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Higuchi MDL, Kawakami JT, Ikegami RN, Reis MM, Pereira JDJ, Ianni BM, Buck P, Oliveira LMDS, Santos MHH, Hajjar LA, Bocchi EA. Archaea Symbiont of T. cruzi Infection May Explain Heart Failure in Chagas Disease. Front Cell Infect Microbiol 2018; 8:412. [PMID: 30519544 PMCID: PMC6259288 DOI: 10.3389/fcimb.2018.00412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/06/2018] [Indexed: 12/20/2022] Open
Abstract
Background: Archaeal genes present in Trypanosoma cruzi may represent symbionts that would explain development of heart failure in 30% of Chagas disease patients. Extracellular vesicles in peripheral blood, called exosomes (< 0.1 μm) or microvesicles (>0.1 μm), present in larger numbers in heart failure, were analyzed to determine whether they are derived from archaea in heart failure Chagas disease. Methods: Exosomes and microvesicles in serum supernatant from 3 groups were analyzed: heart failure Chagas disease (N = 26), asymptomatic indeterminate form (N = 21) and healthy non-chagasic control (N = 16). Samples were quantified with transmission electron microscopy, flow cytometer immunolabeled with anti-archaemetzincin-1 antibody (AMZ 1, archaea collagenase) and probe anti-archaeal DNA and zymography to determine AMZ1 (Archaeal metalloproteinase) activity. Results: Indeterminate form patients had higher median numbers of exosomes/case vs. heart failure patients (58.5 vs. 25.5, P < 0.001), higher exosome content of AMZ1 antigens (2.0 vs. 0.0; P < 0.001), and lower archaeal DNA content (0.2 vs. 1.5, P = 0.02). A positive correlation between exosomes and AMZ1 content was seen in indeterminate form (r = 0.5, P < 0.001), but not in heart failure patients (r = 0.002, P = 0.98). Higher free archaeal DNA (63.0 vs. 11.1, P < 0.001) in correlation with exosome numbers (r = 0.66, P = 0.01) was seen in heart failure but not in indeterminate form (r = 0.29, P = 0.10). Flow cytometer showed higher numbers of AMZ1 microvesicles in indeterminate form (64 vs. 36, P = 0.02) and higher archaeal DNA microvesicles in heart failure (8.1 vs. 0.9, P < 0.001). Zymography showed strong% collagenase activity in HF group, mild activity in IF compared to non-chagasic healthy group (121 ± 14, 106 ± 13 and 100; P < 0.001). Conclusions: Numerous exosomes, possibly removing and degrading abnormal AMZ1 collagenase, are associated with indeterminate form. Archaeal microvesicles and their exosomes, possibly associated with release of archaeal AMZ1 in heart failure, are future candidates of heart failure biomarkers if confirmed in larger series, and the therapeutic focus in the treatment of Chagas disease.
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Affiliation(s)
- Maria de Lourdes Higuchi
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Joyce T Kawakami
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Renata N Ikegami
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Marcia M Reis
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline de Jesus Pereira
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Barbara M Ianni
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Paula Buck
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Luanda Mara da Silva Oliveira
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Marilia H H Santos
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Ludhmila A Hajjar
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Edimar A Bocchi
- Instituto do Coraçao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. BMC Genomics 2018; 19:594. [PMID: 30086717 PMCID: PMC6081845 DOI: 10.1186/s12864-018-4972-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/31/2018] [Indexed: 12/20/2022] Open
Abstract
Background The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues. Results Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Graphia was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development. Conclusion Expression profiles obtained from public RNA-seq datasets – despite being generated by different laboratories using different methodologies – can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4972-7) contains supplementary material, which is available to authorized users.
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Yu AC, Zambrano RM, Cristian I, Price S, Bernhard B, Zucker M, Venkateswaran S, McGowan-Jordan J, Armour CM. Variable developmental delays and characteristic facial features-A novel 7p22.3p22.2 microdeletion syndrome? Am J Med Genet A 2017; 173:1593-1600. [PMID: 28440577 DOI: 10.1002/ajmg.a.38241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 03/08/2017] [Accepted: 03/11/2017] [Indexed: 12/22/2022]
Abstract
Isolated 7p22.3p22.2 deletions are rarely described with only two reports in the literature. Most other reported cases either involve a much larger region of the 7p arm or have an additional copy number variation. Here, we report five patients with overlapping microdeletions at 7p22.3p22.2. The patients presented with variable developmental delays, exhibiting relative weaknesses in expressive language skills and relative strengths in gross, and fine motor skills. The most consistent facial features seen in these patients included a broad nasal root, a prominent forehead a prominent glabella and arched eyebrows. Additional variable features amongst the patients included microcephaly, metopic ridging or craniosynostosis, cleft palate, cardiac defects, and mild hypotonia. Although the patients' deletions varied in size, there was a 0.47 Mb region of overlap which contained 7 OMIM genes: EIP3B, CHST12, LFNG, BRAT1, TTYH3, AMZ1, and GNA12. We propose that monosomy of this region represents a novel microdeletion syndrome. We recommend that individuals with 7p22.3p22.2 deletions should receive a developmental assessment and a thorough cardiac exam, with consideration of an echocardiogram, as part of their initial evaluation.
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Affiliation(s)
- Andrea C Yu
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Regina M Zambrano
- Division of Clinical Genetics, Department of Pediatrics, Louisiana State University Health Science Center, New Orleans, Louisiana
| | - Ingrid Cristian
- Division of Genetics and Metabolism, Department of Pediatrics, Nemours Children's Hospital Orlando, Orlando, Florida
| | - Sue Price
- Oxford Regional Genetic Service, Churchill Hospital, Oxford, UK
| | - Birgitta Bernhard
- North West Thames Regional Genetic Service, North West London Hospitals, Greater London, England
| | - Marc Zucker
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Sunita Venkateswaran
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Jean McGowan-Jordan
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Christine M Armour
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
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4
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Parker JDK, Shen Y, Pleasance E, Li Y, Schein JE, Zhao Y, Moore R, Wegrzyn-Woltosz J, Savage KJ, Weng AP, Gascoyne RD, Jones S, Marra M, Laskin J, Karsan A. Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing. Cold Spring Harb Mol Case Stud 2016; 2:a000679. [PMID: 27148583 PMCID: PMC4849852 DOI: 10.1101/mcs.a000679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In an attempt to assess potential treatment options, whole-genome and transcriptome sequencing were performed on a patient with an unclassifiable small lymphoproliferative disorder. Variants from genome sequencing were prioritized using a combination of comparative variant distributions in a spectrum of lymphomas, and meta-analyses of gene expression profiling. In this patient, the molecular variants that we believe to be most relevant to the disease presentation most strongly resemble a diffuse large B-cell lymphoma (DLBCL), whereas the gene expression data are most consistent with a low-grade chronic lymphocytic leukemia (CLL). The variant of greatest interest was a predicted NOTCH2-truncating mutation, which has been recently reported in various lymphomas.
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Affiliation(s)
- Jeremy D K Parker
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Yvonne Li
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Jacqueline E Schein
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Joanna Wegrzyn-Woltosz
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer and Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory and Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer and Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Steven Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Janessa Laskin
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Aly Karsan
- Genome Sciences Centre and Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
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5
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Jia B, Li Z, Liu J, Sun Y, Jia X, Xuan YH, Zhang J, Jeon CO. A Zinc-Dependent Protease AMZ-tk from a Thermophilic Archaeon is a New Member of the Archaemetzincin Protein Family. Front Microbiol 2015; 6:1380. [PMID: 26733945 PMCID: PMC4681839 DOI: 10.3389/fmicb.2015.01380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/20/2015] [Indexed: 12/23/2022] Open
Abstract
A putative zinc-dependent protease (TK0512) in Thermococcus kodakarensis KOD1 shares a conserved motif with archaemetzincins, which are metalloproteases found in archaea, bacteria, and eukarya. Phylogenetic and sequence analyses showed that TK0512 and its homologues in Thermococcaceae represent new members in the archaemetzincins family, which we named AMZ-tk. We further confirmed its proteolytic activity biochemically by overexpression of the recombinant AMZ-tk in Escherichia coli and characterization of the purified enzyme. In the presence of zinc, the purified enzyme degraded casein, while adding EDTA strongly inhibited the enzyme activity. AMZ-tk also exhibited self-cleavage activity that required Zn2+. These results demonstrated that AMZ-tk is a zinc-dependent protease within the archaemetzincin family. The enzyme displayed activity at alkaline pHs ranging from 7.0 to 10.0, with the optimal pH being 8.0. The optimum temperature for the catalytic activity of AMZ-tk was 55°C. Quantitative reverse transcription-PCR revealed that transcription of AMZ-tk was also up-regulated after exposing the cells to 55 and 65°C. Mutant analysis suggested that Zn2+ binding histidine and catalytic glutamate play key roles in proteolysis. AMZ-tk was thermostable on incubation for 4 h at 70°C in the presence of EDTA. AMZ-tk also retained >50% of its original activity in the presence of both laboratory surfactants and commercial laundry detergents. AMZ-tk further showed antibacterial activity against several bacteria. Therefore, AMZ-tk is of considerable interest for many purposes in view of its activity at alkaline pH, detergents, and thermostability.
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Affiliation(s)
- Baolei Jia
- Department of Life Science, Chung-Ang University Seoul, South Korea
| | - Zhengqun Li
- College of Plant Sciences, Jilin University Changchun, China
| | - Jinliang Liu
- College of Plant Sciences, Jilin University Changchun, China
| | - Ying Sun
- Department of Life Science, Chung-Ang University Seoul, South Korea
| | - Xiaomeng Jia
- Department of Life Science, Chung-Ang University Seoul, South Korea
| | - Yuan Hu Xuan
- College of Plant Protection, Shenyang Agricultural University Shenyang, China
| | - Jiayan Zhang
- College of Plant Sciences, Jilin University Changchun, China
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University Seoul, South Korea
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Jokela T, Oikari S, Takabe P, Rilla K, Kärnä R, Tammi M, Tammi R. Interleukin-1β-induced Reduction of CD44 Ser-325 Phosphorylation in Human Epidermal Keratinocytes Promotes CD44 Homomeric Complexes, Binding to Ezrin, and Extended, Monocyte-adhesive Hyaluronan Coats. J Biol Chem 2015; 290:12379-93. [PMID: 25809479 DOI: 10.1074/jbc.m114.620864] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 12/13/2022] Open
Abstract
The proinflammatory cytokine interleukin-1β (IL-1β) attracts leukocytes to sites of inflammation. One of the recruitment mechanisms involves the formation of extended, hyaluronan-rich pericellular coats on local fibroblasts, endothelial cells, and epithelial cells. In the present work, we studied how IL-1β turns on the monocyte adhesion of the hyaluronan coat on human keratinocytes. IL-1β did not influence hyaluronan synthesis or increase the amount of pericellular hyaluronan in these cells. Instead, we found that the increase in the hyaluronan-dependent monocyte binding was associated with the CD44 of the keratinocytes. Although IL-1β caused a small increase in the total amount of CD44, a more marked impact was the decrease of CD44 phosphorylation at serine 325. At the same time, IL-1β increased the association of CD44 with ezrin and complex formation of CD44 with itself. Treatment of keratinocyte cultures with KN93, an inhibitor of calmodulin kinase 2, known to phosphorylate Ser-325 in CD44, caused similar effects as IL-1β (i.e. homomerization of CD44 and its association with ezrin) and resulted in increased monocyte binding to keratinocytes in a hyaluronan-dependent way. Overexpression of wild type CD44 standard form, but not a corresponding CD44 mutant mimicking the Ser-325-phosphorylated form, was able to induce monocyte binding to keratinocytes. In conclusion, treatment of human keratinocytes with IL-1β changes the structure of their hyaluronan coat by influencing the amount, post-translational modification, and cytoskeletal association of CD44, thus enhancing monocyte retention on keratinocytes.
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Affiliation(s)
- Tiina Jokela
- From the Institute of Biomedicine, Department of Medicine, University of Eastern Finland, Yliopistonranta 1E, P.O. Box 1627, 70211 Kuopio, Finland
| | - Sanna Oikari
- From the Institute of Biomedicine, Department of Medicine, University of Eastern Finland, Yliopistonranta 1E, P.O. Box 1627, 70211 Kuopio, Finland
| | - Piia Takabe
- From the Institute of Biomedicine, Department of Medicine, University of Eastern Finland, Yliopistonranta 1E, P.O. Box 1627, 70211 Kuopio, Finland
| | - Kirsi Rilla
- From the Institute of Biomedicine, Department of Medicine, University of Eastern Finland, Yliopistonranta 1E, P.O. Box 1627, 70211 Kuopio, Finland
| | - Riikka Kärnä
- From the Institute of Biomedicine, Department of Medicine, University of Eastern Finland, Yliopistonranta 1E, P.O. Box 1627, 70211 Kuopio, Finland
| | - Markku Tammi
- From the Institute of Biomedicine, Department of Medicine, University of Eastern Finland, Yliopistonranta 1E, P.O. Box 1627, 70211 Kuopio, Finland
| | - Raija Tammi
- From the Institute of Biomedicine, Department of Medicine, University of Eastern Finland, Yliopistonranta 1E, P.O. Box 1627, 70211 Kuopio, Finland
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7
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Cerdà-Costa N, Gomis-Rüth FX. Architecture and function of metallopeptidase catalytic domains. Protein Sci 2014; 23:123-44. [PMID: 24596965 DOI: 10.1002/pro.2400] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The cleavage of peptide bonds by metallopeptidases (MPs) is essential for life. These ubiquitous enzymes participate in all major physiological processes, and so their deregulation leads to diseases ranging from cancer and metastasis, inflammation, and microbial infection to neurological insults and cardiovascular disorders. MPs cleave their substrates without a covalent intermediate in a single-step reaction involving a solvent molecule, a general base/acid, and a mono- or dinuclear catalytic metal site. Most monometallic MPs comprise a short metal-binding motif (HEXXH), which includes two metal-binding histidines and a general base/acid glutamate, and they are grouped into the zincin tribe of MPs. The latter divides mainly into the gluzincin and metzincin clans. Metzincins consist of globular ∼ 130-270-residue catalytic domains, which are usually preceded by N-terminal pro-segments, typically required for folding and latency maintenance. The catalytic domains are often followed by C-terminal domains for substrate recognition and other protein-protein interactions, anchoring to membranes, oligomerization, and compartmentalization. Metzincin catalytic domains consist of a structurally conserved N-terminal subdomain spanning a five-stranded β-sheet, a backing helix, and an active-site helix. The latter contains most of the metal-binding motif, which is here characteristically extended to HEXXHXXGXX(H,D). Downstream C-terminal subdomains are generally shorter, differ more among metzincins, and mainly share a conserved loop--the Met-turn--and a C-terminal helix. The accumulated structural data from more than 300 deposited structures of the 12 currently characterized metzincin families reviewed here provide detailed knowledge of the molecular features of their catalytic domains, help in our understanding of their working mechanisms, and form the basis for the design of novel drugs.
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8
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Huang CJ, Yang SH, Lee CL, Cheng YC, Tai SY, Chien CC. Ribosomal protein S27-like in colorectal cancer: a candidate for predicting prognoses. PLoS One 2013; 8:e67043. [PMID: 23826192 PMCID: PMC3691124 DOI: 10.1371/journal.pone.0067043] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/13/2013] [Indexed: 01/25/2023] Open
Abstract
Background The development and progression of colorectal cancer (CRC) involve a complex process of multiple genetic changes. Tumor suppressor p53 is capable of determining the fate of CRC cells. However, the role of a p53-inducible modulator, ribosomal protein S27-like (RPS27L), in CRC is unknown. Methods Here, the differential expression of RPS27L was examined in the feces and colonic tissues of CRC patients, to explore its possible correlation with patient survival and to investigate the cellular mechanisms underlying their clinical outcomes. Eighty intermediate-stage CRC patients (42 at stage II and 38 at stage III) were divided into two groups according to their fecal RPS27L mRNA levels. The survival probabilities of the groups were estimated using the Kaplan–Meier method. The RPS27L protein in the colonic tissues of stage III patients with different prognoses was further examined immunohistochemically. RPS27L expression in LoVo cells was manipulated to examine the possible cellular responses in vitro. Results Elevated RPS27L expression, in either feces or tissues, was related to a better prognosis. In vitro, RPS27L-expressing LoVo cells ceased DNA synthesis and apoptotic activity while the expression of their DNA repair molecules was upregulated. Conclusions Elevated RPS27L may improve the prognoses of certain CRC patients by enhancing the DNA repair capacity of their colonic cells, and can be determined in feces. By integrating clinical, molecular, and cellular data, our study demonstrates that fecal RPS27L may be a useful index for predicting prognoses and guiding personalized therapeutic strategies, especially in patients with intermediate-stage CRC.
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Affiliation(s)
- Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
- School of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Shung-Haur Yang
- Department of Surgery, Taipei-Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming University, Taipei, Taiwan
| | - Chia-Long Lee
- Department of Internal Medicine, Hsinchu Cathay General Hospital, Hsinchu, Taiwan
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Che Cheng
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
| | - Szu-Yun Tai
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
| | - Chih-Cheng Chien
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
- School of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
- Department of Anesthesiology, Sijhih Cathay General Hospital, New Taipei, Taiwan
- * E-mail:
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9
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Qian W, Deng L, Lu D, Xu S. Genome-wide landscapes of human local adaptation in Asia. PLoS One 2013; 8:e54224. [PMID: 23349834 PMCID: PMC3551950 DOI: 10.1371/journal.pone.0054224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 12/11/2012] [Indexed: 01/30/2023] Open
Abstract
Genetic studies of human local adaptation have been facilitated greatly by recent advances in high-throughput genotyping and sequencing technologies. However, few studies have investigated local adaptation in Asian populations on a genome-wide scale and with a high geographic resolution. In this study, taking advantage of the dense population coverage in Southeast Asia, which is the part of the world least studied in term of natural selection, we depicted genome-wide landscapes of local adaptations in 63 Asian populations representing the majority of linguistic and ethnic groups in Asia. Using genome-wide data analysis, we discovered many genes showing signs of local adaptation or natural selection. Notable examples, such as FOXQ1, MAST2, and CDH4, were found to play a role in hair follicle development and human cancer, signal transduction, and tumor repression, respectively. These showed strong indications of natural selection in Philippine Negritos, a group of aboriginal hunter-gatherers living in the Philippines. MTTP, which has associations with metabolic syndrome, body mass index, and insulin regulation, showed a strong signature of selection in Southeast Asians, including Indonesians. Functional annotation analysis revealed that genes and genetic variants underlying natural selections were generally enriched in the functional category of alternative splicing. Specifically, many genes showing significant difference with respect to allele frequency between northern and southern Asian populations were found to be associated with human height and growth and various immune pathways. In summary, this study contributes to the overall understanding of human local adaptation in Asia and has identified both known and novel signatures of natural selection in the human genome.
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Affiliation(s)
- Wei Qian
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lian Deng
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Abstract
Recent proteomic analyses of snake venoms show that metalloproteinases represent major components in most of the Crotalid and Viperid venoms. In this chapter we discuss the multiple activities of the SVMPs. In addition to hemorrhagic activity, members of the SVMP family also have fibrin(ogen)olytic activity, act as prothrombin activators, activate blood coagulation factor X, possess apoptotic activity, inhibit platelet aggregation, are pro-inflammatory and inactivate blood serine proteinase inhibitors. Clearly the SVMPs have multiple functions in addition to their well-known hemorrhagic activity. The realization that there are structural variations in the SVMPs and the early studies that led to their classification represents an important event in our understanding of the structural forms of the SVMPs. The SVMPs were subdivided into the P-I, P-II and P-III protein classes. The noticeable characteristic that distinguished the different classes was their size (molecular weight) differences and domain structure: Class I (P-I), the small SVMPs, have molecular masses of 20-30 kDa, contain only a pro domain and the proteinase domain; Class II (P-II), the medium size SVMPs, molecular masses of 30-60 kDa, contain the pro domain, proteinase domain and disintegrin domain; Class III (P-III), the large SVMPs, have molecular masses of 60-100 kDa, contain pro, proteinase, disintegrin-like and cysteine-rich domain structure. Another significant advance in the SVMP field was the characterization of the crystal structure of the first P-I class SVMP. The structures of other P-I SVMPs soon followed and the structures of P-III SVMPs have also been determined. The active site of the metalloproteinase domain has a consensus HEXXHXXGXXHD sequence and a Met-turn. The "Met-turn" structure contains a conserved Met residue that forms a hydrophobic basement for the three zinc-binding histidines in the consensus sequence.
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Affiliation(s)
- Francis S Markland
- University of Southern California, Keck School of Medicine, Cancer Research Laboratory #106, 1303 N. Mission Rd., Los Angeles, CA 90033, USA.
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Crystal structures of archaemetzincin reveal a moldable substrate-binding site. PLoS One 2012; 7:e43863. [PMID: 22937112 PMCID: PMC3427221 DOI: 10.1371/journal.pone.0043863] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 07/30/2012] [Indexed: 12/01/2022] Open
Abstract
Background Archaemetzincins are metalloproteases occurring in archaea and some mammalia. They are distinct from all the other metzincins by their extended active site consensus sequence HEXXHXXGXXHCX4CXMX17CXXC featuring four conserved cysteine residues. Very little is known about their biological importance and structure-function relationships. Principal Findings Here we present three crystal structures of the archaemetzincin AfAmzA (Uniprot O29917) from Archaeoglobus fulgidus, revealing a metzincin architecture featuring a zinc finger-like structural element involving the conserved cysteines of the consensus motif. The active sites in all three structures are occluded to different extents rendering the enzymes proteolytically inactive against a large variety of tested substrates. Owing to the different ligand binding there are significant differences in active site architecture, revealing a large flexibility of the loops covering the active site cleft. Conclusions The crystal structures of AfAmzA provide the structural basis for the lack of activity in standard proteolytic assays and imply a triggered activity onset upon opening of the active site cleft.
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Sneeringer R, Penzias AS, Barrett B, Usheva A. High levels of mineralocorticoids in preovulatory follicular fluid could contribute to oocyte development. Fertil Steril 2011; 95:182-7. [DOI: 10.1016/j.fertnstert.2010.06.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 05/18/2010] [Accepted: 06/15/2010] [Indexed: 10/19/2022]
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Skandalis SS, Kozlova I, Engström U, Hellman U, Heldin P. Proteomic identification of CD44 interacting proteins. IUBMB Life 2010; 62:833-40. [DOI: 10.1002/iub.392] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Waltersperger S, Widmer C, Wang M, Baumann U. Crystal structure of archaemetzincin AmzA from Methanopyrus kandleri at 1.5 A resolution. Proteins 2010; 78:2720-3. [PMID: 20597090 DOI: 10.1002/prot.22777] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sandro Waltersperger
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
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Elías-Arnanz M, Padmanabhan S, Murillo FJ. The regulatory action of the myxobacterial CarD/CarG complex: a bacterial enhanceosome? FEMS Microbiol Rev 2010; 34:764-78. [PMID: 20561058 DOI: 10.1111/j.1574-6976.2010.00235.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A global regulatory complex made up of two unconventional transcriptional factors, CarD and CarG, is implicated in the control of various processes in Myxococcus xanthus, a Gram-negative bacterium that serves as a prokaryotic model system for multicellular development and the response to blue light. CarD has a unique two-domain architecture composed of: (1) a C-terminal DNA-binding domain that resembles eukaryotic high mobility group A (HMGA) proteins, which are relatively abundant, nonhistone components of chromatin that remodel DNA and prime it for the assembly of multiprotein-DNA complexes essential for various DNA transactions, and (2) an N-terminal domain involved in interactions with CarG and RNA polymerase, which is also the founding member of the large CarD_TRCF family of bacterial proteins. CarG, which does not bind DNA directly, has a zinc-binding motif of the type found in the archaemetzincin class of metalloproteases that, in CarG, appears to play a purely structural role. This review aims to provide an overview of the known molecular details and insights emerging from the study of the singular CarD-CarG prokaryotic regulatory complex and its parallels with enhanceosomes, the higher order, nucleoprotein transcription complexes in eukaryotes.
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Affiliation(s)
- Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Area de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
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Abstract
Metalloproteases comprise a heterogeneous group of proteolytic enzymes whose main characteristic is the utilization of a metal ion to polarize a water molecule and perform hydrolytic reactions. These enzymes represent the most densely populated catalytic class of proteases in many organisms and play essential roles in multiple biological processes. In this chapter, we will first present a general description of the complexity of metalloproteases in the context of the degradome, which is defined as the complete set of protease genes encoded by the genome of a certain organism. We will also discuss the functional relevance of these enzymes in a large variety of biological and pathological conditions. Finally, we will analyze in more detail three families of metalloproteases: ADAMs (a disintegrin and metalloproteinase), ADAMTSs (ADAMs with thrombospondin domains), and MMPs (matrix metalloproteinases) which have a growing relevance in a number of human pathologies including cancer, arthritis, neurodegenerative disorders, and cardiovascular diseases.
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Affiliation(s)
- Alejandro P Ugalde
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
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Quesada V, Ordóñez GR, Sánchez LM, Puente XS, López-Otín C. The Degradome database: mammalian proteases and diseases of proteolysis. Nucleic Acids Res 2008; 37:D239-43. [PMID: 18776217 PMCID: PMC2686449 DOI: 10.1093/nar/gkn570] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The degradome is defined as the complete set of proteases present in an organism. The recent availability of whole genomic sequences from multiple organisms has led us to predict the contents of the degradomes of several mammalian species. To ensure the fidelity of these predictions, our methods have included manual curation of individual sequences and, when necessary, direct cloning and sequencing experiments. The results of these studies in human, chimpanzee, mouse and rat have been incorporated into the Degradome database, which can be accessed through a web interface at http://degradome.uniovi.es. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This web site also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes.
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Affiliation(s)
- Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006-Oviedo, Spain
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Peñalver-Mellado M, García-Heras F, Padmanabhan S, García-Moreno D, Murillo FJ, Elías-Arnanz M. Recruitment of a novel zinc-bound transcriptional factor by a bacterial HMGA-type protein is required for regulating multiple processes in Myxococcus xanthus. Mol Microbiol 2006; 61:910-26. [PMID: 16879646 DOI: 10.1111/j.1365-2958.2006.05289.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enhanceosome assembly in eukaryotes often requires high mobility group A (HMGA) proteins. In prokaryotes, the only known transcriptional regulator with HMGA-like physical, structural and DNA-binding properties is Myxococcus xanthus CarD. Here, we report that every CarD-regulated process analysed also requires the product of gene carG, located immediately downstream of and transcriptionally coupled to carD. CarG has the zinc-binding H/C-rich metallopeptidase motif found in archaemetzincins, but with Q replacing a catalytically essential E. CarG, a monomer, binds two zinc atoms, shows no apparent metallopeptidase activity, and its stability in vivo absolutely requires the cysteines. This indicates a strictly structural role for zinc-binding. In vivo CarG localizes to the nucleoid but only if CarD is also present. In vitro CarG shows no DNA-binding but physically interacts with CarD via its N-terminal and not HMGA domain. CarD and CarG thus work as a single, physically linked, transcriptional regulatory unit, and if one exists in a bacterium so does the other. Like zinc-associated eukaryotic transcriptional adaptors in enhanceosome assembly, CarG regulates by interacting not with DNA but with another transcriptional factor.
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Affiliation(s)
- Marcos Peñalver-Mellado
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
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Higuchi ML, Santos MH, Roggério A, Kawakami JT, Bezerra HG, Canzian M. A role for archaeal organisms in development of atherosclerotic vulnerable plaques and myxoid matrices. Clinics (Sao Paulo) 2006; 61:473-8. [PMID: 17072447 DOI: 10.1590/s1807-59322006000500016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 08/07/2006] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Vulnerable plaques are characterized by a myxoid matrix, necrotic lipidic core, reactive oxygen species, and high levels of microorganisms. Aerobic microbes such as Chlamydophila pneumoniae and Mycoplasma pneumoniae usually do not survive in oxidative stress media. Archaea are anaerobic microbes with powerful anti-oxidative enzymes that allow detoxification of free radicals whose presence might favor the survival of aerobic microorganisms. We searched for archaeal organisms in vulnerable plaques, and possible associations with myxoid matrix, chlamydia, and mycoplasma bodies. METHODS Twenty-nine tissue samples from 13 coronary artherectomies from large excentric ostial or bifurcational lesions were studied using optical and electron microscopy. Infectious agents compatible with archaea, chlamydia, and mycoplasma were semiquantified using electron micrographs and correlated with the amounts of fibromuscular tissue, myxoid matrix, and foam cells, as determined from semi-thin sections. Six of the cases were also submitted to polymerase chain reaction with archaeal primers. RESULTS All 13 specimens showed archaeal-compatible structures and chlamydial and mycoplasmal bodies in at least 1 sample. There was a positive correlation between extent of the of myxoid matrix and archaeal bodies (r = 0.44, P = 0.02); between archaeal and mycoplasmal bodies (r = 0.41, P = 0.03), and between chlamydial bodies and foam cells (r = 0.42; P = 0.03). The PCR test was positive for archaeal DNA in 4 of the 6 fragments. DISCUSSION DNA and forms suggestive of archaea are present in vulnerable plaques and may have a fundamental role in the proliferation of mycoplasma and chlamydia. This seems to be the first description of apparently pathogenic archaea in human internal organ lesions.
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Affiliation(s)
- Maria L Higuchi
- Heart Institute, Hospital das Clínicas, São Paulo University Medical School, São Paulo, SP, Brazil
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