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Wang XX, Myakala K, Libby AE, Krawczyk E, Panov J, Jones BA, Bhasin K, Shults N, Qi Y, Krausz KW, Zerfas PM, Takahashi S, Daneshpajouhnejad P, Titievsky A, Taranenko E, Billon C, Chatterjee A, Elgendy B, Walker JK, Albanese C, Kopp JB, Rosenberg AZ, Gonzalez FJ, Guha U, Brodsky L, Burris TP, Levi M. Estrogen-Related Receptor Agonism Reverses Mitochondrial Dysfunction and Inflammation in the Aging Kidney. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1969-1987. [PMID: 37717940 PMCID: PMC10734281 DOI: 10.1016/j.ajpath.2023.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/21/2023] [Accepted: 07/19/2023] [Indexed: 09/19/2023]
Abstract
A gradual decline in renal function occurs even in healthy aging individuals. In addition to aging, per se, concurrent metabolic syndrome and hypertension, which are common in the aging population, can induce mitochondrial dysfunction and inflammation, which collectively contribute to age-related kidney dysfunction and disease. This study examined the role of the nuclear hormone receptors, the estrogen-related receptors (ERRs), in regulation of age-related mitochondrial dysfunction and inflammation. The ERRs were decreased in both aging human and mouse kidneys and were preserved in aging mice with lifelong caloric restriction (CR). A pan-ERR agonist, SLU-PP-332, was used to treat 21-month-old mice for 8 weeks. In addition, 21-month-old mice were treated with a stimulator of interferon genes (STING) inhibitor, C-176, for 3 weeks. Remarkably, similar to CR, an 8-week treatment with a pan-ERR agonist reversed the age-related increases in albuminuria, podocyte loss, mitochondrial dysfunction, and inflammatory cytokines, via the cyclic GMP-AMP synthase-STING and STAT3 signaling pathways. A 3-week treatment of 21-month-old mice with a STING inhibitor reversed the increases in inflammatory cytokines and the senescence marker, p21/cyclin dependent kinase inhibitor 1A (Cdkn1a), but also unexpectedly reversed the age-related decreases in PPARG coactivator (PGC)-1α, ERRα, mitochondrial complexes, and medium chain acyl coenzyme A dehydrogenase (MCAD) expression. These studies identified ERRs as CR mimetics and as important modulators of age-related mitochondrial dysfunction and inflammation. These findings highlight novel druggable pathways that can be further evaluated to prevent progression of age-related kidney disease.
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Affiliation(s)
- Xiaoxin X Wang
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia.
| | - Komuraiah Myakala
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Andrew E Libby
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Ewa Krawczyk
- Department of Pathology, Center for Cell Reprogramming, Georgetown University, Washington, District of Columbia
| | - Julia Panov
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, Israel; Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Bryce A Jones
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, District of Columbia
| | - Kanchan Bhasin
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Nataliia Shults
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Yue Qi
- Thoracic and GI Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Kristopher W Krausz
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Patricia M Zerfas
- Office of Research Services, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Shogo Takahashi
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Parnaz Daneshpajouhnejad
- Renal Pathology Service, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Avi Titievsky
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, Israel
| | | | - Cyrielle Billon
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, St. Louis, Missouri
| | - Arindam Chatterjee
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Bahaa Elgendy
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, St. Louis, Missouri
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Chris Albanese
- Department of Oncology and Center for Translational Imaging, Georgetown University Medical Center, Washington, District of Columbia
| | - Jeffrey B Kopp
- Kidney Diseases Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Avi Z Rosenberg
- Renal Pathology Service, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, Israel
| | - Thomas P Burris
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, St. Louis, Missouri
| | - Moshe Levi
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia.
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2
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Liu X, Liu Y, Chai W, Yan M, Li H, Li J, Sun L, Cao Y, Liu Q, Sun Y, Pan H. CDK12 loss inhibits cell proliferation by regulating TBK1 in non-small cell lung cancer cells. Mol Cell Probes 2023; 71:101923. [PMID: 37517598 DOI: 10.1016/j.mcp.2023.101923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Lung cancer is one of the most common malignant tumors and has a poor prognosis and a low survival rate. Traditional treatments, such as radiotherapy and chemotherapy, still face some challenges because of high drug resistance and toxicity. Therefore, it is necessary to discover a new kind of targeted drug with low toxicity and high efficiency. CDK12 is a cell cycle-dependent kinase whose main function is to activate RNA polymerase II (RNAPII) and promote the transcriptional extension of RNA. However, the role and molecular mechanism of CDK12 in lung cancer are still unclear. In this study, the mutation and RNA-Seq data of CDK12 in lung adenocarcinoma and squamous cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA) database and analyzed with the custom scripts. Cell proliferation was evaluated by Cell Counting Kit-8 (CCK-8) and cell colony formation assays. A subcutaneous tumor experiment in nude mice was used to examine the effects of CDK12 knockdown on the in vivo tumor growth of NSCLC cells. The cell cycle distribution and the apoptosis rate of lung cancer cells were assessed by flow cytometry. Regulation of TANK-binding kinase 1 (TBK1) by CDK12 was evaluated by quantitative PCR, immunoprecipitation and Western blot analysis. In this study we have analyzed the mutation and expression data of The Cancer Genome Atlas (TCGA) database and found that CDK12 is highly expressed in lung cancer tissues. Clinical correlation analysis showed that high expression of CDK12 in NSCLC reduces patient survival, but its high expression is only related to early tumor progression and has no significant correlation with late tumor progression and metastasis. Furthermore, we present evidence that CDK12 depletion in lung cancer cell lines not only leads to the inhibition of cell growth and induces apoptosis but also inhibits tumor growth of NSCLC cells in vivo. CDK12 positively regulates the expression of the oncogene TBK1 in lung cancer cells. These results revealed that CDK12 affects the progression of non-small cell lung cancer through positive regulation of TBK1 expression, suggesting that CDK12 might be a potential molecular target for the treatment of non-small cell lung cancer.
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Affiliation(s)
- Xiaoli Liu
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, No. 688, Hongqu Road, Shanghai, 200032, China
| | - Yangdong Liu
- Department of Hepatobiliary Surgery, Tai'an Hospital of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine Affiliated Hospital, No.58 Dongyue Street, Tai'an City, Shandong Province, 271000, China
| | - Wenjun Chai
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, No. 688, Hongqu Road, Shanghai, 200032, China
| | - Mingxia Yan
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, No. 688, Hongqu Road, Shanghai, 200032, China
| | - Hui Li
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, No. 688, Hongqu Road, Shanghai, 200032, China
| | - Jing Li
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, No. 688, Hongqu Road, Shanghai, 200032, China
| | - Lei Sun
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, No. 688, Hongqu Road, Shanghai, 200032, China
| | - Yue Cao
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, No. 688, Hongqu Road, Shanghai, 200032, China
| | - Qian Liu
- Department of Respiratory Medicine, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
| | - Yuexi Sun
- Department of Emergency, Tongji Hospital of Tongji University, No.389 Xincun Road, Shanghai, 200065, China.
| | - Hongyu Pan
- Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, No. 688, Hongqu Road, Shanghai, 200032, China.
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Maity TK, Kim EY, Cultraro CM, Venugopalan A, Khare L, Poddutoori R, Marappan S, Syed SD, Telford WG, Samajdar S, Ramachandra M, Guha U. Novel CDK12/13 Inhibitors AU-15506 and AU-16770 Are Potent Anti-Cancer Agents in EGFR Mutant Lung Adenocarcinoma with and without Osimertinib Resistance. Cancers (Basel) 2023; 15:cancers15082263. [PMID: 37190191 DOI: 10.3390/cancers15082263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Osimertinib is a third-generation epidermal growth factor receptor and tyrosine kinase inhibitor (EGFR-TKI) approved for the treatment of lung adenocarcinoma patients harboring EGFR mutations. However, acquired resistance to this targeted therapy is inevitable, leading to disease relapse within a few years. Therefore, understanding the molecular mechanisms of osimertinib resistance and identifying novel targets to overcome such resistance are unmet needs of cancer patients. Here, we investigated the efficacy of two novel CDK12/13 inhibitors, AU-15506 and AU-16770, in osimertinib-resistant EGFR mutant lung adenocarcinoma cells in culture and xenograft models in vivo. We demonstrate that these drugs, either alone or in combination with osimertinib, are potent inhibitors of osimertinib-resistant as well as -sensitive lung adenocarcinoma cells in culture. Interestingly, only the CDK12/13 inhibitor in combination with osimertinib, although not as monotherapy, suppresses the growth of resistant tumors in xenograft models in vivo. Taken together, the results of this study suggest that inhibition of CDK12/13 in combination with osimertinib has the potential to overcome osimertinib resistance in EGFR mutant lung adenocarcinoma patients.
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Affiliation(s)
- Tapan K Maity
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Eun Young Kim
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - Leena Khare
- Aurigene Discovery Technologies Ltd., Bangalore 560100, India
| | | | | | - Samiulla D Syed
- Aurigene Discovery Technologies Ltd., Bangalore 560100, India
| | - William G Telford
- Experimental Transplantation & Immunotherapy Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - Udayan Guha
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
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4
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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5
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Aragoneses-Cazorla G, Machuca A, Buendia-Nacarino MP, Anunciação DS, Garcia-Calvo E, Luque-Garcia JL. Super-SILAC Quantitative Proteome Profiling of Zebrafish Larvae. Methods Mol Biol 2023; 2603:199-207. [PMID: 36370281 DOI: 10.1007/978-1-0716-2863-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The super-SILAC approach enables the quantitative proteome profiling of highly complex samples such as biological tissues or whole organisms. In this approach, a super-SILAC mix consisting of heavy isotope-labeled cells representative of the tissue or organism to be analyzed is mixed with the unlabeled samples of interest, such that the labeled proteins act as a spike-in standard, thus allowing the relative quantification of proteins between the samples of interest. In this chapter, we thoroughly describe the protocol to carry out the super-SILAC approach using a common in vivo model such as zebrafish larvae.
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Affiliation(s)
| | - Andres Machuca
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain
| | - M Pilar Buendia-Nacarino
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain
| | - Daniela S Anunciação
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Estefania Garcia-Calvo
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain.
| | - Jose L Luque-Garcia
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain.
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6
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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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7
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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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8
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Alterations in HLA Class I-Presented Immunopeptidome and Class I-Interactome upon Osimertinib Resistance in EGFR Mutant Lung Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13194977. [PMID: 34638461 PMCID: PMC8507780 DOI: 10.3390/cancers13194977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/02/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary We sought to identify molecular mechanisms of lower efficacy of immunotherapy in epidermal growth factor receptor (EGFR) mutant lung adenocarcinoma and the differences in those mechanisms with the emergence of tyrosine kinase inhibitor (TKI)-resistance. To this end, we conducted affinity purification and quantitative mass spectrometry-based proteomic profiling of human leukocyte antigen (HLA) Class I-presented immunopeptides and Class I-interacting proteins. This large-scale dataset revealed that the Class I-presented immunopeptidome was suppressed in two third-generation EGFR TKI, osimertinib-resistant lung adenocarcinoma cell lines compared to their isogenic TKI-sensitive counterparts. The whole-cell proteomic profiling show that antigen presentation complex proteins and immunoproteasome were downregulated upon EGFR TKI resistance. Furthermore, HLA class I-interactome profiling demonstrated altered interaction with key apoptosis and autophagy pathway proteins. In summary, our comprehensive multi-proteomic characterization in antigen presentation machinery provides potentially novel evidence of poor immune response in osimertinib-resistant lung adenocarcinoma. Abstract Immune checkpoint inhibitor (ICI) therapy has been a paradigm shift in the treatment of cancer. ICI therapy results in durable responses and survival benefit for a large number of tumor types. Osimertinib, a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) has shown great efficacy treating EGFR mutant lung cancers; however, all patients eventually develop resistance. ICI therapy has not benefitted EGFR mutant lung cancer. Herein, we employed stable isotope labeling by amino acids in cell culture (SILAC) quantitative mass spectrometry-based proteomics to investigate potential immune escape molecular mechanisms in osimertinib resistant EGFR mutant lung adenocarcinoma by interrogating the alterations in the human leukocyte antigen (HLA) Class I-presented immunopeptidome, Class I-interactome, and the whole cell proteome between isogenic osimertinib-sensitive and -resistant human lung adenocarcinoma cells. Our study demonstrates an overall reduction in HLA class I-presented immunopeptidome and downregulation of antigen presentation core complex (e.g., TAP1 and ERAP1/2) and immunoproteasome in osimertinib resistant lung adenocarcinoma cells. Several key components in autophagy pathway are differentially altered. S100 proteins and SLC3A2 may play critical roles in reduced antigen presentation. Our dataset also includes ~1000 novel HLA class I interaction partners and hundreds of Class I-presented immunopeptides in EGFR mutant lung adenocarcinoma. This large-scale unbiased proteomics study provides novel insights and potential mechanisms of immune evasion of EGFR mutant lung adenocarcinoma.
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Yan F, Zhang X, Tan R, Li M, Xiao Z, Wang H, Zhang Z, Ma Z, Liu Z. Autophagic flux in cancer cells at the invasive front in the tumor-stroma border. Aging (Albany NY) 2021; 13:20229-20245. [PMID: 34483138 PMCID: PMC8436923 DOI: 10.18632/aging.203406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/02/2021] [Indexed: 12/28/2022]
Abstract
Cancer cells at the invasive front directly interact with stromal tissue that provides a microenvironment with mechanical, nutrient, and oxygen supply characteristics distinct from those of intratumoral tissues. It has long been known that cancer cells at the invasive front and cancer cells inside the tumor body exhibit highly differentiated functions and behaviors. However, it is unknown whether cancer cells at different locations exhibit a variety of autophagic flux, an important catabolic process to maintain cellular homeostasis in response to environmental changes. Here, using transmission electron microscopy (TEM), we found that invading cancer cells at the invasive front, which show mesenchymal transcriptomic traits, exhibit higher autophagic flux than cancer cells inside the tumor body in human primary non-small cell lung cancer (NSCLC) tissues. This autophagic feature was further confirmed by a live cell autophagic flux monitoring system combined with a 3D organotypic invasion coculture system. Additionally, the increased autophagic flux endows cancer cells with invasive behavior and positively correlates with the advanced tumor stages and the reduced survival period of lung cancer patients. These findings expand the understanding of autophagic dynamics during cancer invasion.
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Affiliation(s)
- Fei Yan
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Xuexi Zhang
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Rongying Tan
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Mingchen Li
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Zengtuan Xiao
- Department of Lung Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Hao Wang
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Zhenfa Zhang
- Department of Lung Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhenyi Ma
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
| | - Zhe Liu
- Department of Immunology, Biochemistry and Molecular Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, State Key Laboratory of Experimental Hematology, Tianjin Medical University, Tianjin, China
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10
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Qi YA, Maity TK, Cultraro CM, Misra V, Zhang X, Ade C, Gao S, Milewski D, Nguyen KD, Ebrahimabadi MH, Hanada KI, Khan J, Sahinalp C, Yang JC, Guha U. Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma. Mol Cell Proteomics 2021; 20:100136. [PMID: 34391887 PMCID: PMC8724932 DOI: 10.1016/j.mcpro.2021.100136] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/30/2022] Open
Abstract
Immune checkpoint inhibitors and adoptive lymphocyte transfer–based therapies have shown great therapeutic potential in cancers with high tumor mutational burden (TMB), such as melanoma, but not in cancers with low TMB, such as mutant epidermal growth factor receptor (EGFR)–driven lung adenocarcinoma. Precision immunotherapy is an unmet need for most cancers, particularly for cancers that respond inadequately to immune checkpoint inhibitors. Here, we employed large-scale MS-based proteogenomic profiling to identify potential immunogenic human leukocyte antigen (HLA) class I-presented peptides in melanoma and EGFR-mutant lung adenocarcinoma. Similar numbers of peptides were identified from both tumor types. Cell line and patient-specific databases (DBs) were constructed using variants identified from whole-exome sequencing. A de novo search algorithm was used to interrogate the HLA class I immunopeptidome MS data. We identified 12 variant peptides and several classes of tumor-associated antigen-derived peptides. We constructed a cancer germ line (CG) antigen DB with 285 antigens. This allowed us to identify 40 class I-presented CG antigen–derived peptides. The class I immunopeptidome comprised more than 1000 post-translationally modified (PTM) peptides representing 58 different PTMs, underscoring the critical role PTMs may play in HLA binding. Finally, leveraging de novo search algorithm and an annotated long noncoding RNA (lncRNA) DB, we developed a novel lncRNA-encoded peptide discovery pipeline to identify 44 lncRNA-derived peptides that are presented by class I. We validated tandem MS spectra of select variant, CG antigen, and lncRNA-derived peptides using synthetic peptides and performed HLA class I-binding assays to demonstrate binding to class I proteins. In summary, we provide direct evidence of HLA class I presentation of a large number of variant and tumor-associated peptides in both low and high TMB cancer. These results can potentially be useful for precision immunotherapies, such as vaccine or adoptive cell therapies in melanoma and EGFR-mutant lung cancers. Proteogenomics identified ∼35,000 class I-presented peptides. CG antigen and PTM peptides identified in melanoma and lung cancer. De novo search identified variant and lncRNA-derived peptides. A new strategy to identify class I-presented lncRNA-derived peptides developed.
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Affiliation(s)
- Yue A Qi
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA.
| | - Tapan K Maity
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Constance M Cultraro
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Vikram Misra
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Xu Zhang
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Catherine Ade
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Shaojian Gao
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - David Milewski
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Khoa D Nguyen
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Mohammad H Ebrahimabadi
- Cancer Data Science Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA; Department of Computer Science, Indiana University, Bloomington, Indiana, USA
| | - Ken-Ichi Hanada
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Cenk Sahinalp
- Cancer Data Science Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - James C Yang
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA; Bristol-Myers Squibb, Lawrenceville, New Jersey, USA.
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11
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Liu H, Liu K, Dong Z. Targeting CDK12 for Cancer Therapy: Function, Mechanism, and Drug Discovery. Cancer Res 2020; 81:18-26. [PMID: 32958547 DOI: 10.1158/0008-5472.can-20-2245] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/23/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) is a member of the CDK family of proteins (CDK) and is critical for cancer development. Years of study into CDK12 have generated much information regarding the intricacy of its function and mechanism as well as inhibitors against it for oncological research. However, there remains a lack of understanding regarding the role of CDK12 in carcinogenesis and cancer prevention. An exhaustive comprehension of CDK12 will highly stimulate the development of new strategies for treating and preventing cancer. Here, we review the literature of CDK12, with a focus on its function, its role in signaling, and how to use it as a target for discovery of novel drugs for cancer prevention and therapy.
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Affiliation(s)
- Hui Liu
- Department of Pathophysiology, School of Basic Medical Sciences, The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan, China.,China-US (Henan) Hormel Cancer Institute, Jinshui District, Zhengzhou, Henan, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan, China. .,China-US (Henan) Hormel Cancer Institute, Jinshui District, Zhengzhou, Henan, China
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12
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He Y, Mohamedali A, Huang C, Baker MS, Nice EC. Oncoproteomics: Current status and future opportunities. Clin Chim Acta 2019; 495:611-624. [PMID: 31176645 DOI: 10.1016/j.cca.2019.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
Oncoproteomics is the systematic study of cancer samples using omics technologies to detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already opening new avenues for the identification of novel biomarkers for early clinical stage cancer detection, targeted molecular therapies, disease monitoring, and drug development. Such information will lead to new understandings of cancer biology and impact dramatically on the future care of cancer patients. In this review, we will summarize the advantages and limitations of the key technologies used in (onco)proteogenomics, (the Omics Pipeline), explain how they can assist us in understanding the biology behind the overarching "Hallmarks of Cancer", discuss how they can advance the development of precision/personalised medicine and the future directions in the field.
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Affiliation(s)
- Yujia He
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia
| | - Canhua Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia.
| | - Edouard C Nice
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
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