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Sucularli C. Identification of BRIP1, NSMCE2, ANAPC7, RAD18 and TTL from chromosome segregation gene set associated with hepatocellular carcinoma. Cancer Genet 2022; 268-269:28-36. [PMID: 36126360 DOI: 10.1016/j.cancergen.2022.09.003] [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: 02/12/2022] [Revised: 07/12/2022] [Accepted: 09/06/2022] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Hepatocellular carcinoma is one of the most frequent cancers with high mortality rate worldwide. METHODS TCGA LIHC HTseq counts were analyzed. GSEA was performed with GO BP gene sets. GO analysis was performed with differentially expressed genes. The subset of genes contributing most of the enrichment result of GO_BP_CHROMOSOME_SEGREGATION of GSEA were identified. Five genes have been selected in this subset of genes for further analysis. A microarray data set, GSE112790, was analyzed as a validation data set. Survival analysis was performed. RESULTS According to GSEA and GO analysis several gene sets and processes related to chromosome segregation were enriched in LIHC. GO_BP_CHROMOSOME_SEGREGATION gene set from GSEA had the highest size of the genes contributing most of the enrichment. Five genes in this gene set; BRIP1, NSMCE2, ANAPC7, RAD18 and TTL, whose expressions and prognostic values have not been studied in hepatocellular carcinoma in detail, have been selected for further analyses. Expression of these five genes were identified as significantly upregulated in LIHC RNA-seq and HCC microarray data set. Survival analysis showed that high expression of the five genes was associated with poor overall survival in HCC patients. CONCLUSION Selected genes were upregulated and had prognostic value in HCC.
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Affiliation(s)
- Ceren Sucularli
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey.
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Burenina OY, Lazarevich NL, Kustova IF, Shavochkina DA, Moroz EA, Kudashkin NE, Patyutko YI, Metelin AV, Kim EF, Skvortsov DA, Zatsepin TS, Rubtsova MP, Dontsova OA. Panel of potential lncRNA biomarkers can distinguish various types of liver malignant and benign tumors. J Cancer Res Clin Oncol 2020; 147:49-59. [PMID: 32918630 DOI: 10.1007/s00432-020-03378-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE Liver cancers are among the deadliest malignancies due to a limited efficacy of early diagnostics, the lack of appropriate biomarkers and insufficient discrimination of different types of tumors by classic and molecular methods. In this study, we searched for novel long non-coding RNA (lncRNA) as well as validated several known candidates suitable as probable biomarkers for primary liver tumors of various etiology. METHODS We described a novel lncRNA HELIS (aka "HEalthy LIver Specific") and estimated its expression by RT-qPCR in 82 paired tissue samples from patients with hepatocellular carcinoma (HCC), cholangiocarcinoma (CCA), combined HCC-CCA, pediatric hepatoblastoma (HBL) and non-malignant hepatocellular adenoma (HCA) and focal nodular hyperplasia (FNH). Additionally, we examined expression of cancer-associated lncRNAs HULC, MALAT1, UCA1, CYTOR, LINC01093 and H19, which were previously studied mainly in HCC. RESULTS We demonstrated that down-regulation of HELIS strongly correlates with carcinogenesis; whereas in tumors with non-hepatocyte origin (HBL, CCA) or in a number of poorly differentiated HCC, this lncRNA is not expressed. We showed that recently discovered LINC01093 is dramatically down-regulated in all malignant liver cancers; while in benign tumors LINC01093 expression is just twice decreased in comparison to adjacent samples. CONCLUSION Our study revealed that among all measured biomarkers only down-regulated HELIS and LINC01093, up-regulated CYTOR and dysregulated HULC are perspective for differential diagnostics of liver cancers; whereas others demonstrated discordant results and cannot be considered as potential universal biomarkers for this purpose.
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Affiliation(s)
- Olga Y Burenina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia, 143026.
| | - Natalia L Lazarevich
- Institute of Carcinogenesis, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
- Biology Department, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Inna F Kustova
- Institute of Carcinogenesis, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Daria A Shavochkina
- Institute of Carcinogenesis, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Ekaterina A Moroz
- Institute of Clinical Oncology, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Nikolay E Kudashkin
- Institute of Clinical Oncology, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Yuriy I Patyutko
- Institute of Clinical Oncology, FSBI "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia, 115478
| | - Alexey V Metelin
- Petrovsky National Research Centre of Surgery, Moscow, Russia, 119991
| | - Eduard F Kim
- Petrovsky National Research Centre of Surgery, Moscow, Russia, 119991
| | - Dmitry A Skvortsov
- Lomonosov Moscow State University, Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia, 119992
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia, 101000
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia, 143026
- Lomonosov Moscow State University, Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia, 119992
| | - Maria P Rubtsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia, 143026
- Lomonosov Moscow State University, Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia, 119992
| | - Olga A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia, 143026
- Lomonosov Moscow State University, Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia, 119992
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Nouri-Vaskeh M, Alizadeh L, Hajiasgharzadeh K, Mokhtarzadeh A, Halimi M, Baradaran B. The role of HSP90 molecular chaperones in hepatocellular carcinoma. J Cell Physiol 2020; 235:9110-9120. [PMID: 32452023 DOI: 10.1002/jcp.29776] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023]
Abstract
Misfolded proteins have enhanced formation of toxic oligomers and nonfunctional protein copies lead to recruiting wild-type protein types. Heat shock protein 90 (HSP90) is a molecular chaperone generated by cells that are involved in many cellular functions through regulation of folding and/or localization of large multi-protein complexes as well as client proteins. HSP90 can regulate a number of different cellular processes including cell proliferation, motility, angiogenesis, signal transduction, and adaptation to stress. HSP90 makes the mutated oncoproteins able to avoid misfolding and degradation and permits the malignant transformation. As a result, HSP90 is an important factor in several signaling pathways associated with tumorigenicity, therapy resistance, and inhibiting apoptosis. Clinically, the upregulation of HSP90 expression in hepatocellular carcinoma (HCC) is linked with advanced stages and inappropriate survival in cases suffering from this kind of cancer. The present review comprehensively assesses HSP90 functions and its possible usefulness as a potential diagnostic biomarker and therapeutic option for HCC.
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Affiliation(s)
- Masoud Nouri-Vaskeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Alizadeh
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Monireh Halimi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Kiani A, Uyumazturk B, Rajpurkar P, Wang A, Gao R, Jones E, Yu Y, Langlotz CP, Ball RL, Montine TJ, Martin BA, Berry GJ, Ozawa MG, Hazard FK, Brown RA, Chen SB, Wood M, Allard LS, Ylagan L, Ng AY, Shen J. Impact of a deep learning assistant on the histopathologic classification of liver cancer. NPJ Digit Med 2020; 3:23. [PMID: 32140566 PMCID: PMC7044422 DOI: 10.1038/s41746-020-0232-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 02/06/2020] [Indexed: 12/15/2022] Open
Abstract
Artificial intelligence (AI) algorithms continue to rival human performance on a variety of clinical tasks, while their actual impact on human diagnosticians, when incorporated into clinical workflows, remains relatively unexplored. In this study, we developed a deep learning-based assistant to help pathologists differentiate between two subtypes of primary liver cancer, hepatocellular carcinoma and cholangiocarcinoma, on hematoxylin and eosin-stained whole-slide images (WSI), and evaluated its effect on the diagnostic performance of 11 pathologists with varying levels of expertise. Our model achieved accuracies of 0.885 on a validation set of 26 WSI, and 0.842 on an independent test set of 80 WSI. Although use of the assistant did not change the mean accuracy of the 11 pathologists (p = 0.184, OR = 1.281), it significantly improved the accuracy (p = 0.045, OR = 1.499) of a subset of nine pathologists who fell within well-defined experience levels (GI subspecialists, non-GI subspecialists, and trainees). In the assisted state, model accuracy significantly impacted the diagnostic decisions of all 11 pathologists. As expected, when the model's prediction was correct, assistance significantly improved accuracy (p = 0.000, OR = 4.289), whereas when the model's prediction was incorrect, assistance significantly decreased accuracy (p = 0.000, OR = 0.253), with both effects holding across all pathologist experience levels and case difficulty levels. Our results highlight the challenges of translating AI models into the clinical setting, and emphasize the importance of taking into account potential unintended negative consequences of model assistance when designing and testing medical AI-assistance tools.
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Affiliation(s)
- Amirhossein Kiani
- Department of Computer Science, Stanford University, Stanford, CA USA
| | - Bora Uyumazturk
- Department of Computer Science, Stanford University, Stanford, CA USA
| | - Pranav Rajpurkar
- Department of Computer Science, Stanford University, Stanford, CA USA
| | - Alex Wang
- Department of Computer Science, Stanford University, Stanford, CA USA
| | - Rebecca Gao
- Stanford University School of Medicine, Stanford, CA USA
| | - Erik Jones
- Department of Computer Science, Stanford University, Stanford, CA USA
| | - Yifan Yu
- Department of Computer Science, Stanford University, Stanford, CA USA
| | - Curtis P. Langlotz
- Center for Artificial Intelligence in Medicine & Imaging, Stanford University, Stanford, CA USA
- Department of Radiology, Stanford University, Stanford, CA USA
| | - Robyn L. Ball
- Center for Artificial Intelligence in Medicine & Imaging, Stanford University, Stanford, CA USA
| | - Thomas J. Montine
- Center for Artificial Intelligence in Medicine & Imaging, Stanford University, Stanford, CA USA
- Department of Pathology, Stanford University, Stanford, CA USA
| | - Brock A. Martin
- Department of Pathology, Stanford University, Stanford, CA USA
| | - Gerald J. Berry
- Department of Pathology, Stanford University, Stanford, CA USA
| | | | | | - Ryanne A. Brown
- Department of Pathology, Stanford University, Stanford, CA USA
| | - Simon B. Chen
- Department of Pathology, Stanford University, Stanford, CA USA
| | - Mona Wood
- Department of Pathology, Stanford University, Stanford, CA USA
| | - Libby S. Allard
- Department of Pathology, Stanford University, Stanford, CA USA
| | - Lourdes Ylagan
- Department of Pathology, Stanford University, Stanford, CA USA
| | - Andrew Y. Ng
- Department of Computer Science, Stanford University, Stanford, CA USA
| | - Jeanne Shen
- Center for Artificial Intelligence in Medicine & Imaging, Stanford University, Stanford, CA USA
- Department of Pathology, Stanford University, Stanford, CA USA
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