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Sharma J, Jangale V, Swain AK, Yadav P. An optimized instrument variable selection approach to improve causality estimation in association studies. Sci Rep 2024; 14:22781. [PMID: 39354059 PMCID: PMC11445377 DOI: 10.1038/s41598-024-73970-z] [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: 05/01/2024] [Accepted: 09/23/2024] [Indexed: 10/03/2024] Open
Abstract
Mendelian randomization (MR) is an emerging tool for inferring causality in genetic epidemiology. MR studies suffer bias from weak genetic instrument variables (IVs) and horizontal pleiotropy. We introduce a robust integrative framework strictly adhering with STROBE-MR guidelines to improve causality inference through MR studies. We implemented novel t-statistics-based criteria to improve the reliability of selected IVs followed by various MR methods. Further, we include sensitivity analyses to remove horizontal-pleiotropy bias. For functional validation, we perform enrichment analysis of identified causal SNPs. We demonstrate effectiveness of our proposed approach on 5 different MR datasets selected from diverse populations. Our pipeline outperforms its counterpart MR analyses using default parameters on these datasets. Notably, we found a significant association between total cholesterol and coronary artery disease (P = 1.16 × 10-71) in a single-sample dataset using our pipeline. Contrarily, this same association was deemed ambiguous while using default parameters. Moreover, in a two-sample dataset, we uncover 13 new causal SNPs with enhanced statistical significance (P = 1.06 × 10-11) for liver-iron-content and liver-cell-carcinoma. Likewise, these SNPs remained undetected using the default parameters (P = 7.58 × 10-4). Furthermore, our analysis confirmed previously known pathways, such as hyperlipidemia in heart diseases and gene ME1 in liver cancer. In conclusion, we propose a robust and powerful framework to infer causality across diverse populations and easily adaptable to different diseases.
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Affiliation(s)
- Jyoti Sharma
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, 342030, India
| | - Vaishnavi Jangale
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, 342030, India
| | - Asish Kumar Swain
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, 342030, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, 342030, India.
- School of Artificial Intelligence and Data Science, Indian Institute of Technology Jodhpur, Rajasthan, 342030, India.
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2
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Karpova Y, Orlicky DJ, Schmidt EE, Tulin AV. Disrupting Poly(ADP-ribosyl)ating Pathway Creates Premalignant Conditions in Mammalian Liver. Int J Mol Sci 2023; 24:17205. [PMID: 38139034 PMCID: PMC10743425 DOI: 10.3390/ijms242417205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a major global health concern, representing one of the leading causes of cancer-related deaths. Despite various treatment options, the prognosis for HCC patients remains poor, emphasizing the need for a deeper understanding of the factors contributing to HCC development. This study investigates the role of poly(ADP-ribosyl)ation in hepatocyte maturation and its impact on hepatobiliary carcinogenesis. A conditional Parg knockout mouse model was employed, utilizing Cre recombinase under the albumin promoter to target Parg depletion specifically in hepatocytes. The disruption of the poly(ADP-ribosyl)ating pathway in hepatocytes affects the early postnatal liver development. The inability of hepatocytes to finish the late maturation step that occurs early after birth causes intensive apoptosis and acute inflammation, resulting in hypertrophic liver tissue with enlarged hepatocytes. Regeneration nodes with proliferative hepatocytes eventually replace the liver tissue and successfully fulfill the liver function. However, early developmental changes predispose these types of liver to develop pathologies, including with a malignant nature, later in life. In a chemically induced liver cancer model, Parg-depleted livers displayed a higher tendency for hepatocellular carcinoma development. This study underscores the critical role of the poly(ADP-ribosyl)ating pathway in hepatocyte maturation and highlights its involvement in liver pathologies and hepatobiliary carcinogenesis. Understanding these processes may provide valuable insights into liver biology and liver-related diseases, including cancer.
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Affiliation(s)
- Yaroslava Karpova
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Grand Forks, ND 58202, USA;
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 119334 Moscow, Russia
| | - David J. Orlicky
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA;
| | - Edward E. Schmidt
- Microbiology & Cell Biology, Montana State University, Bozeman, MT 59718, USA;
- Department of Microbiology & Immunology, Lewis Hall, Bozeman, MT 59718, USA
- Redox Biology Laboratory, University of Veterinary Medicine, 1078 Budapest, Hungary
| | - Alexei V. Tulin
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Grand Forks, ND 58202, USA;
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Liu TY, Liao CC, Chang YS, Chen YC, Chen HD, Lai IL, Peng CY, Chung CC, Chou YP, Tsai FJ, Jeng LB, Chang JG. Identification of 13 Novel Loci in a Genome-Wide Association Study on Taiwanese with Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:16417. [PMID: 38003606 PMCID: PMC10671380 DOI: 10.3390/ijms242216417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Liver cancer is caused by complex interactions among genetic factors, viral infection, alcohol abuse, and metabolic diseases. We conducted a genome-wide association study and polygenic risk score (PRS) model in Taiwan, employing a nonspecific etiology approach, to identify genetic risk factors for hepatocellular carcinoma (HCC). Our analysis of 2836 HCC cases and 134,549 controls revealed 13 novel associated loci such as the FAM66C gene, noncoding genes, liver-fibrosis-related genes, metabolism-related genes, and HCC-related pathway genes. We incorporated the results from the UK Biobank and Japanese database into our study for meta-analysis to validate our findings. We also identified specific subtypes of the major histocompatibility complex that influence both viral infection and HCC progression. Using this data, we developed a PRS to predict HCC risk in the general population, patients with HCC, and HCC-affected families. The PRS demonstrated higher risk scores in families with multiple HCCs and other cancer cases. This study presents a novel approach to HCC risk analysis, identifies seven new genes associated with HCC development, and introduces a reproducible PRS model for risk assessment.
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Affiliation(s)
- Ting-Yuan Liu
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chi-Chou Liao
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Ya-Sian Chang
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Yu-Chia Chen
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Hong-Da Chen
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - I-Lu Lai
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Cheng-Yuan Peng
- Department of Internal Medicine, Section of Hepatobiliary Tract, China Medical University Hospital, Taichung 40447, Taiwan;
| | - Chin-Chun Chung
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Yu-Pao Chou
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
- Division of Pediatric Genetics, Children’s Hospital of China Medical University, Taichung 40447, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Long-Bin Jeng
- Department of Surgery, Section of Hepatobiliary Tract, China Medical University Hospital, Taichung 40447, Taiwan;
| | - Jan-Gowth Chang
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan
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Wasilewicz MP. Possible Therapies for Hepatocellular Carcinoma-Preparing for the Modern War with the Insidious Enemy. Int J Mol Sci 2023; 24:12536. [PMID: 37628717 PMCID: PMC10454545 DOI: 10.3390/ijms241612536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) accounts for 7% of all malignancies and about 90% of all primary liver malignancies, making it the most common type of malignant liver neoplasm [...].
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Affiliation(s)
- Michał P Wasilewicz
- Liver Unit, Department of Gastroenterology, Pomeranian Medical University in Szczecin, Unii Lubelskiej Str. 1, 71-252 Szczecin, Poland
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Yang S, Pang L, Dai W, Wu S, Ren T, Duan Y, Zheng Y, Bi S, Zhang X, Kong J. Role of Forkhead Box O Proteins in Hepatocellular Carcinoma Biology and Progression (Review). Front Oncol 2021; 11:667730. [PMID: 34123834 PMCID: PMC8190381 DOI: 10.3389/fonc.2021.667730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/28/2021] [Indexed: 12/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC), the most common type of malignant tumor of the digestive system, is associated with high morbidity and mortality. The main treatment for HCC is surgical resection. Advanced disease, recurrence, and metastasis are the main factors affecting prognosis. Chemotherapy and radiotherapy are not sufficiently efficacious for the treatment of primary and metastatic HCC; therefore, optimizing targeted therapy is essential for improving outcomes. Forkhead box O (FOXO) proteins are widely expressed in cells and function to integrate a variety of growth factors, oxidative stress signals, and other stimulatory signals, thereby inducing the specific expression of downstream signal factors and regulation of the cell cycle, senescence, apoptosis, oxidative stress, HCC development, and chemotherapy sensitivity. Accordingly, FOXO proteins are considered multifunctional targets of cancer treatment. The current review discusses the roles of FOXO proteins, particularly FOXO1, FOXO3, FOXO4, and FOXO6, in HCC and establishes a theoretical basis for the potential targeted therapy of HCC.
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Affiliation(s)
- Shaojie Yang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Liwei Pang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Wanlin Dai
- Innovation Institute of China Medical University, Shenyang, China
| | - Shuodong Wu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tengqi Ren
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yunlong Duan
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yuting Zheng
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shiyuan Bi
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaolin Zhang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jing Kong
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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Neuman MG, Cohen LB, Malnick S. Familial non-alcoholic steatohepatitis leading to hepatocellular carcinoma. Chem Biol Interact 2020; 323:109054. [PMID: 32217109 DOI: 10.1016/j.cbi.2020.109054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 02/17/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Non-alcoholic steatohepatitis (NASH) has been associated with fibrosis that may progress to cirrhosis. The purpose of this study was to examine hepatocytes and perisinusoidal cells in liver biopsies of 3 families (3 males and 4 females) with non-cirrhotic and cirrhotic NASH to determine unique histological changes during a period of 2-7 years from diagnosis. METHODS In this study, hepatocytes, stellate cells and Kupffer cells were analyzed using light and electron microscopy, and immunohistochemistry with specific anti-macrophage antibody staining of liver biopsies. RESULTS Body mass index of all patients was over 28, and all viral, metabolic markers were negative. Alcohol consumption was insignificant. In all liver biopsies, diffuse, non-zonal macrovesicular steatosis involved 40-70% of liver samples. The lobular hepatocytes showed prominent ballooning hepatocyte degeneration. No Mallory Denk hyaline bodies (MDBs) were observed in three of the patients. MDBs developed in ballooned hepatocytes of four individuals that also presented foci of lobular inflammation. The apoptotic bodies were stained by cytokeratin 18. The trichrome stain revealed portal to portal bridging fibrosis. In one family, there was a three-fold increase in relative numbers of perisinusoidal macrophages in the older sister with NASH compared to livers of the younger siblings. The special finding in livers of patients with NASH was accumulation of groups of perisinusoidal macrophages, which was not associated with focal necrosis. CONCLUSION Perisinusoidal macrophages appear to accumulate in NASH. It is possible that collections of macrophages are a response to chronic portal endotoxemia or lipotoxic activation of immuno-mediators. The persistent activation of these macrophages could lead to the chronic release of pro-inflammatory cytokines and contribute to chronic inflammation, fibrosis and cirrhosis leading to HCC.
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Affiliation(s)
- Manuela G Neuman
- In Vitro Drug Safety and Biotechnology, Canada; Department of Pharmacology & Toxicology, University of Toronto, Canada.
| | - Lawrence B Cohen
- Division of Gastroenterology, Sunnybrook Health Science Centre, Canada; Department of Medicine, University of Toronto, Toronto, Canada.
| | - Stephen Malnick
- Department of Internal Medicine, Kaplan Medical Centre, Affiliated to Hebrew University, Rehovot, Israel.
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Bailey A, Shah SA. Screening high risk populations for cancer: Hepatobiliary. J Surg Oncol 2019; 120:847-850. [DOI: 10.1002/jso.25633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/28/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Amanda Bailey
- Solid Organ Transplantation, Department of SurgeryUniversity of Cincinnati College of Medicine Cincinnati Ohio
| | - Shimul A. Shah
- Solid Organ Transplantation, Department of SurgeryUniversity of Cincinnati College of Medicine Cincinnati Ohio
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