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Li Z, Yang H, Liu J, Li L, Wang X. TOMM34 serves as a candidate therapeutic target associated with immune cell infiltration in colon cancer. Front Oncol 2023; 13:947364. [PMID: 36845719 PMCID: PMC9948080 DOI: 10.3389/fonc.2023.947364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Background Colon cancer represents one of the most pervasive digestive malignancies worldwide. Translocase of the outer mitochondrial membrane 34 (TOMM34) is considered an oncogene and is implicated in tumor proliferation. However, the correlation between TOMM34 and immune cell infiltration in colon cancer has not been investigated. Materials and methods Based on multiple open online databases, we performed integrated bioinformatics analysis of TOMM34 to evaluate the prognostic value of TOMM34 and its correlation with immune cell infiltration. Results TOMM34 gene and protein expression levels were elevated in tumor tissues compared with normal tissues. Survival analysis revealed that upregulation of TOMM34 was significantly associated with poorer survival time in colon cancer. High TOMM34 expression was dramatically related to low levels of B cells, CD8+ T cells, neutrophils, dendritic cells, PD-1, PD-L1 and CTLA-4. Conclusions Our results confirmed that high expression of TOMM34 in tumor tissue correlates with immune cell infiltration and worse prognosis in colon cancer patients. TOMM34 may serve as a potential prognostic biomarker for colon cancer diagnosis and prognosis prediction.
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Affiliation(s)
- Zhigui Li
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Hongzhao Yang
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jianbo Liu
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Li Li
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaodong Wang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Xiaodong Wang,
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Poverennaya EV, Pyatnitskiy MA, Dolgalev GV, Arzumanian VA, Kiseleva OI, Kurbatov IY, Kurbatov LK, Vakhrushev IV, Romashin DD, Kim YS, Ponomarenko EA. Exploiting Multi-Omics Profiling and Systems Biology to Investigate Functions of TOMM34. BIOLOGY 2023; 12:biology12020198. [PMID: 36829477 PMCID: PMC9952762 DOI: 10.3390/biology12020198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Although modern biology is now in the post-genomic era with vastly increased access to high-quality data, the set of human genes with a known function remains far from complete. This is especially true for hundreds of mitochondria-associated genes, which are under-characterized and lack clear functional annotation. However, with the advent of multi-omics profiling methods coupled with systems biology algorithms, the cellular role of many such genes can be elucidated. Here, we report genes and pathways associated with TOMM34, Translocase of Outer Mitochondrial Membrane, which plays role in the mitochondrial protein import as a part of cytosolic complex together with Hsp70/Hsp90 and is upregulated in various cancers. We identified genes, proteins, and metabolites altered in TOMM34-/- HepG2 cells. To our knowledge, this is the first attempt to study the functional capacity of TOMM34 using a multi-omics strategy. We demonstrate that TOMM34 affects various processes including oxidative phosphorylation, citric acid cycle, metabolism of purine, and several amino acids. Besides the analysis of already known pathways, we utilized de novo network enrichment algorithm to extract novel perturbed subnetworks, thus obtaining evidence that TOMM34 potentially plays role in several other cellular processes, including NOTCH-, MAPK-, and STAT3-signaling. Collectively, our findings provide new insights into TOMM34's cellular functions.
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Affiliation(s)
| | - Mikhail A. Pyatnitskiy
- Institute of Biomedical Chemistry, Moscow 119121, Russia
- Faculty Of Computer Science, National Research University Higher School of Economics, Moscow 101000, Russia
- Correspondence:
| | | | | | | | | | | | | | | | - Yan S. Kim
- Institute of Biomedical Chemistry, Moscow 119121, Russia
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Huang Y, Chen Z, Chen X, Chen X, Xu M. TOMM34 promotes cell proliferation, migration, and invasion of OSCC and modulates mitochondrial function. J Oral Pathol Med 2023; 52:47-55. [PMID: 36367442 DOI: 10.1111/jop.13382] [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: 05/18/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND 34-kDa translocase of the outer mitochondrial membrane (TOMM34) has been reported highly expressed in many cancers and is positively correlated to poorer prognosis. Our prior study showed TOMM34 is highly expressed in oral squamous cell carcinoma (OSCC) and is closely related to TNM classification and tumor size. TOMM34 is also associated with lymph node metastasis and poorer overall survival and disease-free survival in HPV-negative OSCC. METHODS We knocked down TOMM34 in OSCC cells (SCC15, HPV positive; Cal27, HPV negative) with siRNA and over-expressed with plasmids. The effects of TOMM34 on cell proliferation, migration and invasion abilities were detected by EdU assay, CCK-8 assay, wound-healing assay, and Transwell assay. We also detected the mitochondrial morphology and the intracellular Reactive Oxygen Species (ROS) level by fluorescence staining and flow cytometry. Finally, we monitored the protein levels of ERK pathway-related molecules. RESULTS TOMM34 knockdown decreased the proliferation in SCC15 and Cal27, and weakened the migration and invasion abilities as well. Mitochondria became shorter, in the shape of dots or short rods, suggesting that mitochondrial damage occurred. Intracellular ROS levels increased significantly after knockdown TOMM34 and decreased after over-expressing TOMM34. The phosphorylation levels of ERK1/2 and MEK1/2 in SCC15 were significantly higher than in Cal27. Besides, the phosphorylation levels of ERK1/2 and MEK1/2 were inhibited in SCC15 after knockdown of TOMM34, but not in Cal27. CONCLUSION TOMM34 promotes the cell proliferation, migration, and invasion of OSCC. In addition, TOMM34 participates in maintaining the mitochondrial shape and reducing the intracellular ROS level to protect cancer cells. Furthermore, TOMM34 increases the activity of ERK1/2 and MEK1/2 in HPV-positive OSCC cells but not in HPV-negative.
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Affiliation(s)
- Yunyi Huang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Zhipei Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xuanyi Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xiaohua Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Meng Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
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Zhang M, Chiozzi RZ, Skerrett-Byrne DA, Veenendaal T, Klumperman J, Heck AJR, Nixon B, Helms JB, Gadella BM, Bromfield EG. High Resolution Proteomic Analysis of Subcellular Fractionated Boar Spermatozoa Provides Comprehensive Insights Into Perinuclear Theca-Residing Proteins. Front Cell Dev Biol 2022; 10:836208. [PMID: 35252197 PMCID: PMC8894813 DOI: 10.3389/fcell.2022.836208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
Abstract
The perinuclear theca (PT) is a highly condensed, largely insoluble protein structure that surrounds the nucleus of eutherian spermatozoa. Recent reports have indicated that the PT unexpectedly houses several somatic proteins, such as core histones, which may be important post-fertilization during re-modelling of the male pronucleus, yet little is known regarding the overall proteomic composition of the PT. Here, we report the first in depth, label-free proteomic characterization of the PT of boar spermatozoa following the implementation of a long-established subcellular fractionation protocol designed to increase the detection of low abundance proteins. A total of 1,802 proteins were identified, a result that represents unparalleled depth of coverage for the boar sperm proteome and exceeds the entire annotated proteome of the Sus scrofa species so far. In the PT structure itself, we identified 813 proteins and confirmed the presence of previously characterized PT proteins including the core histones H2A, H2B, H3 and H4, as well as Ras-related protein Rab-2A (RAB2A) and Rab-2B (RAB2B) amongst other RAB proteins. In addition to these previously characterized PT proteins, our data revealed that the PT is replete in proteins critical for sperm-egg fusion and egg activation, including: Izumo family members 1–4 (IZUMO1-4) and phosphoinositide specific phospholipase ζ (PLCZ1). Through Ingenuity Pathway Analysis, we found surprising enrichment of endoplasmic reticulum (ER) proteins and the ER-stress response in the PT. This is particularly intriguing as it is currently held that the ER structure is lost during testicular sperm maturation. Using the String and Cytoscape tools to visualize protein-protein interactions revealed an intricate network of PT protein complexes, including numerous proteasome subunits. Collectively, these data suggest that the PT may be a unique site of cellular homeostasis that houses an abundance of protein degradation machinery. This fits with previous observations that the PT structure dissociates first within the oocyte post-fertilization. It remains to be explored whether proteasome subunits within the PT actively assist in the protein degradation of paternal cell structures post-fertilization and how aberrations in PT protein content may delay embryonic development.
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Affiliation(s)
- Min Zhang
- Department of Biomolecular Health Sciences and Department of Farm and Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Netherlands Proteomics Centre, Utrecht, Netherlands
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - David A. Skerrett-Byrne
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Tineke Veenendaal
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Netherlands Proteomics Centre, Utrecht, Netherlands
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Brett Nixon
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - J. Bernd Helms
- Department of Biomolecular Health Sciences and Department of Farm and Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bart M. Gadella
- Department of Biomolecular Health Sciences and Department of Farm and Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- *Correspondence: Bart M. Gadella,
| | - Elizabeth G. Bromfield
- Department of Biomolecular Health Sciences and Department of Farm and Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, University of Newcastle, Callaghan, NSW, Australia
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Liu W, Sun Y, Ge W, Zhang F, Gan L, Zhu Y, Guo T, Liu K. DIA-based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia. Mol Cell Proteomics 2021; 21:100187. [PMID: 34922009 PMCID: PMC8800142 DOI: 10.1016/j.mcpro.2021.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 11/08/2021] [Accepted: 12/13/2021] [Indexed: 11/26/2022] Open
Abstract
Drug resistance is a critical obstacle to effective treatment in patients with chronic myeloid leukemia (CML). To understand the underlying resistance mechanisms in response to imatinib (IMA) and adriamycin (ADR), the parental K562 cells were treated with low doses of IMA or ADR for two months to generate derivative cells with mild, intermediate and severe resistance to the drugs as defined by their increasing resistance index (RI). PulseDIA-based quantitative proteomics was then employed to reveal the proteome changes in these resistant cells. In total, 7082 proteotypic proteins from 98,232 peptides were identified and quantified from the dataset using four DIA software tools including OpenSWATH, Spectronaut, DIA-NN, and EncyclopeDIA. Sirtuin Signaling Pathway was found to be significantly enriched in both ADR- and IMA-resistant K562 cells. In particular, IDH2 was identified as a potential drug target correlated with the drug resistance phenotype, and its inhibition by the antagonist AGI-6780 reversed the acquired resistance in K562 cells to either ADR or IMA. Together, our study has implicated IDH2 as a potential target that can be therapeutically leveraged to alleviate the drug resistance in K562 cells when treated with IMA and ADR.
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Affiliation(s)
- Wei Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yaoting Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, China
| | - Fangfei Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lin Gan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Kexin Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China.
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Shukla P, Singh KK. The mitochondrial landscape of ovarian cancer: emerging insights. Carcinogenesis 2021; 42:663-671. [PMID: 33928357 PMCID: PMC8163040 DOI: 10.1093/carcin/bgab033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/18/2021] [Accepted: 04/20/2021] [Indexed: 02/02/2023] Open
Abstract
Ovarian cancer (OC) is known to be the most lethal cancer in women worldwide, and its etiology is poorly understood. Recent studies show that mitochondrial DNA (mtDNA) content as well as mtDNA and nuclear genes encoding mitochondrial proteins influence OC risk. This review presents an overview of role of mitochondrial genetics in influencing OC development and discusses the contribution of mitochondrial proteome in OC development, progression and therapy. A role of mitochondrial genetics in racial disparity is also highlighted. In-depth understanding of role of mitochondria in OC will help develop strategies toward prevention and treatment and improving overall survival in women with OC.
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Affiliation(s)
- Pallavi Shukla
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Molecular Endocrinology, Indian Council of Medical Research-National Institute for Research in Reproductive Health (ICMR-NIRRH), Mumbai, India
| | - Keshav K Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
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7
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Cai M, Tan R, Huang Y, Chen X, Kong Q, Guo K, Xu M. High Expression of Tomm34 and Its Correlations With Clinicopathology in Oral Squamous Cell Carcinoma. Pathol Oncol Res 2021; 27:641042. [PMID: 34257607 PMCID: PMC8262227 DOI: 10.3389/pore.2021.641042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/02/2021] [Indexed: 11/23/2022]
Abstract
Tomm34, as a member of the outer mitochondrial membrane proteins, is evenly distributed between the cytoplasm and the outer mitochondrial membrane. It is up-regulated in a variety of tumors and correlates with poor prognosis. This study aimed to investigate expression of Tomm34 and its correlations with clinicopathology in oral squamous cell carcinoma (OSCC). Oncomine database and UALCAN database were utilized to predict the expression and prognosis values of Tomm34 in head and neck squamous cell carcinoma (HNSCC). By immunohistochemistry, a retrospective study was performed to verify the bioinformatics results to evaluate the Tomm34 expression and clinicopathological variables in both HPV-positive OSCC and HPV-negative OSCC. Immunohistochemistry of our cohort revealed that 48 cases fulfilled the Tomm34 high expression judgment criteria, and the overall positive rate was 60% (48/80), and 27 cases fulfilled the p16 expression judgment criteria (33.75%, 27/80). The high expression of Tomm34 was closely related with the TNM classification of OSCC (p < 0.01) and tumor size (p < 0.01) both in HPV-negative OSCC and HPV-positive OSCC, while related with lymph node metastasis (p = 0.001) in HPV-negative OSCC and drinking history (p = 0.044) in HPV-positive OSCC. In addition, the Kaplan-Meier curves indicated that higher level of Tomm34 was correlated with poorer overall survival (OS) and disease-free survival (DFS) in HPV-negative OSCC (OS, p = 0.046; DFS, p = 0.020) but not in HPV-positive OSCC (OS, p = 0.824; DFS, p = 0.782). In conclusion, Tomm34 is highly expressed in OSCC and may be a useful factor to provide prognostic information, especially in HPV-negative OSCC group.
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Affiliation(s)
- Min Cai
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Rukeng Tan
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Yunyi Huang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Xuanyi Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Qingci Kong
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Kaixin Guo
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Meng Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
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Zhang T, Nie Y, Gu J, Cai K, Chen X, Li H, Wang J. Identification of Mitochondrial-Related Prognostic Biomarkers Associated With Primary Bile Acid Biosynthesis and Tumor Microenvironment of Hepatocellular Carcinoma. Front Oncol 2021; 11:587479. [PMID: 33868990 PMCID: PMC8047479 DOI: 10.3389/fonc.2021.587479] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of tumor-associated deaths worldwide. Despite great progress in early diagnosis and multidisciplinary tumor management, the long-term prognosis of HCC remains poor. Currently, metabolic reprogramming during tumor development is widely observed to support rapid growth and proliferation of cancer cells, and several metabolic targets that could be used as cancer biomarkers have been identified. The liver and mitochondria are the two centers of human metabolism at the whole organism and cellular levels, respectively. Thus, identification of prognostic biomarkers based on mitochondrial-related genes (Mito-RGs)—the coding-genes of proteins located in the mitochondria—that reflect metabolic changes associated with HCC could lead to better interventions for HCC patients. In the present study, we used HCC data from The Cancer Genome Atlas (TCGA) database to construct a classifier containing 10 Mito-RGs (ACOT7, ADPRHL2, ATAD3A, BSG, FAM72A, PDK3, PDSS1, RAD51C, TOMM34, and TRMU) for predicting the prognosis of HCC by using 10-fold Least Absolute Shrinkage and Selection Operation (LASSO) cross-validation Cox regression. Based on the risk score calculated by the classifier, the samples were divided into high- and low-risk groups. Gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), t-distributed stochastic neighbor embedding (t-SNE), and consensus clusterPlus algorithms were used to identify metabolic pathways that were significantly different between the high- and low-risk groups. We further investigated the relationship between metabolic status and infiltration of immune cells into HCC tumor samples by using the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm combined with the Tumor Immune Estimation Resource (TIMER) database. Our results showed that the classifier based on Mito-RGs could act as an independent biomarker for predicting survival of HCC patients. Repression of primary bile acid biosynthesis plays a vital role in the development and poor prognosis of HCC, which provides a potential approach to treatment. Our study revealed cross-talk between bile acid and infiltration of tumors by immune cells, which may provide novel insight into immunotherapy of HCC. Furthermore, our research may provide a novel method for HCC metabolic therapy based on modulation of mitochondrial function.
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Affiliation(s)
- Tao Zhang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingli Nie
- Department of Dermatology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian Gu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kailin Cai
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangdong Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huili Li
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiliang Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Dean ME, Johnson JL. Human Hsp90 cochaperones: perspectives on tissue-specific expression and identification of cochaperones with similar in vivo functions. Cell Stress Chaperones 2021; 26:3-13. [PMID: 33037995 PMCID: PMC7736379 DOI: 10.1007/s12192-020-01167-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
The Hsp90 molecular chaperone is required for the function of hundreds of different cellular proteins. Hsp90 and a cohort of interacting proteins called cochaperones interact with clients in an ATP-dependent cycle. Cochaperone functions include targeting clients to Hsp90, regulating Hsp90 ATPase activity, and/or promoting Hsp90 conformational changes as it progresses through the cycle. Over the last 20 years, the list of cochaperones identified in human cells has grown from the initial six identified in complex with steroid hormone receptors and protein kinases to about fifty different cochaperones found in Hsp90-client complexes. These cochaperones may be placed into three groups based on shared Hsp90 interaction domains. Available evidence indicates that cochaperones vary in client specificity, abundance, and tissue distribution. Many of the cochaperones have critical roles in regulation of cancer and neurodegeneration. A more limited set of cochaperones have cellular functions that may be limited to tissues such as muscle and testis. It is likely that a small set of cochaperones are part of the core Hsp90 machinery required for the folding of a wide range of clients. The presence of more selective cochaperones may allow greater control of Hsp90 activities across different tissues or during development.
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Affiliation(s)
- Marissa E Dean
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844-3051, USA
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844-3051, USA.
- Center for Reproductive Biology, University of Idaho, Moscow, ID, 83844-3051, USA.
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10
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MR image-based radiomics to differentiate type Ι and type ΙΙ epithelial ovarian cancers. Eur Radiol 2020; 31:403-410. [PMID: 32743768 DOI: 10.1007/s00330-020-07091-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022]
Abstract
OBJECTIVES Epithelial ovarian cancers (EOC) can be divided into type I and type II according to etiology and prognosis. Accurate subtype differentiation can substantially impact patient management. In this study, we aimed to construct an MR image-based radiomics model to differentiate between type I and type II EOC. METHODS In this multicenter retrospective study, a total of 294 EOC patients from January 2010 to February 2019 were enrolled. Quantitative MR imaging features were extracted from the following axial sequences: T2WI FS, DWI, ADC, and CE-T1WI. A combined model was constructed based on the combination of these four MR sequences. The diagnostic performance was evaluated by ROC-AUC. In addition, an occlusion test was carried out to identify the most critical region for EOC differentiation. RESULTS The combined radiomics model exhibited superior diagnostic capability over all four single-parametric radiomics models, both in internal and external validation cohorts (AUC of 0.806 and 0.847, respectively). The occlusion test revealed that the most critical region for differential diagnosis was the border zone between the solid and cystic components, or the less compact areas of solid component on direct visual inspection. CONCLUSIONS MR image-based radiomics modeling can differentiate between type I and type II EOC and identify the most critical region for differential diagnosis. KEY POINTS • Combined radiomics models exhibited superior diagnostic capability over all four single-parametric radiomics models, both in internal and external validation cohorts (AUC of 0.834 and 0.847, respectively). • The occlusion test revealed that the most crucial region for differentiating type Ι and type ΙΙ EOC was the border zone between the solid and cystic components, or the less compact areas of solid component on direct visual inspection on T2WI FS. • The light-combined model (constructed by T2WI FS, DWI, and ADC sequences) can be used for patients who are not suitable for contrast agent use.
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Trcka F, Durech M, Vankova P, Vandova V, Simoncik O, Kavan D, Vojtesek B, Muller P, Man P. The interaction of the mitochondrial protein importer TOMM34 with HSP70 is regulated by TOMM34 phosphorylation and binding to 14-3-3 adaptors. J Biol Chem 2020; 295:8928-8944. [PMID: 32371396 PMCID: PMC7335785 DOI: 10.1074/jbc.ra120.012624] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/28/2020] [Indexed: 01/17/2023] Open
Abstract
Translocase of outer mitochondrial membrane 34 (TOMM34) orchestrates heat shock protein 70 (HSP70)/HSP90-mediated transport of mitochondrial precursor proteins. Here, using in vitro phosphorylation and refolding assays, analytical size-exclusion chromatography, and hydrogen/deuterium exchange MS, we found that TOMM34 associates with 14-3-3 proteins after its phosphorylation by protein kinase A (PKA). PKA preferentially targeted two serine residues in TOMM34: Ser93 and Ser160, located in the tetratricopeptide repeat 1 (TPR1) domain and the interdomain linker, respectively. Both of these residues were necessary for efficient 14-3-3 protein binding. We determined that phosphorylation-induced structural changes in TOMM34 are further augmented by binding to 14-3-3, leading to destabilization of TOMM34's secondary structure. We also observed that this interaction with 14-3-3 occludes the TOMM34 interaction interface with ATP-bound HSP70 dimers, which leaves them intact and thereby eliminates an inhibitory effect of TOMM34 on HSP70-mediated refolding in vitro In contrast, we noted that TOMM34 in complex with 14-3-3 could bind HSP90. Both TOMM34 and 14-3-3 participated in cytosolic precursor protein transport mediated by the coordinated activities of HSP70 and HSP90. Our results provide important insights into how PKA-mediated phosphorylation and 14-3-3 binding regulate the availability of TOMM34 for its interaction with HSP70.
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Affiliation(s)
- Filip Trcka
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Michal Durech
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Pavla Vankova
- BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Veronika Vandova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Oliver Simoncik
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Daniel Kavan
- BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Borivoj Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Petr Muller
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
| | - Petr Man
- BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic.
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