still mostly an incurable and fatal disease. With diminishing returns from traditional drug discovery strategies, and high clinical failure rates, more emphasis is being placed on alternative drug discovery platforms, such as ex vivo approaches. Ex vivo approaches aim to embed biological relevance and inter-patient variability at an earlier stage of drug discovery, and to offer more precise treatment stratification for patients. However, these techniques also have a high potential to offer personalised therapies to patients, complementing and enhancing genomic medicine. Although an array of approaches are available to researchers, only a minority of techniques have made it through to direct patient treatment within robust clinical trials. Within this review, we discuss the current challenges to ex vivo approaches within clinical practice and summarise the contemporary literature which has directed patient treatment. Finally, we map out how ex vivo approaches could transition from a small-scale, predominantly research based technology to a robust and validated predictive tool. In future, these pre-clinical approaches may be integrated into clinical cancer pathways to assist in the personalisation of therapy choices and to hopefully improve patient experiences and outcomes.
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10
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Dai W, Wu J, Peng X, Hou W, Huang H, Cheng Q, Liu Z, Luyten W, Schoofs L, Zhou J, Liu S. CDK12 orchestrates super-enhancer-associated CCDC137 transcription to direct hepatic metastasis in colorectal cancer. Clin Transl Med 2022; 12:e1087. [PMID: 36254394 PMCID: PMC9577262 DOI: 10.1002/ctm2.1087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/22/2022] [Accepted: 09/29/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatic metastasis is the primary and direct cause of death in individuals with colorectal cancer (CRC) attribute to lack of effective therapeutic targets. The present study aimed to identify potential druggable candidate targets for patients with liver metastatic CRC. METHODS The transcriptional profiles of super-enhancers (SEs) in primary and liver metastatic CRC were evaluated in publicly accessible CRC datasets. Immunohistochemistry of human CRC tissues was conducted to determine the expression level of CDK12. Cellular proliferation, survival and stemness were examined upon CDK12 inhibition by shCDK12 or a selective CDK12 inhibitor named SR-4835 with multiple in vitro and in vivo assays. RNA sequencing and bioinformatics analyses were carried out to investigate the mechanisms of CDK12 inhibition in CRC cells. RESULTS We identified CDK12 as a driver gene for direct hepatic metastasis in CRC. Suppression of CDK12 led to robust inhibition of proliferation, survival and stemness. Mechanistically, CDK12 intervention preferentially repressed the transcription of SE-associated genes. Integration of the SE landscape and RNA sequencing, BCL2L1 and CCDC137 were identified as SE-associated oncogenic genes to strengthen the abilities of cellular survival, proliferation and stemness, eventually increasing liver metastasis of CRC. CONCLUSIONS Our data highlight the potential of CDK12 and SE-associated oncogenic transcripts as therapeutic targets for patients with liver metastatic CRC.
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Affiliation(s)
- Wei Dai
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Junhong Wu
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Xiaopeng Peng
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Wen Hou
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Hao Huang
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Qilai Cheng
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
| | - Zhiping Liu
- Center for ImmunologyGannan Medical UniversityGanzhouJiangxiChina
| | | | | | - Jingfeng Zhou
- Department of Hematology and OncologyInternational Cancer CenterShenzhen Key LaboratoryShenzhen University General HospitalShenzhen University Clinical Medical AcademyShenzhen University Health Science CenterShenzhenChina
| | - Shenglan Liu
- School of PharmacyGannan Medical UniversityGanzhouJiangxiChina
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11
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CYCLIN K down-regulation induces androgen receptor gene intronic polyadenylation, variant expression and PARP inhibitor vulnerability in castration-resistant prostate cancer. Proc Natl Acad Sci U S A 2022; 119:e2205509119. [PMID: 36129942 PMCID: PMC9522376 DOI: 10.1073/pnas.2205509119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Expression of androgen receptor variants (AR-Vs) is implicated in the development of castration-resistant prostate cancer (PCa). Others have shown that androgen depletion or antiandrogen treatment induces AR-V expression in PCa cell lines, xenografts, and patient samples, although the underlying mechanism remains unclear. Our findings reveal that hormonal therapy–induced CYCLIN K down-regulation represents a key mechanism that drives intronic polyadenylation (IPA) usage in the AR gene and AR-V expression and castration resistance in PCa, and that this mechanism of action can be therapeutically targeted by the PARP inhibitor. Androgen receptor (AR) messenger RNA (mRNA) alternative splicing variants (AR-Vs) are implicated in castration-resistant progression of prostate cancer (PCa), although the molecular mechanism underlying the genesis of AR-Vs remains poorly understood. The CDK12 gene is often deleted or mutated in PCa and CDK12 deficiency is known to cause homologous recombination repair gene alteration or BRCAness via alternative polyadenylation (APA). Here, we demonstrate that pharmacological inhibition or genetic inactivation of CDK12 induces AR gene intronic (intron 3) polyadenylation (IPA) usage, AR-V expression, and PCa cell resistance to the antiandrogen enzalutamide (ENZ). We further show that AR binds to the CCNK gene promoter and up-regulates CYCLIN K expression. In contrast, ENZ decreases AR occupancy at the CCNK gene promoter and suppresses CYCLIN K expression. Similar to the effect of the CDK12 inhibitor, CYCLIN K degrader or ENZ treatment promotes AR gene IPA usage, AR-V expression, and ENZ-resistant growth of PCa cells. Importantly, we show that targeting BRCAness induced by CYCLIN K down-regulation with the PARP inhibitor overcomes ENZ resistance. Our findings identify CYCLIN K down-regulation as a key driver of IPA usage, hormonal therapy–induced AR-V expression, and castration resistance in PCa. These results suggest that hormonal therapy–induced AR-V expression and therapy resistance are vulnerable to PARP inhibitor treatment.
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12
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Magnuson B, Bedi K, Narayanan IV, Bartkowiak B, Blinkiewicz H, Paulsen MT, Greenleaf A, Ljungman M. CDK12 regulates co-transcriptional splicing and RNA turnover in human cells. iScience 2022; 25:105030. [PMID: 36111258 PMCID: PMC9468413 DOI: 10.1016/j.isci.2022.105030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
The cyclin-dependent kinase CDK12 has garnered interest as a cancer therapeutic target as DNA damage response genes are particularly suppressed by loss of CDK12 activity. In this study, we assessed the acute effects of CDK12 inhibition on transcription and RNA processing using nascent RNA Bru-seq and BruChase-seq. Acute transcriptional changes were overall small after CDK12 inhibition but over 600 genes showed intragenic premature termination, including DNA repair and cell cycle genes. Furthermore, many genes showed reduced transcriptional readthrough past the end of genes in the absence of CDK12 activity. RNA turnover was dramatically affected by CDK12 inhibition and importantly, caused increased degradation of many transcripts from DNA damage response genes. We also show that co-transcriptional splicing was suppressed by CDK12 inhibition. Taken together, these studies reveal the roles of CDK12 in regulating transcription elongation, transcription termination, co-transcriptional splicing, and RNA turnover. Over 600 genes showed prematurely terminated transcription when CDK12 was inhibited CDK12 promotes transcriptional readthrough past transcription end sites (TESs) CDK12 promotes splicing and affects transcript stability
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Affiliation(s)
- Brian Magnuson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karan Bedi
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Bartlomiej Bartkowiak
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hailey Blinkiewicz
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T. Paulsen
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arno Greenleaf
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mats Ljungman
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author
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13
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Chilà R, Chiappa M, Guffanti F, Panini N, Conconi D, Rinaldi A, Cascione L, Bertoni F, Fratelli M, Damia G. Stable CDK12 Knock-Out Ovarian Cancer Cells Do Not Show Increased Sensitivity to Cisplatin and PARP Inhibitor Treatment. Front Oncol 2022; 12:903536. [PMID: 35912188 PMCID: PMC9328802 DOI: 10.3389/fonc.2022.903536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a serine/threonine kinase involved in the regulation of RNA polymerase II and in the transcription of a subset of genes involved in the DNA damage response. CDK12 is one of the most mutated genes in ovarian carcinoma. These mutations result in loss-of-function and can predict the responses to PARP1/2 inhibitor and platinum. To investigate the role of CDK12 in ovarian cancer, CRISPR/Cas9 technology was used to generate a stable CDK12 knockout (KO) clone in A2780 ovarian carcinoma cells. This is the first report on a CDK12 null cell line. The clone had slower cell growth and was less clonogenic than parental cells. These data were confirmed in vivo, where CDK12 KO transplanted cells had a much longer time lag and slightly slower growth rate than CDK12-expressing cells. The slower growth was associated with a higher basal level of apoptosis, but there were no differences in the basal level of autophagy and senescence. While cell cycle distribution was similar in parental and knockout cells, there was a doubling in DNA content, with an almost double modal number of chromosomes in the CDK12 KO clone which, however did not display any increase in γH2AX, a marker of DNA damage. We found partial down-regulation of the expression of DNA repair genes at the mRNA level and, among the down-regulated genes, an enrichment in the G2/M checkpoint genes. Although the biological features of CDK12 KO cells are compatible with the function of CDK12, contrary to some reports, we could not find any difference in the sensitivity to cisplatin and olaparib between wild-type and CDK12 KO cells.
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Affiliation(s)
- Rosaria Chilà
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Michela Chiappa
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Federica Guffanti
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Nicolò Panini
- Laboratory of Cancer Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - Maddalena Fratelli
- Department of Biochemistry, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giovanna Damia
- Laboratory of Experimental Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri Istituito di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- *Correspondence: Giovanna Damia,
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14
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Lei P, Zhang J, Liao P, Ren C, Wang J, Wang Y. Current progress and novel strategies that target CDK12 for drug discovery. Eur J Med Chem 2022; 240:114603. [PMID: 35868123 DOI: 10.1016/j.ejmech.2022.114603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023]
Abstract
CDK12 is a cyclin-dependent kinase that plays critical roles in DNA replication, transcription, mRNA splicing, and DNA damage repair. CDK12 genomic changes, including mutation, amplification, deletion, and fusion, lead to various cancers, such as colorectal cancer, gastric cancer, and ovarian cancer. An increasing number of CDK12 inhibitors have been reported since CDK12 was identified as a biomarker and cancer therapeutic target. A major challenge lies in that CDK12 and CDK13 share highly similar sequences, which leads to great difficulties in the development of highly selective CDK12 inhibitors. In recent years, great efforts were made in developing selective CDK12 blockers. Techniques including PROTAC and molecular glue degraders were also applied to facilitate their development. Also, the drug combination strategy of CDK12 small molecule inhibitors were studied. This review discusses the latest studies on CDK12 inhibitors and analyzes their structure-activity relationships, shedding light on their further development.
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Affiliation(s)
- Peng Lei
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China
| | - Peiyu Liao
- School of Pharmacy, Chengdu Medical College, Chengdu, 610500, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China.
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15
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Mills LJ, Scott MC, Shah P, Cunanan AR, Deshpande A, Auch B, Curtin B, Beckman KB, Spector LG, Sarver AL, Subramanian S, Richmond TA, Modiano JF. Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma. Bone 2022; 158:115716. [PMID: 33127576 PMCID: PMC8076342 DOI: 10.1016/j.bone.2020.115716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/24/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023]
Abstract
Osteosarcoma is an aggressive tumor of the bone that primarily affects young adults and adolescents. Osteosarcoma is characterized by genomic chaos and heterogeneity. While inactivation of tumor protein p53 (TP53) is nearly universal other high frequency mutations or structural variations have not been identified. Despite this genomic heterogeneity, key conserved transcriptional programs associated with survival have been identified across human, canine and induced murine osteosarcoma. The epigenomic landscape, including DNA methylation, plays a key role in establishing transcriptional programs in all cell types. The role of epigenetic dysregulation has been studied in a variety of cancers but has yet to be explored at scale in osteosarcoma. Here we examined genome-wide DNA methylation patterns in 24 human and 44 canine osteosarcoma samples identifying groups of highly correlated DNA methylation marks in human and canine osteosarcoma samples. We also link specific DNA methylation patterns to key transcriptional programs in both human and canine osteosarcoma. Building on previous work, we built a DNA methylation-based measure for the presence and abundance of various immune cell types in osteosarcoma. Finally, we determined that the underlying state of the tumor, and not changes in cell composition, were the main driver of differences in DNA methylation across the human and canine samples. SIGNIFICANCE: Genome wide comparison of DNA methylation patterns in osteosarcoma across two species lays the ground work for the exploration of DNA methylation programs that help establish conserved transcriptional programs in the context of varied mutational landscapes.
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Affiliation(s)
- Lauren J Mills
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Childhood Cancer Genomics Group, Department of Pediatric, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Milcah C Scott
- Department of Microbiology and Immunology, Center for Immunology, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pankti Shah
- Roche Sequencing Solution, Pleasanton, CA, USA
| | | | | | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Bridget Curtin
- Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Logan G Spector
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Childhood Cancer Genomics Group, Department of Pediatric, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron L Sarver
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul 55108, USA; Institute of Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Subbaya Subramanian
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Jaime F Modiano
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul 55108, USA; Institute of Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, UDS Institute for Engineering in Medicine, Minneapolis, MN 55455, USA
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16
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Wong CH, Li CH, Man Tong JH, Zheng D, He Q, Luo Z, Lou UK, Wang J, To KF, Chen Y. The Establishment of CDK9/ RNA PolII/H3K4me3/DNA Methylation Feedback Promotes HOTAIR Expression by RNA Elongation Enhancement in Cancer. Mol Ther 2022; 30:1597-1609. [PMID: 35121112 PMCID: PMC9077372 DOI: 10.1016/j.ymthe.2022.01.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/07/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Long non-coding RNA HOX Transcript Antisense RNA (HOTAIR) is overexpressed in multiple cancers with diverse genetic profiles. Importantly, since HOTAIR heavily contributes to cancer progression by promoting tumor growth and metastasis, HOTAIR becomes a potential target for cancer therapy. However, the underlying mechanism leading to HOTAIR deregulation is largely unexplored. Here, we performed a pan-cancer analysis using more than 4,200 samples and found that intragenic exon CpG island (Ex-CGI) was hypermethylated and was positively correlated to HOTAIR expression. Also, we revealed that Ex-CGI methylation promotes HOTAIR expression through enhancing the transcription elongation process. Furthermore, we linked up the aberrant intragenic tri-methylation on H3 at lysine 4 (H3K4me3) and Ex-CGI DNA methylation in promoting transcription elongation of HOTAIR. Targeting the oncogenic CDK7-CDK9-H3K4me3 axis downregulated HOTAIR expression and inhibited cell growth in many cancers. To our knowledge, this is the first time that a positive feedback loop that involved CDK9-mediated phosphorylation of RNA Polymerase II Serine 2 (RNA PolII Ser2), H3K4me3, and intragenic DNA methylation, which induced robust transcriptional elongation and heavily contributed to the upregulation of oncogenic lncRNA in cancer has been demonstrated. Targeting the oncogenic CDK7-CDK9-H3K4me3 axis could be a novel therapy in many cancers through inhibiting the HOTAIR expression.
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Affiliation(s)
- Chi Hin Wong
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Chi Han Li
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Joanna Hung Man Tong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Duo Zheng
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen University International Cancer Center, Department of Cell Biology and Genetics, School of Medicine, Shenzhen University, Shenzhen 518055, China
| | - Qifang He
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Zhiyuan Luo
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Ut Kei Lou
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Jiatong Wang
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yangchao Chen
- A School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518087, China.
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17
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Liu QH, Dai GR, Wang XN, Wang L, Li LL, Wu ZS, Xia RX. CDK12 activates MYC to repress miR-28-5p/EZH2 and amplifies tonic BCR signaling to promote the development of diffuse large B-cell lymphoma. Cancer Gene Ther 2022; 29:1207-1216. [PMID: 35082399 DOI: 10.1038/s41417-021-00415-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 10/11/2021] [Accepted: 12/03/2021] [Indexed: 11/09/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) is a transcription-associated kinase that participates in various cellular processes. However, its regulatory role in the progression of diffuse large B-cell lymphoma (DLBCL), which is the most prevalent subtype of non-Hodgkin lymphoma (NHL), is still elusive and controversial.The expression of CDK12 was detected by immunohistochemistry (IHC), RT-qPCR was performed to detect miR-28-5p expression of OCI-LY3 and SU-DHL-4 cells. MTT and soft agarose colony formation assays were used to detect cell proliferation. The cell apoptosis was determined by flow cytometry. The protein expressions changes of MYC, EZH2 and the biomarkers of BCR signaling were also detected. A subcutaneous transplantation tumor model of OCI-LY3 cells in nude mice was established to evaluate anticarcinogenic activities of CDK12 knockdown. Elevated expression of CDK12 was observed while miR-28-5p was downregulated in DLBCL tissues. CDK12 knockdown or miR-28-5p overexpression could inhibit proliferation and promote apoptosis of DLBCL cells. miR-28-5p inhibition could reverse the effect of CDK12 knockdown on proliferation and apoptosis of DLBCL cells. In addition, CDK12 knockdown could inhibit DLBCL tumor growth in the mice model. CDK12 activated MYC to repress miR-28-5p/EZH2 and amplified tonic BCR signaling to promote the development of DLBCL, which might provide potential therapeutic targets for future therapeutic intervention in DLBCL.
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Affiliation(s)
- Qin-Hua Liu
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Guan-Rong Dai
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Xiao-Nan Wang
- Laboratory of Pathogenic Microbiology and Immunology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Lin Wang
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Li-Li Li
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Zheng-Sheng Wu
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Rui-Xiang Xia
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China.
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18
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Jiang B, Gao Y, Che J, Lu W, Kaltheuner IH, Dries R, Kalocsay M, Berberich MJ, Jiang J, You I, Kwiatkowski N, Riching KM, Daniels DL, Sorger PK, Geyer M, Zhang T, Gray NS. Discovery and resistance mechanism of a selective CDK12 degrader. Nat Chem Biol 2021; 17:675-683. [PMID: 33753926 PMCID: PMC8590456 DOI: 10.1038/s41589-021-00765-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 01/09/2021] [Accepted: 02/04/2021] [Indexed: 01/31/2023]
Abstract
Cyclin-dependent kinase 12 (CDK12) is an emerging therapeutic target due to its role in regulating transcription of DNA-damage response (DDR) genes. However, development of selective small molecules targeting CDK12 has been challenging due to the high degree of homology between kinase domains of CDK12 and other transcriptional CDKs, most notably CDK13. In the present study, we report the rational design and characterization of a CDK12-specific degrader, BSJ-4-116. BSJ-4-116 selectively degraded CDK12 as assessed through quantitative proteomics. Selective degradation of CDK12 resulted in premature cleavage and poly(adenylation) of DDR genes. Moreover, BSJ-4-116 exhibited potent antiproliferative effects, alone and in combination with the poly(ADP-ribose) polymerase inhibitor olaparib, as well as when used as a single agent against cell lines resistant to covalent CDK12 inhibitors. Two point mutations in CDK12 were identified that confer resistance to BSJ-4-116, demonstrating a potential mechanism that tumor cells can use to evade bivalent degrader molecules.
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Affiliation(s)
- Baishan Jiang
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,These authors contributed equally: Baishan Jiang, Yang Gao and Jianwei Che
| | - Yang Gao
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,These authors contributed equally: Baishan Jiang, Yang Gao and Jianwei Che
| | - Jianwei Che
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,These authors contributed equally: Baishan Jiang, Yang Gao and Jianwei Che
| | - Wenchao Lu
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Ruben Dries
- Department of Hematology and Oncology, Boston University, Boston, Massachusetts, USA.,Department of Computational Medicine, Boston University, Boston, Massachusetts, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew J. Berberich
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jie Jiang
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Inchul You
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Kwiatkowski
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Peter K. Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Tinghu Zhang
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Correspondence should be addressed to Tinghu Zhang (); Nathanael S. Gray ()
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana–Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Correspondence should be addressed to Tinghu Zhang (); Nathanael S. Gray ()
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19
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Wang L, Wu J, Song S, Chen H, Hu Y, Xu B, Liu J. Plasma Exosome-Derived Sentrin SUMO-Specific Protease 1: A Prognostic Biomarker in Patients With Osteosarcoma. Front Oncol 2021; 11:625109. [PMID: 33791211 PMCID: PMC8006461 DOI: 10.3389/fonc.2021.625109] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Background The exosomes contain many important proteins that can be used for early tumor diagnosis or patient prognosis analysis. In this study, we investigated plasma exosome-derived sentrin SUMO-specific protease 1 (SENP1) levels as a prognostic biomarker in patients with osteosarcoma. Methods The expression of SENP1 protein in osteosarcoma tissues and adjacent tissues was detected by immunohistochemistry (IHC). The exosomes were identified by transmission electron microscopy, nanoparticle tracking analysis, and western blotting. ELISA was used to detect plasma exosome-derived SENP1 levels to assess prognosis in patients with osteosarcoma. Results IHC showed that the positive expression rate of SENP1 in osteosarcoma tissues was 88.33%, whereas that in adjacent tissues was 46.67% (P < 0.05). Plasma exosome-derived SENP1 levels were related to tumor size, tumor location, necrosis rate, pulmonary metastasis, and surgical stage. Both disease-free survival (DFS) and overall survival (OS) were worse in patients who had higher plasma exosome-derived SENP1 levels compared with those in patients with lower plasma exosome-derived SENP1 levels (P < 0.001). The area under the receiver operating characteristic curve (AUROC) of plasma exosome-derived SENP1, as 1-year DFS and 3-year DFS prognostic biomarkers, was 0.90 (95% CI: 0.83-0.98) and 0.96 (95% CI: 0.94-0.99), respectively. As to OS, the AUROC of plasma exosome-derived SENP1 for 1-year and 3-year prediction was 0.90 (95% CI: 0.82-0.99) and 0.96 (0.93-0.98), respectively. The plasma exosome-derived SENP1 was better than plasma SENP1 as a prognostic biomarker both in DFS and OS. Conclusions Our findings show that the plasma exosome-derived SENP1 may serve as a novel and independent prognostic predictor in clinical applications.
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Affiliation(s)
- Li Wang
- Department of Orthopedics, The Third People's Hospital of Yancheng City, Yancheng, China
| | - Jian Wu
- Department of Laboratory Medicine, The First People's Hospital of Yancheng City, Yancheng, China
| | - Shu Song
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Haining Chen
- Department of Orthopedics, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yong Hu
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Buwei Xu
- Department of Orthopedics, The Third People's Hospital of Yancheng City, Yancheng, China
| | - Jinbo Liu
- Department of Spine, The Third Affiliated Hospital of Soochow University, Changzhou, China
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Li N, Zheng S, Xue Z, Xiong Z, Zou Y, Tang Y, Wei WD, Yang L. Expression and prognostic value of transcription-associated cyclin-dependent kinases in human breast cancer. Aging (Albany NY) 2021; 13:8095-8114. [PMID: 33686962 PMCID: PMC8034920 DOI: 10.18632/aging.202595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/14/2021] [Indexed: 12/24/2022]
Abstract
The expression and prognostic significance of transcription-associated cyclin-dependent kinases (TA-CDKs) in breast cancer have not been systematically investigated. Using Oncomine, GEPIA2, the Human Protein Atlas, the Kaplan-Meier Plotter, cBioPortal, Metascape, and DAVID 6.8, we profiled the expression of TA-CDKs in breast cancer, inferred their biological functions, and assessed their effect on prognosis. The expression of CDK7/10/13/19 mRNAs in breast cancer tissues was significantly higher than in normal breast tissues. Survival analysis of breast cancer patients revealed that increased CDK8 expression was associated with inferior overall survival (OS), higher expression of CDK7 or CDK8 was associated with inferior relapse-free survival (RFS), but higher expression of CDK13 was associated with favorable RFS and OS. In addition, a high genetic alteration rate (56%) in TA-CDKs was associated with shorter OS. On functional enrichment analysis, top GO enrichment items for TA-CDKs and their neighboring genes included cyclin-dependent protein serine/threonine kinase activity and transferase complex. The top KEGG pathways included cell cycle and mismatch repair. These results suggest that CDK7/8/13 are potential prognostic biomarkers for breast cancer patients and provide novel insight for future studies examining their usefulness as therapeutic targets.
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Affiliation(s)
- Ning Li
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shaoquan Zheng
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhicheng Xue
- Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhenchong Xiong
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yutian Zou
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yuhui Tang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wei-Dong Wei
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lu Yang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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21
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The promise and current status of CDK12/13 inhibition for the treatment of cancer. Future Med Chem 2020; 13:117-141. [PMID: 33295810 DOI: 10.4155/fmc-2020-0240] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CDK12 and CDK13 are Ser/Thr protein kinases that regulate transcription and co-transcriptional processes. Genetic silencing of CDK12 is associated with genomic instability in a variety of cancers, including difficult-to-treat breast, ovarian, colorectal, brain and pancreatic cancers, and is synthetic lethal with PARP, MYC or EWS/FLI inhibition. CDK13 is amplified in hepatocellular carcinoma. Consequently, selective CDK12/13 inhibitors constitute powerful research tools as well as promising anti-cancer therapeutics, either alone or in combination therapy. Herein the authors discuss the role of CDK12 and CDK13 in normal and cancer cells, describe their utility as a biomarker and therapeutic target, review the medicinal chemistry optimization of existing CDK12/13 inhibitors and outline strategies for the rational design of CDK12/13 selective inhibitors.
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22
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Beyond Kinases: Targeting Replication Stress Proteins in Cancer Therapy. Trends Cancer 2020; 7:430-446. [PMID: 33203609 DOI: 10.1016/j.trecan.2020.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/19/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022]
Abstract
DNA replication stress describes a state of impaired replication fork progress that triggers a cellular stress response to maintain genome stability and complete DNA synthesis. Replication stress is a common state that must be tolerated in many cancers. One promising therapeutic approach is targeting replication stress response factors such as the ataxia telangiectasia and rad 3-related kinase (ATR) or checkpoint kinase 1 (CHK1) kinases that some cancers depend upon to survive endogenous replication stress. However, research revealing the complexity of the replication stress response suggests new genetic interactions and candidate therapeutic targets. Many of these candidates regulate DNA transactions around reversed replication forks, including helicases, nucleases and alternative polymerases that promote fork stability and restart. Here we review emerging strategies to exploit replication stress for cancer therapy.
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23
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CDK12: a potential therapeutic target in cancer. Drug Discov Today 2020; 25:2257-2267. [PMID: 33038524 DOI: 10.1016/j.drudis.2020.09.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/30/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]
Abstract
Cyclin-dependent kinase (CDK) 12 engages in diversified biological functions, from transcription, post-transcriptional modification, cell cycle, and translation to cellular proliferation. Moreover, it regulates the expression of cancer-related genes involved in DNA damage response (DDR) and replication, which are responsible for maintaining genomic stability. CDK12 emerges as an oncogene or tumor suppressor in different cellular contexts, where its dysregulation results in tumorigenesis. Current CDK12 inhibitors are nonselective, which impedes the process of pharmacological target validation and drug development. Herein, we discuss the latest understanding of the biological roles of CDK12 in cancers and provide molecular analyses of CDK12 inhibitors to guide the rational design of selective inhibitors.
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24
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Thanindratarn P, Dean DC, Feng W, Wei R, Nelson SD, Hornicek FJ, Duan Z. Cyclin-dependent kinase 12 (CDK12) in chordoma: prognostic and therapeutic value. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2020; 29:3214-3228. [PMID: 32691223 DOI: 10.1007/s00586-020-06543-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/14/2020] [Indexed: 01/22/2023]
Abstract
PURPOSE To determine the cyclin-dependent kinase 12 (CDK12) expression in chordoma patient tissues and cell lines, its correlation with oncologic outcomes, and its function in chordoma cell proliferation. METHODS A chordoma tissue microarray was constructed from fifty-six patient specimens and examined by immunohistochemistry to measure CDK12 expression and its correlation to patient clinical characteristics and survival. CDK12 expression in chordoma cell lines and patient tissues was evaluated via western blot. CDK12 specific small interfering RNA (siRNA) was applied to determine whether its inhibition attenuated chordoma cell growth and proliferation. RESULTS CDK12 was expressed in the majority of chordoma specimens, with notably higher expression in patients with recurrent or metastatic disease. High CDK12 expression was an independent prognostic predictor for shorter overall and progression-free survival in chordoma by univariate and multivariate analysis. Western blot analysis revealed that CDK12 was also highly expressed in chordoma cell lines, with CDK12 specific small interfering RNA (siRNA) mediated knockdown decreasing proliferation and inducing apoptosis. Mechanistically, inhibition of CDK12 decreased phosphorylation of RNA polymerase II (RNAP II) and the anti-apoptotic proteins Survivin and Mcl-1. CONCLUSION High expression of CDK12 is an independent predictor of poor prognosis in chordoma. Inhibition of CDK12 significantly decreased chordoma cell proliferation and induced apoptosis. Our results support CDK12 as a novel prognostic biomarker and therapeutic target in chordoma.
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Affiliation(s)
- Pichaya Thanindratarn
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA.,Department of Orthopedic Surgery, Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Dylan C Dean
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA
| | - Wenlong Feng
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ran Wei
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA.,Musculoskeletal Tumor Center, Beijing Key Laboratory of Musculoskeletal Tumor, Peking University People's Hospital, Beijing, China
| | - Scott D Nelson
- Department of Pathology, University of California, Los Angeles, CA, USA
| | - Francis J Hornicek
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA
| | - Zhenfeng Duan
- Department of Orthopaedic Surgery, Sarcoma Biology Laboratory, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young. Dr. South, Los Angeles, CA, 90095, USA.
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25
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Liang S, Hu L, Wu Z, Chen Z, Liu S, Xu X, Qian A. CDK12: A Potent Target and Biomarker for Human Cancer Therapy. Cells 2020; 9:E1483. [PMID: 32570740 PMCID: PMC7349380 DOI: 10.3390/cells9061483] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are a group of serine/threonine protein kinases and play crucial roles in various cellular processes by regulating cell cycle and gene transcription. Cyclin-dependent kinase 12 (CDK12) is an important transcription-associated CDK. It shows versatile roles in regulating gene transcription, RNA splicing, translation, DNA damage response (DDR), cell cycle progression and cell proliferation. Recently, increasing evidence demonstrates the important role of CDK12 in various human cancers, illustrating it as both a biomarker of cancer and a potential target for cancer therapy. Here, we summarize the current knowledge of CDK12, and review the research advances of CDK12's biological functions, especially its role in human cancers and as a potential target and biomarker for cancer therapy.
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Affiliation(s)
- Shujing Liang
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Lifang Hu
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Zixiang Wu
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Zhihao Chen
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Shuyu Liu
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Xia Xu
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Airong Qian
- Laboratory for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi’an 710072, China; (S.L.); (L.H.); (Z.W.); (Z.C.); (S.L.); (X.X.)
- Key Laboratory for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
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Pilarova K, Herudek J, Blazek D. CDK12: cellular functions and therapeutic potential of versatile player in cancer. NAR Cancer 2020; 2:zcaa003. [PMID: 34316683 PMCID: PMC8210036 DOI: 10.1093/narcan/zcaa003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) phosphorylates the C-terminal domain of RNA polymerase II and is needed for the optimal transcription elongation and translation of a subset of human protein-coding genes. The kinase has a pleiotropic effect on the maintenance of genome stability, and its inactivation in prostate and ovarian tumours results in focal tandem duplications, a CDK12-unique genome instability phenotype. CDK12 aberrations were found in many other malignancies and have the potential to be used as biomarkers for therapeutic intervention. Moreover, the inhibition of CDK12 emerges as a promising strategy for treatment in several types of cancers. In this review, we summarize mechanisms that CDK12 utilizes for the regulation of gene expression and discuss how the perturbation of CDK12-sensitive genes contributes to the disruption of cell cycle progression and the onset of genome instability. Furthermore, we describe tumour-suppressive and oncogenic functions of CDK12 and its potential as a biomarker and inhibition target in anti-tumour treatments.
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Affiliation(s)
- Kveta Pilarova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Jan Herudek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
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27
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Chou J, Quigley DA, Robinson TM, Feng FY, Ashworth A. Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy. Cancer Discov 2020; 10:351-370. [DOI: 10.1158/2159-8290.cd-19-0528] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022]
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28
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Fan TM, Roberts RD, Lizardo MM. Understanding and Modeling Metastasis Biology to Improve Therapeutic Strategies for Combating Osteosarcoma Progression. Front Oncol 2020; 10:13. [PMID: 32082995 PMCID: PMC7006476 DOI: 10.3389/fonc.2020.00013] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma is a malignant primary tumor of bone, arising from transformed progenitor cells with osteoblastic differentiation and osteoid production. While categorized as a rare tumor, most patients diagnosed with osteosarcoma are adolescents in their second decade of life and underscores the potential for life changing consequences in this vulnerable population. In the setting of localized disease, conventional treatment for osteosarcoma affords a cure rate approaching 70%; however, survival for patients suffering from metastatic disease remain disappointing with only 20% of individuals being alive past 5 years post-diagnosis. In patients with incurable disease, pulmonary metastases remain the leading cause for osteosarcoma-associated mortality; yet identifying new strategies for combating metastatic progression remains at a scientific and clinical impasse, with no significant advancements for the past four decades. While there is resonating clinical urgency for newer and more effective treatment options for managing osteosarcoma metastases, the discovery of druggable targets and development of innovative therapies for inhibiting metastatic progression will require a deeper and more detailed understanding of osteosarcoma metastasis biology. Toward the goal of illuminating the processes involved in cancer metastasis, a convergent science approach inclusive of diverse disciplines spanning the biology and physical science domains can offer novel and synergistic perspectives, inventive, and sophisticated model systems, and disruptive experimental approaches that can accelerate the discovery and characterization of key processes operative during metastatic progression. Through the lens of trans-disciplinary research, the field of comparative oncology is uniquely positioned to advance new discoveries in metastasis biology toward impactful clinical translation through the inclusion of pet dogs diagnosed with metastatic osteosarcoma. Given the spontaneous course of osteosarcoma development in the context of real-time tumor microenvironmental cues and immune mechanisms, pet dogs are distinctively valuable in translational modeling given their faithful recapitulation of metastatic disease progression as occurs in humans. Pet dogs can be leveraged for the exploration of novel therapies that exploit tumor cell vulnerabilities, perturb local microenvironmental cues, and amplify immunologic recognition. In this capacity, pet dogs can serve as valuable corroborative models for realizing the science and best clinical practices necessary for understanding and combating osteosarcoma metastases.
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Affiliation(s)
- Timothy M Fan
- Comparative Oncology Research Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Ryan D Roberts
- Center for Childhood Cancer and Blood Disorders, Abigail Wexner Research Institute at Nationwide Children's Hospital, The James Comprehensive Cancer Center at The Ohio State University, Columbus, OH, United States
| | - Michael M Lizardo
- Poul Sorensen Laboratory, Department of Molecular Oncology, BC Cancer, Part of the Provincial Health Services Authority in British Columbia, Vancouver, BC, Canada
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Schott C, Shah AT, Sweet-Cordero EA. Genomic Complexity of Osteosarcoma and Its Implication for Preclinical and Clinical Targeted Therapies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1258:1-19. [PMID: 32767231 DOI: 10.1007/978-3-030-43085-6_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Osteosarcoma is a genomically complex disease characterized by few recurrent single-nucleotide mutations or in-frame fusions. In contrast, structural alterations, including copy number changes, chromothripsis, kataegis, loss of heterozygosity (LOH), and other large-scale genomic alterations, are frequent and widespread across the osteosarcoma genome. These observed structural alterations lead to activation of oncogenes and loss of tumor suppressors which together contribute to oncogenesis. To date, few targeted therapies for osteosarcoma have been identified. It is likely that effectiveness of targeted therapies will vary greatly in subsets of tumors with distinct key driver events. Model systems which can recapitulate the genetic heterogeneity of this disease are needed to test this hypothesis. One possible approach is to use patient-derived xenograft (PDX) models characterized with regards to their similarity to the human tumor samples from which they were derived. Here we review evidence pointing to the genomic complexity of osteosarcoma and how this is reflected in available model systems. We also review the current state of preclinical testing for targeted therapies using these models.
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Affiliation(s)
- Courtney Schott
- Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Avanthi Tayi Shah
- Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, USA
| | - E Alejandro Sweet-Cordero
- Department of Pediatrics, Division of Hematology and Oncology, University of California San Francisco, San Francisco, CA, USA.
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30
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Targeting the Cancer Epigenome with Histone Deacetylase Inhibitors in Osteosarcoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1258:55-75. [PMID: 32767234 DOI: 10.1007/978-3-030-43085-6_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Epigenetic deregulation is an emerging hallmark of cancer that enables tumor cells to escape surveillance by tumor suppressors and ultimately progress. The structure of the epigenome consists of covalent modifications of chromatin components, including acetylation by histone acetyltransferases (HATs) and deacetylation by histone deacetylases (HDACs). Targeting these enzymes with inhibitors to restore epigenetic homeostasis has been explored for many cancers. Osteosarcoma, an aggressive bone malignancy that primarily affects children and young adults, is notable for widespread genetic and epigenetic instability. This may explain why therapy directed at unique molecular pathways has failed to substantially improve outcomes in osteosarcoma over the past four decades. In this review, we discuss the potential of targeting the cancer epigenome, with a focus on histone deacetylase inhibitors (HDACi) for osteosarcoma. We additionally highlight the safety and tolerance of HDACi, combination chemotherapy with HDACi, and the ongoing challenges in the development of these agents.
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