1
|
Veyel D, Wenger K, Broermann A, Bretschneider T, Luippold AH, Krawczyk B, Rist W, Simon E. Biomarker discovery for chronic liver diseases by multi-omics - a preclinical case study. Sci Rep 2020; 10:1314. [PMID: 31992752 PMCID: PMC6987209 DOI: 10.1038/s41598-020-58030-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is a major cause of liver fibrosis with increasing prevalence worldwide. Currently there are no approved drugs available. The development of new therapies is difficult as diagnosis and staging requires biopsies. Consequently, predictive plasma biomarkers would be useful for drug development. Here we present a multi-omics approach to characterize the molecular pathophysiology and to identify new plasma biomarkers in a choline-deficient L-amino acid-defined diet rat NASH model. We analyzed liver samples by RNA-Seq and proteomics, revealing disease relevant signatures and a high correlation between mRNA and protein changes. Comparison to human data showed an overlap of inflammatory, metabolic, and developmental pathways. Using proteomics analysis of plasma we identified mainly secreted proteins that correlate with liver RNA and protein levels. We developed a multi-dimensional attribute ranking approach integrating multi-omics data with liver histology and prior knowledge uncovering known human markers, but also novel candidates. Using regression analysis, we show that the top-ranked markers were highly predictive for fibrosis in our model and hence can serve as preclinical plasma biomarkers. Our approach presented here illustrates the power of multi-omics analyses combined with plasma proteomics and is readily applicable to human biomarker discovery.
Collapse
Affiliation(s)
- Daniel Veyel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany
| | - Kathrin Wenger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany
| | - Andre Broermann
- Boehringer Ingelheim Pharma GmbH & Co. KG, CardioMetabolic Diseases Research, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany
| | - Tom Bretschneider
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany
| | - Andreas H Luippold
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany
| | - Bartlomiej Krawczyk
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany
| | - Wolfgang Rist
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany.
| | - Eric Simon
- Boehringer Ingelheim Pharma GmbH & Co. KG, Computational Biology, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany.
| |
Collapse
|
2
|
Choi Y, Bose S, Shin NR, Song EJ, Nam YD, Kim H. Lactate-Fortified Puerariae Radix Fermented by Bifidobacterium breve Improved Diet-Induced Metabolic Dysregulation via Alteration of Gut Microbial Communities. Nutrients 2020; 12:E276. [PMID: 31973042 PMCID: PMC7070547 DOI: 10.3390/nu12020276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/15/2020] [Accepted: 01/19/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Puerariae Radix (PR), the dried root of Pueraria lobata, is reported to possess therapeutic efficacies against various diseases including obesity, diabetes, and hypertension. Fermentation-driven bioactivation of herbal medicines can result in improved therapeutic potencies and efficacies. METHODS C57BL/6J mice were fed a high-fat diet and fructose in water with PR (400 mg/kg) or PR fermented by Bifidobacterium breve (400 mg/kg) for 10 weeks. Histological staining, qPCR, Western blot, and 16s rRNA sequencing were used to determine the protective effects of PR and fermented PR (fPR) against metabolic dysfunction. RESULTS Treatment with both PR and fPR for 10 weeks resulted in a reduction in body weight gain with a more significant reduction in the latter group. Lactate, important for energy metabolism and homeostasis, was increased during fermentation. Both PR and fPR caused significant down-regulation of the intestinal expression of the MCP-1, IL-6, and TNF-α genes. However, for the IL-6 and TNF-α gene expressions, the inhibitory effect of fPR was more pronounced (p < 0.01) than that of PR (p < 0.05). Oral glucose tolerance test results showed that both PR and fPR treatments improved glucose homeostasis. In addition, there was a significant reduction in the expression of hepatic gene PPARγ, a key regulator of lipid and glucose metabolism, following fPR but not PR treatment. Activation of hepatic AMPK phosphorylation was significantly enhanced by both PR and fPR treatment. In addition, both PR and fPR reduced adipocyte size in highly significant manners (p < 0.001). Treatment by fPR but not PR significantly reduced the expression of PPARγ and low-density lipoproteins in adipose tissue. CONCLUSION Treatment with fPR appears to be more potent than that of PR in improving the pathways related to glucose and lipid metabolism in high-fat diet (HFD)+fructose-fed animals. The results revealed that the process of fermentation of PR enhanced lactate and facilitated the enrichment of certain microbial communities that contribute to anti-obesity and anti-inflammatory activities.
Collapse
Affiliation(s)
- Yura Choi
- Department of Rehabilitation Medicine of Korean Medicine, Dongguk University, 27 Donggukro, Ilsan-donggu, Goyang 10326, Korea; (Y.C.); (N.R.S.)
| | | | - Na Rae Shin
- Department of Rehabilitation Medicine of Korean Medicine, Dongguk University, 27 Donggukro, Ilsan-donggu, Goyang 10326, Korea; (Y.C.); (N.R.S.)
| | - Eun-Ji Song
- Research Group of Gut Microbiome, Korea Food Research Institute, Wanju-gun 24 55365, Korea; (E.-J.S.); (Y.-D.N.)
- Department of Food Biotechnology, Korea University of Science and Technology, Wanju-gun 34113, Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Korea Food Research Institute, Wanju-gun 24 55365, Korea; (E.-J.S.); (Y.-D.N.)
- Department of Food Biotechnology, Korea University of Science and Technology, Wanju-gun 34113, Korea
| | - Hojun Kim
- Department of Rehabilitation Medicine of Korean Medicine, Dongguk University, 27 Donggukro, Ilsan-donggu, Goyang 10326, Korea; (Y.C.); (N.R.S.)
| |
Collapse
|
3
|
Beck JR, Cabral F, Rasineni K, Casey CA, Harris EN, Stains CI. A Panel of Protein Kinase Chemosensors Distinguishes Different Types of Fatty Liver Disease. Biochemistry 2019; 58:3911-3917. [PMID: 31433166 DOI: 10.1021/acs.biochem.9b00547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The worldwide incidence of fatty liver disease continues to rise, which may account for concurrent increases in the frequencies of more aggressive liver ailments. Given the existence of histologically identical fatty liver disease subtypes, there is a critical need for the identification of methods that can classify disease and potentially predict progression. Herein, we show that a panel of protein kinase chemosensors can distinguish fatty liver disease subtypes. These direct activity measurements highlight distinct differences between histologically identical fatty liver diseases arising from diets rich in fat versus alcohol and identify a previously unreported decrease in p38α activity associated with a high-fat diet. In addition, we have profiled kinase activities in both benign (diet-induced) and progressive (STAM) disease models. These experiments provide temporal insights into kinase activity during disease development and progression. Altogether, this work provides the basis for the future development of clinical diagnostics and potential treatment strategies.
Collapse
Affiliation(s)
- Jon R Beck
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Fatima Cabral
- Department of Biochemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Karuna Rasineni
- Division of Gastroenterology-Hepatology , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Research Service, Veterans' Affairs , Nebraska-Western Iowa Health Care System , Omaha , Nebraska 68105 , United States
| | - Carol A Casey
- Division of Gastroenterology-Hepatology , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Research Service, Veterans' Affairs , Nebraska-Western Iowa Health Care System , Omaha , Nebraska 68105 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States
| | - Edward N Harris
- Department of Biochemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States
| | - Cliff I Stains
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Nebraska Center for Integrated Biomolecular Communication , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , United States.,Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States.,Department of Chemistry , University of Virginia , Charlottesville , Virginia 22904 , United States
| |
Collapse
|
4
|
Loomba R, Lawitz E, Mantry PS, Jayakumar S, Caldwell SH, Arnold H, Diehl AM, Djedjos CS, Han L, Myers RP, Subramanian GM, McHutchison JG, Goodman ZD, Afdhal NH, Charlton MR. The ASK1 inhibitor selonsertib in patients with nonalcoholic steatohepatitis: A randomized, phase 2 trial. Hepatology 2018; 67:549-559. [PMID: 28892558 PMCID: PMC5814892 DOI: 10.1002/hep.29514] [Citation(s) in RCA: 395] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/28/2017] [Accepted: 09/06/2017] [Indexed: 12/12/2022]
Abstract
Inhibition of apoptosis signal-regulating kinase 1, a serine/threonine kinase, leads to improvement in inflammation and fibrosis in animal models of nonalcoholic steatohepatitis. We evaluated the safety and efficacy of selonsertib, a selective inhibitor of apoptosis signal-regulating kinase 1, alone or in combination with simtuzumab, in patients with nonalcoholic steatohepatitis and stage 2 or 3 liver fibrosis. In this multicenter phase 2 trial, 72 patients were randomized to receive 24 weeks of open-label treatment with either 6 or 18 mg of selonsertib orally once daily with or without once-weekly injections of 125 mg of simtuzumab or simtuzumab alone. The effect of treatment was assessed by paired pretreatment and posttreatment liver biopsies, magnetic resonance elastography, magnetic resonance imaging-estimated proton density fat fraction, quantitative collagen content, and noninvasive markers of liver injury. Due to the lack of effect of simtuzumab on histology or selonsertib pharmacokinetics, selonsertib groups with and without simtuzumab were pooled. After 24 weeks of treatment, the proportion of patients with a one or more stage reduction in fibrosis in the 18-mg selonsertib group was 13 of 30 (43%; 95% confidence interval, 26-63); in the 6-mg selonsertib group, 8 of 27 (30%; 95% confidence interval, 14-50); and in the simtuzumab-alone group, 2 of 10 (20%; 95% confidence interval, 3-56). Improvement in fibrosis was associated with reductions in liver stiffness on magnetic resonance elastography, collagen content and lobular inflammation on liver biopsy, as well as improvements in serum biomarkers of apoptosis and necrosis. There were no significant differences in adverse events between the treatment groups. Conclusion: These findings suggest that selonsertib may reduce liver fibrosis in patients with nonalcoholic steatohepatitis and stage 2-3 fibrosis. (Hepatology 2018;67:549-559).
Collapse
Affiliation(s)
- Rohit Loomba
- University of California at San DiegoSan DiegoCA
| | - Eric Lawitz
- Texas Liver InstituteUniversity of Texas Health San AntonioSan AntonioTX
| | | | | | | | - Hays Arnold
- Gastroenterology Consultants of San AntonioSan AntonioTX
| | | | | | - Ling Han
- Gilead Sciences, Inc.Foster CityCA
| | | | | | | | | | - Nezam H. Afdhal
- Beth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMA
| | | | | |
Collapse
|
5
|
Visual Liver Score to Stratify Non-Alcoholic Steatohepatitis Risk and Determine Selective Intraoperative Liver Biopsy in Obesity. Obes Surg 2017; 28:427-436. [DOI: 10.1007/s11695-017-2859-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|