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Chen R, Chen H, Hu C. HADHA promotes glioma progression by accelerating MDM2-mediated p53 ubiquitination. Cancer Gene Ther 2024:10.1038/s41417-024-00801-8. [PMID: 39039194 DOI: 10.1038/s41417-024-00801-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 04/09/2024] [Accepted: 06/17/2024] [Indexed: 07/24/2024]
Abstract
Glioma represents a notoriously aggressive and malignant tumor that targets the central nervous system, with a poor prognosis for patients. In this research, we set out to examine the role of hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha (HADHA) in glioma, its clinical significance, as well as its potential biological mechanisms. In this study, we used immunohistochemistry staining to assess the expression level of HADHA in glioma tissues. We also evaluated the correlation between HADHA expression and patient survival using the Kaplan-Meier method. To determine the role of HADHA in glioma cells, we conducted loss-of-function assays in vitro and in vivo. Additionally, we utilized co-immunoprecipitation and protein stability assays to investigate the potential mechanisms involving HADHA, MDM2, and p53 in glioma. Our research findings indicate that gliomas exhibit high levels of HADHA. Clinically, high expression of HADHA suggests an increased risk of malignant tumors, recurrence, and reduced survival rates. Functionally, knocking down HADHA can lead to decreased proliferation, enhanced apoptosis, and inhibited migration of glioma cells. Mechanistically, HADHA accelerates MDM2-mediated p53 ubiquitination through interaction with MDM2. Consistently, MDM2 knockdown or overexpression of p53 can attenuate the promoting effect of HADHA overexpression on the malignant progression of glioma. We have discovered a novel role of HADHA in promoting MDM2-mediated p53 ubiquitination, which contributes to the progression of glioma. This finding provides a new perspective to understand the pathogenesis of glioma and offers a potential target for developing innovative therapeutic strategies.
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Affiliation(s)
- Rudong Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan City, Hubei province, 430030, China
| | - Hao Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan City, Hubei province, 430030, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430030, China
| | - Changchen Hu
- Department of Neurosurgery, Shanxi provincial people's Hospital, Shanxi Medical University, Taiyuan City, Shanxi province, 030012, China.
- Department of Neurourgery, Shuozhou People's hospital, Shuozhou, China.
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2
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Liu Y, Xiong Y. HADHA promotes ovarian cancer outgrowth via up-regulating CDK1. Cancer Cell Int 2023; 23:283. [PMID: 37986001 PMCID: PMC10658966 DOI: 10.1186/s12935-023-03120-4] [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: 03/24/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Ovarian cancer, a prevalent cause of cancer-related mortality among gynecological cancers, still lacks a clear understanding of its pathogenesis. In this study, our objective was to investigate the functional roles and pathogenic mechanisms of HADHA in ovarian cancer. METHODS We utilized an ovarian cancer tissue microarray and three ovarian cancer cell lines (HO-8910, A2780, and SK-OV-3) for our analysis. Lentiviral-mediated short hairpin RNA (shRNA) was employed to interfere with HADHA expression in ovarian cancer cells. Various cellular events associated with tumor development were assessed using techniques such as Celigo cell counting assay, wound healing assay, Transwell assay, and flow cytometry analysis. Additionally, xenograft tumor models were developed to visualize the impacts of HADHA/CDK1 on ovarian cancer progression. RESULTS Our data revealed significant HADHA overexpression in both ovarian cancer tissues and cell lines. Patients with elevated HADHA levels tended to experience poor survival outcomes. Moreover, HADHA upregulation correlated with several pathological parameters, including pathological stage, tumor size, tumor infiltrate, metastasis, and recurrence. Loss-of-function experiments targeting HADHA demonstrated that its suppression in ovarian cancer cells hindered cell growth and migration, while promoting apoptosis. To elucidate the underlying mechanism by which HADHA regulates ovarian cancer, we identified CDK1 as a target of HADHA. HADHA upregulated CDK1 expression by inhibiting its ubiquitination-dependent proteasomal degradation. Significantly, the overexpression of CDK1 reversed the impaired cell development caused by HADHA depletion, both in vitro and in vivo. CONCLUSION Our study highlights the involvement of HADHA in ovarian cancer tumorigenesis and suggests its potential as a promising prognostic marker in ovarian cancer. Through its regulation of CDK1, HADHA influences critical cellular processes in ovarian cancer, providing insights into its pathogenic mechanism.
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Affiliation(s)
- Yinglan Liu
- Department of Obsdetrics and Gynecology, First Affiliated Hospital of Harbin Medical University, No.23, Youzheng Road, Harbin city, 150001, Heilongjiang Province, China
| | - Ying Xiong
- Department of Gynecology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, No.651, Dongfengdong Road, Guangzhou, 5100160, Guangdong Province, China.
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Szrok-Jurga S, Czumaj A, Turyn J, Hebanowska A, Swierczynski J, Sledzinski T, Stelmanska E. The Physiological and Pathological Role of Acyl-CoA Oxidation. Int J Mol Sci 2023; 24:14857. [PMID: 37834305 PMCID: PMC10573383 DOI: 10.3390/ijms241914857] [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: 08/25/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Fatty acid metabolism, including β-oxidation (βOX), plays an important role in human physiology and pathology. βOX is an essential process in the energy metabolism of most human cells. Moreover, βOX is also the source of acetyl-CoA, the substrate for (a) ketone bodies synthesis, (b) cholesterol synthesis, (c) phase II detoxication, (d) protein acetylation, and (d) the synthesis of many other compounds, including N-acetylglutamate-an important regulator of urea synthesis. This review describes the current knowledge on the importance of the mitochondrial and peroxisomal βOX in various organs, including the liver, heart, kidney, lung, gastrointestinal tract, peripheral white blood cells, and other cells. In addition, the diseases associated with a disturbance of fatty acid oxidation (FAO) in the liver, heart, kidney, lung, alimentary tract, and other organs or cells are presented. Special attention was paid to abnormalities of FAO in cancer cells and the diseases caused by mutations in gene-encoding enzymes involved in FAO. Finally, issues related to α- and ω- fatty acid oxidation are discussed.
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Affiliation(s)
- Sylwia Szrok-Jurga
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Aleksandra Czumaj
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Jacek Turyn
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Areta Hebanowska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Julian Swierczynski
- Institue of Nursing and Medical Rescue, State University of Applied Sciences in Koszalin, 75-582 Koszalin, Poland;
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Ewa Stelmanska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
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Wang X, Song H, Liang J, Jia Y, Zhang Y. Abnormal expression of HADH, an enzyme of fatty acid oxidation, affects tumor development and prognosis (Review). Mol Med Rep 2022; 26:355. [PMID: 36239258 PMCID: PMC9607826 DOI: 10.3892/mmr.2022.12871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Tumor occurrence and progression are closely associated with abnormal energy metabolism and energy metabolism associated with glucose, proteins and lipids. The reprogramming of energy metabolism is one of the hallmarks of cancer. As a form of energy metabolism, fatty acid metabolism includes fatty acid uptake, de novo synthesis and β‑oxidation. In recent years, the role of abnormal fatty acid β‑oxidation in tumors has gradually been recognized. Mitochondrial trifunctional protein (MTP) serves an important role in fatty acid β‑oxidation and HADH (two subtypes: α subunit, HADHA and β subunit, HADHB) are important subunits of MTP. HADH participates in the steps of 2, 3 and 4 fatty acid β‑oxidation. However, there is no review summarizing the specific role of HADH in tumors. Therefore, the present study focused on HADH as the main indicator to explore the changes in fatty acid β‑oxidation in several types of tumors. The present review summarized the changes in HADH in 11 organs (cerebrum, oral cavity, esophagus, liver, pancreas, stomach, colorectum, lymph, lung, breast, kidney), the effect of up‑ and downregulation and the relationship of HADH with prognosis. In summary, HADH can be either a suppressor or a promoter depending on where the tumor is located, which is closely associated with prognostic assessment. HADHA and HADHB have similar prognostic roles in known and comparable tumors.
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Affiliation(s)
- Xiaoqing Wang
- Department of Pediatric Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China
- Post-doctoral Research Station of Clinical Medicine, Liaocheng People's Hospital, Jinan, Shandong 252004, P.R. China
| | - Honghao Song
- Department of Pediatric Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Junyu Liang
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Yang Jia
- Post-doctoral Research Station of Clinical Medicine, Liaocheng People's Hospital, Jinan, Shandong 252004, P.R. China
- Department of Thoracic Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Yongfei Zhang
- Department of Dermatology, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250021, P.R. China
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Chen M, Wang L, Li M, Budai MM, Wang J. Mitochondrion-Mediated Cell Death through Erk1-Alox5 Independent of Caspase-9 Signaling. Cells 2022; 11:cells11193053. [PMID: 36231015 PMCID: PMC9564198 DOI: 10.3390/cells11193053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/22/2022] [Accepted: 09/25/2022] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial disruption leads to the release of cytochrome c to activate caspase-9 and the downstream caspase cascade for the execution of apoptosis. However, cell death can proceed efficiently in the absence of caspase-9 following mitochondrial disruption, suggesting the existence of caspase-9-independent cell death mechanisms. Through a genome-wide siRNA library screening, we identified a network of genes that mediate caspase-9-independent cell death, through ROS production and Alox5-dependent membrane lipid peroxidation. Erk1-dependent phosphorylation of Alox5 is critical for targeting Alox5 to the nuclear membrane to mediate lipid peroxidation, resulting in nuclear translocation of cytolytic molecules to induce DNA damage and cell death. Consistently, double knockouts of caspase-9 and Alox5 in mice, but not deletion of either gene alone, led to significant T cell expansion with inhibited cell death, indicating that caspase-9- and Alox5-dependent pathways function in parallel to regulate T cell death in vivo. This unbiased whole-genome screening reveals an Erk1-Alox5-mediated pathway that promotes membrane lipid peroxidation and nuclear translocation of cytolytic molecules, leading to the execution of cell death in parallel to the caspase-9 signaling cascade.
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Affiliation(s)
- Min Chen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (M.C.); (J.W.)
| | - Lei Wang
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Min Li
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Marietta M. Budai
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Jin Wang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
- Correspondence: (M.C.); (J.W.)
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Mazorra-Carrillo JL, De León-Rodríguez A, Huerta-Ocampo JA, Velarde-Salcedo AJ, González de Mejía E, Barba de la Rosa AP. Proteomic analysis of chemically transformed NIH-3T3 cells reveals novel mechanisms of action of amaranth lunasin-like peptide. Food Res Int 2022; 157:111374. [DOI: 10.1016/j.foodres.2022.111374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/02/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
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Wu X, Feng R, Wang X, Guo F, Liu W. Roles of hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha, a lipid metabolism enzyme, in Wilms tumor patients. J Cancer Res Ther 2021; 17:1281-1285. [PMID: 34850779 DOI: 10.4103/jcrt.jcrt_1388_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Objectives Wilms tumor is a common pediatric malignant tumor that accounts for approximately 95% of kidney tumors in children. The role of lipid metabolism in tumors has attracted increased attention in recent years. We examined the role of hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha (HADHA), a lipid metabolism enzyme, in the pathogenesis of Wilms tumor. Materials and Methods In a previous study, we screened Wilms tumors and adjacent normal tissues for differentially expressed proteins by mass spectrometry and verified the results by western blot analysis. The Oncomine database and quantitative reverse transcription-polymerase chain reaction were used to verify the expression of HADHA at the genetic level. Immunohistochemistry and immunofluorescence were also used to validate the differential expression of the HADHA protein. The relationship between histopathological typing, clinical pathology, and HADHA expression was analyzed in 65 paraffin-embedded specimens from pediatric Wilms tumor patients. Kaplan-Meier survival curves were used to analyze the relationship between the expression of HADHA and patient prognosis. Results HADHA was expressed at low levels in Wilms tumor tissue compared with the corresponding normal tissue. The expression of HADHA was closely associated with histopathological typing (P = 0.030). The prognostic analysis of 65 children with Wilms tumor showed that high expression of HADHA was closely associated with poor prognosis (P = 0.046). Conclusions HADHA expression is downregulated in Wilms tumor tissues, but high expression in tumor tissues is associated with clinical stage and the prognosis of children with this tumor.
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Affiliation(s)
- Xiangyu Wu
- Department of Pediatric Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Run Feng
- Department of Pediatric Surgery, Zibo Municipal Hospital, Zibo, China
| | - Xiaoqing Wang
- Department of Pediatric Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Feng Guo
- Department of Pediatric Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wei Liu
- Department of Pediatric Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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Huang YW, Lin CW, Pan P, Echeveste CE, Dong A, Oshima K, Yearsley M, Yu J, Wang LS. Dysregulated Free Fatty Acid Receptor 2 Exacerbates Colonic Adenoma Formation in Apc Min/+ Mice: Relation to Metabolism and Gut Microbiota Composition. J Cancer Prev 2021; 26:32-40. [PMID: 33842404 PMCID: PMC8020170 DOI: 10.15430/jcp.2021.26.1.32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Free fatty acid receptor 2 (FFAR2) has been reported as a tumor suppressor in colon cancer development. The current study investigated the effects of FFAR2 signaling on energy metabolism and gut microbiota profiling in a colorectal cancer mouse model (Apc Min/+ ). Ffar2 deficiency promoted colonic polyp development and enhanced fatty acid oxidation and bile acid metabolism. Gut microbiome sequencing analysis showed distinct clustering among wild-type, Apc Min/+ , and Apc Min/+ -Ffar2 -/- mice. The relative abundance of Flavobacteriaceae and Verrucomicrobiaceae was significantly increased in the Apc Min/+ -Ffar2 -/- mice compared to the Apc Min/+ mice. In addition, knocking-down FFAR2 in the human colon cancer cell lines (SW480 and HT29) resulted in increased expression of several key enzymes in fatty acid oxidation, such as carnitine palmitoyltransferase 2, acyl-CoA dehydrogenase, long-chain acyl-CoA dehydrogenase, C-2 to C-3 short chain, and hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase, alpha subunit. Collectively, these results demonstrated that Ffar2 deficiency significantly altered profiles of fatty acid metabolites and gut microbiome, which might promote colorectal cancer development.
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Affiliation(s)
- Yi-Wen Huang
- Department of Obstetrics & Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Pan Pan
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Carla Elena Echeveste
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Athena Dong
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kiyoko Oshima
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Martha Yearsley
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, Comprehensive Cancer Center, City of Hope National Medical Center, Duarte, CA, USA
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
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Screening and identification of potential prognostic biomarkers in bladder urothelial carcinoma: Evidence from bioinformatics analysis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Le-Tian Z, Cheng-Zhang H, Xuan Z, Zhang Q, Zhen-Gui Y, Qing-Qing W, Sheng-Xuan W, Zhong-Jin X, Ran-Ran L, Ting-Jun L, Zhong-Qu S, Zhong-Hua W, Ke-Rong S. Protein acetylation in mitochondria plays critical functions in the pathogenesis of fatty liver disease. BMC Genomics 2020; 21:435. [PMID: 32586350 PMCID: PMC7318365 DOI: 10.1186/s12864-020-06837-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fatty liver is a high incidence of perinatal disease in dairy cows caused by negative energy balance, which seriously threatens the postpartum health and milk production. It has been reported that lysine acetylation plays an important role in substance and energy metabolism. Predictably, most metabolic processes in the liver, as a vital metabolic organ, are subjected to acetylation. Comparative acetylome study were used to quantify the hepatic tissues from the severe fatty liver group and normal group. Combined with bioinformatics analysis, this study provides new insights for the role of acetylation modification in fatty liver disease of dairy cows. RESULTS We identified 1841 differential acetylation sites on 665 proteins. Among of them, 1072 sites on 393 proteins were quantified. Functional enrichment analysis shows that higher acetylated proteins are significantly enriched in energy metabolic pathways, while lower acetylated proteins are significantly enriched in pathways related to immune response, such as drug metabolism and cancer. Among significantly acetylated proteins, many mitochondrial proteins were identified to be interacting with multiple proteins and involving in lipid metabolism. Furthermore, this study identified potential important proteins, such as HADHA, ACAT1, and EHHADH, which may be important regulatory factors through modification of acetylation in the development of fatty liver disease in dairy cows and possible therapeutic targets for NAFLD in human beings. CONCLUSION This study provided a comprehensive acetylome profile of fatty liver of dairy cows, and revealed important biological pathways associated with protein acetylation occurred in mitochondria, which were involved in the regulation of the pathogenesis of fatty liver disease. Furthermore, potential important proteins, such as HADHA, ACAT1, EHHADH, were predicted to be essential regulators during the pathogenesis of fatty liver disease. The work would contribute to the understanding the pathogenesis of NAFLD, and inspire in the development of new therapeutic strategies for NAFLD.
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Affiliation(s)
- Zhang Le-Tian
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Hu Cheng-Zhang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Zhang Xuan
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Qin Zhang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Yan Zhen-Gui
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Wei Qing-Qing
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Wang Sheng-Xuan
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Xu Zhong-Jin
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Li Ran-Ran
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Liu Ting-Jun
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Su Zhong-Qu
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Wang Zhong-Hua
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Shi Ke-Rong
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China.
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Pechalrieu D, Assemat F, Halby L, Marcellin M, Yan P, Chaoui K, Sharma S, Chiosis G, Burlet-Schiltz O, Arimondo PB, Lopez M. Bisubstrate-Type Chemical Probes Identify GRP94 as a Potential Target of Cytosine-Containing Adenosine Analogs. ACS Chem Biol 2020; 15:952-961. [PMID: 32191434 DOI: 10.1021/acschembio.9b00965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We synthesized affinity-based chemical probes of cytosine-adenosine bisubstrate analogs and identified several potential targets by proteomic analysis. The validation of the proteomic analysis identified the chemical probe as a specific inhibitor of glucose-regulated protein 94 (GRP94), a potential drug target for several types of cancers. Therefore, as a result of the use of bisubstrate-type chemical probes and a chemical-biology methodology, this work opens the way to the development of a new family of GRP94 inhibitors that could potentially be of therapeutic interest.
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Affiliation(s)
- Dany Pechalrieu
- ETaC, CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
| | - Fanny Assemat
- ETaC, CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
| | - Ludovic Halby
- ETaC, CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
- EpiCBio, Epigenetic Chemical Biology, Department Structural Biology and Chemistry, Institut Pasteur, CNRS UMR no. 3523, 28 rue du Dr Roux, 75015 Paris, France
| | - Marlene Marcellin
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pengrong Yan
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Karima Chaoui
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sahil Sharma
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Gabriela Chiosis
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Paola B. Arimondo
- ETaC, CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
- EpiCBio, Epigenetic Chemical Biology, Department Structural Biology and Chemistry, Institut Pasteur, CNRS UMR no. 3523, 28 rue du Dr Roux, 75015 Paris, France
| | - Marie Lopez
- ETaC, CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Univ Montpellier, ENSCM UMR 5247, 240 Avenue du Prof. E. Jeanbrau, 34296 Montpellier Cedex 5, France
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Liu S, Liu X, Wu F, Zhang X, Zhang H, Gao D, Bi D, Qu H, Ge J, Xu Y, Zhao Z. HADHA overexpression disrupts lipid metabolism and inhibits tumor growth in clear cell renal cell carcinoma. Exp Cell Res 2019; 384:111558. [DOI: 10.1016/j.yexcr.2019.111558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
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Shen C, Song YH, Xie Y, Wang X, Wang Y, Wang C, Liu S, Xue SL, Li Y, Liu B, Tang Z, Chen W, Song J, Amin HM, Zhou J. Downregulation of HADH promotes gastric cancer progression via Akt signaling pathway. Oncotarget 2017; 8:76279-76289. [PMID: 29100311 PMCID: PMC5652705 DOI: 10.18632/oncotarget.19348] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 06/30/2017] [Indexed: 01/23/2023] Open
Abstract
HADH is a key enzyme in fatty acid oxidation. The aim of this study was to identify the role of HADH in gastric cancer. We analyzed the expression of HADH in 102 pairs of gastric cancer samples. Western blot analysis revealed that HADH was decreased in stage I/II gastric cancer samples compared to matched adjacent normal gastric tissue, and its expression was further decreased in stage III/IV samples. Importantly, the reduced expression of HADH was associated with increased expression of p-Akt and reduced expression of PTEN in the gastric carcinoma tumor samples. To determine the significance of HADH downregulation in gastric cancer progression, we tested the impact of HADH knockdown or overexpression on the migration and invasion of the gastric cancer cells using a transwell assay. Knockdown of HADH significantly promoted gastric cancer cell migration and invasion, which was associated with increased expression of p-Akt. The PI3K inhibitor LY294002 inhibited HADH shRNA induced migration/invasion, and abolished the upregulation of p-Akt. By contrast, HADH overexpression inhibited the migration and invasion of MKN45 cells. Herein, for the first time, we demonstrate that downregulation of HADH promotes gastric cancer progression via activation of Akt signaling pathway.
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Affiliation(s)
- Congcong Shen
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Yufeng Xie
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, P. R. China
| | - Xiaoxiao Wang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Yunliang Wang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, P. R. China
| | - Chao Wang
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, P. R. China
| | - Songbai Liu
- Suzhou Vocational Health College, Suzhou Key Laboratory of Biotechnology for Laboratory Medicine, Suzhou, P. R. China
| | - Sheng-Li Xue
- Department of Hematology, The First Affiliated Hospital of Soochow University, Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Yangxin Li
- Department of Cardiovascular Surgery & Institute of Cardiovascular Science, First Affiliated Hospital of Soochow University, Suzhou, P. R. China
| | - Bin Liu
- Department of Cardiology, Second Hospital of Jilin University, Changchun, P. R. China
| | - Zaixiang Tang
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China
| | - Weichang Chen
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, P. R. China
| | - Jenny Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Hesham M Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jin Zhou
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, P. R. China
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14
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Tremblay MP, Armero VES, Allaire A, Boudreault S, Martenon-Brodeur C, Durand M, Lapointe E, Thibault P, Tremblay-Létourneau M, Perreault JP, Scott MS, Bisaillon M. Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma. BMC Genomics 2016; 17:683. [PMID: 27565572 PMCID: PMC5002109 DOI: 10.1186/s12864-016-3029-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/20/2016] [Indexed: 12/13/2022] Open
Abstract
Background Dysregulations in alternative splicing (AS) patterns have been associated with many human diseases including cancer. In the present study, alterations to the global RNA splicing landscape of cellular genes were investigated in a large-scale screen from 377 liver tissue samples using high-throughput RNA sequencing data. Results Our study identifies modifications in the AS patterns of transcripts encoded by more than 2500 genes such as tumor suppressor genes, transcription factors, and kinases. These findings provide insights into the molecular differences between various types of hepatocellular carcinoma (HCC). Our analysis allowed the identification of 761 unique transcripts for which AS is misregulated in HBV-associated HCC, while 68 are unique to HCV-associated HCC, 54 to HBV&HCV-associated HCC, and 299 to virus-free HCC. Moreover, we demonstrate that the expression pattern of the RNA splicing factor hnRNPC in HCC tissues significantly correlates with patient survival. We also show that the expression of the HBx protein from HBV leads to modifications in the AS profiles of cellular genes. Finally, using RNA interference and a reverse transcription-PCR screening platform, we examined the implications of cellular proteins involved in the splicing of transcripts involved in apoptosis and demonstrate the potential contribution of these proteins in AS control. Conclusions This study provides the first comprehensive portrait of global changes in the RNA splicing signatures that occur in hepatocellular carcinoma. Moreover, these data allowed us to identify unique signatures of genes for which AS is misregulated in the different types of HCC. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3029-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie-Pier Tremblay
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Victoria E S Armero
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Andréa Allaire
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Simon Boudreault
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Camille Martenon-Brodeur
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Mathieu Durand
- Plateforme RNomique, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Elvy Lapointe
- Plateforme RNomique, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Philippe Thibault
- Plateforme RNomique, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Maude Tremblay-Létourneau
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Martin Bisaillon
- Département de biochimie, Pavillon de recherche appliquée sur le cancer, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada.
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15
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Zhao Z, Lu J, Han L, Wang X, Man Q, Liu S. Prognostic significance of two lipid metabolism enzymes, HADHA and ACAT2, in clear cell renal cell carcinoma. Tumour Biol 2016; 37:8121-30. [PMID: 26715271 DOI: 10.1007/s13277-015-4720-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 12/21/2015] [Indexed: 01/26/2023] Open
Abstract
Renal cell carcinoma (RCC) is one of the leading causes of cancer mortality in adults, but there is still no acknowledged biomarker for its prognostic evaluation. Our previous proteomic data had demonstrated the dysregulation of some lipid metabolism enzymes in clear cell RCC (ccRCC). In the present study, we elucidated the expression of two lipid metabolism enzymes, hydroxyl-coenzyme A dehydrogenase, alpha subunit (HADHA) and acetyl-coenzyme A acetyltransferase 2 (ACAT2), using Western blotting analysis, then assessed the prognostic potential of HADHA and ACAT2 using immunohistochemistry (IHC) on a tissue microarray of 145 ccRCC tissues. HADHA and ACAT2 were downregulated in ccRCC (P < 0.05); further IHC analysis revealed that HADHA expression was significantly associated with tumor grade, stage, size, metastasis, and cancer-specific survival (P = 0.004, P < 0.001, P < 0.001, P = 0.049, P < 0.001, respectively) and ACAT2 expression was significantly associated with tumor stage, size, and cancer-specific survival (P < 0.001, P = 0.001, P < 0.001, respectively). In addition, a strong correlation was found between HADHA and ACAT2 expression (R = 0.655, P < 0.001). Further univariate survival analysis demonstrated that high stage, big tumor size, metastasis, and HADHA and ACAT2 down-expression were associated with poorer prognosis on cancer-specific survival (P = 0.007, P = 0.005, P = 0.006, P < 0.001, P = 0.001, respectively), and multivariate analysis revealed that HADHA, stage, and metastasis were identified as independent prognostic factors for cancer-specific survival in patients with ccRCC (P = 0.018, P = 0.046, P = 0.001, respectively). Collectively, these findings indicated that HADHA could serve as a promising prognostic marker in ccRCC, which indicated lipid metabolism abnormality might be involved in ccRCC tumorigenesis.
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Affiliation(s)
- Zuohui Zhao
- Department of Pediatric Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jingshi Road, No. 16766, Jinan, Shandong, 250014, China
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jingwu Road, No. 324, Jinan, Shandong, 250021, China
| | - Jiaju Lu
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jingwu Road, No. 324, Jinan, Shandong, 250021, China
| | - Liping Han
- Department of Neurology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jingshi Road, No. 16766, Jinan, Shandong, 250014, China
| | - Xiaoqing Wang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jingwu Road, No. 324, Jinan, Shandong, 250021, China
| | - Quanzhan Man
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jingwu Road, No. 324, Jinan, Shandong, 250021, China
| | - Shuai Liu
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jingwu Road, No. 324, Jinan, Shandong, 250021, China.
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16
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Chen Y. Disease Comorbidity Network Guides the Detection of Molecular Evidence for the Link Between Colorectal Cancer and Obesity. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2015; 2015:201-6. [PMID: 26306270 PMCID: PMC4525229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Epidemiological studies suggested that obesity increases the risk of colorectal cancer (CRC). The genetic connection between CRC and obesity is multifactorial and inconclusive. In this study, we hypothesize that the study of shared comorbid diseases between CRC and obesity can offer unique insights into common genetic basis of these two diseases. We constructed a comorbidity network based on mining health data for millions of patients. We developed a novel approach and extracted the diseases that play critical roles in connecting obesity and CRC in the comorbidity network. Our approach was able to prioritize metabolic syndrome and diabetes, which are known to be associated with obesity and CRC through insulin resistance pathways. Interestingly, we found that osteoporosis was highly associated with the connection between obesity and CRC. Through gene expression meta-analysis, we identified novel genes shared among CRC, obesity and osteoporosis. Literature evidences support that these genes may contribute in explaining the genetic overlaps between obesity and CRC.
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17
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Kočevar N, Grazio SF, Komel R. Two-dimensional gel electrophoresis of gastric tissue in an alkaline pH range. Proteomics 2014; 14:311-21. [PMID: 24293252 DOI: 10.1002/pmic.201200574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 10/09/2013] [Accepted: 11/13/2013] [Indexed: 12/17/2022]
Abstract
2DE in combination with MS has facilitated the discovery of several proteins with altered abundance in gastric cancer. While acidic and wide pH ranges have been widely investigated, analysis in the alkaline pH range has not been specifically performed in gastric cancer to date. In the present study, we initially optimized the 2DE in alkaline pH range (pH 7-11) for gastric tissue samples. Using a modified lysis buffer, we analyzed pooled nontumor and tumor samples for proteins with altered abundance in gastric adenocarcinoma. We successfully identified 38 silver-stained spots as 24 different proteins. Four of these were chosen for investigation with immunoblotting on individual paired samples to determine whether the changes seen in 2DE represent the overall abundance of the protein or possibly only a single form. While mitochondrial trifunctional protein (MTP) subunits were decreased in 2DE gels, immunoblotting identified their overall abundance as being differently dysregulated: in the gastric tumor samples, the MTP-α subunit was decreased, and the MTP-β subunit was increased. On the other hand, heterogenous nuclear ribonucleoprotein M and galectin-4 were increased in the gastric tumor samples in both 2DE and immunoblotting.
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Affiliation(s)
- Nina Kočevar
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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18
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Kalender Atak Z, Gianfelici V, Hulselmans G, De Keersmaecker K, Devasia AG, Geerdens E, Mentens N, Chiaretti S, Durinck K, Uyttebroeck A, Vandenberghe P, Wlodarska I, Cloos J, Foà R, Speleman F, Cools J, Aerts S. Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. PLoS Genet 2013; 9:e1003997. [PMID: 24367274 PMCID: PMC3868543 DOI: 10.1371/journal.pgen.1003997] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/16/2013] [Indexed: 12/22/2022] Open
Abstract
RNA-seq is a promising technology to re-sequence protein coding genes for the identification of single nucleotide variants (SNV), while simultaneously obtaining information on structural variations and gene expression perturbations. We asked whether RNA-seq is suitable for the detection of driver mutations in T-cell acute lymphoblastic leukemia (T-ALL). These leukemias are caused by a combination of gene fusions, over-expression of transcription factors and cooperative point mutations in oncogenes and tumor suppressor genes. We analyzed 31 T-ALL patient samples and 18 T-ALL cell lines by high-coverage paired-end RNA-seq. First, we optimized the detection of SNVs in RNA-seq data by comparing the results with exome re-sequencing data. We identified known driver genes with recurrent protein altering variations, as well as several new candidates including H3F3A, PTK2B, and STAT5B. Next, we determined accurate gene expression levels from the RNA-seq data through normalizations and batch effect removal, and used these to classify patients into T-ALL subtypes. Finally, we detected gene fusions, of which several can explain the over-expression of key driver genes such as TLX1, PLAG1, LMO1, or NKX2-1; and others result in novel fusion transcripts encoding activated kinases (SSBP2-FER and TPM3-JAK2) or involving MLLT10. In conclusion, we present novel analysis pipelines for variant calling, variant filtering, and expression normalization on RNA-seq data, and successfully applied these for the detection of translocations, point mutations, INDELs, exon-skipping events, and expression perturbations in T-ALL. The quest for somatic mutations underlying oncogenic processes is a central theme in today's cancer research. High-throughput genomics approaches including amplicon re-sequencing, exome re-sequencing, full genome re-sequencing, and SNP arrays have contributed to cataloguing driver genes across cancer types. Thus far transcriptome sequencing by RNA-seq has been mainly used for the detection of fusion genes, while few studies have assessed its value for the combined detection of SNPs, INDELs, fusions, gene expression changes, and alternative transcript events. Here we apply RNA-seq to 49 T-ALL samples and perform a critical assessment of the bioinformatics pipelines and filters to identify each type of aberration. By comparing to exome re-sequencing, and by exploiting the catalogues of known cancer drivers, we identified many known and several novel driver genes in T-ALL. We also determined an optimal normalization strategy to obtain accurate gene expression levels and used these to identify over-expressed transcription factors that characterize different T-ALL subtypes. Finally, by PCR, cloning, and in vitro cellular assays we uncover new fusion genes that have consequences at the level of gene expression, oncogenic chimaeras, and tumor suppressor inactivation. In conclusion, we present the first RNA-seq data set across T-ALL patients and identify new driver events.
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Affiliation(s)
- Zeynep Kalender Atak
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Valentina Gianfelici
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, ‘Sapienza’ University of Rome, Rome, Italy
| | - Gert Hulselmans
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Kim De Keersmaecker
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Arun George Devasia
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Ellen Geerdens
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Nicole Mentens
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Sabina Chiaretti
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, ‘Sapienza’ University of Rome, Rome, Italy
| | - Kaat Durinck
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Anne Uyttebroeck
- Pediatric Hemato-Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Iwona Wlodarska
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Jacqueline Cloos
- Pediatric Oncology/Hematology and Hematology, VU Medical Center, Amsterdam, The Netherlands
| | - Robin Foà
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, ‘Sapienza’ University of Rome, Rome, Italy
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Jan Cools
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
- * E-mail: (JC); (SA)
| | - Stein Aerts
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
- * E-mail: (JC); (SA)
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