1
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Wu Q, Gu Z, Shang B, Wan D, Zhang Q, Zhang X, Xie P, Cheng S, Zhang W, Zhang K. Circulating tumor cell clustering modulates RNA splicing and polyadenylation to facilitate metastasis. Cancer Lett 2024; 588:216757. [PMID: 38417668 DOI: 10.1016/j.canlet.2024.216757] [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] [Received: 10/11/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Circulating tumor cell (CTC) clusters exhibit significantly higher metastatic potential compared to single CTCs. However, the underlying mechanism behind this phenomenon remains unclear, and the role of posttranscriptional RNA regulation in CTC clusters has not been explored. Here, we conducted a comparative analysis of alternative splicing (AS) and alternative polyadenylation (APA) profiles between single CTCs and CTC clusters. We identified 994 and 836 AS events in single CTCs and CTC clusters, respectively, with ∼20% of AS events showing differential regulation between the two cell types. A key event in this differential splicing was observed in SRSF6, which disrupted AS profiles and contributed to the increased malignancy of CTC clusters. Regarding APA, we found a global lengthening of 3' UTRs in CTC clusters compared to single CTCs. This alteration was primarily governed by 14 core APA factors, particularly PPP1CA. The modified APA profiles facilitated the cell cycle progression of CTC clusters and indicated their reduced susceptibility to oxidative stress. Further investigation revealed that the proportion of H2AFY mRNA with long 3' UTR instead of short 3' UTR was higher in CTC clusters than single CTCs. The AU-rich elements (AREs) within the long 3' UTR of H2AFY mRNA enhance mRNA stability and translation activity, resulting in promoting cell proliferation and invasion, which potentially facilitate the establishment and rapid formation of metastatic tumors mediated by CTC clusters. These findings provide new insights into the mechanisms driving CTC cluster metastasis.
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Affiliation(s)
- Quanyou Wu
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China; State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Zhaoru Gu
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Bingqing Shang
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Duo Wan
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Qi Zhang
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Xiaoli Zhang
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Peipei Xie
- State Key Laboratory of Molecular Oncology, 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, 100021, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, 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, 100021, China.
| | - Wen Zhang
- Department of Immunology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, 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, 100021, China.
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2
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Liu M, Wang Z, Li S, Deng Y, He N. Identification of PHB2 as a Potential Biomarker of Luminal A Breast Cancer Cells Using a Cell-Specific Aptamer. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51593-51601. [PMID: 36346944 DOI: 10.1021/acsami.2c12291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Precise diagnosis of breast cancer molecular subtypes remains a great challenge in clinics. The present molecular biomarkers are not specific enough to classify breast cancer subtypes precisely, which requests for more accurate and specific molecular biomarkers to be discovered. Aptamers evolved by the cell-systematic evolution of ligands by exponential enrichment (SELEX) method show great potential in the discovery and identification of cell membrane targets via aptamer-based cell membrane protein pull-down, which has been regarded as a novel and powerful weapon for the discovery and identification of new molecular biomarkers. Herein, a cell membrane protein PHB2 was identified as a potential molecular biomarker specifically expressed in the cell membranes of MCF-7 breast cancer cells using a DNA aptamer MF3Ec. Further experiments demonstrated that the PHB2 protein is differentially expressed in the cell membranes of MCF-7, SK-BR-3, and MDA-MB-231 breast cancer cells and MCF-10A cells, and the binding molecular domains of aptamer MF3Ec and anti-PHB2 antibodies to the PHB2 protein are different due to there being no obvious competitions between aptamer MF3Ec and anti-PHB2 antibodies in the binding to the cell membranes of target MCF-7 cells. Due to those four cells belonging to luminal A, HER2-positive, and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, respectively, the PHB2 protein in the cell membrane may be a potential biomarker for precise diagnosis of the luminal A breast cancer cell subtype, which is endowed with the ability to differentiate the luminal A breast cancer cell subtype from HER2-positive and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, providing a new molecular biomarker and therapeutic target for the accurate and precise classification and diagnostics and personalized therapy of breast cancer.
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Affiliation(s)
- Mei Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, P. R. China
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, P. R. China
| | - Zhifei Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
| | - Song Li
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Yan Deng
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
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3
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Gu L, Zhang J, Liu D, Chen J, Liu S, Peng Q, Tian Y, Du M, Zhang J, Xiao W, Shen S, Wang J. Development of artesunate intelligent prodrug liposomes based on mitochondrial targeting strategy. J Nanobiotechnology 2022; 20:376. [PMID: 35964052 PMCID: PMC9375379 DOI: 10.1186/s12951-022-01569-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022] Open
Abstract
Breast cancer is the leading cause of cancer-related deaths in women and remains a formidable therapeutic challenge. Mitochondria participate in a myriad of essential cellular processes, such as metabolism, and are becoming an ideal target for cancer therapy. Artemisinin and its derivatives have demonstrated multiple activities in the context of various cancers. Mitochondrial autophagy(mitophagy) is one of the important anti-tumor mechanisms of artemisinin drugs. However, the lack of specific tumor targeting ability limits the anti-tumor efficacy of artemisinin drugs. In this study, a GSH-sensitive artesunate smart conjugate (TPP-SS-ATS) was synthesized and liposomes (TPP-SS-ATS-LS) that target tumor cells and mitochondria were further prepared. The advantages of TPP-SS-ATS-LS targeting to the breast tumor were verified by in vivo and in vitro evaluations. In our study, the cytotoxicity was obviously enhanced in vitro and tumor growth inhibition rate was increased from 37.7% to 56.4% at equivalent artesunate dosage in breast cancer orthotopic implanted mice. Meanwhile, mitochondrial dysfunction, suppression of ATP production and respiratory capacity were detected in breast cancer cells. We further discovered that TPP-SS-ATS-LS inhibited tumor cells proliferation through mitophagy by regulating PHB2 and PINK1 expression. These results provide new research strategies for the development of new artemisinin-based anti-tumor drugs.
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Affiliation(s)
- Liwei Gu
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Jiaxing Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Dandan Liu
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Jiayun Chen
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Shuzhi Liu
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Qing Peng
- Institute of Basic Medical Sciences of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, People's Republic of China
| | - Ya Tian
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Maobo Du
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Junzhe Zhang
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Wei Xiao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Shuo Shen
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China.
| | - Jigang Wang
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China. .,School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, People's Republic of China.
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4
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Toki S, Yoshimaru T, Matsushita Y, Aihara H, Ono M, Tsuneyama K, Sairyo K, Katagiri T. The survival and proliferation of osteosarcoma cells are dependent on the mitochondrial BIG3-PHB2 complex formation. Cancer Sci 2021; 112:4208-4219. [PMID: 34363714 PMCID: PMC8486206 DOI: 10.1111/cas.15099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022] Open
Abstract
Previous studies reported the critical role of the brefeldin A-inhibited guanine nucleotide exchange protein 3-prohibitin 2 (BIG3-PHB2) complex in modulating estrogen signaling activation in breast cancer cells, yet its pathophysiological roles in osteosarcoma (OS) cells remain elusive. Here, we report a novel function of BIG3-PHB2 in OS malignancy. BIG3-PHB2 complexes were localized mainly in mitochondria in OS cells, unlike in estrogen-dependent breast cancer cells. Depletion of endogenous BIG3 expression by small interfering RNA (siRNA) treatment led to significant inhibition of OS cell growth. Disruption of BIG3-PHB2 complex formation by treatment with specific peptide inhibitor also resulted in significant dose-dependent suppression of OS cell growth, migration, and invasion resulting from G2/M-phase arrest and in PARP cleavage, ultimately leading to PARP-1/apoptosis-inducing factor (AIF) pathway activation-dependent apoptosis in OS cells. Subsequent proteomic and bioinformatic pathway analyses revealed that disruption of the BIG3-PHB2 complex might lead to downregulation of inner mitochondrial membrane protein complex activity. Our findings indicate that the mitochondrial BIG3-PHB2 complex might regulate PARP-1/AIF pathway-dependent apoptosis during OS cell proliferation and progression and that disruption of this complex may be a promising therapeutic strategy for OS.
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Affiliation(s)
- Shunichi Toki
- Division of Genome Medicine, Advanced Institute of Medical Sciences, Tokushima University, Tokushima, Japan.,Department of Orthopedics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Tetsuro Yoshimaru
- Division of Genome Medicine, Advanced Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Yosuke Matsushita
- Division of Genome Medicine, Advanced Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Hitoshi Aihara
- Division of Genome Medicine, Advanced Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Masaya Ono
- Department of Proteomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Koichi Sairyo
- Department of Orthopedics, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Toyomasa Katagiri
- Division of Genome Medicine, Advanced Institute of Medical Sciences, Tokushima University, Tokushima, Japan
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5
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Functional genomics for breast cancer drug target discovery. J Hum Genet 2021; 66:927-935. [PMID: 34285339 PMCID: PMC8384626 DOI: 10.1038/s10038-021-00962-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 01/14/2023]
Abstract
Breast cancer is a heterogeneous disease that develops through a multistep process via the accumulation of genetic/epigenetic alterations in various cancer-related genes. Current treatment options for breast cancer patients include surgery, radiotherapy, and chemotherapy including conventional cytotoxic and molecular-targeted anticancer drugs for each intrinsic subtype, such as endocrine therapy and antihuman epidermal growth factor receptor 2 (HER2) therapy. However, these therapies often fail to prevent recurrence and metastasis due to resistance. Overall, understanding the molecular mechanisms of breast carcinogenesis and progression will help to establish therapeutic modalities to improve treatment. The recent development of comprehensive omics technologies has led to the discovery of driver genes, including oncogenes and tumor-suppressor genes, contributing to the development of molecular-targeted anticancer drugs. Here, we review the development of anticancer drugs targeting cancer-specific functional therapeutic targets, namely, MELK (maternal embryonic leucine zipper kinase), TOPK (T-lymphokine-activated killer cell-originated protein kinase), and BIG3 (brefeldin A-inhibited guanine nucleotide-exchange protein 3), as identified through comprehensive breast cancer transcriptomics.
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6
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Zhang F, Shi W, Zhang J, Zeng M, Li M, Kurgan L. PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection. Bioinformatics 2020; 36:i735-i744. [DOI: 10.1093/bioinformatics/btaa806] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract
Motivation
Knowledge of protein-binding residues (PBRs) improves our understanding of protein−protein interactions, contributes to the prediction of protein functions and facilitates protein−protein docking calculations. While many sequence-based predictors of PBRs were published, they offer modest levels of predictive performance and most of them cross-predict residues that interact with other partners. One unexplored option to improve the predictive quality is to design consensus predictors that combine results produced by multiple methods.
Results
We empirically investigate predictive performance of a representative set of nine predictors of PBRs. We report substantial differences in predictive quality when these methods are used to predict individual proteins, which contrast with the dataset-level benchmarks that are currently used to assess and compare these methods. Our analysis provides new insights for the cross-prediction concern, dissects complementarity between predictors and demonstrates that predictive performance of the top methods depends on unique characteristics of the input protein sequence. Using these insights, we developed PROBselect, first-of-its-kind consensus predictor of PBRs. Our design is based on the dynamic predictor selection at the protein level, where the selection relies on regression-based models that accurately estimate predictive performance of selected predictors directly from the sequence. Empirical assessment using a low-similarity test dataset shows that PROBselect provides significantly improved predictive quality when compared with the current predictors and conventional consensuses that combine residue-level predictions. Moreover, PROBselect informs the users about the expected predictive quality for the prediction generated from a given input protein.
Availability and implementation
PROBselect is available at http://bioinformatics.csu.edu.cn/PROBselect/home/index.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fuhao Zhang
- Hunan Provincial Key Laboratory on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Wenbo Shi
- Hunan Provincial Key Laboratory on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Jian Zhang
- School of Computer and Information Technology, Xinyang Normal University, Xinyang 464000, China
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Min Zeng
- Hunan Provincial Key Laboratory on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Min Li
- Hunan Provincial Key Laboratory on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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7
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Protein phosphatase 1 in tumorigenesis: is it worth a closer look? Biochim Biophys Acta Rev Cancer 2020; 1874:188433. [PMID: 32956763 DOI: 10.1016/j.bbcan.2020.188433] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/26/2020] [Accepted: 09/12/2020] [Indexed: 02/06/2023]
Abstract
Cancer cells take advantage of signaling cascades to meet their requirements for sustained growth and survival. Cell signaling is tightly controlled by reversible protein phosphorylation mechanisms, which require the counterbalanced action of protein kinases and protein phosphatases. Imbalances on this system are associated with cancer development and progression. Protein phosphatase 1 (PP1) is one of the most relevant protein phosphatases in eukaryotic cells. Despite the widely recognized involvement of PP1 in key biological processes, both in health and disease, its relevance in cancer has been largely neglected. Here, we provide compelling evidence that support major roles for PP1 in tumorigenesis.
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8
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Wang D, Tabti R, Elderwish S, Abou-Hamdan H, Djehal A, Yu P, Yurugi H, Rajalingam K, Nebigil CG, Désaubry L. Prohibitin ligands: a growing armamentarium to tackle cancers, osteoporosis, inflammatory, cardiac and neurological diseases. Cell Mol Life Sci 2020; 77:3525-3546. [PMID: 32062751 PMCID: PMC11104971 DOI: 10.1007/s00018-020-03475-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 02/08/2023]
Abstract
Over the last three decades, the scaffold proteins prohibitins-1 and -2 (PHB1/2) have emerged as key signaling proteins regulating a myriad of signaling pathways in health and diseases. Small molecules targeting PHBs display promising effects against cancers, osteoporosis, inflammatory, cardiac and neurodegenerative diseases. This review provides an updated overview of the various classes of PHB ligands, with an emphasis on their mechanism of action and therapeutic potential. We also describe how these ligands have been used to explore PHB signaling in different physiological and pathological settings.
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Affiliation(s)
- Dong Wang
- Sino-French Joint Lab of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Redouane Tabti
- Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081, Strasbourg, France
| | - Sabria Elderwish
- Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081, Strasbourg, France
| | - Hussein Abou-Hamdan
- Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081, Strasbourg, France
| | - Amel Djehal
- Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081, Strasbourg, France
- Superior National School Biotechnology Taoufik Khaznadar, Ville universitaire Ali Mendjeli, BP E66 25100, Constantine, Algeria
| | - Peng Yu
- Sino-French Joint Lab of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Hajime Yurugi
- Cell Biology Unit, University Medical Center Mainz, JGU-Mainz, Mainz, Germany
| | | | - Canan G Nebigil
- Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081, Strasbourg, France
| | - Laurent Désaubry
- Sino-French Joint Lab of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.
- Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081, Strasbourg, France.
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Terkelsen T, Russo F, Gromov P, Haakensen VD, Brunak S, Gromova I, Krogh A, Papaleo E. Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration. Breast Cancer Res 2020; 22:73. [PMID: 32605588 PMCID: PMC7329449 DOI: 10.1186/s13058-020-01295-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/14/2020] [Indexed: 12/21/2022] Open
Abstract
Background Studies on tumor-secreted microRNAs point to a functional role of these in cellular communication and reprogramming of the tumor microenvironment. Uptake of tumor-secreted microRNAs by neighboring cells may result in the silencing of mRNA targets and, in turn, modulation of the transcriptome. Studying miRNAs externalized from tumors could improve cancer patient diagnosis and disease monitoring and help to pinpoint which miRNA-gene interactions are central for tumor properties such as invasiveness and metastasis. Methods Using a bioinformatics approach, we analyzed the profiles of secreted tumor and normal interstitial fluid (IF) microRNAs, from women with breast cancer (BC). We carried out differential abundance analysis (DAA), to obtain miRNAs, which were enriched or depleted in IFs, from patients with different clinical traits. Subsequently, miRNA family enrichment analysis was performed to assess whether any families were over-represented in the specific sets. We identified dysregulated genes in tumor tissues from the same cohort of patients and constructed weighted gene co-expression networks, to extract sets of co-expressed genes and co-abundant miRNAs. Lastly, we integrated miRNAs and mRNAs to obtain interaction networks and supported our findings using prediction tools and cancer gene databases. Results Network analysis showed co-expressed genes and miRNA regulators, associated with tumor lymphocyte infiltration. All of the genes were involved in immune system processes, and many had previously been associated with cancer immunity. A subset of these, BTLA, CXCL13, IL7R, LAMP3, and LTB, was linked to the presence of tertiary lymphoid structures and high endothelial venules within tumors. Co-abundant tumor interstitial fluid miRNAs within this network, including miR-146a and miR-494, were annotated as negative regulators of immune-stimulatory responses. One co-expression network encompassed differences between BC subtypes. Genes differentially co-expressed between luminal B and triple-negative breast cancer (TNBC) were connected with sphingolipid metabolism and predicted to be co-regulated by miR-23a. Co-expressed genes and TIF miRNAs associated with tumor grade were BTRC, CHST1, miR-10a/b, miR-107, miR-301a, and miR-454. Conclusion Integration of IF miRNAs and mRNAs unveiled networks associated with patient clinicopathological traits, and underlined molecular mechanisms, specific to BC sub-groups. Our results highlight the benefits of an integrative approach to biomarker discovery, placing secreted miRNAs within a biological context.
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Affiliation(s)
- Thilde Terkelsen
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Francesco Russo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pavel Gromov
- Breast Cancer Biology Group, Genome Integrity Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Vilde Drageset Haakensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Irina Gromova
- Breast Cancer Biology Group, Genome Integrity Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Anders Krogh
- Unit of Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark. .,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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10
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Zhang J, Kurgan L. SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences. Bioinformatics 2020; 35:i343-i353. [PMID: 31510679 PMCID: PMC6612887 DOI: 10.1093/bioinformatics/btz324] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Motivation Accurate predictions of protein-binding residues (PBRs) enhances understanding of molecular-level rules governing protein–protein interactions, helps protein–protein docking and facilitates annotation of protein functions. Recent studies show that current sequence-based predictors of PBRs severely cross-predict residues that interact with other types of protein partners (e.g. RNA and DNA) as PBRs. Moreover, these methods are relatively slow, prohibiting genome-scale use. Results We propose a novel, accurate and fast sequence-based predictor of PBRs that minimizes the cross-predictions. Our SCRIBER (SeleCtive pRoteIn-Binding rEsidue pRedictor) method takes advantage of three innovations: comprehensive dataset that covers multiple types of binding residues, novel types of inputs that are relevant to the prediction of PBRs, and an architecture that is tailored to reduce the cross-predictions. The dataset includes complete protein chains and offers improved coverage of binding annotations that are transferred from multiple protein–protein complexes. We utilize innovative two-layer architecture where the first layer generates a prediction of protein-binding, RNA-binding, DNA-binding and small ligand-binding residues. The second layer re-predicts PBRs by reducing overlap between PBRs and the other types of binding residues produced in the first layer. Empirical tests on an independent test dataset reveal that SCRIBER significantly outperforms current predictors and that all three innovations contribute to its high predictive performance. SCRIBER reduces cross-predictions by between 41% and 69% and our conservative estimates show that it is at least 3 times faster. We provide putative PBRs produced by SCRIBER for the entire human proteome and use these results to hypothesize that about 14% of currently known human protein domains bind proteins. Availability and implementation SCRIBER webserver is available at http://biomine.cs.vcu.edu/servers/SCRIBER/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jian Zhang
- School of Computer and Information Technology, Xinyang Normal University, Xinyang, China.,Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
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Chigira T, Nagatoishi S, Takeda H, Yoshimaru T, Katagiri T, Tsumoto K. Biophysical characterization of the breast cancer-related BIG3-PHB2 interaction: Effect of non-conserved loop region of BIG3 on the structure and the interaction. Biochem Biophys Res Commun 2019; 518:183-189. [PMID: 31421830 DOI: 10.1016/j.bbrc.2019.08.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/06/2019] [Indexed: 01/07/2023]
Abstract
Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) interacts with and inhibits the tumor suppressor function of prohibitin-2 (PHB2), and recent in vivo studies have demonstrated that the BIG3-PHB2 interaction is a promising target for breast cancer therapy. However, little biophysical characterization on BIG3 and its interaction with PHB2 has been reported. Here we compared the calculated 8-class secondary structure of the N-terminal domains of BIG family proteins and identified a loop region unique to BIG3. Our biophysical characterization demonstrated that this loop region significantly affects the colloidal and thermodynamic stability of BIG3 and the thermodynamic and kinetic profile of its interaction with PHB2. These results establish a model for the BIG3-PHB2 interaction and an entry for drug discovery for breast cancer.
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Affiliation(s)
- Takeru Chigira
- Department of Chemistry & Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoru Nagatoishi
- Department of Chemistry & Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| | - Hiroyuki Takeda
- Divison of Proteo-Drug-Discovery Sciences, Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama, Ehime, 790-8577, Japan
| | - Tetsuro Yoshimaru
- Division of Genome Medicine, Institute for Genome Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, 770-8503, Japan
| | - Toyomasa Katagiri
- Division of Genome Medicine, Institute for Genome Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, 770-8503, Japan
| | - Kouhei Tsumoto
- Department of Chemistry & Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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12
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Mitophagy in Cancer: A Tale of Adaptation. Cells 2019; 8:cells8050493. [PMID: 31121959 PMCID: PMC6562743 DOI: 10.3390/cells8050493] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023] Open
Abstract
:In the past years, we have learnt that tumors co-evolve with their microenvironment, and that the active interaction between cancer cells and stromal cells plays a pivotal role in cancer initiation, progression and treatment response. Among the players involved, the pathways regulating mitochondrial functions have been shown to be crucial for both cancer and stromal cells. This is perhaps not surprising, considering that mitochondria in both cancerous and non-cancerous cells are decisive for vital metabolic and bioenergetic functions and to elicit cell death. The central part played by mitochondria also implies the existence of stringent mitochondrial quality control mechanisms, where a specialized autophagy pathway (mitophagy) ensures the selective removal of damaged or dysfunctional mitochondria. Although the molecular underpinnings of mitophagy regulation in mammalian cells remain incomplete, it is becoming clear that mitophagy pathways are intricately linked to the metabolic rewiring of cancer cells to support the high bioenergetic demand of the tumor. In this review, after a brief introduction of the main mitophagy regulators operating in mammalian cells, we discuss emerging cell autonomous roles of mitochondria quality control in cancer onset and progression. We also discuss the relevance of mitophagy in the cellular crosstalk with the tumor microenvironment and in anti-cancer therapy responses.
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Hojo N, Huisken AL, Wang H, Chirshev E, Kim NS, Nguyen SM, Campos H, Glackin CA, Ioffe YJ, Unternaehrer JJ. Snail knockdown reverses stemness and inhibits tumour growth in ovarian cancer. Sci Rep 2018; 8:8704. [PMID: 29880891 PMCID: PMC5992154 DOI: 10.1038/s41598-018-27021-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/23/2018] [Indexed: 12/29/2022] Open
Abstract
To develop effective therapies for advanced high grade serous ovarian cancer (HGSOC), understanding mechanisms of recurrence and metastasis is necessary. In this study, we define the epithelial/mesenchymal status of cell lines that accurately model HGSOC, and evaluate the therapeutic potential of targeting Snai1 (Snail), a master regulator of the epithelial/mesenchymal transition (EMT) in vitro and in vivo. The ratio of Snail to E-cadherin (S/E index) at RNA and protein levels was correlated with mesenchymal morphology in four cell lines. The cell lines with high S/E index (OVCAR8 and COV318) showed more CSC-like, motile, and chemoresistant phenotypes than those with low S/E index (OVSAHO and Kuramochi). We tested the role of Snail in regulation of malignant phenotypes including stemness, cell motility, and chemotherapy resistance: shRNA-mediated knockdown of Snail reversed these malignant phenotypes. Interestingly, the expression of let-7 tumour suppressor miRNA was upregulated in Snail knockdown cells. Furthermore, knockdown of Snail decreased tumour burden in an orthotopic xenograft mouse model. We conclude that Snail is important in controlling HGSOC malignant phenotypes and suggest that the Snail/Let-7 axis may be an attractive target for HGSOC treatment.
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Affiliation(s)
- N Hojo
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA, USA
| | - A L Huisken
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA, USA
| | - H Wang
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA, USA
| | - E Chirshev
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA, USA
| | - N S Kim
- Department of Molecular Biology, Chonbuk National University, Dukjindong 664-14, Jeonju, Jeollabuk-do, 561-756, Republic of Korea
| | - S M Nguyen
- University of California, Riverside - School of Medicine, Riverside, CA, USA
| | - H Campos
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA, USA.,Center for Health Disparities and Molecular Medicine, Loma Linda University, Loma Linda, CA, USA
| | - C A Glackin
- Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Y J Ioffe
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Loma Linda University Medical Center, Loma Linda, CA, USA
| | - J J Unternaehrer
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA, USA.
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14
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Librizzi M, Caradonna F, Cruciata I, Dębski J, Sansook S, Dadlez M, Spencer J, Luparello C. Molecular Signatures Associated with Treatment of Triple-Negative MDA-MB231 Breast Cancer Cells with Histone Deacetylase Inhibitors JAHA and SAHA. Chem Res Toxicol 2017; 30:2187-2196. [PMID: 29129070 DOI: 10.1021/acs.chemrestox.7b00269] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Jay Amin hydroxamic acid (JAHA; N8-ferrocenylN1-hydroxy-octanediamide) is a ferrocene-containing analogue of the histone deacetylase inhibitor (HDACi) suberoylanilide hydroxamic acid (SAHA). JAHA's cytotoxic activity on MDA-MB231 triple negative breast cancer (TNBC) cells at 72 h has been previously demonstrated with an IC50 of 8.45 μM. JAHA's lethal effect was found linked to perturbations of cell cycle, mitochondrial activity, signal transduction, and autophagy mechanisms. To glean novel insights on how MDA-MB231 breast cancer cells respond to the cytotoxic effect induced by JAHA, and to compare the biological effect with the related compound SAHA, we have employed a combination of differential display-PCR, proteome analysis, and COMET assay techniques and shown some differences in the molecular signature profiles induced by exposure to either HDACis. In particular, in contrast to the more numerous and diversified changes induced by SAHA, JAHA has shown a more selective impact on expression of molecular signatures involved in antioxidant activity and DNA repair. Besides expanding the biological knowledge of the effect exerted by the modifications in compound structures on cell phenotype, the molecular elements put in evidence in our study may provide promising targets for therapeutic interventions on TNBCs.
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Affiliation(s)
- Mariangela Librizzi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo , Viale delle Scienze, 90128 Palermo, Italy
| | - Fabio Caradonna
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo , Viale delle Scienze, 90128 Palermo, Italy
| | - Ilenia Cruciata
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo , Viale delle Scienze, 90128 Palermo, Italy
| | - Janusz Dębski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Supojjanee Sansook
- Department of Chemistry, School of Life Sciences, University of Sussex , Falmer, Brighton BN1 9QJ, United Kingdom
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Pawinskiego 5a, 02-106 Warsaw, Poland
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex , Falmer, Brighton BN1 9QJ, United Kingdom
| | - Claudio Luparello
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo , Viale delle Scienze, 90128 Palermo, Italy
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