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van Huizen NA, Coebergh van den Braak RRJ, Doukas M, Dekker LJM, IJzermans JNM, Luider TM. Up-regulation of collagen proteins in colorectal liver metastasis compared with normal liver tissue. J Biol Chem 2018; 294:281-289. [PMID: 30409905 DOI: 10.1074/jbc.ra118.005087] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/07/2018] [Indexed: 01/30/2023] Open
Abstract
Changes to extracellular matrix (ECM) structures are linked to tumor cell proliferation and metastasis. We previously reported that naturally occurring peptides of collagen type I are elevated in urine of patients with colorectal liver metastasis (CRLM). In the present study, we took an MS-based proteomic approach to identify specific collagen types that are up-regulated in CRLM tissues compared with healthy, adjacent liver tissues from the same patients. We found that 19 of 22 collagen-α chains are significantly up-regulated (p < 0.05) in CRLM tissues compared with the healthy tissues. At least four collagen-α chains were absent or had low expression in healthy colon and adjacent tissues, but were highly abundant in both colorectal cancer (CRC) and CRLM tissues. This expression pattern was also observed for six noncollagen colon-specific proteins, two of which (CDH17 and PPP1R1B/DARP-32) had not previously been linked to CRLM. Furthermore, we observed CRLM-associated up-regulation of 16 proteins (of 20 associated proteins identified) known to be required for collagen synthesis, indicating increased collagen production in CRLM. Immunohistochemistry validated that collagen type XII is significantly up-regulated in CRLM. The results of this study indicate that most collagen isoforms are up-regulated in CRLM compared with healthy tissues, most likely as a result of an increased collagen production in the metastatic cells. Our findings provide further insight into morphological changes in the ECM in CRLM and help explain the finding of tumor metastasis-associated proteins and peptides in urine, suggesting their utility as metastasis biomarkers.
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Affiliation(s)
- Nick A van Huizen
- Department of Surgery, Erasmus University Medical Center, P.O. Box 1738, 3015 GE Rotterdam, The Netherlands; Department of Neurology, Erasmus University Medical Center, P.O. Box 1738, 3015 GE Rotterdam, The Netherlands
| | | | - Michael Doukas
- Department of Pathology, Erasmus University Medical Center, P.O. Box 1738, 3015 GE Rotterdam, The Netherlands
| | - Lennard J M Dekker
- Department of Neurology, Erasmus University Medical Center, P.O. Box 1738, 3015 GE Rotterdam, The Netherlands
| | - Jan N M IJzermans
- Department of Surgery, Erasmus University Medical Center, P.O. Box 1738, 3015 GE Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center, P.O. Box 1738, 3015 GE Rotterdam, The Netherlands.
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154
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Wang T, Holt MV, Young NL. Early butyrate induced acetylation of histone H4 is proteoform specific and linked to methylation state. Epigenetics 2018; 13:519-535. [PMID: 29940793 DOI: 10.1080/15592294.2018.1475979] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Histone posttranslational modifications (PTMs) help regulate DNA templated processes; however, relatively little work has unbiasedly explored the single-molecule combinations of histone PTMs, their dynamics on short timescales, or how these preexisting histone PTMs modulate further histone modifying enzyme activity. We use quantitative top down proteomics to unbiasedly measure histone H4 proteoforms (single-molecule combinations of PTMs) upon butyrate treatment. Our results show that histone proteoforms change in cells within 10 minutes of application of sodium butyrate. Cells recover from treatment within 30 minutes after removal of butyrate. Surprisingly, K20me2 containing proteoforms are the near-exclusive substrate of histone acetyltransferases upon butyrate treatment. Single-molecule hierarchies of progressive PTMs mostly dictate the addition and removal of histone PTMs (K16ac > K12ac ≥ K8ac > K5ac, and the reverse on recovery). This reveals the underlying single-molecule mechanism that explains the previously reported but indistinct and unexplained patterns of H4 acetylation. Thus, preexisting histone PTMs strongly modulate histone modifying enzyme activity and this suggests that proteoform constrained reaction pathways are crucial mechanisms that enable the long-term stability of the cellular epigenetic state.
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Affiliation(s)
- Tao Wang
- a Verna & Marrs McLean Department of Biochemistry & Molecular Biology , Baylor College of Medicine , Houston , TX
| | - Matthew V Holt
- a Verna & Marrs McLean Department of Biochemistry & Molecular Biology , Baylor College of Medicine , Houston , TX
| | - Nicolas L Young
- a Verna & Marrs McLean Department of Biochemistry & Molecular Biology , Baylor College of Medicine , Houston , TX.,b Department of Molecular and Cellular Biology , Baylor College of Medicine , Houston , TX
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155
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Chua MD, Hipolito KJ, Singerr OB, Solway J, Guttman JA. SM22 is required for the maintenance of actin-rich structures generated during bacterial infections. Exp Cell Res 2018; 369:139-146. [PMID: 29778753 DOI: 10.1016/j.yexcr.2018.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 11/19/2022]
Abstract
The host actin cytoskeleton is utilized by an assortment of pathogenic bacteria to colonize and cause disease in their hosts. Two prominently studied actin-hijacking bacteria are enteropathogenic Escherichia coli (EPEC) and Listeria monocytogenes. EPEC form actin-rich pedestals atop its host cells to move across the intestinal epithelia, while Listeria monocytogenes generate branched actin networks arranged as actin clouds around the bacteria and as comet tails for propulsion within and amongst their host cells. Previous mass spectrometry analysis revealed that a member of the calponin family of actin-bundling proteins, transgelin/SM22 was enriched in EPEC pedestals. To validate that finding and examine the role of SM22 during infections, we initially immunolocalized SM22 in EPEC and L. monocytogenes infected cells, used siRNA to deplete SM22 and EGFP-SM22 to overexpress SM22, then quantified the alterations to the bacterially generated actin structures. SM22 concentrated at all bacterially-generated actin structures. Depletion of SM22 resulted in fewer pedestals and comet tails and caused comet tails to shorten. The decrease in comet tail abundance caused a proportional increase in actin clouds whereas overexpression of SM22 reversed the actin cloud to comet tail proportions and increased comet tail length, while not influencing EPEC pedestal abundance. Thus, we demonstrate that SM22 plays a role in regulating the transitions and morphological appearance of bacterially generated actin-rich structures during infections.
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Affiliation(s)
- Michael Dominic Chua
- Department of Biological Sciences, Simon Fraser University, 8888 University Dr Shrum Science Centre Rm B7239, Burnaby, BC, Canada V5A1S6
| | - Kevin Jay Hipolito
- Department of Biological Sciences, Simon Fraser University, 8888 University Dr Shrum Science Centre Rm B7239, Burnaby, BC, Canada V5A1S6
| | - Onisokumen Benny Singerr
- Department of Biological Sciences, Simon Fraser University, 8888 University Dr Shrum Science Centre Rm B7239, Burnaby, BC, Canada V5A1S6
| | - Julian Solway
- Department of Medicine, University of Chicago, 5841 S. Maryland Ave, MC6026, Rm BH-M644, Chicago, IL 60637, USA
| | - Julian Andrew Guttman
- Department of Biological Sciences, Simon Fraser University, 8888 University Dr Shrum Science Centre Rm B7239, Burnaby, BC, Canada V5A1S6.
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156
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Wong JKL, Gui H, Kwok M, Ng PW, Lui CHT, Baum L, Sham PC, Kwan P, Cherny SS. Rare variants and de novo variants in mesial temporal lobe epilepsy with hippocampal sclerosis. NEUROLOGY-GENETICS 2018; 4:e245. [PMID: 29904720 PMCID: PMC5999346 DOI: 10.1212/nxg.0000000000000245] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 04/13/2018] [Indexed: 12/03/2022]
Abstract
Objective We investigated the role of rare genetic variants and of de novo variants in the pathogenesis of mesial temporal lobe epilepsy related to hippocampal sclerosis (MTLE-HS). Methods Whole-exome sequencing (WES) was performed in patients with MTLE-HS and their unaffected parents (trios). Genes or gene sets that were enriched with predicted damaging rare variants in the patients as compared to population controls were identified. Patients and their parents were compared to identify whether the variants were de novo or inherited. Results After quality control, WES data from 47 patients (26 female), including 23 complete trios, were available for analysis. Compared with population controls, significant enrichment of rare variants was observed in SEC24B. Integration of gene set data describing neuronal functions and psychiatric disorders showed enrichment signal on fragile X mental retardation protein (FMRP) targets. Twenty-one de novo variants were identified, with many known to cause neuropsychiatric disorders. The FMRP-targeted genes also carried more de novo variants. Inherited compound heterozygous and homozygous variants were identified. Conclusions The genetic architecture underlying MTHE-HS is complex. Multiple genes carrying de novo variants and rare variants among FMRP targets were identified, suggesting a pathogenic role. MTLE-HS and other neuropsychiatric disorders may have shared biology.
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Affiliation(s)
- John K L Wong
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
| | - Hongsheng Gui
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
| | - Maxwell Kwok
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
| | - Ping Wing Ng
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
| | - Colin H T Lui
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
| | - Larry Baum
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
| | - Pak Chung Sham
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
| | - Patrick Kwan
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
| | - Stacey S Cherny
- Centre for Genomic Sciences and Department of Psychiatry (J.K.L.W., H.G., L.B., P.C.S., S.S.C.), Li Ka Shing Faculty of Medicine, The University of Hong Kong; Department of Medicine and Therapeutics (M.K., P.K.), The Chinese University of Hong Kong; Department of Medicine (P.W.N.), United Christian Hospital; Department of Medicine (C.H.T.L.), Queen Elizabeth Hospital, Hong Kong, China; Departments of Medicine and Neurology (P.K.), The University of Melbourne, Royal Melbourne Hospital, Australia; Department of Epidemiology and Preventive Medicine (S.S.C.) and Department of Anatomy and Anthropology (S.S.C.), Sackler Faculty of Medicine, Tel Aviv University, Israel; and The State Key Laboratory of Brain and Cognitive Sciences (P.C.S., S.S.C.)
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157
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Zecha J, Meng C, Zolg DP, Samaras P, Wilhelm M, Kuster B. Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics. Mol Cell Proteomics 2018; 17:974-992. [PMID: 29414762 PMCID: PMC5930408 DOI: 10.1074/mcp.ra118.000583] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/31/2018] [Indexed: 11/06/2022] Open
Abstract
The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass spectrometry-based technologies allow determination of endogenous protein turnover on a proteome-wide scale. However, standard dynamic SILAC (Stable Isotope Labeling in Cell Culture) approaches can suffer from missing data across pulse time-points limiting the accuracy of such analysis. This issue is of particular relevance when studying protein stability at the level of proteoforms because often only single peptides distinguish between different protein products of the same gene. To address this shortcoming, we evaluated the merits of combining dynamic SILAC and tandem mass tag (TMT)-labeling of ten pulse time-points in a single experiment. Although the comparison to the standard dynamic SILAC method showed a high concordance of protein turnover rates, the pulsed SILAC-TMT approach yielded more comprehensive data (6000 proteins on average) without missing values. Replicate analysis further established that the same reproducibility of turnover rate determination can be obtained for peptides and proteins facilitating proteoform resolved investigation of protein stability. We provide several examples of differentially turned over splice variants and show that post-translational modifications can affect cellular protein half-lives. For example, N-terminally processed peptides exhibited both faster and slower turnover behavior compared with other peptides of the same protein. In addition, the suspected proteolytic processing of the fusion protein FAU was substantiated by measuring vastly different stabilities of the cleavage products. Furthermore, differential peptide turnover suggested a previously unknown mechanism of activity regulation by post-translational destabilization of cathepsin D as well as the DNA helicase BLM. Finally, our comprehensive data set facilitated a detailed evaluation of the impact of protein properties and functions on protein stability in steady-state cells and uncovered that the high turnover of respiratory chain complex I proteins might be explained by oxidative stress.
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Affiliation(s)
- Jana Zecha
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- §German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- ¶German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Chen Meng
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Daniel Paul Zolg
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Patroklos Samaras
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Bernhard Kuster
- From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany;
- §German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- ¶German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- ‖Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, 85354 Freising, Germany
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