151
|
Liu X, Kang WY, Shang LL, Ge SH. [Sitagliptin inhibits lipopolysaccharide-induced inflammatory response in human gingival fibroblasts by blocking nuclear factor-κB signaling pathway]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2021; 39:153-163. [PMID: 33834669 DOI: 10.7518/hxkq.2021.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OBJECTIVES This study was performed to clarify the effects of sitagliptin on Porphyromonas gingivalis-lipopolysaccharide (LPS)-induced inflammatory response in human gingival fibroblasts (HGFs), explore the molecular mechanism of its roles, and provide a foundation for clinical therapeutics in periodontitis. METHODS Healthy gingival samples were collected from the donors. HGFs were isolated with enzymic digestion method and identified. The effects of LPS and sitagliptin on cell viability were detected by cell-counting kit-8 (CCK8). The mRNA levels of inflammatory cytokines, namely, interleukin (IL)-6, IL-8, C-C motif ligand 2 (CCL2), and superoxide dismutase 2 (SOD2), were evaluated by quantity real-time polymerase chain reaction (qRT-PCR) and enzyme-linked immune sorbent assay (ELISA) was used to measure the secretion protein levels of IL-6, IL-8, and CCL2. Western blot analysis was used to further investigate the activation of nuclear factor (NF)-κB signaling pathway. The effect of NF-κB pathway inhibitor BAY11-7082 on LPS-induced HGF inflammatory cytokines at the gene level was verified by qRT-PCR. RESULTS Low concentrations of sitagliptin (0.1, 0.25, and 0.5 µmol·L-1) did not affect HGF growth in 24 and 48 h, whereas high concentrations of sitagliptin (5-1 000 µmol·L-1) significantly inhibited cell proliferation. Sitagliptin suppressed 5 µg·mL-1 of LPS-induced IL-6, IL-8, CCL2, and SOD2 gene expression levels in HGF in a concentration-dependent manner. Furthermore, sitagliptin significantly decreased the elevated secretion of IL-6, IL-8, and CCL2 protein induced by LPS. Western blot analysis showed that 0.5 µmol·L-1 of sitagliptin significantly inhibited LPS-induced NF-κB signaling pathway activation. Results of qRT-PCR analysis indicated that 0.5 µmol·L-1 of sitagliptin and 5 µmol·L-1 of BAY11-7082 significantly inhibited LPS-induced IL-6, IL-8, CCL2, and SOD2 gene expressions. CONCLUSIONS Sitagliptin could significantly inhibit LPS-induced HGF inflammatory response by blocking the NF-κB signaling pathway activation.
Collapse
Affiliation(s)
- Xiang Liu
- Dept. of Periodonto-logy, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan 250012, China
| | - Wen-Yan Kang
- Dept. of Periodonto-logy, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan 250012, China
| | - Ling-Ling Shang
- Dept. of Periodonto-logy, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan 250012, China
| | - Shao-Hua Ge
- Dept. of Periodonto-logy, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan 250012, China
| |
Collapse
|
152
|
Luo JH, Wang M, Jia GF, He Y. Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2933-2946. [PMID: 33606877 PMCID: PMC8023220 DOI: 10.1093/jxb/erab074] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/12/2021] [Indexed: 05/14/2023]
Abstract
Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.
Collapse
Affiliation(s)
- Jin-Hong Luo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Min Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Gui-Fang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
- Correspondence:
| |
Collapse
|
153
|
Drzewiecka EM, Kozlowska W, Zmijewska A, Wydorski PJ, Franczak A. Electromagnetic Field (EMF) Radiation Alters Estrogen Release from the Pig Myometrium during the Peri-Implantation Period. Int J Mol Sci 2021; 22:ijms22062920. [PMID: 33805726 PMCID: PMC7999543 DOI: 10.3390/ijms22062920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/17/2022] Open
Abstract
An electromagnetic field (EMF) may affect the functions of uterine tissues. This study hypothesized that EMF changes the estrogenic activity of pig myometrium during the peri-implantation period. Tissue was collected on days 15-16 of the gestation and incubated in the presence of EMF (50 and 120 Hz, 2 and 4 h). The cytochrome P450 aromatase type 3 (CYP19A3) and hydroxysteroid 17β dehydrogenase type 4 (HSD17B4) mRNA transcript abundance, cytochrome P450arom (aromatase), and 17β hydroxysteroid dehydrogenase 17βHSD) protein abundance and estrone (E1) and estradiol-17β (E2) release were examined using Real-Time PCR, Western blot and radioimmunoassay. Selected myometrial slices were treated with progesterone (P4) to determine whether it functions as a protector against EMF. CYP19A3 mRNA transcript abundance in slices treated with EMF was less at 50 Hz (2 h) and greater at 120 Hz (2 and 4 h). HSD17B4 mRNA transcript was greater in slices treated with EMF at 120 Hz (2 h). Progesterone diminished EMF-related effects on CYP19A3 and HSD17B4. When P4 was added, EMF had suppressive (50 and 120 Hz, 2 h) or enhancing (50 Hz, 4 h) effects on aromatase abundance. The E1 release was lower after 4 h of EMF treatment at 50 Hz and P4 did not protect myometrial E1 release. In conclusion, EMF alters the synthesis and release of E1 and did not affect E2 release in the myometrium during the peri-implantation period.
Collapse
Affiliation(s)
| | | | | | | | - Anita Franczak
- Correspondence: (E.M.D.); (A.F.); Tel.: +48-89-523-32-01 (E.M.D. & A.F.)
| |
Collapse
|
154
|
Smolle MA, Herbsthofer L, Goda M, Granegger B, Brcic I, Bergovec M, Scheipl S, Prietl B, El-Heliebi A, Pichler M, Gerger A, Posch F, Tomberger M, López-García P, Feichtinger J, Baumgartner C, Leithner A, Liegl-Atzwanger B, Szkandera J. Influence of tumor-infiltrating immune cells on local control rate, distant metastasis, and survival in patients with soft tissue sarcoma. Oncoimmunology 2021; 10:1896658. [PMID: 33763294 PMCID: PMC7954425 DOI: 10.1080/2162402x.2021.1896658] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Soft tissue sarcomas (STS) are considered non-immunogenic, although distinct entities respond to anti-tumor agents targeting the tumor microenvironment. This study’s aims were to investigate relationships between tumor-infiltrating immune cells and patient/tumor-related factors, and assess their prognostic value for local recurrence (LR), distant metastasis (DM), and overall survival (OS). One-hundred-eighty-eight STS-patients (87 females [46.3%]; median age: 62.5 years) were retrospectively analyzed. Tissue microarrays (in total 1266 cores) were stained with multiplex immunohistochemistry and analyzed with multispectral imaging. Seven cell types were differentiated depending on marker profiles (CD3+, CD3+ CD4+ helper, CD3+ CD8+ cytotoxic, CD3+ CD4+ CD45RO+ helper memory, CD3+ CD8+ CD45RO+ cytotoxic memory T-cells; CD20 + B-cells; CD68+ macrophages). Correlations between phenotype abundance and variables were analyzed. Uni- and multivariate Fine&Gray and Cox-regression models were constructed to investigate prognostic variables. Model calibration was assessed with C-index. IHC-findings were validated with TCGA-SARC gene expression data of genes specific for macrophages, T- and B-cells. B-cell percentage was lower in patients older than 62.5 years (p = .013), whilst macrophage percentage was higher (p = .002). High B-cell (p = .035) and macrophage levels (p = .003) were associated with increased LR-risk in the univariate analysis. In the multivariate setting, high macrophage levels (p = .014) were associated with increased LR-risk, irrespective of margins, age, gender or B-cells. Other immune cells were not associated with outcome events. High macrophage levels were a poor prognostic factor for LR, irrespective of margins, B-cells, gender and age. Thus, anti-tumor, macrophage-targeting agents may be applied more frequently in tumors with enhanced macrophage infiltration.
Collapse
Affiliation(s)
- Maria A Smolle
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | | | - Mark Goda
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Barbara Granegger
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Iva Brcic
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Marko Bergovec
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Susanne Scheipl
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Barbara Prietl
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria.,Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
| | - Amin El-Heliebi
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria.,Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Martin Pichler
- Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Florian Posch
- Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | | | | | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Claudia Baumgartner
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Andreas Leithner
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Bernadette Liegl-Atzwanger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Joanna Szkandera
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| |
Collapse
|
155
|
Park HE, Park JS, Park HT, Choi JG, Shin JI, Jung M, Kang HL, Baik SC, Lee WK, Kim D, Yoo HS, Shin MK. Alpha-2-Macroglobulin as a New Promising Biomarker Improving the Diagnostic Sensitivity of Bovine Paratuberculosis. Front Vet Sci 2021; 8:637716. [PMID: 33748212 PMCID: PMC7973028 DOI: 10.3389/fvets.2021.637716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/08/2021] [Indexed: 12/18/2022] Open
Abstract
Johne's disease (JD) is a chronic granulomatous enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), which induces persistent diarrhea and cachexia. JD causes huge economic losses to the dairy industry due to reduced milk production and premature culling. Infected animals excrete MAP via feces during the prolonged subclinical stage without exhibiting any clinical signs. Therefore, accurate detection of subclinical stage animals is crucial for successful eradication of JD in the herd. In the current study, we analyzed serum samples of MAP-infected and non-infected cattle to identify potential biomarker candidates. First, we identified 12 differentially expressed serum proteins in subclinical and clinical shedder groups compared to the healthy control group. Second, we conducted ELISA for three selected biomarkers (alpha-2-macroglobulin (A2M), alpha-1-beta glycoprotein, and transthyretin) and compared their diagnostic performance with that of two commercial ELISA diagnostic kits. Serum A2M levels were significantly higher in the MAP-exposed, subclinical shedder, subclinical non-shedder, and clinical shedder groups than in the healthy control group, suggesting its possible use as a diagnostic biomarker for MAP infection. Furthermore, A2M demonstrated a sensitivity of 90.4%, and a specificity of 100% while the two commercial ELISA kits demonstrated a sensitivity of 67.83 and 73.04% and a specificity of 100%, respectively. In conclusion, our results suggest that measuring A2M by ELISA can be used as a diagnostic tool to detect MAP infection, considerably improving the detection rate of subclinical shedders and MAP-exposed animals that are undetectable using current diagnostic tools.
Collapse
Affiliation(s)
- Hyun-Eui Park
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea.,Department of Infectious Diseases, College of Veterinary Medicine, BK21Four and Bio-Max/N-Bio Institute, Seoul National University, Seoul, South Korea
| | - Jin-Sik Park
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea
| | - Hong-Tae Park
- Department of Infectious Diseases, College of Veterinary Medicine, BK21Four and Bio-Max/N-Bio Institute, Seoul National University, Seoul, South Korea
| | - Jeong-Gyu Choi
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea.,Department of Convergence Medical Sciences, Gyeongsang National University, Jinju, South Korea
| | - Jeong-Ih Shin
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea.,Department of Convergence Medical Sciences, Gyeongsang National University, Jinju, South Korea
| | - Myunghwan Jung
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea.,Department of Convergence Medical Sciences, Gyeongsang National University, Jinju, South Korea
| | - Hyung-Lyun Kang
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea.,Department of Convergence Medical Sciences, Gyeongsang National University, Jinju, South Korea
| | - Seung-Chul Baik
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea.,Department of Convergence Medical Sciences, Gyeongsang National University, Jinju, South Korea
| | - Woo-Kon Lee
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea.,Department of Convergence Medical Sciences, Gyeongsang National University, Jinju, South Korea
| | - Donghyuk Kim
- Schools of Energy & Chemical Engineering and Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, BK21Four and Bio-Max/N-Bio Institute, Seoul National University, Seoul, South Korea
| | - Min-Kyoung Shin
- Department of Microbiology, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea.,Department of Convergence Medical Sciences, Gyeongsang National University, Jinju, South Korea
| |
Collapse
|
156
|
Robins C, Liu Y, Fan W, Duong DM, Meigs J, Harerimana NV, Gerasimov ES, Dammer EB, Cutler DJ, Beach TG, Reiman EM, De Jager PL, Bennett DA, Lah JJ, Wingo AP, Levey AI, Seyfried NT, Wingo TS. Genetic control of the human brain proteome. Am J Hum Genet 2021; 108:400-410. [PMID: 33571421 PMCID: PMC8008492 DOI: 10.1016/j.ajhg.2021.01.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
We generated an online brain pQTL resource for 7,376 proteins through the analysis of genetic and proteomic data derived from post-mortem samples of the dorsolateral prefrontal cortex of 330 older adults. The identified pQTLs tend to be non-synonymous variation, are over-represented among variants associated with brain diseases, and replicate well (77%) in an independent brain dataset. Comparison to a large study of brain eQTLs revealed that about 75% of pQTLs are also eQTLs. In contrast, about 40% of eQTLs were identified as pQTLs. These results are consistent with lower pQTL mapping power and greater evolutionary constraint on protein abundance. The latter is additionally supported by observations of pQTLs with large effects' tending to be rare, deleterious, and associated with proteins that have evidence for fewer protein-protein interactions. Mediation analyses using matched transcriptomic and proteomic data provided additional evidence that pQTL effects are often, but not always, mediated by mRNA. Specifically, we identified roughly 1.6 times more mRNA-mediated pQTLs than mRNA-independent pQTLs (550 versus 341). Our pQTL resource provides insight into the functional consequences of genetic variation in the human brain and a basis for novel investigations of genetics and disease.
Collapse
|
157
|
Sullivan DI, Jiang M, Hinchie AM, Roth MG, Bahudhanapati H, Nouraie M, Liu J, McDyer JF, Mallampalli RK, Zhang Y, Kass DJ, Finkel T, Alder JK. Transcriptional and Proteomic Characterization of Telomere-Induced Senescence in a Human Alveolar Epithelial Cell Line. Front Med (Lausanne) 2021; 8:600626. [PMID: 33634147 PMCID: PMC7902064 DOI: 10.3389/fmed.2021.600626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/05/2021] [Indexed: 01/16/2023] Open
Abstract
Cellular senescence due to telomere dysfunction has been hypothesized to play a role in age-associated diseases including idiopathic pulmonary fibrosis (IPF). It has been postulated that paracrine mediators originating from senescent alveolar epithelia signal to surrounding mesenchymal cells and contribute to disease pathogenesis. However, murine models of telomere-induced alveolar epithelial senescence fail to display the canonical senescence-associated secretory phenotype (SASP) that is observed in senescent human cells. In an effort to understand human-specific responses to telomere dysfunction, we modeled telomere dysfunction-induced senescence in a human alveolar epithelial cell line. We hypothesized that this system would enable us to probe for differences in transcriptional and proteomic senescence pathways in vitro and to identify novel secreted protein (secretome) changes that potentially contribute to the pathogenesis of IPF. Following induction of telomere dysfunction, a robust senescence phenotype was observed. RNA-seq analysis of the senescent cells revealed the SASP and comparisons to previous murine data highlighted differences in response to telomere dysfunction. We conducted a proteomic analysis of the senescent cells using a novel biotin ligase capable of labeling secreted proteins. Candidate biomarkers selected from our transcriptional and secretome data were then evaluated in IPF and control patient plasma. Four novel proteins were found to be differentially expressed between the patient groups: stanniocalcin-1, contactin-1, tenascin C, and total inhibin. Our data show that human telomere-induced, alveolar epithelial senescence results in a transcriptional SASP that is distinct from that seen in analogous murine cells. Our findings suggest that studies in animal models should be carefully validated given the possibility of species-specific responses to telomere dysfunction. We also describe a pragmatic approach for the study of the consequences of telomere-induced alveolar epithelial cell senescence in humans.
Collapse
Affiliation(s)
- Daniel I. Sullivan
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Pittsburgh, PA, United States
| | - Mao Jiang
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States,The Third Xiangya Hospital, Central South University, Changsha, China
| | - Angela M. Hinchie
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mark G. Roth
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Harinath Bahudhanapati
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Pittsburgh, PA, United States
| | - Mehdi Nouraie
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Pittsburgh, PA, United States
| | - Jie Liu
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, United States,University of Pittsburgh Medical Center, Pittsburgh, PA, United States,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - John F. McDyer
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rama K. Mallampalli
- Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Yingze Zhang
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Pittsburgh, PA, United States
| | - Daniel J. Kass
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Pittsburgh, PA, United States
| | - Toren Finkel
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, United States,University of Pittsburgh Medical Center, Pittsburgh, PA, United States,Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jonathan K. Alder
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Pittsburgh, PA, United States,*Correspondence: Jonathan K. Alder
| |
Collapse
|
158
|
Asai M, Sheehan G, Li Y, Robertson BD, Kavanagh K, Langford PR, Newton SM. Innate Immune Responses of Galleria mellonella to Mycobacterium bovis BCG Challenge Identified Using Proteomic and Molecular Approaches. Front Cell Infect Microbiol 2021; 11:619981. [PMID: 33634038 PMCID: PMC7900627 DOI: 10.3389/fcimb.2021.619981] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/04/2021] [Indexed: 01/10/2023] Open
Abstract
The larvae of the insect Galleria mellonella, have recently been established as a non-mammalian infection model for the Mycobacterium tuberculosis complex (MTBC). To gain further insight into the potential of this model, we applied proteomic (label-free quantification) and transcriptomic (gene expression) approaches to characterise the innate immune response of G. mellonella to infection with Mycobacterium bovis BCG lux over a 168 h time course. Proteomic analysis of the haemolymph from infected larvae revealed distinct changes in the proteome at all time points (4, 48, 168 h). Reverse transcriptase quantitative PCR confirmed induction of five genes (gloverin, cecropin, IMPI, hemolin, and Hdd11), which encoded proteins found to be differentially abundant from the proteomic analysis. However, the trend between gene expression and protein abundance were largely inconsistent (20%). Overall, the data are in agreement with previous phenotypic observations such as haemocyte internalization of mycobacterial bacilli (hemolin/β-actin), formation of granuloma-like structures (Hdd11), and melanization (phenoloxidase activating enzyme 3 and serpins). Furthermore, similarities in immune expression in G. mellonella, mouse, zebrafish and in vitro cell-line models of tuberculosis infection were also identified for the mechanism of phagocytosis (β-actin). Cecropins (antimicrobial peptides), which share the same α-helical motif as a highly potent peptide expressed in humans (h-CAP-18), were induced in G. mellonella in response to infection, giving insight into a potential starting point for novel antimycobacterial agents. We believe that these novel insights into the innate immune response further contribute to the validation of this cost-effective and ethically acceptable insect model to study members of the MTBC.
Collapse
Affiliation(s)
- Masanori Asai
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gerard Sheehan
- SSPC Pharma Research Centre, Department of Biology, Maynooth University, Maynooth, Ireland.,Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Yanwen Li
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Kevin Kavanagh
- SSPC Pharma Research Centre, Department of Biology, Maynooth University, Maynooth, Ireland
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sandra M Newton
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| |
Collapse
|
159
|
Guo Z, Pan F, Peng L, Tian S, Jiao J, Liao L, Lu C, Zhai G, Wu Z, Dong H, Xu X, Wu J, Chen P, Bai X, Lin D, Xu L, Li E, Zhang K. Systematic Proteome and Lysine Succinylome Analysis Reveals Enhanced Cell Migration by Hyposuccinylation in Esophageal Squamous Cell Carcinoma. Mol Cell Proteomics 2021; 20:100053. [PMID: 33561546 PMCID: PMC7970140 DOI: 10.1074/mcp.ra120.002150] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is an aggressive malignancy with poor therapeutic outcomes. However, the alterations in proteins and posttranslational modifications (PTMs) leading to the pathogenesis of ESCC remain unclear. Here, we provide the comprehensive characterization of the proteome, phosphorylome, lysine acetylome, and succinylome for ESCC and matched control cells using quantitative proteomic approach. We identify abnormal protein and PTM pathways, including significantly downregulated lysine succinylation sites in cancer cells. Focusing on hyposuccinylation, we reveal that this altered PTM was enriched on enzymes of metabolic pathways inextricably linked with cancer metabolism. Importantly, ESCC malignant behaviors such as cell migration are inhibited once the level of succinylation was restored in vitro or in vivo. This effect was further verified by mutations to disrupt succinylation sites in candidate proteins. Meanwhile, we found that succinylation has a negative regulatory effect on histone methylation to promote cancer migration. Finally, hyposuccinylation is confirmed in primary ESCC specimens. Our findings together demonstrate that lysine succinylation may alter ESCC metabolism and migration, providing new insights into the functional significance of PTM in cancer biology.
Collapse
Affiliation(s)
- Zhenchang Guo
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China; The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Feng Pan
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Liu Peng
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Shanshan Tian
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jiwei Jiao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Liandi Liao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, China
| | - Congcong Lu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadephia, Pennsylvania, USA
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Zhiyong Wu
- Departments of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou, China
| | - Hanyang Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiue Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, China
| | - Jianyi Wu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Pu Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Dechen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Liyan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China.
| | - Enmin Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| |
Collapse
|
160
|
Jia X, Yu T, Xiao C, Sheng D, Yang M, Cheng Q, Wu J, Lian T, Zhao Y, Zhang S. Expression of transient receptor potential vanilloid genes and proteins in diabetic rat heart. Mol Biol Rep 2021; 48:1217-1223. [PMID: 33523372 DOI: 10.1007/s11033-021-06182-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 11/27/2022]
Abstract
Cardiac complications are leading causes of death in diabetic patients. Imbalance of Ca2+ homeostasis is a hallmark of cardiac dysfunction in diabetes, while TRPV channels are non-selective for cations and are permeable to Ca2+. Our aim was to evaluate the expression levels of TRPV1, TRPV2, TRPV3, TRPV4, TRPV5, and TRPV6 genes and proteins in cardiac tissue at 3 days and 4, 8, and 12 weeks after induction of diabetes. Sprague-Dawley rats were assigned to control and DM groups. DM was induced by intraperitoneal injection of streptozotocin (60 mg/kg). The expression levels of TRPV genes were analyzed by the quantitative reverse transcription polymerase chain reaction, and TRPV proteins were determined by western blotting. Compared to controls, the expression levels of TRPV2, TRPV3, and TRPV6 in diabetic myocardium did not change, while TRPV1 decreased at 4, 8, and 12 weeks, TRPV4 was upregulated at 3 days and 4, 8, and 12 weeks, TRPV5 mRNA increased at 8 and 12 weeks, and TRPV5 protein increased at 4, 8, and 12 weeks. Our findings showed that TRPV1, TRPV4, and TRPV5 are associated with the diabetic heart.
Collapse
Affiliation(s)
- Xiaoli Jia
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China
| | - Tao Yu
- Renhe Hospital of China Three Gorges University, Yichang, China
| | - Chao Xiao
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China
| | - Deqiao Sheng
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China
| | - Mengcheng Yang
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China
| | - Quanyi Cheng
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China
| | - Jing Wu
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China
| | - Ting Lian
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China
| | - Yun Zhao
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China.
| | - Shizhong Zhang
- Department of Physiology, Medical Science College of China Three Gorges University, Yichang, China.
| |
Collapse
|
161
|
Chronic exposure of humans to high level natural background radiation leads to robust expression of protective stress response proteins. Sci Rep 2021; 11:1777. [PMID: 33469066 PMCID: PMC7815775 DOI: 10.1038/s41598-020-80405-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding exposures to low doses of ionizing radiation are relevant since most environmental, diagnostic radiology and occupational exposures lie in this region. However, the molecular mechanisms that drive cellular responses at these doses, and the subsequent health outcomes, remain unclear. A local monazite-rich high level natural radiation area (HLNRA) in the state of Kerala on the south-west coast of Indian subcontinent show radiation doses extending from ≤ 1 to ≥ 45 mGy/y and thus, serve as a model resource to understand low dose mechanisms directly on healthy humans. We performed quantitative discovery proteomics based on multiplexed isobaric tags (iTRAQ) coupled with LC–MS/MS on human peripheral blood mononuclear cells from HLNRA individuals. Several proteins involved in diverse biological processes such as DNA repair, RNA processing, chromatin modifications and cytoskeletal organization showed distinct expression in HLNRA individuals, suggestive of both recovery and adaptation to low dose radiation. In protein–protein interaction (PPI) networks, YWHAZ (14-3-3ζ) emerged as the top-most hub protein that may direct phosphorylation driven pro-survival cellular processes against radiation stress. PPI networks also identified an integral role for the cytoskeletal protein ACTB, signaling protein PRKACA; and the molecular chaperone HSPA8. The data will allow better integration of radiation biology and epidemiology for risk assessment [Data are available via ProteomeXchange with identifier PXD022380].
Collapse
|
162
|
Boero G, Tyler RE, Todd CA, O'Buckley TK, Balan I, Besheer J, Morrow AL. (3α,5α)3-hydroxypregnan-20-one (3α,5α-THP) regulation of hypothalamic and extrahypothalamic corticotropin releasing factor (CRF): Sexual dimorphism and brain region specificity in Sprague Dawley rats. Neuropharmacology 2021; 186:108463. [PMID: 33460689 DOI: 10.1016/j.neuropharm.2021.108463] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 11/25/2022]
Abstract
CRF is the main activator of the hypothalamic-pituitary-adrenal (HPA) axis in response to stress. CRF neurons are found mainly in the hypothalamus, but CRF positive cells and CRF1 receptors are also found in extrahypothalamic structures, including amygdala (CeA), hippocampus, NAc and VTA. CRF release in the hypothalamus is regulated by inhibitory GABAergic interneurons and extrahypothalamic glutamatergic inputs, and disruption of this balance is found in stress-related disorders and addiction. (3α,5α)3-hydroxypregnan-20-one (3α,5α-THP), the most potent positive modulator of GABAA receptors, attenuates the stress response reducing hypothalamic CRF mRNA expression and ACTH and corticosterone serum levels. In this study, we explored 3α,5α-THP regulation of hypothalamic and extrahypothalamic CRF mRNA and peptide expression, in male and female Sprague Dawley rats, following vehicle or 3α,5α-THP administration (15 mg/kg). In the hypothalamus, we found sex differences in CRF mRNA expression (females +74%, p < 0.01) and CRF peptide levels (females -71%, p < 0.001). 3α,5α-THP administration reduced hypothalamic CRF mRNA expression only in males (-50%, p < 0.05) and did not alter CRF peptide expression in either sex. In hippocampus and CeA, 3α,5α-THP administration reduced CRF peptide concentrations only in the male (hippocampus -29%, p < 0.05; CeA -62%, p < 0.01). In contrast, 3α,5α-THP injection increased CRF peptide concentration in the VTA of both males (+32%, p < 0.01) and females (+26%, p < 0.01). The results show sex and region-specific regulation of CRF signals and the response to 3α,5α-THP administration. This data may be key to successful development of therapeutic approaches for stress-related disorders and addiction.
Collapse
Affiliation(s)
- Giorgia Boero
- Department of Psychiatry, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA; Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ryan E Tyler
- Department of Pharmacology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA; Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - Caroline A Todd
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - Todd K O'Buckley
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - Irina Balan
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - Joyce Besheer
- Department of Psychiatry, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA; Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - A Leslie Morrow
- Department of Psychiatry, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA; Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA.
| |
Collapse
|
163
|
Curdy N, Lanvin O, Cadot S, Laurent C, Fournié JJ, Franchini DM. Stress Granules in the Post-transcriptional Regulation of Immune Cells. Front Cell Dev Biol 2021; 8:611185. [PMID: 33520991 PMCID: PMC7841200 DOI: 10.3389/fcell.2020.611185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022] Open
Abstract
Immune cell activation triggers transcriptional and translational programs eliciting cellular processes, such as differentiation or proliferation, essential for an efficient immune response. These dynamic processes require an intricate orchestration of regulatory mechanisms to control the precise spatiotemporal expression of proteins. Post-transcriptional regulation ensures the control of messenger RNA metabolism and appropriate translation. Among these post-transcriptional regulatory mechanisms, stress granules participate in the control of protein synthesis. Stress granules are ribonucleoprotein complexes that form upon stress, typically under control of the integrated stress response. Such structures assemble upon stimulation of immune cells where they control selective translational programs ensuring the establishment of accurate effector functions. In this review, we summarize the current knowledge about post-transcriptional regulation in immune cells and highlight the role of stress sensors and stress granules in such regulation.
Collapse
Affiliation(s)
- Nicolas Curdy
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Olivia Lanvin
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Sarah Cadot
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Camille Laurent
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France.,Département de Pathologie, Centre Hospitalier Universitaire (CHU) de Toulouse, Toulouse, France
| | - Jean-Jacques Fournié
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Don-Marc Franchini
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| |
Collapse
|
164
|
Biological Applications for LC-MS-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:17-29. [PMID: 34628625 DOI: 10.1007/978-3-030-77252-9_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Since its inception, liquid chromatography-mass spectrometry (LC-MS) has been continuously improved upon in many aspects, including instrument capabilities, sensitivity, and resolution. Moreover, the costs to purchase and operate mass spectrometers and liquid chromatography systems have decreased, thus increasing affordability and availability in sectors outside of academic and industrial research. Processing power has also grown immensely, cutting the time required to analyze samples, allowing more data to be feasibly processed, and allowing for standardized processing pipelines. As a result, proteomics via LC-MS has become popular in many areas of biological sciences, forging an important seat for itself in targeted and untargeted assays, pure and applied science, the laboratory, and the clinic. In this chapter, many of these applications of LC-MS-based proteomics and an outline of how they can be executed will be covered. Since the field of personalized medicine has matured alongside proteomics, it has also come to rely on various mass spectrometry methods and will be elaborated upon as well. As time goes on and mass spectrometry evolves, there is no doubt that its presence in these areas, and others, will only continue to grow.
Collapse
|
165
|
Goedtke L, Sprenger H, Hofmann U, Schmidt FF, Hammer HS, Zanger UM, Poetz O, Seidel A, Braeuning A, Hessel-Pras S. Polycyclic Aromatic Hydrocarbons Activate the Aryl Hydrocarbon Receptor and the Constitutive Androstane Receptor to Regulate Xenobiotic Metabolism in Human Liver Cells. Int J Mol Sci 2020; 22:ijms22010372. [PMID: 33396476 PMCID: PMC7796163 DOI: 10.3390/ijms22010372] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/18/2020] [Accepted: 12/26/2020] [Indexed: 12/19/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants produced by incomplete combustion of organic matter. They induce their own metabolism by upregulating xenobiotic-metabolizing enzymes such as cytochrome P450 monooxygenase 1A1 (CYP1A1) by activating the aryl hydrocarbon receptor (AHR). However, previous studies showed that individual PAHs may also interact with the constitutive androstane receptor (CAR). Here, we studied ten PAHs, different in carcinogenicity classification, for their potential to activate AHR- and CAR-dependent luciferase reporter genes in human liver cells. The majority of investigated PAHs activated AHR, while non-carcinogenic PAHs tended to activate CAR. We further characterized gene expression, protein abundancies and activities of the AHR targets CYP1A1 and 1A2, and the CAR target CYP2B6 in human HepaRG hepatoma cells. Enzyme induction patterns strongly resembled the profiles obtained at the receptor level, with AHR-activating PAHs inducing CYP1A1/1A2 and CAR-activating PAHs inducing CYP2B6. In summary, this study provides evidence that beside well-known activation of AHR, some PAHs also activate CAR, followed by subsequent expression of respective target genes. Furthermore, we found that an increased PAH ring number is associated with AHR activation as well as the induction of DNA double-strand breaks, whereas smaller PAHs activated CAR but showed no DNA-damaging potential.
Collapse
Affiliation(s)
- Lisa Goedtke
- Department Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (L.G.); (H.S.); (A.B.)
| | - Heike Sprenger
- Department Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (L.G.); (H.S.); (A.B.)
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstr. 112, 70376 Stuttgart, and University of Tübingen, 72074 Tübingen, Germany; (U.H.); (U.M.Z.)
| | - Felix F. Schmidt
- SIGNATOPE GmbH, Markwiesenstraße 55, 72770 Reutlingen, Germany; (F.F.S.); (H.S.H.); (O.P.)
| | - Helen S. Hammer
- SIGNATOPE GmbH, Markwiesenstraße 55, 72770 Reutlingen, Germany; (F.F.S.); (H.S.H.); (O.P.)
| | - Ulrich M. Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstr. 112, 70376 Stuttgart, and University of Tübingen, 72074 Tübingen, Germany; (U.H.); (U.M.Z.)
| | - Oliver Poetz
- SIGNATOPE GmbH, Markwiesenstraße 55, 72770 Reutlingen, Germany; (F.F.S.); (H.S.H.); (O.P.)
| | - Albrecht Seidel
- Biochemical Institute for Environmental Carcinogens, Prof. Dr. Gernot Grimmer Foundation, Lurup 4, 22927 Grosshansdorf, Germany;
| | - Albert Braeuning
- Department Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (L.G.); (H.S.); (A.B.)
| | - Stefanie Hessel-Pras
- Department Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (L.G.); (H.S.); (A.B.)
- Correspondence: ; Tel.: +49-30-18412-25203
| |
Collapse
|
166
|
Mapping the Transcriptional and Fitness Landscapes of a Pathogenic E. coli Strain: The Effects of Organic Acid Stress under Aerobic and Anaerobic Conditions. Genes (Basel) 2020; 12:genes12010053. [PMID: 33396416 PMCID: PMC7824302 DOI: 10.3390/genes12010053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/31/2022] Open
Abstract
Several methods are available to probe cellular responses to external stresses at the whole genome level. RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism’s ability to survive the stress. The relative contribution of each non-essential gene in the genome to the fitness of the organism under stress can be obtained using methods that use sequencing to estimate the frequencies of members of a dense transposon library grown under different conditions, for example by transposon-directed insertion sequencing (TraDIS). These two methods thus probe different aspects of the underlying biology of the organism. We were interested to determine the extent to which the data from these two methods converge on related genes and pathways. To do this, we looked at a combination of biologically meaningful stresses. The human gut contains different organic short-chain fatty acids (SCFAs) produced by fermentation of carbon compounds, and Escherichia coli is exposed to these in its passage through the gut. Their effect is likely to depend on both the ambient pH and the level of oxygen present. We, therefore, generated RNAseq and TraDIS data on a uropathogenic E. coli strain grown at either pH 7 or pH 5.5 in the presence or absence of three SCFAs (acetic, propionic and butyric), either aerobically or anaerobically. Our analysis identifies both known and novel pathways as being likely to be important under these conditions. There is no simple correlation between gene expression and fitness, but we found a significant overlap in KEGG pathways that are predicted to be enriched following analysis of the data from the two methods, and the majority of these showed a fitness signature that would be predicted from the gene expression data, assuming expression to be adaptive. Genes which are not in the E. coli core genome were found to be particularly likely to show a positive correlation between level of expression and contribution to fitness.
Collapse
|
167
|
The Nuclear Pore Complex and mRNA Export in Cancer. Cancers (Basel) 2020; 13:cancers13010042. [PMID: 33375634 PMCID: PMC7796397 DOI: 10.3390/cancers13010042] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
Export of mRNAs from the nucleus to the cytoplasm is a key regulatory step in the expression of proteins. mRNAs are transported through the nuclear pore complex (NPC). Export of mRNAs responds to a variety of cellular stimuli and stresses. Revelations of the specific effects elicited by NPC components and associated co-factors provides a molecular basis for the export of selected RNAs, independent of bulk mRNA export. Aberrant RNA export has been observed in primary human cancer specimens. These cargo RNAs encode factors involved in nearly all facets of malignancy. Indeed, the NPC components involved in RNA export as well as the RNA export machinery can be found to be dysregulated, mutated, or impacted by chromosomal translocations in cancer. The basic mechanisms associated with RNA export with relation to export machinery and relevant NPC components are described. Therapeutic strategies targeting this machinery in clinical trials is also discussed. These findings firmly position RNA export as a targetable feature of cancer along with transcription and translation.
Collapse
|
168
|
Wojtysiak K, Ryszka W, Stefaniak T, Król J, Kozdrowski R. Changes in the Secretion of Anti-Inflammatory Cytokines and Acute-Phase Proteins in the Uterus after Artificial Insemination in the Mare. Animals (Basel) 2020; 10:ani10122438. [PMID: 33352707 PMCID: PMC7766701 DOI: 10.3390/ani10122438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Semen deposition into the uterus during mating or artificial insemination induces a rapid inflammatory response, and, in susceptible mares, persistent endometritis can develop. Cytokines are mediators involved in the regulation of the inflammatory process, and acute phase proteins are the most sensitive indicators of the inflammatory process. Therefore, the aim of this research was to determine the secretion of anti-inflammatory cytokines and acute-phase proteins in the uterus before and after artificial insemination in the mare. The obtained results indicate that the status of the mare before artificial insemination has little effect on the response measured shortly after artificial insemination. The presence of intrauterine fluid during estrus is not connected with the inflammation parameters investigated in this study at 7 h post artificial insemination. Detailed examination of the mare’s reproductive tract before and after artificial insemination guarantees high fertility. Abstract The objective of the study was to evaluate the concentrations of interleukin-1 receptor antagonist (IL-1RA), interleukin-10 (IL-10), serum amyloid A (SAA) and haptoglobin (Hp) in uterine lavage fluid before and after artificial insemination (AI). Based on ultrasound examination, mares were divided into: Group 1 (n = 9), no fluid was detected in the uterus during estrus and 7 h after AI; Group 2 (n = 8), no fluid was detected in the uterus during estrus but 7 h after AI fluid was detected in the uterus; Group 3 (n = 8), fluid was detected in the uterus during estrus and also 7 h after AI. In all groups of mares, a significant increase in polymorphonuclear cells (PMN) and a significant increase in IL-1RA and SAA were recorded 7 h after AI. The obtained results show that, regardless of the status of the mare before AI, the endometrial response characterized by PMN influx, and SAA, Hp, IL-1RA and IL-10 production, is similar. The presence of intrauterine fluid during estrus is not connected with PMN influx but can impact uterine IL-1RA production at this time.
Collapse
Affiliation(s)
- Katarzyna Wojtysiak
- Department of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 49, 50-366 Wroclaw, Poland;
| | | | - Tadeusz Stefaniak
- Department of Immunology, Pathophysiology and Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, C.K. Norwida 31, 50-375 Wroclaw, Poland;
| | - Jarosław Król
- Department of Pathology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, C.K. Norwida 31, 50-375 Wroclaw, Poland;
| | - Roland Kozdrowski
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Gagarina 11, 87-100 Toruń, Poland
- Correspondence:
| |
Collapse
|
169
|
Zhang F, Deng CK, Wang M, Deng B, Barber R, Huang G. Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq. BMC Bioinformatics 2020; 21:541. [PMID: 33272210 PMCID: PMC7713335 DOI: 10.1186/s12859-020-03824-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 01/12/2023] Open
Abstract
Background Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functionally diverse proteins from a single gene. The emergence of next-generation sequencing technologies, especially RNA-seq, provides novel insights into large-scale detection and analysis of alternative splicing at the transcriptional level. Advances in Proteomic Technologies such as liquid chromatography coupled tandem mass spectrometry (LC–MS/MS), have shown tremendous power for the parallel characterization of large amount of proteins in biological samples. Although poor correspondence has been generally found from previous qualitative comparative analysis between proteomics and microarray data, significantly higher degrees of correlation have been observed at the level of exon. Combining protein and RNA data by searching LC–MS/MS data against a customized protein database from RNA-Seq may produce a subset of alternatively spliced protein isoform candidates that have higher confidence. Results We developed a bioinformatics workflow to discover alternative splicing biomarkers from LC–MS/MS using RNA-Seq. First, we retrieved high confident, novel alternative splicing biomarkers from the breast cancer RNA-Seq database. Then, we translated these sequences into in silico Isoform Junction Peptides, and created a customized alternative splicing database for MS searching. Lastly, we ran the Open Mass spectrometry Search Algorithm against the customized alternative splicing database with breast cancer plasma proteome. Twenty six alternative splicing biomarker peptides with one single intron event and one exon skipping event were identified. Further interpretation of biological pathways with our Integrated Pathway Analysis Database showed that these 26 peptides are associated with Cancer, Signaling, Metabolism, Regulation, Immune System and Hemostasis pathways, which are consistent with the 256 alternative splicing biomarkers from the RNA-Seq. Conclusions This paper presents a bioinformatics workflow for using RNA-seq data to discover novel alternative splicing biomarkers from the breast cancer proteome. As a complement to synthetic alternative splicing database technique for alternative splicing identification, this method combines the advantages of two platforms: mass spectrometry and next generation sequencing and can help identify potentially highly sample-specific alternative splicing isoform biomarkers at early-stage of cancer.
Collapse
Affiliation(s)
- Fan Zhang
- Vermont Biomedical Research Network and Department of Biology, University of Vermont, Burlington, VT, 05405, USA. .,Institute for Translational Research and Department of Family Medicine, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Chris K Deng
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Mu Wang
- Department of Biochemistry and Molecular Biology, IU School of Medicine, Indianapolis, IN, 46202, USA.,Indiana Center for Systems Biology and Personalized Medicine, Indianapolis, IN, 46202, USA
| | - Bin Deng
- Vermont Biomedical Research Network and Department of Biology, University of Vermont, Burlington, VT, 05405, USA.,Institute for Translational Research and Department of Family Medicine, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Robert Barber
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Gang Huang
- Shanghai Key Laboratory for Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, People's Republic of China.
| |
Collapse
|
170
|
Speidel JT, Affandi T, Jones DNM, Ferrara SE, Reyland ME. Functional proteomic analysis reveals roles for PKCδ in regulation of cell survival and cell death: Implications for cancer pathogenesis and therapy. Adv Biol Regul 2020; 78:100757. [PMID: 33045516 PMCID: PMC8294469 DOI: 10.1016/j.jbior.2020.100757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/18/2022]
Abstract
Protein Kinase C-δ (PKCδ), regulates a broad group of biological functions and disease processes, including well-defined roles in immune function, cell survival and apoptosis. PKCδ primarily regulates apoptosis in normal tissues and non-transformed cells, and genetic disruption of the PRKCD gene in mice is protective in many diseases and tissue damage models. However pro-survival/pro-proliferative functions have also been described in some transformed cells and in mouse models of cancer. Recent evidence suggests that the contribution of PKCδ to specific cancers may depend in part on the oncogenic context of the tumor, consistent with its paradoxical role in cell survival and cell death. Here we will discuss what is currently known about biological functions of PKCδ and potential paradigms for PKCδ function in cancer. To further understand mechanisms of regulation by PKCδ, and to gain insight into the plasticity of PKCδ signaling, we have used functional proteomics to identify pathways that are dependent on PKCδ. Understanding how these distinct functions of PKCδ are regulated will be critical for the logical design of therapeutics to target this pathway.
Collapse
Affiliation(s)
- Jordan T Speidel
- Department of Craniofacial Biology, School of Dental Medicine, USA
| | - Trisiani Affandi
- Department of Craniofacial Biology, School of Dental Medicine, USA
| | | | - Sarah E Ferrara
- University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mary E Reyland
- Department of Craniofacial Biology, School of Dental Medicine, USA.
| |
Collapse
|
171
|
Li Z, Zhu A, Song Q, Chen HY, Harmon FG, Chen ZJ. Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis. THE PLANT CELL 2020; 32:3706-3722. [PMID: 33004616 PMCID: PMC7721322 DOI: 10.1105/tpc.20.00320] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/17/2020] [Accepted: 09/29/2020] [Indexed: 05/04/2023]
Abstract
Heterosis or hybrid vigor is widespread in plants and animals. Although the molecular basis for heterosis has been extensively studied, metabolic and proteomic contributions to heterosis remain elusive. Here we report an integrative analysis of time-series metabolome and proteome data in maize (Zea mays) hybrids and their inbred parents. Many maize metabolites and proteins are diurnally regulated, and many of these show nonadditive abundance in the hybrids, including key enzymes and metabolites involved in carbon assimilation. Compared with robust trait heterosis, metabolic heterosis is relatively mild. Interestingly, most amino acids display negative mid-parent heterosis (MPH), i.e., having lower values than the average of the parents, while sugars, alcohols, and nucleoside metabolites show positive MPH. From the network perspective, metabolites in the photosynthetic pathway show positive MPH, whereas metabolites in the photorespiratory pathway show negative MPH, which corresponds to nonadditive protein abundance and enzyme activities of key enzymes in the respective pathways in the hybrids. Moreover, diurnally expressed proteins that are upregulated in the hybrids are enriched in photosynthesis-related gene-ontology terms. Hybrids may more effectively remove toxic metabolites generated during photorespiration, and thus maintain higher photosynthetic efficiency. These metabolic and proteomic resources provide unique insight into heterosis and its utilization for high yielding maize and other crop plants.
Collapse
Affiliation(s)
- Zhi Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Andan Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Helen Y Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Frank G Harmon
- Plant Gene Expression Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710
- Department of Plant & Microbial Biology, University of California, Berkeley, California 94720
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| |
Collapse
|
172
|
Young S, Fenn J, Arriero E, Lowe A, Poulin B, MacColl AD, Bradley JE. Relationships between immune gene expression and circulating cytokine levels in wild house mice. Ecol Evol 2020; 10:13860-13871. [PMID: 33391686 PMCID: PMC7771139 DOI: 10.1002/ece3.6976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/28/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022] Open
Abstract
Quantitative PCR (qPCR) has been commonly used to measure gene expression in a number of research contexts, but the measured RNA concentrations do not always represent the concentrations of active proteins which they encode. This can be due to transcriptional regulation or post-translational modifications, or localization of immune environments, as can occur during infection. However, in studies using free-living non-model species, such as in ecoimmunological research, qPCR may be the only available option to measure a parameter of interest, and so understanding the quantitative link between gene expression and associated effector protein levels is vital.Here, we use qPCR to measure concentrations of RNA from mesenteric lymph node (MLN) and spleen tissue, and multiplex ELISA of blood serum to measure circulating cytokine concentrations in a wild population of a model species, Mus musculus domesticus.Few significant correlations were found between gene expression levels and circulating cytokines of the same immune genes or proteins, or related functional groups. Where significant correlations were observed, these were most frequently within the measured tissue (i.e., the expression levels of genes measured from spleen tissue were more likely to correlate with each other rather than with genes measured from MLN tissue, or with cytokine concentrations measured from blood).Potential reasons for discrepancies between measures including differences in decay rates and transcriptional regulation networks are discussed. We highlight the relative usefulness of different measures under different research questions and consider what might be inferred from immune assays.
Collapse
Affiliation(s)
- Stuart Young
- School of Life SciencesUniversity of NottinghamNottinghamUK
- North of England Zoological SocietyChesterUK
| | - Jonathan Fenn
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Elena Arriero
- School of Life SciencesUniversity of NottinghamNottinghamUK
- Department of Biodiversity, Ecology and EvolutionUniversity Complutense of MadridMadridSpain
| | - Ann Lowe
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Benoit Poulin
- School of Life SciencesUniversity of NottinghamNottinghamUK
- Leicester Biomedical Research CentreUniversity Hospitals of Leicester NHS TrustGeneral HospitalLeicesterUK
| | | | | |
Collapse
|
173
|
Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Cell 2020; 183:1665-1681.e18. [PMID: 33188776 DOI: 10.1016/j.cell.2020.10.026] [Citation(s) in RCA: 372] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 07/31/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022]
Abstract
We present deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq) for co-mapping of mRNAs and proteins in a formaldehyde-fixed tissue slide via next-generation sequencing (NGS). Parallel microfluidic channels were used to deliver DNA barcodes to the surface of a tissue slide, and crossflow of two sets of barcodes, A1-50 and B1-50, followed by ligation in situ, yielded a 2D mosaic of tissue pixels, each containing a unique full barcode AB. Application to mouse embryos revealed major tissue types in early organogenesis as well as fine features like microvasculature in a brain and pigmented epithelium in an eye field. Gene expression profiles in 10-μm pixels conformed into the clusters of single-cell transcriptomes, allowing for rapid identification of cell types and spatial distributions. DBiT-seq can be adopted by researchers with no experience in microfluidics and may find applications in a range of fields including developmental biology, cancer biology, neuroscience, and clinical pathology.
Collapse
Affiliation(s)
- Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mingyu Yang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Cindy C Guo
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Toma Tebaldi
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Eileen Norris
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Alisia Pan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Jiatong Li
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Stephanie Halene
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
174
|
Liu W, Liu Q, Zhang B, Lin Z, Li X, Yang X, Pu M, Zou R, He Z, Wang F, Dou K. The mRNA of TCTP functions as a sponge to maintain homeostasis of TCTP protein levels in hepatocellular carcinoma. Cell Death Dis 2020; 11:974. [PMID: 33184257 PMCID: PMC7665032 DOI: 10.1038/s41419-020-03149-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023]
Abstract
Translationally controlled tumor protein (TCTP) is a highly conserved protein that accumulated in the tumorigenesis of various malignancies. Despite the important role of TCTP protein in tumor progression, the precise function and underlying mechanistic regulation of TCTP mRNA in hepatocellular carcinoma (HCC) remain unclear. In this study, we found that TCTP protein was overexpressed in HCC patients but TCTP mRNA expression levels were reversed. TCTP knockout HCC cells exhibited attenuated abilities of proliferation, migration, and invasion. The knockdown of TCTP by siRNA effectively reduced TCTP mRNA levels but not protein levels in HCC cells. Moreover, although the constitutive knockdown of TCTP inhibited almost 80% of TCTP protein expression levels in tumors of wildtype transgenic mice (TCTP KD/WT), partial restoration of TCTP protein expression was observed in the tumors of heterozygous TCTP mice (TCTP KD/TCTP±). The blockage of mRNA synthesis with ActD stimulated TCTP protein expression in HCC cells. In contrast, combined treatment with ActD and CHX or MG132 treatment alone did not lead to the TCTP protein accumulation in cells. Furthermore, following the introduction of exogenous TCTP in cells and orthotopic HCC tumor models, the endogenous TCTP protein did not change with the recombinational TCTP expression and kept a rather stable level. Dual-luciferase assays revealed that the coding sequence of TCTP mRNA functions as a sponge to regulate the TCTP protein expression. Collectively, our results indicated that the TCTP mRNA and protein formed a closed regulatory circuit and works as a buffering system to keep the homeostasis of TCTP protein levels in HCC.
Collapse
Affiliation(s)
- Wei Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University, Shanghai, 200123, China.,Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, 710032, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China
| | - Qi Liu
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Beilei Zhang
- Department of Gynecology and Obstetrics, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, 710038, China
| | - Zhibin Lin
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Xia Li
- Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China
| | - Xisheng Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Meng Pu
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Rongzhi Zou
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, 710032, China
| | - Zhiying He
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University, Shanghai, 200123, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China.
| | - Fu Wang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, China.
| | - Kefeng Dou
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi Province, 710032, China.
| |
Collapse
|
175
|
Skeletal muscle healing by M1-like macrophages produced by transient expression of exogenous GM-CSF. Stem Cell Res Ther 2020; 11:473. [PMID: 33158459 PMCID: PMC7648431 DOI: 10.1186/s13287-020-01992-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/22/2020] [Indexed: 12/23/2022] Open
Abstract
Background After traumatic skeletal muscle injury, muscle healing is often incomplete and produces extensive fibrosis. The sequence of M1 and M2 macrophage accumulation and the duration of each subtype in the injured area may help to direct the relative extent of fibrogenesis and myogenesis during healing. We hypothesized that increasing the number of M1 macrophages early after traumatic muscle injury would produce more cellular and molecular substrates for myogenesis and fewer substrates for fibrosis, leading to better muscle healing. Methods To test this hypothesis, we transfected skeletal muscle with a plasmid vector to transiently express GM-CSF shortly after injury to drive the polarization of macrophages towards the M1 subset. C57BL/6 mouse tibialis anterior (TA) muscles were injured by contusion and electroporated with uP-mGM, which is a plasmid vector that transiently expresses GM-CSF. Myogenesis, angiogenesis, and fibrosis were evaluated by histology, immunohistochemistry, and RT-qPCR; subpopulations of macrophages by flow cytometry; and muscle functioning by the maximum running speed on the treadmill and the recovery of muscle mass. Results Muscle injury increased the number of local M1-like macrophages and decreased the number of M2-like macrophages on day 4, and uP-mGM treatment enhanced this variation. uP-mGM treatment decreased TGF-β1 protein expression on day 4, and the Sirius Red-positive area decreased from 35.93 ± 15.45% (no treatment) to 2.9% ± 6.5% (p < 0.01) on day 30. uP-mGM electroporation also increased Hgf, Hif1α, and Mtor gene expression; arteriole density; and muscle fiber number during regeneration. The improvement in the quality of the muscle tissue after treatment with uP-mGM affected the increase in the TA muscle mass and the maximum running speed on a treadmill. Conclusion Collectively, our data show that increasing the number of M1-like macrophages immediately after traumatic muscle injury promotes muscle recovery with less fibrosis, and this can be achieved by the transient expression of GM-CSF.
Collapse
|
176
|
Yagi R, Masuda T, Ogata S, Mori A, Ito S, Ohtsuki S. Proteomic Evaluation of Plasma Membrane Fraction Prepared from a Mouse Liver and Kidney Using a Bead Homogenizer: Enrichment of Drug-Related Transporter Proteins. Mol Pharm 2020; 17:4101-4113. [PMID: 32902293 DOI: 10.1021/acs.molpharmaceut.0c00547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Quantifying the protein levels of drug transporters in plasma membrane fraction helps elucidate the function of these transporters. In this study, we conducted a proteomic evaluation of enriched drug-related transporter proteins in plasma membrane fraction prepared from mouse liver and kidney tissues using the membrane protein extraction kit and a bead homogenizer. Crude and plasma membrane fractions were prepared using either the Dounce or bead homogenizer, and protein levels were determined using quantitative proteomics. In liver tissues, the plasma membrane fractions were more enriched in transporter proteins than the crude membrane fractions; the average enrichment ratios of plasma-to-crude membrane fractions were 3.31 and 6.93 using the Dounce and bead homogenizers, respectively. The concentrations of transporter proteins in plasma membrane fractions determined using the bead homogenizer were higher than those determined using the Dounce homogenizer. Meanwhile, in kidney tissues, the plasma membrane fractions were enriched in transporters localized in the brush-border membrane to the same degree for both the homogenizers; however, the membrane fractions obtained using either homogenizer were not enriched in Na+/K+-ATPase and transporters localized in the basolateral membrane. These results indicate that fractionation, using the bead homogenizer, yielded transporter-enriched plasma membrane fractions from mouse liver and kidney tissues; however, no enrichment of basolateral transporters was observed in plasma membrane fractions prepared from kidney tissues.
Collapse
Affiliation(s)
- Ryotaro Yagi
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Seiryo Ogata
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Ayano Mori
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| |
Collapse
|
177
|
Ngcala MG, Goche T, Brown AP, Chivasa S, Ngara R. Heat Stress Triggers Differential Protein Accumulation in the Extracellular Matrix of Sorghum Cell Suspension Cultures. Proteomes 2020; 8:29. [PMID: 33105781 PMCID: PMC7709130 DOI: 10.3390/proteomes8040029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 01/13/2023] Open
Abstract
Plants reprogram gene expression as an adaptive response to survive high temperatures. While the identity and functions of intracellular heat stress-responsive proteins have been extensively studied, the heat response of proteins secreted to the extracellular matrix is unknown. Here, we used Sorghum bicolor, a species adapted for growth in hot climates, to investigate the extracellular heat-induced responses. When exposed to 40 C for 72 h, heat-sensitive Arabidopsis cell suspension cultures died, while ICSB338 sorghum cell cultures survived by activation of a transcriptional response characterized by the induction of HSP70 and HSP90 genes. Quantitative proteomic analysis of proteins recovered from cell culture medium revealed specific heat stress-induced protein accumulation within the sorghum secretome. Of the 265 secreted proteins identified, 31 responded to heat (2-fold change), with 84% possessing a predicted signal peptide for targeting to the classical secretory pathway. The differentially accumulated proteins have putative functions in metabolism, detoxification, and protein modifications. A germin (SORBI_3003G427700) was highly heat-inducible at both protein and gene level. Overall, our study reveals new insights into sorghum responses to heat and provides a useful resource of extracellular proteins that could serve as targets for developing thermotolerant crops. Data are available via ProteomeXchange with identifier PXD021536.
Collapse
Affiliation(s)
- Mamosa G. Ngcala
- Department of Plant Sciences, Qwaqwa campus, University of the Free State, Phuthadithjaba 9866, South Africa;
| | - Tatenda Goche
- Department of Crop Sciences, Epoch Mine Campus, Gwanda State University, Filabusi, Zimbabwe;
| | - Adrian P. Brown
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (A.P.B.); (S.C.)
| | - Stephen Chivasa
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (A.P.B.); (S.C.)
| | - Rudo Ngara
- Department of Plant Sciences, Qwaqwa campus, University of the Free State, Phuthadithjaba 9866, South Africa;
| |
Collapse
|
178
|
Gorchs L, Ahmed S, Mayer C, Knauf A, Fernández Moro C, Svensson M, Heuchel R, Rangelova E, Bergman P, Kaipe H. The vitamin D analogue calcipotriol promotes an anti-tumorigenic phenotype of human pancreatic CAFs but reduces T cell mediated immunity. Sci Rep 2020; 10:17444. [PMID: 33060625 PMCID: PMC7562723 DOI: 10.1038/s41598-020-74368-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
The pancreatic tumour stroma is composed of phenotypically heterogenous cancer-associated fibroblasts (CAFs) with both pro- and anti-tumorigenic functions. Here, we studied the impact of calcipotriol, a vitamin D3 analogue, on the activation of human pancreatic CAFs and T cells using 2- and 3-dimensional (2D, 3D) cell culture models. We found that calcipotriol decreased CAF proliferation and migration and reduced the release of the pro-tumorigenic factors prostaglandin E2, IL-6, periostin, and leukemia inhibitory factor. However, calcipotriol promoted PD-L1 upregulation, which could influence T cell mediated tumour immune surveillance. Calcipotriol reduced T cell proliferation and production of IFN-γ, granzyme B and IL-17, but increased IL-10 secretion. These effects were even more profound in the presence of CAFs in 2D cultures and in the presence of CAFs and pancreatic tumour cell line (PANC-1) spheroids in 3D cultures. Functional assays on tumour infiltrating lymphocytes also showed a reduction in T cell activation by calcipotriol. This suggests that calcipotriol reduces the tumour supportive activity of CAFs but at the same time reduces T cell effector functions, which could compromise the patients’ tumour immune surveillance. Thus, vitamin D3 analogues appear to have dual functions in the context of pancreatic cancer, which could have important clinical implications.
Collapse
Affiliation(s)
- Laia Gorchs
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Sultan Ahmed
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chanté Mayer
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Alisa Knauf
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Carlos Fernández Moro
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Mattias Svensson
- Department of Medicine, Centre for Infectious Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Rainer Heuchel
- Department of CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - Elena Rangelova
- Department of CLINTEC, Karolinska Institutet, Stockholm, Sweden.,Pancreatic Surgery Unit, Centre for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Bergman
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Infectious Disease Clinic, The Immunodeficiency Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Helen Kaipe
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden. .,Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
179
|
Hanson RL, Batchelor E. Rucaparib Treatment Alters p53 Oscillations in Single Cells to Enhance DNA-Double-Strand-Break-Induced Cell Cycle Arrest. Cell Rep 2020; 33:108240. [PMID: 33053351 DOI: 10.1016/j.celrep.2020.108240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 08/12/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
DNA double strand breaks induce oscillatory expression of the transcription factor p53 that is dependent on ataxia telangiectasia mutated (ATM) activity and the rate of double strand break resolution. Although p53 dynamics are known to play a role in the regulation of cell fate determination, the consequences of the variability in dynamics associated with differences in repair rates and utilized repair pathways are unknown. Using single-cell time-lapse microscopy, we found that disruption of specific repair pathways has distinct impacts on p53 dynamics. The small-molecule rucaparib, an inhibitor of the alternative end-joining-associated protein poly (ADP-ribose) polymerase (PARP), increased p53 pulse duration, altering the temporal expression of multiple p53 target genes. As a result, combination treatments of the radiomimetic drug neocarzinostatin with rucaparib drove prolonged growth arrest beyond that of DNA damage alone. This study highlights how pharmacological manipulation of DNA repair pathways may be used to alter p53 dynamics to enhance therapeutic regimens.
Collapse
Affiliation(s)
- Ryan L Hanson
- Department of Integrative Biology and Physiology, University of Minnesota, Cancer and Cardiovascular Research Building 3-136, 2231 6th Street SE, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric Batchelor
- Department of Integrative Biology and Physiology, University of Minnesota, Cancer and Cardiovascular Research Building 3-136, 2231 6th Street SE, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
180
|
OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data. Genes (Basel) 2020; 11:genes11101165. [PMID: 33023248 PMCID: PMC7650687 DOI: 10.3390/genes11101165] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023] Open
Abstract
Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by biologists, we developed a web application called OneStopRNAseq for the one-stop analysis of RNA-seq data. OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. Users only need to select the desired analyses and genome build, and provide a Gene Expression Omnibus (GEO) accession number or Dropbox links to sequence files, alignment files, gene-expression-count tables, or rank files with the corresponding metadata. Our pipeline facilitates the comprehensive and efficient analysis of private and public RNA-seq data.
Collapse
|
181
|
Mangleburg CG, Wu T, Yalamanchili HK, Guo C, Hsieh YC, Duong DM, Dammer EB, De Jager PL, Seyfried NT, Liu Z, Shulman JM. Integrated analysis of the aging brain transcriptome and proteome in tauopathy. Mol Neurodegener 2020; 15:56. [PMID: 32993812 PMCID: PMC7526226 DOI: 10.1186/s13024-020-00405-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 09/18/2020] [Indexed: 01/09/2023] Open
Abstract
Background Tau neurofibrillary tangle pathology characterizes Alzheimer’s disease and other neurodegenerative tauopathies. Brain gene expression profiles can reveal mechanisms; however, few studies have systematically examined both the transcriptome and proteome or differentiated Tau- versus age-dependent changes. Methods Paired, longitudinal RNA-sequencing and mass-spectrometry were performed in a Drosophila model of tauopathy, based on pan-neuronal expression of human wildtype Tau (TauWT) or a mutant form causing frontotemporal dementia (TauR406W). Tau-induced, differentially expressed transcripts and proteins were examined cross-sectionally or using linear regression and adjusting for age. Hierarchical clustering was performed to highlight network perturbations, and we examined overlaps with human brain gene expression profiles in tauopathy. Results TauWT induced 1514 and 213 differentially expressed transcripts and proteins, respectively. TauR406W had a substantially greater impact, causing changes in 5494 transcripts and 697 proteins. There was a ~ 70% overlap between age- and Tau-induced changes and our analyses reveal pervasive bi-directional interactions. Strikingly, 42% of Tau-induced transcripts were discordant in the proteome, showing opposite direction of change. Tau-responsive gene expression networks strongly implicate innate immune activation. Cross-species analyses pinpoint human brain gene perturbations specifically triggered by Tau pathology and/or aging, and further differentiate between disease amplifying and protective changes. Conclusions Our results comprise a powerful, cross-species functional genomics resource for tauopathy, revealing Tau-mediated disruption of gene expression, including dynamic, age-dependent interactions between the brain transcriptome and proteome.
Collapse
Affiliation(s)
- Carl Grant Mangleburg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hari K Yalamanchili
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Caiwei Guo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yi-Chen Hsieh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and Taub Institute for the study of Alzheimer's disease and the aging brain, Columbia University Medical Center, New York, NY, 10032, USA.,Cell Circuits Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, 1250 Moursund St., Suite N.1150, Houston, TX, 77030, USA
| | - Joshua M Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA. .,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, 1250 Moursund St., Suite N.1150, Houston, TX, 77030, USA. .,Department of Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
182
|
Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana. Int J Mol Sci 2020; 21:ijms21186946. [PMID: 32971781 PMCID: PMC7554720 DOI: 10.3390/ijms21186946] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/24/2022] Open
Abstract
Nutrient limited conditions are common in natural phytoplankton communities and are often used to increase the yield of lipids from industrial microalgae cultivations. Here we studied the effects of bioavailable nitrogen (N) and phosphorus (P) deprivation on the proteome and transcriptome of the oleaginous marine microalga Nannochloropsis gaditana. Turbidostat cultures were used to selectively apply either N or P deprivation, controlling for variables including the light intensity. Global (cell-wide) changes in the proteome were measured using Tandem Mass Tag (TMT) and LC-MS/MS, whilst gene transcript expression of the same samples was quantified by Illumina RNA-sequencing. We detected 3423 proteins, where 1543 and 113 proteins showed significant changes in abundance in N and P treatments, respectively. The analysis includes the global correlation between proteomic and transcriptomic data, the regulation of subcellular proteomes in different compartments, gene/protein functional groups, and metabolic pathways. The results show that triacylglycerol (TAG) accumulation under nitrogen deprivation was associated with substantial downregulation of protein synthesis and photosynthetic activity. Oil accumulation was also accompanied by a diverse set of responses including the upregulation of diacylglycerol acyltransferase (DGAT), lipase, and lipid body associated proteins. Deprivation of phosphorus had comparatively fewer, weaker effects, some of which were linked to the remodeling of respiratory metabolism.
Collapse
|
183
|
Comparative Proteomic Analysis Identifies EphA2 as a Specific Cell Surface Marker for Wharton's Jelly-Derived Mesenchymal Stem Cells. Int J Mol Sci 2020; 21:ijms21176437. [PMID: 32899389 PMCID: PMC7503404 DOI: 10.3390/ijms21176437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022] Open
Abstract
Wharton’s jelly-derived mesenchymal stem cells (WJ-MSCs) are a valuable tool in stem cell research due to their high proliferation rate, multi-lineage differentiation potential, and immunotolerance properties. However, fibroblast impurity during WJ-MSCs isolation is unavoidable because of morphological similarities and shared surface markers. Here, a proteomic approach was employed to identify specific proteins differentially expressed by WJ-MSCs in comparison to those by neonatal foreskin and adult skin fibroblasts (NFFs and ASFs, respectively). Mass spectrometry analysis identified 454 proteins with a transmembrane domain. These proteins were then compared across the different cell-lines and categorized based on their cellular localizations, biological processes, and molecular functions. The expression patterns of a selected set of proteins were further confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR), Western blotting, and immunofluorescence assays. As anticipated, most of the studied proteins had common expression patterns. However, EphA2, SLC25A4, and SOD2 were predominantly expressed by WJ-MSCs, while CDH2 and Talin2 were specific to NFFs and ASFs, respectively. Here, EphA2 was established as a potential surface-specific marker to distinguish WJ-MSCs from fibroblasts and for prospective use to prepare pure primary cultures of WJ-MSCs. Additionally, CDH2 could be used for a negative-selection isolation/depletion method to remove neonatal fibroblasts contaminating preparations of WJ-MSCs.
Collapse
|
184
|
Chang S, Wang LHC, Chen BS. Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. Biomedicines 2020; 8:biomedicines8090320. [PMID: 32878239 PMCID: PMC7555687 DOI: 10.3390/biomedicines8090320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B Virus (HBV) infection is a major cause of morbidity and mortality worldwide. However, poor understanding of its pathogenesis often gives rise to intractable immune escape and prognosis recurrence. Thus, a valid systematic approach based on big data mining and genome-wide RNA-seq data is imperative to further investigate the pathogenetic mechanism and identify biomarkers for drug design. In this study, systems biology method was applied to trim false positives from the host/pathogen genetic and epigenetic interaction network (HPI-GEN) under HBV infection by two-side RNA-seq data. Then, via the principal network projection (PNP) approach and the annotation of KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, significant biomarkers related to cellular dysfunctions were identified from the core cross-talk signaling pathways as drug targets. Further, based on the pre-trained deep learning-based drug-target interaction (DTI) model and the validated pharmacological properties from databases, i.e., drug regulation ability, toxicity, and sensitivity, a combination of promising multi-target drugs was designed as a multiple-molecule drug to create more possibility for the treatment of HBV infection. Therefore, with the proposed systems medicine discovery and repositioning procedure, we not only shed light on the etiologic mechanism during HBV infection but also efficiently provided a potential drug combination for therapeutic treatment of Hepatitis B.
Collapse
Affiliation(s)
- Shen Chang
- Laboratory of Automatic Control, Signal Processing and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan;
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan;
| | - Bor-Sen Chen
- Laboratory of Automatic Control, Signal Processing and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan;
- Correspondence:
| |
Collapse
|
185
|
Jacqueline C, Lee A, Frey N, Minden JS, Finn OJ. Inflammation-Induced Abnormal Expression of Self-molecules on Epithelial Cells: Targets for Tumor Immunoprevention. Cancer Immunol Res 2020; 8:1027-1038. [PMID: 32467324 PMCID: PMC7415557 DOI: 10.1158/2326-6066.cir-19-0870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/11/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023]
Abstract
Tumor-associated antigens (TAA) are self-molecules abnormally expressed on tumor cells, which elicit humoral and cellular immunity and are targets of immunosurveillance. Immunity to TAAs is found in some healthy individuals with no history of cancer and correlates positively with a history of acute inflammatory and infectious events and cancer risk reduction. This suggests a potential role in cancer immunosurveillance for the immune memory elicited against disease-associated antigens (DAA) expressed on infected and inflamed tissues that are later recognized on tumors as TAAs. To understand probable sources for DAA generation, we investigated in vitro the role of inflammation that accompanies both infection and carcinogenesis. After exposure of normal primary breast epithelial cells to proinflammatory cytokines IL1β, IL6, and TNFα, or macrophages producing these cytokines, we saw transient overexpression of well-known TAAs, carcinoembryonic antigen and Her-2/neu, and overexpression and hypoglycosylation of MUC1. We documented inflammation-induced changes in the global cellular proteome by 2D difference gel electrophoresis combined with mass spectrometry and identified seven new DAAs. Through gene profiling, we showed that the cytokine treatment activated NF-κB and transcription of the identified DAAs. We tested three in vitro-identified DAAs, Serpin B1, S100A9, and SOD2, and found them overexpressed in premalignant and malignant breast tissues as well as in inflammatory conditions of the colon, stomach, and liver. This new category of TAAs, which are also DAAs, represent a potentially large number of predictable, shared, immunogenic, and safe antigens to use in preventative cancer vaccines and as targets for cancer therapies.
Collapse
Affiliation(s)
- Camille Jacqueline
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Amanda Lee
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Nolan Frey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Jonathan S Minden
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Olivera J Finn
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
| |
Collapse
|
186
|
Sadick JS, Crawford LA, Cramer HC, Franck C, Liddelow SA, Darling EM. Generating Cell Type-Specific Protein Signatures from Non-symptomatic and Diseased Tissues. Ann Biomed Eng 2020; 48:2218-2232. [PMID: 32303872 PMCID: PMC7416432 DOI: 10.1007/s10439-020-02507-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
Abstract
Here we demonstrate a technique to generate proteomic signatures of specific cell types within heterogeneous populations. While our method is broadly applicable across biological systems, we have limited the current work to study neural cell types isolated from human, post-mortem Alzheimer's disease (AD) and aged-matched non-symptomatic (NS) brains. Motivating the need for this tool, we conducted an initial meta-analysis of current, human AD proteomics studies. While the results broadly corroborated major neurodegenerative disease hypotheses, cell type-specific predictions were limited. By adapting our Formaldehyde-fixed Intracellular Target-Sorted Antigen Retrieval (FITSAR) method for proteomics and applying this technique to characterize AD and NS brains, we generated enriched neuron and astrocyte proteomic profiles for a sample set of donors (available at www.fitsarpro.appspot.com ). Results showed the feasibility for using FITSAR to evaluate cell-type specific hypotheses. Our overall methodological approach provides an accessible platform to determine protein presence in specific cell types and emphasizes the need for protein-compatible techniques to resolve systems complicated by cellular heterogeneity.
Collapse
Affiliation(s)
- Jessica S Sadick
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, 02912, USA
- Neuroscience Institute, NYU Langone Medical Center, New York, NY, 10016, USA
| | - Lorin A Crawford
- Department of Biostatistics, Brown University, Providence, RI, 02912, USA
- Center for Statistical Sciences, Brown University, Providence, RI, 02912, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA
| | - Harry C Cramer
- Center for Biomedical Engineering, Brown University, Providence, RI, 02912, USA
- School of Engineering, Brown University, Providence, RI, 02912, USA
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Christian Franck
- Center for Biomedical Engineering, Brown University, Providence, RI, 02912, USA
- School of Engineering, Brown University, Providence, RI, 02912, USA
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Langone Medical Center, New York, NY, 10016, USA
- Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY, 10016, USA
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Eric M Darling
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, 02912, USA.
- Center for Biomedical Engineering, Brown University, Providence, RI, 02912, USA.
- School of Engineering, Brown University, Providence, RI, 02912, USA.
- Department of Orthopaedics, Brown University, Providence, RI, 02912, USA.
| |
Collapse
|
187
|
Boldrup L, Coates P, Gu X, Wang L, Fåhraeus R, Wilms T, Sgaramella N, Baumgarth J, Norberg-Spaak L, Nylander K. Levels of MUC1 in tumours and serum of patients with different sub-types of squamous cell carcinoma of the head and neck. Oncol Lett 2020; 20:1709-1718. [PMID: 32724413 PMCID: PMC7377060 DOI: 10.3892/ol.2020.11746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/14/2020] [Indexed: 01/27/2023] Open
Abstract
Mucin 1 (MUC1) is a membrane-bound and secreted glycoprotein that has a protective role in surface epithelia. We recently demonstrated that MUC1 mRNA expression was upregulated in tumour-free tongue tissues adjacent to squamous cell carcinoma of the oral tongue (SCCOT) compared with that in the tumour tissues. The present study investigated MUC1 protein in SCCOT tissue and serum from patients with squamous cell carcinoma of the head and neck (SCCHN) at different sub-sites. The results from immunohistochemistry demonstrated that all SCCOT tissues expressed MUC1; however, the protein levels were not correlated with MUC1 mRNA levels in the same tumours. Furthermore, serum MUC1 level was lower in patients with SCCOT, tonsil SCC and gingival SCC compared with that in healthy subjects; however, the difference was only significant for patients with SCCOT (P=0.0421). No correlation was seen between MUC1 level in tumour tissues and MUCI level in serum from the same patients. The absence of correlation between MUC1 protein and mRNA levels in SCCOT tissues emphasized the importance of validating genomic data in clinical samples. Although significant MUC1 downregulation was observed in the serum of patients with SCCOT, there was a large variation within the groups, suggesting that MUC1 may not be used as a biomarker for these types of tumors.
Collapse
Affiliation(s)
- Linda Boldrup
- Department of Medical Biosciences, Umeå University, Umeå, Västerbotten 901 87, Sweden
| | - Philip Coates
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Southern Moravia 656 53, Czech Republic
| | - Xiaolian Gu
- Department of Medical Biosciences, Umeå University, Umeå, Västerbotten 901 87, Sweden
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, Umeå, Västerbotten 901 87, Sweden
| | - Robin Fåhraeus
- Department of Medical Biosciences, Umeå University, Umeå, Västerbotten 901 87, Sweden.,Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Southern Moravia 656 53, Czech Republic.,Institute of Molecular Genetics, University of Paris St. Louis Hospital, Paris, Île-de-France 750 10, France
| | - Torben Wilms
- Department of Clinical Sciences, Umeå University Hospital, Umeå, Västerbotten 901 87, Sweden
| | - Nicola Sgaramella
- Department of Medical Biosciences, Umeå University, Umeå, Västerbotten 901 87, Sweden
| | - Jonathan Baumgarth
- Department of Clinical Sciences, Umeå University Hospital, Umeå, Västerbotten 901 87, Sweden
| | - Lena Norberg-Spaak
- Department of Clinical Sciences, Umeå University Hospital, Umeå, Västerbotten 901 87, Sweden
| | - Karin Nylander
- Department of Medical Biosciences, Umeå University, Umeå, Västerbotten 901 87, Sweden
| |
Collapse
|
188
|
Dobrzyn K, Kiezun M, Zaobidna E, Kisielewska K, Rytelewska E, Gudelska M, Kopij G, Bors K, Szymanska K, Kaminska B, Kaminski T, Smolinska N. The In Vitro Effect of Prostaglandin E 2 and F 2α on the Chemerin System in the Porcine Endometrium during Gestation. Int J Mol Sci 2020; 21:E5213. [PMID: 32717877 PMCID: PMC7432131 DOI: 10.3390/ijms21155213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
Chemerin belongs to the group of adipocyte-derived hormones known as adipokines, which are responsible mainly for the control of energy homeostasis. Adipokine exerts its influence through three receptors: Chemokine-like receptor 1 (CMKLR1), G protein-coupled receptor 1 (GPR1), and C-C motif chemokine receptor-like 2 (CCRL2). A growing body of evidence indicates that chemerin participates in the regulation of the female reproductive system. According to the literature, the expression of chemerin and its receptors in reproductive structures depends on the local hormonal milieu. The aim of this study was to investigate the in vitro effect of prostaglandins E2 (PGE2) and F2α (PGF2α) on chemerin and chemerin receptor (chemerin system) mRNAs (qPCR) and proteins (ELISA, Western blotting) in endometrial tissue explants collected from early-pregnant gilts. Both PGE2 and PGF2α significantly influenced the expression of the chemerin gene, hormone secretion, and the expression of chemerin receptor genes and proteins. The influence of both prostaglandins on the expression of the chemerin system varied between different stages of gestation. This is the first study to describe the modulatory effect of PGE2 and PGF2α on the expression of the chemerin system in the porcine uterus during early gestation.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Nina Smolinska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn-Kortowo, Poland; (M.K.); (E.Z.); (K.K.); (E.R.); (M.G.); (G.K.); (K.B.); (K.S.); (B.K.); (T.K.)
| |
Collapse
|
189
|
Widyastuti HP, Norden-Krichmar TM, Grosberg A, Zaragoza MV. Gene expression profiling of fibroblasts in a family with LMNA-related cardiomyopathy reveals molecular pathways implicated in disease pathogenesis. BMC MEDICAL GENETICS 2020; 21:152. [PMID: 32698886 PMCID: PMC7374820 DOI: 10.1186/s12881-020-01088-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/06/2020] [Indexed: 12/22/2022]
Abstract
Background Intermediate filament proteins that construct the nuclear lamina of a cell include the Lamin A/C proteins encoded by the LMNA gene, and are implicated in fundamental processes such as nuclear structure, gene expression, and signal transduction. LMNA mutations predominantly affect mesoderm-derived cell lineages in diseases collectively termed as laminopathies that include dilated cardiomyopathy with conduction defects, different forms of muscular dystrophies, and premature aging syndromes as Hutchinson-Gilford Progeria Syndrome. At present, our understanding of the molecular mechanisms regulating tissue-specific manifestations of laminopathies are still limited. Methods To gain deeper insight into the molecular mechanism of a novel LMNA splice-site mutation (c.357-2A > G) in an affected family with cardiac disease, we conducted deep RNA sequencing and pathway analysis for nine fibroblast samples obtained from three patients with cardiomyopathy, three unaffected family members, and three unrelated, unaffected individuals. We validated our findings by quantitative PCR and protein studies. Results We identified eight significantly differentially expressed genes between the mutant and non-mutant fibroblasts, that included downregulated insulin growth factor binding factor protein 5 (IGFBP5) in patient samples. Pathway analysis showed involvement of the ERK/MAPK signaling pathway consistent with previous studies. We found no significant differences in gene expression for Lamin A/C and B-type lamins between the groups. In mutant fibroblasts, RNA-seq confirmed that only the LMNA wild type allele predominately was expressed, and Western Blot showed normal Lamin A/C protein levels. Conclusions IGFBP5 may contribute in maintaining signaling pathway homeostasis, which may lead to the absence of notable molecular and structural abnormalities in unaffected tissues such as fibroblasts. Compensatory mechanisms from other nuclear membrane proteins were not found. Our results also demonstrate that only one copy of the wild type allele is sufficient for normal levels of Lamin A/C protein to maintain physiological function in an unaffected cell type. This suggests that affected cell types such as cardiac tissues may be more sensitive to haploinsufficiency of Lamin A/C. These results provide insight into the molecular mechanism of disease with a possible explanation for the tissue specificity of LMNA-related dilated cardiomyopathy.
Collapse
Affiliation(s)
- Halida P Widyastuti
- UCI Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Chemistry, University of California, Irvine, School of Medicine, 2042 Hewitt Hall, Irvine, CA, 92697-3940, USA
| | - Trina M Norden-Krichmar
- Department of Epidemiology, University of California, Irvine, School of Medicine, 3062 Anteater Instruction and Research Building, Irvine, CA, 92697-7550, USA.
| | - Anna Grosberg
- Department of Biomedical Engineering and The Edwards Lifesciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, California, USA
| | - Michael V Zaragoza
- UCI Cardiogenomics Program, Department of Pediatrics, Division of Genetics & Genomics and Department of Biological Chemistry, University of California, Irvine, School of Medicine, 2042 Hewitt Hall, Irvine, CA, 92697-3940, USA.
| |
Collapse
|
190
|
Wang SE, Brooks AES, Poole AM, Simoes-Barbosa A. Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis. BMC Mol Cell Biol 2020; 21:54. [PMID: 32689943 PMCID: PMC7370421 DOI: 10.1186/s12860-020-00297-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Trichomonas vaginalis, the causative agent of a prevalent urogenital infection in humans, is an evolutionarily divergent protozoan. Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5' UTRs. The specific mechanisms adopted by T. vaginalis to fine-tune the translation efficiency (TE) of mRNAs remain largely unknown. RESULTS Using both computational and experimental approaches, this study investigated two key factors influencing TE in T. vaginalis: codon usage and mRNA secondary structure. Statistical dependence between TE and codon adaptation index (CAI) highlighted the impact of codon usage on mRNA translation in T. vaginalis. A genome-wide interrogation revealed that low structural complexity at the 5' end of mRNA followed closely by a highly structured downstream region correlates with TE variation in this organism. To validate these findings, a synthetic library of 15 synonymous iLOV genes was created, representing five mRNA folding profiles and three codon usage profiles. Fluorescence signals produced by the expression of these synonymous iLOV genes in T. vaginalis were consistent with and validated our in silico predictions. CONCLUSIONS This study demonstrates the role of codon usage bias and mRNA secondary structure in TE of T. vaginalis mRNAs, contributing to a better understanding of the factors that influence, and possibly regulate, gene expression in this human pathogen.
Collapse
Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, USA
| | - Anna E S Brooks
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
| | | |
Collapse
|
191
|
Wieczfinska J, Sitarek P, Kowalczyk T, Pawliczak R. Leonurus sibiricus root extracts decrease airway remodeling markers expression in fibroblasts. Clin Exp Immunol 2020; 202:28-46. [PMID: 32562256 DOI: 10.1111/cei.13481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/27/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022] Open
Abstract
Bronchial asthma is believed to be provoked by the interaction between airway inflammation and remodeling. Airway remodeling is a complex and poorly understood process, and controlling it appears key for halting the progression of asthma and other obstructive lung diseases. Plants synthesize a number of valuable compounds as constitutive products and as secondary metabolites, many of which have curative properties. The aim of this study was to evaluate the anti-remodeling properties of extracts from transformed and transgenic Leonurus sibiricus roots with transformed L. sibiricus roots extract with transcriptional factor AtPAP1 overexpression (AtPAP1). Two fibroblast cell lines, Wistar Institute-38 (WI-38) and human fetal lung fibroblast (HFL1), were incubated with extracts from transformed L. sibiricus roots (TR) and roots with transcriptional factor AtPAP1 over-expression (AtPAP1 TR). Additionally, remodeling conditions were induced in the cultures with rhinovirus 16 (HRV16). The expressions of metalloproteinase 9 (MMP)-9, tissue inhibitor of metalloproteinases 1 (TIMP-1), arginase I and transforming growth factor (TGF)-β were determined by quantitative polymerase chain reaction (qPCR) and immunoblotting methods. AtPAP1 TR decreased arginase I and MMP-9 expression with no effect on TIMP-1 or TGF-β mRNA expression. This extract also inhibited HRV16-induced expression of arginase I, MMP-9 and TGF-β in both cell lines (P < 0·05) Our study shows for the first time to our knowledge, that transformed AtPAP1 TR extract from L. sibiricus root may affect the remodeling process. Its effect can be attributed an increased amount of phenolic acids such as: chlorogenic acid, caffeic acid or ferulic acid and demonstrates the value of biotechnology in medicinal research.
Collapse
Affiliation(s)
- J Wieczfinska
- Department of Immunopathology, Medical University of Lodz, Lodz, Poland
| | - P Sitarek
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, Lodz, Poland
| | - T Kowalczyk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Lodz, Poland
| | - R Pawliczak
- Department of Immunopathology, Medical University of Lodz, Lodz, Poland
| |
Collapse
|
192
|
Mori MP, Souza-Pinto NCD. PPRC1, but not PGC-1α, levels directly correlate with expression of mitochondrial proteins in human dermal fibroblasts. Genet Mol Biol 2020; 43:e20190083. [PMID: 32639509 PMCID: PMC7341727 DOI: 10.1590/1678-4685-gmb-2019-0083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/15/2020] [Indexed: 11/22/2022] Open
Abstract
The XPC protein, which is mutated in xeroderma pigmentosum (XP) complementation group C (XP-C), is a lesion recognition factor in NER, but it has also been shown to interact with and stimulate DNA glycosylases, to act as transcriptional co-activator and on energy metabolism adaptation. We have previously demonstrated that XP-C cells show increased mitochondrial H2O2 production with a shift between respiratory complexes I and II, leading to sensitivity to mitochondrial stress. Here we report a marked decrease in expression of the transcriptional co-activator PGC-1α, a master regulator of mitochondrial biogenesis, in XP-C cells. A transcriptional role for XPC in PGC-1α expression was discarded, as XPC knockdown did not downregulate PGC-1α expression and XPC-corrected cells still showed lower PGC-1α expression. DNA methylation alone did not explain PGC-1α silencing. In four different XP-C cell lines tested, reduction of PGC-1α expression was detected in three, all of them carrying the c.1643_1644delTG mutation (ΔTG) in XPC. Indeed, all cell lines carrying XPC ΔTG mutation, whether homozygous or heterozygous, presented decreased PGC-1α expression. However, this alteration in gene expression was not exclusive to XPC ΔTG cell lines, for other non-related cell lines also showed altered PGC-1α expression. Moreover, PGC1-α expression did not correlate with expression levels of TFAM and SDHA, known PGC-1α target-genes. In turn, PPRC1, another member of the PGC family of transcription co-activators controlling mitochondrial biogenesis, displayed a good correlation between its expression in 10 cell lines and TFAM and SDHA. Nonetheless, PGC-1α knockdown led to a slight decrease of its target-gene protein level, TFAM, and subsequently of a mtDNA-encoded gene, MT-CO2. These results indicate that PGC-1α and PPRC1 cooperate as regulators of mitochondrial biogenesis and maintenance in fibroblasts.
Collapse
Affiliation(s)
- Mateus Prates Mori
- Universidade de São Paulo, Departamento de Bioquímica, Instituto de Química, São Paulo, SP, Brazil
| | | |
Collapse
|
193
|
Martinez-Arroyo O, Ortega A, Perez-Hernandez J, Chaves FJ, Redon J, Cortes R. The Rab-Rabphilin system in injured human podocytes stressed by glucose overload and angiotensin II. Am J Physiol Renal Physiol 2020; 319:F178-F191. [PMID: 32567349 PMCID: PMC7473899 DOI: 10.1152/ajprenal.00077.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Kidney injury in hypertension and diabetes entails, among in other structures, damage in a key cell of the glomerular filtration barrier, the podocyte. Podocytes are polarized and highly differentiated cells in which vesicular transport, partly driven by Rab GTPases, is a relevant process. The aim of the present study was to analyze Rab GTPases of the Rab-Rabphilin system in human immortalized podocytes and the impact of high glucose and angiotensin II. Furthermore, alterations of the system in urine cell pellets from patients with hypertension and diabetes were studied. Apoptosis was analyzed in podocytes, and mRNA level quantification, Western blot analysis, and immunofluorescence were developed to quantify podocyte-specific molecules and Rab-Rabphilin components (Rab3A, Rab27A, and Rabphilin3A). Quantitative RT-PCR was performed on urinary cell pellet from patients. The results showed that differentiated cells had reduced protein levels of the Rab-rabphillin system compared with undifferentiated cells. After glucose overload and angiotensin II treatment, apoptosis was increased and podocyte-specific proteins were reduced. Rab3A and Rab27A protein levels were increased under glucose overload, and Rabphilin3A decreased. Furthermore, this system exhibited higher levels under stress conditions in a manner of angiotensin II dose and time treatment. Immunofluorescence imaging indicated different expression patterns of podocyte markers and Rab27A under treatments. Finally, Rab3A and Rab27A were increased in patient urine pellets and showed a direct relationship with albuminuria. Collectively, these results suggest that the Rab-Rabphilin system could be involved in the alterations observed in injured podocytes and that a mechanism may be activated to reduce damage through the vesicular transport enhancement directed by this system.
Collapse
Affiliation(s)
- Olga Martinez-Arroyo
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Ana Ortega
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Javier Perez-Hernandez
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Felipe J Chaves
- Genomics and Diabetes Unit, INCLIVA Biomedical Research Institute, Valencia, Spain.,CIBER of Diabetes and Associated Metabolic Diseases, Institute of Health Carlos III, Minister of Health, Barcelona, Spain
| | - Josep Redon
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, Valencia, Spain.,Internal Medicine Unit, Hospital Clínico Universitario, Valencia, Spain.,CIBER of Physiopathology of Obesity and Nutrition, Institute of Health Carlos III, Minister of Health, Madrid, Spain
| | - Raquel Cortes
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, Valencia, Spain
| |
Collapse
|
194
|
Jia Y, Liu H, Qu Z, Wang J, Wang X, Wang Z, Yang L, Zhang D, Zou D, Zhao H. Transcriptome Sequencing and iTRAQ of Different Rice Cultivars Provide Insight into Molecular Mechanisms of Cold-Tolerance Response in Japonica Rice. RICE (NEW YORK, N.Y.) 2020; 13:43. [PMID: 32572635 PMCID: PMC7310054 DOI: 10.1186/s12284-020-00401-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/11/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions. However, it has a high sensitivity to cold stress and chilling stress limits its nitrogen uptake and metabolism. To identify the genes and pathways involved in cold tolerance, specifically within nitrogen metabolism pathways, we compared gene and protein expression differences between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10 (SJ). RESULTS Using isobaric tags for relative or absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5549 genes and 450 proteins in DN and 6145 genes and 790 proteins in SJ, which were differentially expressed during low water temperature (Tw) treatments. There were 354 transcription factor (TF) genes (212 downregulated, 142 upregulated) and 366 TF genes (220 downregulated, 146 upregulated), including 47 gene families, differentially expressed in DN under control (CKDN) vs. DN under low-Tw (D15DN) and SJ under control (CKSJ) vs. SJ under low-Tw D15SJ, respectively. Genes associated with rice cold-related biosynthesis pathways, particularly the mitogen-activated protein kinase (MAPK) signaling, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) associated with rice cold-related biosynthesis pathways, and particularly glutathione metabolism, were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins that participated in γ-aminobutyric acid (GABA) and glutamine synthesis were downregulated under cold stress. CONCLUSION Cold stress conditions during reproductive growth, resulted in genes and proteins related to cold stress biosynthesis pathways being significantly differentially expressed in DN and SJ. The present study confirmed the known cold stress-associated genes and identified new putative cold-responsive genes. We also found that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-Tw treatments affected N uptake and N metabolism in rice, as well as promoted Glu metabolism and the synthesis of ornithine and proline in cold-sensitive SJ.
Collapse
Affiliation(s)
- Yan Jia
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agriculture University, Harbin, 150030, Heilongjiang, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agriculture University, Harbin, 150030, Heilongjiang, China
| | - Zhaojun Qu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agriculture University, Harbin, 150030, Heilongjiang, China
| | - Jin Wang
- Bei Da Huang Kenfeng Seed Limited Company, Harbin, 150431, Heilongjiang, China
| | - Xinpeng Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agriculture University, Harbin, 150030, Heilongjiang, China
| | - Zhuoqian Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agriculture University, Harbin, 150030, Heilongjiang, China
| | - Liang Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agriculture University, Harbin, 150030, Heilongjiang, China
| | - Dong Zhang
- PlantTech Biotechnology Co., Ltd., Beijing, 100000, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agriculture University, Harbin, 150030, Heilongjiang, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agriculture University, Harbin, 150030, Heilongjiang, China.
| |
Collapse
|
195
|
Hafner A, Reyes J, Stewart-Ornstein J, Tsabar M, Jambhekar A, Lahav G. Quantifying the Central Dogma in the p53 Pathway in Live Single Cells. Cell Syst 2020; 10:495-505.e4. [PMID: 32533938 DOI: 10.1016/j.cels.2020.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/08/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
Transcription factors (TFs) integrate signals to regulate target gene expression, but we generally lack a quantitative understanding of how changes in TF levels regulate mRNA and protein production. Here, we established a system to simultaneously monitor the levels of p53, a TF that shows oscillations following DNA damage, and the transcription and protein levels of its target p21 in individual cells. p21 transcription tracked p53 dynamics, while p21 protein steadily accumulated. p21 transcriptional activation showed bursts of mRNA production, with p53 levels regulating the probability but not magnitude of activation. Variations in p53 levels between cells contributed to heterogeneous p21 transcription while independent p21 alleles exhibited highly correlated behaviors. Pharmacologically elevating p53 increased the probability of p21 transcription with minor effects on its magnitude, leading to a strong increase in p21 protein levels. Our results reveal quantitative mechanisms by which TF dynamics can regulate protein levels of its targets. A record of this paper's transparent peer review process is included in the Supplemental Information.
Collapse
Affiliation(s)
- Antonina Hafner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - José Reyes
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Michael Tsabar
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashwini Jambhekar
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
196
|
Makowczenko KG, Jastrzebski JP, Szeszko K, Smolinska N, Paukszto L, Dobrzyn K, Kiezun M, Rytelewska E, Kaminska B, Kaminski T. Transcription Analysis of the Chemerin Impact on Gene Expression Profile in the Luteal Cells of Gilts. Genes (Basel) 2020; 11:E651. [PMID: 32545672 PMCID: PMC7349926 DOI: 10.3390/genes11060651] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/07/2023] Open
Abstract
Chemerin is a recently discovered adipokine that participates in the regulation of many physiological and disorder-related processes in mammals, including metabolism, inflammatory reactions, obesity, and reproduction. We investigated how chemerin affects the transcriptome profile of porcine luteal cells. The luteal cells were acquired from mature gilts. After the in vitro culturing with and without chemerin, the total RNAs were isolated and high-throughput sequencing was performed. Obtained datasets were processed using bioinformatic tools. The study revealed 509 differentially expressed genes under the chemerin influence. Their products take part in many processes, important for the functions of the corpus luteum, such as steroids and prostaglandins synthesis, NF-κB and JAK/STAT signal transducing pathways, and apoptosis. The expression of the CASP3, HSD3B7, IL1B, and PTGS2 genes, due to their important role in the physiology of the corpus luteum, was validated using the quantitative real-time polymerase chain reaction (qPCR) method. The qPCR confirmed the changes of gene expression. Chemerin in physiological concentrations significantly affects the expression of many genes in luteal cells of pigs, which is likely to result in modification of physiological processes related to reproduction.
Collapse
Affiliation(s)
- Karol G. Makowczenko
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (K.G.M.); (K.S.); (N.S.); (K.D.); (M.K.); (E.R.); (B.K.)
| | - Jan P. Jastrzebski
- Bioinformatics Core Facility, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (J.P.J.); (L.P.)
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Karol Szeszko
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (K.G.M.); (K.S.); (N.S.); (K.D.); (M.K.); (E.R.); (B.K.)
| | - Nina Smolinska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (K.G.M.); (K.S.); (N.S.); (K.D.); (M.K.); (E.R.); (B.K.)
| | - Lukasz Paukszto
- Bioinformatics Core Facility, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (J.P.J.); (L.P.)
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Kamil Dobrzyn
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (K.G.M.); (K.S.); (N.S.); (K.D.); (M.K.); (E.R.); (B.K.)
| | - Marta Kiezun
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (K.G.M.); (K.S.); (N.S.); (K.D.); (M.K.); (E.R.); (B.K.)
| | - Edyta Rytelewska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (K.G.M.); (K.S.); (N.S.); (K.D.); (M.K.); (E.R.); (B.K.)
| | - Barbara Kaminska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (K.G.M.); (K.S.); (N.S.); (K.D.); (M.K.); (E.R.); (B.K.)
| | - Tadeusz Kaminski
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (K.G.M.); (K.S.); (N.S.); (K.D.); (M.K.); (E.R.); (B.K.)
| |
Collapse
|
197
|
Nguyen HT, Yamamoto K, Iida M, Agusa T, Ochiai M, Guo J, Karthikraj R, Kannan K, Kim EY, Iwata H. Effects of prenatal bisphenol A exposure on the hepatic transcriptome and proteome in rat offspring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137568. [PMID: 32145629 DOI: 10.1016/j.scitotenv.2020.137568] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/06/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Developmental exposure to bisphenol A (BPA) is associated with liver dysfunction and diseases in adulthood. The aims of this study were to assess the effects of prenatal BPA exposure on the hepatic transcriptome and proteome in female and male offspring and to understand adverse outcome pathways (AOPs) to observed phenotypic effects. Pregnant Wistar rats were exposed to 50 or 5000 μg BPA/kg bw/day, or 17β-estradiol (E2, 50 μg/kg bw/day) from embryonic day 3 to 18. The liver transcriptome and proteome profiles were analyzed in the newborn (postnatal day 1; PND1) and weaning (PND21) rat offspring. Based on the differentially expressed genes/proteins derived from transcriptome and proteome profiles, we performed pathway, transcription factor, and disease enrichment analyses. A principal component analysis of transcriptome data demonstrated that prenatal BPA exposure caused masculinization of the hepatic transcriptome in females. Both of transcriptomic and proteomic data showed that prenatal BPA exposure led to the disruption of cell cycle, lipid homeostasis, and hormone balance in offspring. Most of the effects at the transcript level were extended from newborn to weaning in males, but were moderated until weaning in females. The alterations at the transcript and protein levels were accordant with the observation of increases in body weight and anogenital distance and changes in hepatosomatic index in the offspring. Collectively, we constructed AOPs with evidence of sex- and age-specific actions of prenatal BPA exposure in the offspring.
Collapse
Affiliation(s)
- Hoa Thanh Nguyen
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan
| | - Kimika Yamamoto
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan
| | - Midori Iida
- Graduate School of Computer Science and System Engineering, Kyushu Institute of Technology, Iizuka, 820-0067, Japan
| | - Tetsuro Agusa
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan
| | - Mari Ochiai
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan
| | - Jiahua Guo
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan
| | - Rajendiran Karthikraj
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201-0509, United States
| | - Kurunthachalam Kannan
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201-0509, United States
| | - Eun-Young Kim
- Department of Life and Nanopharmaceutical Science and Department of Biology, Kyung Hee University, Seoul, 130-701, Republic of Korea
| | - Hisato Iwata
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan.
| |
Collapse
|
198
|
Borden KLB, Volpon L. The diversity, plasticity, and adaptability of cap-dependent translation initiation and the associated machinery. RNA Biol 2020; 17:1239-1251. [PMID: 32496897 PMCID: PMC7549709 DOI: 10.1080/15476286.2020.1766179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Translation initiation is a critical facet of gene expression with important impacts that underlie cellular responses to stresses and environmental cues. Its dysregulation in many diseases position this process as an important area for the development of new therapeutics. The gateway translation factor eIF4E is typically considered responsible for ‘global’ or ‘canonical’ m7G cap-dependent translation. However, eIF4E impacts translation of specific transcripts rather than the entire translatome. There are many alternative cap-dependent translation mechanisms that also contribute to the translation capacity of the cell. We review the diversity of these, juxtaposing more recently identified mechanisms with eIF4E-dependent modalities. We also explore the multiplicity of functions played by translation factors, both within and outside protein synthesis, and discuss how these differentially contribute to their ultimate physiological impacts. For comparison, we discuss some modalities for cap-independent translation. In all, this review highlights the diverse mechanisms that engage and control translation in eukaryotes.
Collapse
Affiliation(s)
- Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
| | - Laurent Volpon
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
| |
Collapse
|
199
|
Piran M, Karbalaei R, Piran M, Aldahdooh J, Mirzaie M, Ansari-Pour N, Tang J, Jafari M. Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity? Biomolecules 2020; 10:biom10060850. [PMID: 32503292 PMCID: PMC7355924 DOI: 10.3390/biom10060850] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/17/2022] Open
Abstract
Studying relationships among gene products by expression profile analysis is a common approach in systems biology. Many studies have generalized the outcomes to the different levels of central dogma information flow and assumed a correlation of transcript and protein expression levels. However, the relation between the various types of interaction (i.e., activation and inhibition) of gene products to their expression profiles has not been widely studied. In fact, looking for any perturbation according to differentially expressed genes is the common approach, while analyzing the effects of altered expression on the activity of signaling pathways is often ignored. In this study, we examine whether significant changes in gene expression necessarily lead to dysregulated signaling pathways. Using four commonly used and comprehensive databases, we extracted all relevant gene expression data and all relationships among directly linked gene pairs. We aimed to evaluate the ratio of coherency or sign consistency between the expression level as well as the causal relationships among the gene pairs. Through a comparison with random unconnected gene pairs, we illustrate that the signaling network is incoherent, and inconsistent with the recorded expression profile. Finally, we demonstrate that, to infer perturbed signaling pathways, we need to consider the type of relationships in addition to gene-product expression data, especially at the transcript level. We assert that identifying enriched biological processes via differentially expressed genes is limited when attempting to infer dysregulated pathways.
Collapse
Affiliation(s)
- Mehran Piran
- Bioinformatics and Computational Biology Research Center, Shiraz University of Medical Sciences, Shiraz P.O. Box 71336-54361, Iran;
| | - Reza Karbalaei
- Department of Biology, Temple University, Philadelphia, PA 19122, USA;
| | - Mehrdad Piran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 14177-55469, Iran;
| | - Jehad Aldahdooh
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00270 Helsinki, Finland;
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-134, Iran;
| | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK;
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00270 Helsinki, Finland;
- Correspondence: (J.T.); (M.J.)
| | - Mohieddin Jafari
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00270 Helsinki, Finland;
- Correspondence: (J.T.); (M.J.)
| |
Collapse
|
200
|
Waszkiewicz EM, Kozlowska W, Zmijewska A, Franczak A. Expression of Insulin-Like Growth Factor 1 (IGF-1) and Epidermal Growth Factor (EGF) Receptors and the Effect of IGF-1 and EGF on Androgen and Estrogen Release in the Myometrium of Pigs-In Vitro Study. Animals (Basel) 2020; 10:E915. [PMID: 32466279 PMCID: PMC7278463 DOI: 10.3390/ani10050915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023] Open
Abstract
Porcine myometrium possesses steroidogenic activity but its regulation is not well understood. It was hypothesized that the regulators of myometrial steroidogenesis are insulin-like growth factor 1 (IGF-1) and epidermal growth factor (EGF), which were found to modulate the steroidogenic activity of the endometrium and embryos. Myometrial slices were collected from gravid and nongravid pigs on days 10 or 11, 12 or 13 and 15 or 16 and studied for: (1) the relative abundance of IGF-1R and EGFR mRNA transcripts and proteins, to determine myometrial readiness to response growth factors treatment and (2) the effect of IGF-1 or EGF on the myometrial release of androstenedione (A4), testosterone (T), estrone (E1) and estradiol-17β (E2). The results showed that the relative expression and abundance of IGF-1R and EGFR in the myometrium were altered regarding the female reproductive status. During the estrous cycle, EGF increased myometrial release of A4 on days 12-13 and E2 on days 15-16. In gravid pigs (days 15-16), IGF-1 and EGF increased the E1 release. In conclusion: (1) porcine myometrium possesses the potential to respond to IGF-1 and EGF treatment, (2) EGF significantly increases myometrial A4 and E2 release in cyclic pigs, while IGF-1 and EGF increase the E1 release in gravid pigs.
Collapse
Affiliation(s)
| | | | | | - Anita Franczak
- Department of Animal Anatomy and Physiology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland; (E.M.W.); (W.K.); (A.Z.)
| |
Collapse
|