1
|
Jiang T, Huang J, Li S, Xu Q, Zhang T, Wang X, Chen D. Bioinformatics analysis of carotid vulnerable plaques associated with the SARS-CoV-2 pattern. Gene 2023; 888:147754. [PMID: 37659598 DOI: 10.1016/j.gene.2023.147754] [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: 06/16/2023] [Revised: 08/03/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
The rupture of carotid artery vulnerable plaque plays a critical role in ischemic stroke, and the widely spread new coronavirus in recent years plays a certain role in the development of human carotid artery vulnerable plaque, we screened out 27 differential expression genes (DEGs) of stable plaque and vulnerable plaque associated with the new coronavirus. Through the construction of the protein-protein interaction (PPI) network, the Cathepsin B (CTSB) and Niemann-Pick Disease Type 2 (NPC2) were identified as crucial expression genes, and further, we confirmed the validity of core gene expression in two validation sets. Additionally, we discovered a significant connection between CTSB, NPC2 and 28 different kinds of immune cells in carotid plaque tissue. We screened out 65 target interacting drugs based on 10 differentially expressed genes through online tools and finally verified the high expression of 2 core genes in fragile plaques through clinical sample experiments. These findings imply that two core genes may be novel targets for molecular diagnostics and immunotherapy of vulnerable plaques.
Collapse
Affiliation(s)
- Tao Jiang
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China; China Medical University, Shenyang, China
| | - Jiaming Huang
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China
| | - Shupeng Li
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China
| | - Qiushi Xu
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China
| | - Tianding Zhang
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China
| | - Xianwei Wang
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China; China Medical University, Shenyang, China.
| | - Dong Chen
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian 116033, China; China Medical University, Shenyang, China.
| |
Collapse
|
2
|
Chen C, Wen M, Jin Y. 1DE-MS Profiling for Proteoform-Correlated Proteomic Analysis, by Combining SDS-PAGE, Whole-Gel Slicing, Quantitative LC-MS/MS, and Reconstruction of Gel Distributions of Several Thousands of Proteins. J Proteome Res 2022; 21:2311-2330. [PMID: 36018058 DOI: 10.1021/acs.jproteome.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SDS-PAGE has often been used in proteomic analysis, but generally for sample prefractionation although the technique separates proteins by molecular masses (Mws) and the information would contribute to proteoform-level analysis. Here, we report a method that combines SDS-PAGE, whole-gel slicing, and quantitative LC-MS/MS for establishing gel distributions of several thousand proteins in a proteome. A previously obtained data set on rat cerebral cortex with cerebral ischemia-reperfusion injury1 was analyzed, and the gel distributions of 5906 proteins were reconstructed. These distributions, referred to as 1DE-MS profiles, revealed that about 30% of the proteins had more than one proteoform detected in the gels. The profiles were categorized into six types by distribution (narrow, dispersed, or broad) and relative deviations between the abundance-peak apparent Mws and calculated Mws. Only 56% of the proteins showed narrow distributions and matched Mws, while the others had rather complex profiles. Bioinformatic analysis on example profiles showed the resolved proteoforms involved alternative splicing, proteolytic processing, glycosylation and ubiquitination, fragmentation, and probably transmembrane structures. Profile-based differential analysis revealed that many of the disease-caused changes were proteoform dependent. This work provided a proteome-scale view of protein distributions in SDS-PAGE gels, and the method would be useful to obtain proteoform-correlated information for in-depth proteomics.
Collapse
Affiliation(s)
- Changming Chen
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Meiling Wen
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Ya Jin
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| |
Collapse
|
3
|
TFE3 Regulates the Function of the Autophagy-Lysosome Pathway to Drive the Invasion and Metastasis of Papillary Thyroid Carcinoma. ACTA ACUST UNITED AC 2021; 2021:3081491. [PMID: 34660181 PMCID: PMC8516586 DOI: 10.1155/2021/3081491] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 09/13/2021] [Indexed: 01/06/2023]
Abstract
Background Accumulating evidence shows that autophagy plays a vital role in tumor occurrence, development, and metastasis and even determines tumor prognosis. However, little is known about its role in papillary thyroid carcinoma (PTC) or the potentially oncogenic role of TFE3 in regulating the autophagy-lysosome system. Methods Immunohistochemistry and quantitative real-time PCR (qRT-PCR) were used to examine the expression of TFE3, P62/SQSTM1, and LC3 in PTC and paracancerous tissues. TFE3, P62/SQSTM1, LC3, cathepsin L (CTSL), and cathepsin B (CTSB) were evaluated using Western blot analysis. After inducing TFE3 overexpression by plasmid or TFE3 downregulation by small interfering RNA (siRNA) transfection, MTT, wound healing, and cell migration and invasion assays were used to verify the effects on invasion, migration, and the levels of autophagy-lysosome system-related proteins such as P62/SQSTM1, LC3, CTSL, and CTSB. Results TFE3 was overexpressed in PTC tissues compared with paracancerous tissues. Analysis of the clinicopathological characteristics of PTC patients showed that high TFE3 expression was significantly correlated with lymph node metastasis. TFE3 overexpression in the PTC cell lines KTC-1 and BCPAP promoted proliferation, invasion, and migration, while TFE3 knockdown had the opposite effects. Furthermore, we identified a positive relationship among the expression levels of TFE3, P62/SQSTM1, LC3, CTSL, and CTSB. We found that silencing TFE3 inhibited the expression of P62/SQSTM1, LC3, CTSL, and CTSB in PTC cells. However, TFE3 overexpression had the opposite effects. Conclusions The present study provided evidence for the underlying mechanisms by which TFE3 induces autophagy-lysosome system activity in PTC.
Collapse
|
4
|
Xu Y, Jin X, Zhang J, Wang K, Jin X, Xu D, Tian X, Liu L. Antitumor Activity of a Novel Double-Targeted System for Folate Receptor-Mediated Delivery of Mitomycin C. ACS OMEGA 2020; 5:26864-26870. [PMID: 33111012 PMCID: PMC7581226 DOI: 10.1021/acsomega.0c04042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
In this study, we designed, formulated, and investigated the potential antitumor activity of a folate receptor (FR)-mediated double-targeted drug delivery system. The system comprised of the FR ligand folic acid (FA), glycine-phenylalanine-leucine-glycine (Gly-Phe-Leu-Gly, GFLG), which can be specifically cleaved by cathepsin B, and the anticancer drug mitomycin C (MMC). The antitumor effect of FA-GFLG-MMC was compared to that of MMC. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay revealed that FA-GFLG-MMC has a significantly higher inhibitory effect on HeLa, SiHa, and PC9 cells (high FR expression) than that on 16HBE and A549 cells (low FR expression). Furthermore, FA-GFLG-MMC inhibited cancer cell proliferation in a dose-dependent manner. Free MMC was toxic to both cancer and normal cells. Apoptosis of the HeLa, SiHa, and PC9 cells was higher than that of the A549 cells; however, the apoptotic effect on 16HBE cells was minimal. Proapoptotic protein bcl-2-associated X-protein (BAX) and antiapoptotic protein BCL-2 play critical roles in cellular defense and apoptotic signal transduction. BAX/BCL-2 ratio is used to determine the intensity of an apoptotic signal and assess whether a cell will survive or undergo apoptosis. BAX and BCL-2 expression in cells treated with 5 μM FA-GFLG-MMC was studied by Western blotting. FA-GFLG-MMC increased the BAX/BCL-2 ratio in HeLa, SiHa, and PC9 cells. The results show that FA-GFLG-MMC can effectively inhibit tumor cell proliferation by inducing apoptosis. Therefore, the system developed can enhance the delivery of anticancer drugs to cancer cells and thereby reduce their toxic effects on normal cells.
Collapse
Affiliation(s)
- Yan Xu
- Center
of Morphological Experiment, Yanbian University, Yanji 133002, Jilin, China
| | - Xiangmei Jin
- Department
of Chemistry, Yanbian University, Yanji 133002, Jilin, China
| | - Jun Zhang
- Center
of Morphological Experiment, Yanbian University, Yanji 133002, Jilin, China
| | - Kun Wang
- Department
of Chemistry, Yanbian University, Yanji 133002, Jilin, China
| | - Xiaoyan Jin
- Department
of Chemistry, Yanbian University, Yanji 133002, Jilin, China
| | - Dongyuan Xu
- Center
of Morphological Experiment, Yanbian University, Yanji 133002, Jilin, China
| | - Xizhe Tian
- Department
of Chemistry, Yanbian University, Yanji 133002, Jilin, China
| | - Lan Liu
- Department
of Pathology, Yanbian University Hospital, Yanji 133000, Jilin, China
| |
Collapse
|
5
|
Cathepsin B: A sellsword of cancer progression. Cancer Lett 2019; 449:207-214. [PMID: 30796968 DOI: 10.1016/j.canlet.2019.02.035] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 12/13/2022]
Abstract
Clinical, biochemical and molecular biology studies have identified lysosome-encapsulated cellular proteases as critical risk factors for cancer progression. Cathepsins represent a group of such proteases aimed at maintenance of cellular homeostasis. Nevertheless, recent reports suggest that Cathepsin B executes other cellular programs such as controlling tumor growth, migration, invasion, angiogenesis, and metastases development. In fact, elevated levels of Cathepsins are found under different pathological conditions including inflammation, infection, neurodegenerative disease, and cancer. Furthermore, the discovery of Cathepsin B secretion and function as an extracellular matrix protein has broadened our appreciation for the impact of Cathepsin B on cancer progression. Underneath a façade of an intracellular protease with limited therapeutic potential hides a central role of cathepsins in extracellular functions. Moreover, this role is incredibly diverse from one condition to the next - from driving caspase-dependent apoptosis to facilitating tumor neovascularization and metastasis. Here we discuss the role of Cathepsin B in the oncogenic process and perspective the use of Cathepsin B for diagnostic and therapeutic applications.
Collapse
|
6
|
Chen CY, Melo E, Jakob P, Friedlein A, Elsässer B, Goettig P, Kueppers V, Delobel F, Stucki C, Dunkley T, Fauser S, Schilling O, Iacone R. N-Terminomics identifies HtrA1 cleavage of thrombospondin-1 with generation of a proangiogenic fragment in the polarized retinal pigment epithelial cell model of age-related macular degeneration. Matrix Biol 2018; 70:84-101. [PMID: 29572155 DOI: 10.1016/j.matbio.2018.03.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 02/08/2023]
Abstract
Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in the elderly population. Variants in the HTRA1-ARMS2 locus have been linked to increased AMD risk. In the present study we investigated the impact of elevated HtrA1 levels on the retina pigment epithelial (RPE) secretome using a polarized culture system. Upregulation of HtrA1 alters the abundance of key proteins involved in angiogenesis and extracellular matrix remodeling. Thrombospondin-1, an angiogenesis modulator, was identified as a substrate for HtrA1 using terminal amine isotope labeling of substrates in conjunction with HtrA1 specificity profiling. HtrA1 cleavage of thrombospondin-1 was further corroborated by in vitro cleavage assays and targeted proteomics together with small molecule inhibition of HtrA1. While thrombospondin-1 is anti-angiogenic, the proteolytically released N-terminal fragment promotes the formation of tube-like structure by endothelial cells. Taken together, our findings suggest a mechanism by which increased levels of HtrA1 may contribute to AMD pathogenesis. The proteomic data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier. For quantitative secretome analysis, project accession: PXD007691, username: reviewer45093@ebi.ac.uk, password: 1FUpS6Yq. For TAILS analysis, project accession: PXD007139, username: reviewer76731@ebi.ac.uk, password: sNbMp7xK.
Collapse
Affiliation(s)
- Chia-Yi Chen
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Esther Melo
- Roche Pharma Research and Early Development, Neuroscience Ophthalmology and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Peter Jakob
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Arno Friedlein
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Brigitta Elsässer
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Peter Goettig
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Verena Kueppers
- Roche Pharma Research and Early Development, Neuroscience Ophthalmology and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Frederic Delobel
- Roche Pharma Research and Early Development, Neuroscience Ophthalmology and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Corinne Stucki
- Roche Pharma Research and Early Development, Neuroscience Ophthalmology and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tom Dunkley
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sascha Fauser
- Roche Pharma Research and Early Development, Neuroscience Ophthalmology and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Roberto Iacone
- Roche Pharma Research and Early Development, Neuroscience Ophthalmology and Rare Diseases Discovery & Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| |
Collapse
|
7
|
Oria VO, Bronsert P, Thomsen AR, Föll MC, Zamboglou C, Hannibal L, Behringer S, Biniossek ML, Schreiber C, Grosu AL, Bolm L, Rades D, Keck T, Werner M, Wellner UF, Schilling O. Proteome Profiling of Primary Pancreatic Ductal Adenocarcinomas Undergoing Additive Chemoradiation Link ALDH1A1 to Early Local Recurrence and Chemoradiation Resistance. Transl Oncol 2018; 11:1307-1322. [PMID: 30172883 PMCID: PMC6121830 DOI: 10.1016/j.tranon.2018.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis with frequent post-surgical local recurrence. The combination of adjuvant chemotherapy with radiotherapy is under consideration to achieve a prolonged progression-free survival (PFS). To date, few studies have determined the proteome profiles associated with response to adjuvant chemoradiation. We herein analyzed the proteomes of primary PDAC tumors subjected to additive chemoradiation after surgical resection and achieving short PFS (median 6 months) versus prolonged PFS (median 28 months). Proteomic analysis revealed the overexpression of Aldehyde Dehydrogenase 1 Family Member A1 (ALDH1A1) and Monoamine Oxidase A (MAOA) in the short PFS cohort, which were corroborated by immunohistochemistry. In vitro, specific inhibition of ALDH1A1 by A37 in combination with gemcitabine, radiation, and chemoradiation lowered cell viability and augmented cell death in MiaPaCa-2 and Panc 05.04 cells. ALDH1A1 silencing in both cell lines dampened cell proliferation, cell metabolism, and colony formation. In MiaPaCa-2 cells, ALDH1A1 silencing sensitized cells towards treatment with gemcitabine, radiation or chemoradiation. In Panc 05.04, increased cell death was observed upon gemcitabine treatment only. These findings are in line with previous studies that have suggested a role of ALDH1A1 chemoradiation resistance, e.g., in esophageal cancer. In summary, we present one of the first proteome studies to investigate the responsiveness of PDAC to chemoradiation and provide further evidence for a role of ALDH1A1 in therapy resistance.
Collapse
Affiliation(s)
- V O Oria
- Institute of Molecular Medicine and Cell Research, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine, Freiburg, Germany
| | - P Bronsert
- Institute of Surgical Pathology, University Medical Center, Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Heidelberg, Germany; Tumorbank Comprehensive Cancer Center Freiburg, Medical Center- University of Freiburg, Germany; Faculty of Medicine, University of Freiburg, Germany
| | - A R Thomsen
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Heidelberg, Germany; Faculty of Medicine, University of Freiburg, Germany; Department of Radiation Oncology, Medical Center - University of Freiburg, Germany
| | - M C Föll
- Institute of Molecular Medicine and Cell Research, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - C Zamboglou
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Heidelberg, Germany; Faculty of Medicine, University of Freiburg, Germany; Department of Radiation Oncology, Medical Center - University of Freiburg, Germany
| | - Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department for Pediatrics, Medical Center, University of Freiburg, Freiburg, Germany
| | - S Behringer
- Laboratory of Clinical Biochemistry and Metabolism, Department for Pediatrics, Medical Center, University of Freiburg, Freiburg, Germany
| | - M L Biniossek
- Institute of Molecular Medicine and Cell Research, Freiburg, Germany
| | - C Schreiber
- Institute of Pathology, UKSH Campus Lübeck, Lübeck, Germany
| | - A L Grosu
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Heidelberg, Germany; Faculty of Medicine, University of Freiburg, Germany; Department of Radiation Oncology, Medical Center - University of Freiburg, Germany
| | - L Bolm
- Clinic of Surgery, UKSH Campus Lübeck, Lübeck, Germany
| | - D Rades
- Department of Radiation Oncology, UKSH Campus Lübeck, Lübeck, Germany
| | - T Keck
- Clinic of Surgery, UKSH Campus Lübeck, Lübeck, Germany
| | - M Werner
- Institute of Surgical Pathology, University Medical Center, Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Heidelberg, Germany; Tumorbank Comprehensive Cancer Center Freiburg, Medical Center- University of Freiburg, Germany; Faculty of Medicine, University of Freiburg, Germany
| | - U F Wellner
- Clinic of Surgery, UKSH Campus Lübeck, Lübeck, Germany
| | - O Schilling
- Institute of Molecular Medicine and Cell Research, Freiburg, Germany; Institute of Surgical Pathology, University Medical Center, Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Heidelberg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
8
|
Lindén M, Ramírez Sepúlveda JI, James T, Thorlacius GE, Brauner S, Gómez-Cabrero D, Olsson T, Kockum I, Wahren-Herlenius M. Sex influences eQTL effects of SLE and Sjögren's syndrome-associated genetic polymorphisms. Biol Sex Differ 2017; 8:34. [PMID: 29070082 PMCID: PMC5657123 DOI: 10.1186/s13293-017-0153-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/09/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) are autoimmune disorders characterized by autoantibodies, dysregulated B cells, and notably high female-to-male incidence ratios. Genome-wide association studies have identified several susceptibility SNPs for both diseases. Many SNPs in the genome are expression quantitative trait loci (eQTLs), with context-dependent effects. Assuming that sex is a biological context, we investigated whether SLE/pSS SNPs act as eQTLs in B cells and used a disease-targeted approach to understand if they display sex-specific effects. METHODS We used genome-wide genotype and gene expression data from primary B cells from 125 males and 162 females. The MatrixEQTL R package was used to identify eQTLs within a genomic window of 2 Mb centered on each of 22 established SLE and/or pSS susceptibility SNPs. To find sex-specific eQTLs, we used a linear model with a SNP * sex interaction term. RESULTS We found ten SNPs affecting the expression of 16 different genes (FDR < 0.05). rs7574865-INPP1, rs7574865-MYO1B, rs4938573-CD3D, rs11755393-SNRPC, and rs4963128-PHRF1 were novel observations for the immune compartment and B cells. By analyzing the SNP * sex interaction terms, we identified six genes with differentially regulated expression in females compared to males, depending on the genotype of SLE/pSS-associated SNPs: SLC39A8 (BANK1 locus), CD74 (TNIP1 locus), PXK, CTSB (BLK/FAM167A locus), ARCN1 (CXCR5 locus), and DHX9 (NCF2 locus). CONCLUSIONS We identified several unknown sex-specific eQTL effects of SLE/pSS-associated genetic polymorphisms and provide novel insight into how gene-sex interactions may contribute to the sex bias in systemic autoimmune diseases.
Collapse
Affiliation(s)
- Magdalena Lindén
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jorge I Ramírez Sepúlveda
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Tojo James
- Unit of Neuroimmunology, Department of Clinical Neuroscience, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Gudny Ella Thorlacius
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Brauner
- Unit of Neuroimmunology, Department of Clinical Neuroscience, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - David Gómez-Cabrero
- Unit of Computational Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.,Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, 17121, Solna, Sweden.,Mucosal and Salivary Biology Division, King's College London Dental Institute, London, SE1 9RT, UK
| | - Tomas Olsson
- Unit of Neuroimmunology, Department of Clinical Neuroscience, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Unit of Neuroimmunology, Department of Clinical Neuroscience, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
9
|
Sigloch FC, Tholen M, Gomez-Auli A, Biniossek ML, Reinheckel T, Schilling O. Proteomic analysis of lung metastases in a murine breast cancer model reveals divergent influence of CTSB and CTSL overexpression. J Cancer 2017; 8:4065-4074. [PMID: 29187882 PMCID: PMC5706009 DOI: 10.7150/jca.21401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/09/2017] [Indexed: 12/26/2022] Open
Abstract
Studies in the MMTV-PyMT (PyMT) breast cancer mouse model have shown a strong influence of the lysosomal cysteine cathepsins B or L on lung metastasis formation. Transgenic expression of human CTSB (tgCTSB) or CTSL (tgCTSL) both led to similar metastatic phenotypes with increased metastatic burden in the PyMT mice. However, recent studies in other tumor models proved marked differences in effects of either cathepsin on the proteome composition. We sought to analyze and compare proteome changes in the metastatic proteome of PyMT mice expressing either tgCTSB or tgCTSL to evaluate similarities and differences in those models. Performing an explorative, quantitative proteome comparison based on LC-MS/MS, we identified up to 3,000 proteins from murine lung metastases in three independent biological replicates per genotype. In both cases, when compared to wild-type (WT) mice, we noticed a pronounced impact of transgene cathepsin expression on the metastasis proteome. Highlights include increased moesin, integrin beta 1 and vinexin levels in the tgCTSB dataset and increased saposin and granulin levels in the tgCTSL dataset. Importantly, non-supervised hierarchical clustering clearly separated tgCTSB vs. tgCTSL induced proteome changes. In summary, tgCTSB and tgCTSL both display a strong and distinct impact on proteome composition of lung macrometastases in the PyMT model. Our observations suggest that they impact malignant behavior in distinct ways, thus further emphasizing interest into their tumor-contextual functionality.
Collapse
Affiliation(s)
- Florian Christoph Sigloch
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Martina Tholen
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, D-79104 Freiburg, Germany.,Present address: Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Alejandro Gomez-Auli
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, D-79104 Freiburg, Germany
| | - Martin Lothar Biniossek
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, D-79104 Freiburg, Germany
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, Medical Faculty, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
10
|
Proteome profiling of clear cell renal cell carcinoma in von Hippel-Lindau patients highlights upregulation of Xaa-Pro aminopeptidase-1, an anti-proliferative and anti-migratory exoprotease. Oncotarget 2017; 8:100066-100078. [PMID: 29245961 PMCID: PMC5725003 DOI: 10.18632/oncotarget.21929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/08/2017] [Indexed: 12/21/2022] Open
Abstract
Patients of the von Hippel-Lindau (VHL) disease frequently develop clear cell renal cell carcinoma (ccRCC). Using archived, formalin-fixed, paraffin-embedded (FFPE) samples, we sought to determine global proteome alterations that distinguish ccRCC tissue from adjacent, non-malignant kidney tissue in VHL-patients. Our quantitative proteomic analysis clearly discriminated tumor and non-malignant tissue. Significantly dysregulated proteins were distinguished using the linear models for microarray data algorithm. In the ccRCC tissue, we noticed a predominant under-representation of proteins involved in the tricarboxylic acid cycle and an increase in proteins involved in glycolysis. This profile possibly represents a proteomic fingerprint of the "Warburg effect", which is a molecular hallmark of ccRCC. Furthermore, we observed an increase in proteins involved in extracellular matrix organization. We also noticed differential expression of many exoproteases in the ccRCC tissue. Of particular note were opposing alterations of Xaa-Pro Aminopeptidases-1 and -2 (XPNPEP-1 and -2): a strong decrease of XPNPEP-2 in ccRCC was accompanied by abundant presence of the related protease XPNPEP-1. In both cases, we corroborated the proteomic results by immunohistochemical analysis of ccRCC and adjacent, non-malignant kidney tissue of VHL patients. To functionally investigate the role of XPNPEP-1 in ccRCC, we performed small-hairpin RNA mediated XPNPEP-1 expression silencing in 786-O ccRCC cells harboring a mutated VHL gene. We found that XPNPEP-1 expression dampens cellular proliferation and migration. These results suggest that XPNPEP-1 is likely an anti-target in ccRCC. Methodologically, our work further validates the robustness of using FFPE material for quantitative proteomics.
Collapse
|