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Kandagalla S, Sharath BS, Sherapura A, Grishina M, Potemkin V, Lee J, Ramaswamy G, Prabhakar BT, Hanumanthappa M. A systems biology investigation of curcumin potency against TGF-β-induced EMT signaling in lung cancer. 3 Biotech 2022; 12:306. [PMID: 36276461 PMCID: PMC9526769 DOI: 10.1007/s13205-022-03360-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/12/2022] [Indexed: 11/01/2022] Open
Abstract
Curcumin (diferuloylmethane) is bioactive phenolic compound which exerts diverse antimetastatic effect. Several studies have reported the antimetastatic effect of curcumin by its ability to modulate the epithelial-to-mesenchymal transition (EMT) process in different cancers, but underlying molecular mechanism is poorly understood. EMT is a highly conserved biological process in which epithelial cells acquire mesenchymal-like characteristics by losing their cell-cell junctions and polarity. As a consequence, deviation in cellular mechanism leads to cancer metastasis and thereby death. In this perspective, we explored the antimetastatic potential and mechanism of curcumin on the EMT process by establishing in vitro EMT model in lungs cancer (A549) cells induced by TGF-β1. Our results showed that curcumin mitigates EMT by regulating the expression of crucial mesenchymal markers such as MMP2, vimentin and N-cadherin. Besides, the transcriptional analysis revealed that the curcumin treatment differentially regulated the expression of 75 genes in NanoString nCounter platform. Further protein-protein interaction network and clusters analysis of differentially expressed genes revealed their involvement in essential biological processes that plays a key role during EMT transition. Altogether, the study provides a comprehensive overview of the antimetastatic potential of curcumin in TGF-β1-induced EMT in lung cancer cells. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03360-7.
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Affiliation(s)
- Shivananda Kandagalla
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta, Shivamogga, Karnataka India
- Laboratory of Computational Modeling of Drugs, Higher Medical & Biological School, South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk, Russia
| | - B. S. Sharath
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta, Shivamogga, Karnataka India
- School of Systems Biomedical Science and Department of Bioinformatics and Life Science, Soongsil University, Seoul, South Korea
| | - Ankith Sherapura
- Molecular Biomedicine Laboratory, Postgraduate Department of Studies and Research in Biotechnology, Sahyadri Science College, Kuvempu University, Shivamogga, Karnataka India
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical & Biological School, South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical & Biological School, South Ural State University, 20-A, Tchaikovsky Str., Chelyabinsk, Russia
| | - Julian Lee
- School of Systems Biomedical Science and Department of Bioinformatics and Life Science, Soongsil University, Seoul, South Korea
| | | | - B. T. Prabhakar
- Molecular Biomedicine Laboratory, Postgraduate Department of Studies and Research in Biotechnology, Sahyadri Science College, Kuvempu University, Shivamogga, Karnataka India
| | - Manjunatha Hanumanthappa
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta, Shivamogga, Karnataka India
- Department of Biochemistry, Jnana Bharathi Campus, Bangalore University, Bangalore, Karnataka India
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Taniue K, Tanu T, Shimoura Y, Mitsutomi S, Han H, Kakisaka R, Ono Y, Tamamura N, Takahashi K, Wada Y, Mizukami Y, Akimitsu N. RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival. Int J Mol Sci 2022; 23:496. [PMID: 35008922 PMCID: PMC8745236 DOI: 10.3390/ijms23010496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
The RNA exosome is a multi-subunit ribonuclease complex that is evolutionally conserved and the major cellular machinery for the surveillance, processing, degradation, and turnover of diverse RNAs essential for cell viability. Here we performed integrated genomic and clinicopathological analyses of 27 RNA exosome components across 32 tumor types using The Cancer Genome Atlas PanCancer Atlas Studies' datasets. We discovered that the EXOSC4 gene, which encodes a barrel component of the RNA exosome, was amplified across multiple cancer types. We further found that EXOSC4 alteration is associated with a poor prognosis of pancreatic cancer patients. Moreover, we demonstrated that EXOSC4 is required for the survival of pancreatic cancer cells. EXOSC4 also repressed BIK expression and destabilized SESN2 mRNA by promoting its degradation. Furthermore, knockdown of BIK and SESN2 could partially rescue pancreatic cells from the reduction in cell viability caused by EXOSC4 knockdown. Our study provides evidence for EXOSC4-mediated regulation of BIK and SESN2 mRNA in the survival of pancreatic tumor cells.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yuki Shimoura
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Shuhei Mitsutomi
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Nobue Tamamura
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Kenji Takahashi
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yusuke Mizukami
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
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Abstract
Large-scale exome sequencing of tumors has enabled the identification of cancer drivers using recurrence-based approaches. Some of these methods also employ 3D protein structures to identify mutational hotspots in cancer-associated genes. In determining such mutational clusters in structures, existing approaches overlook protein dynamics, despite its essential role in protein function. We present a framework to identify cancer driver genes using a dynamics-based search of mutational hotspot communities. Mutations are mapped to protein structures, which are partitioned into distinct residue communities. These communities are identified in a framework where residue-residue contact edges are weighted by correlated motions (as inferred by dynamics-based models). We then search for signals of positive selection among these residue communities to identify putative driver genes, while applying our method to the TCGA (The Cancer Genome Atlas) PanCancer Atlas missense mutation catalog. Overall, we predict 1 or more mutational hotspots within the resolved structures of proteins encoded by 434 genes. These genes were enriched among biological processes associated with tumor progression. Additionally, a comparison between our approach and existing cancer hotspot detection methods using structural data suggests that including protein dynamics significantly increases the sensitivity of driver detection.
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Omarini C, Bettelli S, Caprera C, Manfredini S, Caggia F, Guaitoli G, Moscetti L, Toss A, Cortesi L, Kaleci S, Maiorana A, Cascinu S, Conte PF, Piacentini F. Clinical and molecular predictors of long-term response in HER2 positive metastatic breast cancer patients. Cancer Biol Ther 2018; 19:879-886. [PMID: 30067438 DOI: 10.1080/15384047.2018.1480287] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND HER2+ metastatic breast cancer (MBC) is a poor prognosis disease, unusually curable. To date, no predictive factors have been clearly correlated with long-term response to anti-HER2 agents. METHODS 54 HER2+ MBC patients treated with HER2 targeted therapy as first line treatment were analysed: 40 with a time to progression longer than 3 years in Long Responders (LR) group and 14 with a progression disease within one year of anti-HER2 therapy in a control group named Early Progressors (EP). The expression of 770 genes and 13 molecular pathways were evaluated using Nanostring PanCancer pathway panel performed on FFPE BC tissues. RESULTS Considering baseline patients and tumor characteristics, EP women had more CNS spread and more metastatic burden of disease compared to LR (p > 0.05). Gene expression analysis identified 30 genes with significantly different expression in the two cohorts; five were driver genes (BRCA1, PDGFRA, AR, PHF6 and MSH2). The majority of these genes were over-expressed, mainly in LR patients, and encoded growth factors, pro- or anti-inflammatory interleukins and DNA repair factors. Only four genes were down regulated, all in EP group (TNFSF10, CACNG1, IL20RB and BRCA1). Most of these genes were involved in MAPK and PI3K pathways. MAPK pathway was differently expressed between LR and EP (p = 0.05). PI3K was the only pathway overexpressed in EP patients. CONCLUSIONS Whole genome expression analysis comparing LR vs. EP identified a group of genes that may predict more favourable long-term outcomes. Up-regulation of MAPK and down-regulation of PI3K pathway could be a positive predictive factors. Further clinical implications are warranted. ABBREVIATIONS BC: breast cancer; MBC: metastatic breast cancer; LR: long responder; EP: early progressor; FFPE: formalin-fixed paraffin-embedded; CNS: central nervous system; PFS: progression free survival; OS: overall survival.
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Affiliation(s)
- Claudia Omarini
- a Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults , University Hospital of Modena , Modena , Italy
| | - Stefania Bettelli
- b Division of Pathological Anatomy, Department of Diagnostic, Clinical Medicine and Public Health , University Hospital of Modena , Modena , Italy
| | - Cecilia Caprera
- b Division of Pathological Anatomy, Department of Diagnostic, Clinical Medicine and Public Health , University Hospital of Modena , Modena , Italy
| | - Samantha Manfredini
- b Division of Pathological Anatomy, Department of Diagnostic, Clinical Medicine and Public Health , University Hospital of Modena , Modena , Italy
| | - Federica Caggia
- a Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults , University Hospital of Modena , Modena , Italy
| | - Giorgia Guaitoli
- a Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults , University Hospital of Modena , Modena , Italy
| | - Luca Moscetti
- a Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults , University Hospital of Modena , Modena , Italy
| | - Angela Toss
- a Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults , University Hospital of Modena , Modena , Italy
| | - Laura Cortesi
- a Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults , University Hospital of Modena , Modena , Italy
| | - Shaniko Kaleci
- b Division of Pathological Anatomy, Department of Diagnostic, Clinical Medicine and Public Health , University Hospital of Modena , Modena , Italy
| | - Antonino Maiorana
- b Division of Pathological Anatomy, Department of Diagnostic, Clinical Medicine and Public Health , University Hospital of Modena , Modena , Italy
| | - Stefano Cascinu
- a Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults , University Hospital of Modena , Modena , Italy
| | - Pier Franco Conte
- c Department of Surgery, Oncology, and Gastroenterology , University of Padova , Padova , Italy
| | - Federico Piacentini
- a Division of Medical Oncology, Department of Medical and Surgical Sciences for Children & Adults , University Hospital of Modena , Modena , Italy
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Cooper LAD, Demicco EG, Saltz JH, Powell RT, Rao A, Lazar AJ. PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective. J Pathol 2018; 244:512-524. [PMID: 29288495 PMCID: PMC6240356 DOI: 10.1002/path.5028] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 02/06/2023]
Abstract
The Cancer Genome Atlas (TCGA) represents one of several international consortia dedicated to performing comprehensive genomic and epigenomic analyses of selected tumour types to advance our understanding of disease and provide an open-access resource for worldwide cancer research. Thirty-three tumour types (selected by histology or tissue of origin, to include both common and rare diseases), comprising >11 000 specimens, were subjected to DNA sequencing, copy number and methylation analysis, and transcriptomic, proteomic and histological evaluation. Each cancer type was analysed individually to identify tissue-specific alterations, and make correlations across different molecular platforms. The final dataset was then normalized and combined for the PanCancer Initiative, which seeks to identify commonalities across different cancer types or cells of origin/lineage, or within anatomically or morphologically related groups. An important resource generated along with the rich molecular studies is an extensive digital pathology slide archive, composed of frozen section tissue directly related to the tissues analysed as part of TCGA, and representative formalin-fixed paraffin-embedded, haematoxylin and eosin (H&E)-stained diagnostic slides. These H&E image resources have primarily been used to verify diagnoses and histological subtypes with some limited extraction of standard pathological variables such as mitotic activity, grade, and lymphocytic infiltrates. Largely overlooked is the richness of these scanned images for more sophisticated feature extraction approaches coupled with machine learning, and ultimately correlation with molecular features and clinical endpoints. Here, we document initial attempts to exploit TCGA imaging archives, and describe some of the tools, and the rapidly evolving image analysis/feature extraction landscape. Our hope is to inform, and ultimately inspire and challenge, the pathology and cancer research communities to exploit these imaging resources so that the full potential of this integral platform of TCGA can be used to complement and enhance the insightful integrated analyses from the genomic and epigenomic platforms. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Lee AD Cooper
- Department of Biomedical Informatics, Emory University, Atlanta, GA, USA
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada
| | - Joel H Saltz
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Reid T Powell
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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