1
|
Sayed K, Dolin CE, Wilkey DW, Li J, Sato T, Beier JI, Argemi J, Bataller R, Wahed AS, Merchant ML, Benos PV, Arteel GE. A plasma peptidomic signature reveals extracellular matrix remodeling and predicts prognosis in alcohol-related hepatitis. medRxiv 2023:2023.12.13.23299905. [PMID: 38168372 PMCID: PMC10760272 DOI: 10.1101/2023.12.13.23299905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Alcohol-related hepatitis (AH) is plagued with high mortality and difficulty in identifying at-risk patients. The extracellular matrix undergoes significant remodeling during inflammatory liver injury that can be detected in biological fluids and potentially used for mortality prediction. EDTA plasma samples were collected from AH patients (n= 62); Model for End-Stage Liver Disease (MELD) score defined AH severity as moderate (12-20; n=28) and severe (>20; n=34). The peptidome data was collected by high resolution, high mass accuracy UPLC-MS. Univariate and multivariate analyses identified differentially abundant peptides, which were used for Gene Ontology, parent protein matrisomal composition and protease involvement. Machine learning methods were used on patient-specific peptidome and clinical data to develop mortality predictors. Analysis of plasma peptides from AH patients and healthy controls identified over 1,600 significant peptide features corresponding to 130 proteins. These were enriched for ECM fragments in AH samples, likely related to turnover of hepatic-derived proteins. Analysis of moderate versus severe AH peptidomes showed a shift in abundance of peptides from collagen 1A1 and fibrinogen A proteins. The dominant proteases for the AH peptidome spectrum appear to be CAPN1 and MMP12. Increase in hepatic expression of these proteases was orthogonally-validated in RNA-seq data of livers from AH patients. Causal graphical modeling identified four peptides directly linked to 90-day mortality in >90% of the learned graphs. These peptides improved the accuracy of mortality prediction over MELD score and were used to create a clinically applicable mortality prediction assay. A signature based on plasma peptidome is a novel, non-invasive method for prognosis stratification in AH patients. Our results could also lead to new mechanistic and/or surrogate biomarkers to identify new AH mechanisms. Lay summary We used degraded proteins found the blood of alcohol-related hepatitis patients to identify new potential mechanisms of injury and to predict 90 day mortality.
Collapse
|
2
|
Sato T, Head KZ, Li J, Dolin CE, Wilkey D, Skirtich N, Smith K, McCreary DD, Liu S, Beier JI, Singhi AD, McEnaney RM, Merchant ML, Arteel GE. Fibrosis resolution in the mouse liver: Role of Mmp12 and potential role of calpain 1/2. Matrix Biol Plus 2023; 17:100127. [PMID: 36632559 PMCID: PMC9826883 DOI: 10.1016/j.mbplus.2022.100127] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/05/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
Although most work has focused on resolution of collagen ECM, fibrosis resolution involves changes to several ECM proteins. The purpose of the current study was twofold: 1) to examine the role of MMP12 and elastin; and 2) to investigate the changes in degraded proteins in plasma (i.e., the "degradome") in a preclinical model of fibrosis resolution. Fibrosis was induced by 4 weeks carbon tetrachloride (CCl4) exposure, and recovery was monitored for an additional 4 weeks. Some mice were treated with daily MMP12 inhibitor (MMP408) during the resolution phase. Liver injury and fibrosis was monitored by clinical chemistry, histology and gene expression. The release of degraded ECM peptides in the plasma was analyzed using by 1D-LC-MS/MS, coupled with PEAKS Studio (v10) peptide identification. Hepatic fibrosis and liver injury rapidly resolved in this mouse model. However, some collagen fibrils were still present 28d after cessation of CCl4. Despite this persistent collagen presence, expression of canonical markers of fibrosis were also normalized. The inhibition of MMP12 dramatically delayed fibrosis resolution under these conditions. LC-MS/MS analysis identified that several proteins were being degraded even at late stages of fibrosis resolution. Calpains 1/2 were identified as potential new proteases involved in fibrosis resolution. CONCLUSION. The results of this study indicate that remodeling of the liver during recovery from fibrosis is a complex and highly coordinated process that extends well beyond the degradation of the collagenous scar. These results also indicate that analysis of the plasma degradome may yield new insight into the mechanisms of fibrosis recovery, and by extension, new "theragnostic" targets. Lastly, a novel potential role for calpain activation in the degradation and turnover of proteins was identified.
Collapse
Affiliation(s)
- Toshifumi Sato
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, United States
| | - Kimberly Z. Head
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Jiang Li
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, United States
| | - Christine E. Dolin
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Daniel Wilkey
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville, Louisville, KY 40292, United States
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40292, United States
| | - Nolan Skirtich
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Katelyn Smith
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Dylan D. McCreary
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Sylvia Liu
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Juliane I. Beier
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Aatur D. Singhi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Ryan M. McEnaney
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Michael L. Merchant
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville, Louisville, KY 40292, United States
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40292, United States
| | - Gavin E. Arteel
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, United States
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15213, United States
| |
Collapse
|
3
|
Abstract
Chronic fatty liver disease is common worldwide. This disease is a spectrum of disease states, ranging from simple steatosis (fat accumulation) to inflammation, and eventually to fibrosis and cirrhosis if untreated. The fibrotic stage of chronic liver disease is primarily characterized by robust accumulation of extracellular matrix (ECM) proteins (collagens) that ultimately impairs the function of the organ. The role of the ECM in early stages of chronic liver disease is less well-understood, but recent research has demonstrated that several changes in the hepatic ECM in prefibrotic liver disease are not only present but may also contribute to disease progression. The purpose of this review is to summarize the established and proposed changes to the hepatic ECM that may contribute to inflammation during earlier stages of disease development, and to discuss potential mechanisms by which these changes may mediate the progression of the disease.
Collapse
Affiliation(s)
- Christine E. Dolin
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, Kentucky
| | - Gavin E. Arteel
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania,Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
4
|
Hudson SV, Dolin CE, Poole LG, Massey VL, Wilkey D, Beier JI, Merchant ML, Frieboes HB, Arteel GE. Modeling the Kinetics of Integrin Receptor Binding to Hepatic Extracellular Matrix Proteins. Sci Rep 2017; 7:12444. [PMID: 28963535 PMCID: PMC5622105 DOI: 10.1038/s41598-017-12691-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/14/2017] [Indexed: 02/06/2023] Open
Abstract
The composition of the extracellular matrix (ECM) proteins and the expression of their cognate receptors dictate cell behavior and dynamics. In particular, the interactions of ECM proteins with integrin receptors are key mediators of these cellular processes, playing a crucial role in the progression of several diseases of the liver, including inflammation, fibrosis/cirrhosis and cancer. This study establishes a modeling approach combining computation and experiments to evaluate the kinetics of integrin receptor binding to hepatic ECM proteins. ECM ligand concentration was derived from LC-MS/MS quantification of the hepatic ECM from mice exposed to chronic carbon tetrachloride (CCl4); receptor density was derived from published literature. Mathematical models for ECM-integrin binding kinetics that were developed incorporate receptor divalence and an aggregation scheme to represent clustering. The computer simulations reproduced positive cooperativity in the receptor aggregation model when the aggregation equilibrium constant (Ka) was positive and greater than Keq for divalent complex formation. Importantly, the modeling projected an increase in integrin binding for several receptors for which signaling is known to be increased after CCl4 exposure in the liver. The proposed modeling approach may be of use to elucidate the kinetics of integrin receptor binding to ECM proteins for homeostatic and diseased livers.
Collapse
Affiliation(s)
- Shanice V Hudson
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
- Department of Bioengineering, University of Louisville, Louisville, KY, 40208, USA
| | - Christine E Dolin
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Lauren G Poole
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Veronica L Massey
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Daniel Wilkey
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Juliane I Beier
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Michael L Merchant
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Hermann B Frieboes
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
- Department of Bioengineering, University of Louisville, Louisville, KY, 40208, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA
| | - Gavin E Arteel
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA.
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, 40202, KY, USA.
| |
Collapse
|
5
|
Dent LL, Mandape SN, Pratap S, Dong J, Davis J, Gaddy JA, Amoah K, Damo S, Marshall DR, Jones J, Brandt T, Diaz G, Wang Q, Gary T, Yenamandra A, Ghattas MZ, Elrakaiby M, Aziz RK, Zedan HH, Elmassry M, ElRakaiby M, Aziz RK, Lotfy M, Elmassry M, Marcel J, Khattab RA, Abdelfattah MM, Gilbert JA, Aziz RK, Dini P, Loux SC, Scoggin KE, Esteller-Vico A, Squires EL, Troedsson MHT, Daels P, Ball BA, De Silva K, Bailey E, Stephens JC, Kalbfleisch TS, Dolin CE, Poole LG, Wilkey DW, Rouchka EC, Arteel GE, Barati MT, Merchant ML, Higashi RM, Fan TWM, Moseley H, Lane AN. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings. BMC Proc 2017. [PMCID: PMC5667591 DOI: 10.1186/s12919-017-0078-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
6
|
Massey VL, Dolin CE, Poole LG, Hudson SV, Siow DL, Brock GN, Merchant ML, Wilkey DW, Arteel GE. The hepatic "matrisome" responds dynamically to injury: Characterization of transitional changes to the extracellular matrix in mice. Hepatology 2017; 65:969-982. [PMID: 28035785 PMCID: PMC5319876 DOI: 10.1002/hep.28918] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/14/2016] [Accepted: 10/16/2016] [Indexed: 12/13/2022]
Abstract
UNLABELLED The extracellular matrix (ECM) consists of diverse components that work bidirectionally with surrounding cells to create a responsive microenvironment. In some contexts (e.g., hepatic fibrosis), changes to the ECM are well recognized and understood. However, it is becoming increasingly accepted that the hepatic ECM proteome (i.e., matrisome) responds dynamically to stress well before fibrosis. The term "transitional tissue remodeling" describes qualitative and quantitative ECM changes in response to injury that do not alter the overall architecture of the organ; these changes in ECM may contribute to early disease initiation and/or progression. The nature and magnitude of these changes to the ECM in liver injury are poorly understood. The goals of this work were to validate analysis of the ECM proteome and compare the impact of 6 weeks of ethanol diet and/or acute lipopolysaccharide (LPS). Liver sections were processed in a series of increasingly rigorous extraction buffers to separate proteins by solubility. Extracted proteins were identified using liquid chromatography/tandem mass spectrometry (LC-MS/MS). Both ethanol and LPS dramatically increased the number of matrisome proteins ∼25%. The enhancement of LPS-induced liver damage by ethanol preexposure was associated with unique protein changes. CONCLUSION An extraction method to enrich the hepatic ECM was characterized. The results demonstrate that the hepatic matrisome responds dynamically to both acute (LPS) and chronic (ethanol) stresses, long before more-dramatic fibrotic changes to the liver occur. The changes to the mastrisome may contribute, at least in part, to the pathological responses to these stresses. It is also interesting that several ECM proteins responded similarly to both stresses, suggesting a common mechanism in both models. Nevertheless, there were responses that were unique to the individual and combined exposures. (Hepatology 2017;65:969-982).
Collapse
Affiliation(s)
- Veronica L. Massey
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Christine E. Dolin
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Lauren G. Poole
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Shanice V. Hudson
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Deanna L. Siow
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Guy N. Brock
- Department of Bioinformatics and Biostatistics, University of Louisville Health Sciences Center, Louisville, KY
| | - Michael L. Merchant
- University of Louisville Alcohol Research Center, Louisville, KY,Department of Medicine, University of Louisville Health Sciences Center, Louisville, KY
| | - Daniel W. Wilkey
- University of Louisville Alcohol Research Center, Louisville, KY,Department of Medicine, University of Louisville Health Sciences Center, Louisville, KY
| | - Gavin E. Arteel
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| |
Collapse
|