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Mala U, Baral TK, Somasundaram K. Integrative analysis of cell adhesion molecules in glioblastoma identified prostaglandin F2 receptor inhibitor (PTGFRN) as an essential gene. BMC Cancer 2022; 22:642. [PMID: 35690717 PMCID: PMC9188228 DOI: 10.1186/s12885-022-09682-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/13/2022] [Indexed: 11/27/2022] Open
Abstract
Background Glioblastoma (GBM) is the most common primary malignant brain tumor in adults exhibiting infiltration into surrounding tissues, recurrence, and resistance to therapy. GBM infiltration is accomplished by many deregulated factors such as cell adhesion molecules (CAMs), which are membrane proteins that participate in cell-cell and cell-ECM interactions to regulate survival, proliferation, migration, and stemness. Methods A comprehensive bioinformatics analysis of CAMs (n = 518) in multiple available datasets revealed genetic and epigenetic alterations among CAMs in GBM. Univariate Cox regression analysis using TCGA dataset identified 127 CAMs to be significantly correlated with survival. The poor prognostic indicator PTGFRN was chosen to study its role in glioma. Silencing of PTGFRN in glioma cell lines was achieved by the stable expression of short hairpin RNA (shRNA) against the PTGFRN gene. PTGFRN was silenced and performed cell growth, migration, invasion, cell cycle, and apoptosis assays. Neurosphere and limiting dilution assays were also performed after silencing of PTGFRN in GSCs. Results Among the differentially regulated CAMs (n = 181, 34.9%), major proportion of them were found to be regulated by miRNAs (n = 95, 49.7%) followed by DNA methylation (n = 32, 16.7%), and gene copy number variation (n = 12, 6.2%). We found that PTGFRN to be upregulated in GBM tumor samples and cell lines with a significant poor prognostic correlation with patient survival. Silencing PTGFRN diminished cell growth, colony formation, anchorage-independent growth, migration, and invasion and led to cell cycle arrest and induction of apoptosis. At the mechanistic level, silencing of PTGFRN reduced pro-proliferative and promigratory signaling pathways such as ERK, AKT, and mTOR. PTGFRN upregulation was found to be due to the loss of its promoter methylation and downregulation of miR-137 in GBM. PTGFRN was also found to be higher in glioma stem-like cells (GSCs) than the matched differentiated glioma cells (DGCs) and is required for GSC growth and survival. Silencing of PTGFRN in GSCs reduced transcript levels of reprogramming factors (Olig2, Pou3f2, Sall2, and Sox2). Conclusion In this study, we provide a comprehensive overview of the differential regulation of CAMs and the probable causes for their deregulation in GBM. We also establish an oncogenic role of PTGFRN and its regulation by miR-137 in GBM, thus signifying it as a potential therapeutic target. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09682-2.
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Affiliation(s)
- Uchurappa Mala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Tapan Kumar Baral
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.
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Morais MA, Franco B, Holanda ASS, Simino LADP, Manconi M, Torsoni A, Esteves AM. PTPRD as a candidate druggable target for therapies for restless legs syndrome? J Sleep Res 2020; 30:e13216. [PMID: 33111449 DOI: 10.1111/jsr.13216] [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: 05/14/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/18/2022]
Abstract
The gene that encodes the protein tyrosine phosphatase D (PTPRD) may be related to brain circuits associated with sleep, and has been seen as an interesting molecule, a "druggable" drug target. This gene is a potential candidate for increasing therapeutic advances in restless legs syndrome, a sleep-related movement disorder, that manifests as an uncontrollable desire to move limbs (legs) to relieve uncomfortable sensations. Changes in the PTPRD gene expression may increase the chance of developing this syndrome. Treatment with pramipexole is used in restless legs syndrome. This study aims to verify the effect of treatment with pramipexole on the PTPRD expression, as well as on the sleep pattern in an animal model for restless legs syndrome. For this, an animal model of sleep-related movement disorders (spontaneously hypertensive rats) was distributed in groups: (a) spontaneously hypertensive rats-control; (b) spontaneously hypertensive rats-pramipexole (0.125 mg kg-1 for 4 weeks). The analyses of PTPRD gene and protein expression were performed in the striatum and spinal cord by quantitative real-time polymerase chain reaction and indirect enzyme-linked immunosorbent assay, respectively. Electrocorticographic and electromyographic analyses were performed. There was no difference in the PTPRD mRNA levels, as well as in the protein levels, although a tendency has been observed for decreased gene expression in the striatum and increased protein expression in the spinal cord in the spontaneously hypertensive rats-pramipexole group. Pramipexole improved the animals' sleep pattern. Thus, the treatment with pramipexole in the evaluated dose and time tended to alter the expression of the PTPRD protein in the spinal cord, in addition to significantly improving the sleep pattern.
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Affiliation(s)
- Milca A Morais
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, Limeira, Brazil
| | - Beatriz Franco
- Faculdade de Educação Física, Universidade Estadual de Campinas, Campinas, Brazil
| | | | | | - Mauro Manconi
- Sleep and Epilepsy Center, Neurocenter of Southern Switzerland, Civic Hospital of Lugano (EOC), Lugano, Switzerland
| | - Adriana Torsoni
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, Limeira, Brazil
| | - Andrea M Esteves
- Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, Limeira, Brazil
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Sadeghi L, Arvidsson G, Merrien M, Wasik AM, Görgens A, Smith CE, Sander B, P. Wright A. Differential B-Cell Receptor Signaling Requirement for Adhesion of Mantle Cell Lymphoma Cells to Stromal Cells. Cancers (Basel) 2020; 12:cancers12051143. [PMID: 32370190 PMCID: PMC7281289 DOI: 10.3390/cancers12051143] [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: 03/27/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 01/01/2023] Open
Abstract
Interactions between lymphoma cells and stromal cells play a key role in promoting tumor survival and development of drug resistance. We identified differences in key signaling pathways between the JeKo-1 and REC-1 mantle cell lymphoma (MCL) cell lines, displaying different patterns of stromal cell adhesion and chemotaxis towards stroma-conditioned medium. The identified adhesion-regulated genes reciprocated important aspects of microenvironment-mediated gene modulation in MCL patients. Five-hundred and ninety genes were differently regulated between the cell lines upon adhesion to stromal cells, while 32 genes were similarly regulated in both cell lines. Regulation of B-cell Receptor (BCR) signature genes in adherent cells was specific for JeKo-1. Inhibition of BCR using siRNA or clinically approved inhibitors, Ibrutinib and Acalabrutinib, decreased adhesion of JeKo-1, but not REC-1 cells. Cell surface levels of chemokine receptor CXCR4 were higher in JeKo-1, facilitating migration and adhesion of JeKo-1 but not REC-1 cells. Surface levels of ICAM1 adhesion protein differ for REC-1 and JeKo-1. While ICAM1 played a positive role in adherence of both cell lines to stromal cells, S1PR1 had an inhibitory effect. Our results provide a model framework for further investigation of mechanistic differences in patient-response to new pathway-specific drugs.
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Affiliation(s)
- Laia Sadeghi
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
| | - Gustav Arvidsson
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
| | - Magali Merrien
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 52 Stockholm, Sweden; (M.M.); (A.M.W.); (B.S.)
| | - Agata M. Wasik
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 52 Stockholm, Sweden; (M.M.); (A.M.W.); (B.S.)
| | - André Görgens
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg, 45 147 Essen, Germany
| | - C.I. Edvard Smith
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
| | - Birgitta Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 52 Stockholm, Sweden; (M.M.); (A.M.W.); (B.S.)
| | - Anthony P. Wright
- Department of Laboratory Medicine, Division of Biomedical and Cellular Medicine, Karolinska Institutet, 141 57 Stockholm, Sweden; (L.S.); (G.A.); (A.G.); (C.I.E.S.)
- Correspondence:
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Abijo T, Blum K, Gondré-Lewis MC. Neuropharmacological and Neurogenetic Correlates of Opioid Use Disorder (OUD) As a Function of Ethnicity: Relevance to Precision Addiction Medicine. Curr Neuropharmacol 2020; 18:578-595. [PMID: 31744450 PMCID: PMC7457418 DOI: 10.2174/1570159x17666191118125702] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/31/2019] [Accepted: 11/16/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Over 100 people die daily from opioid overdose and $78.5B per year is spent on treatment efforts, however, the real societal cost is multifold greater. Alternative strategies to eradicate/manage drug misuse and addiction need consideration. The perception of opioid addiction as a social/criminal problem has evolved to evidence-based considerations of them as clinical disorders with a genetic basis. We present evaluations of the genetics of addiction with ancestryspecific risk profiles for consideration. OBJECTIVE Studies of gene variants associated with predisposition to substance use disorders (SUDs) are monolithic, and exclude many ethnic groups, especially Hispanics and African Americans. We evaluate gene polymorphisms that impact brain reward and predispose individuals to opioid addictions, with a focus on the disparity of research which includes individuals of African and Hispanic descent. METHODOLOGY PubMed and Google Scholar were searched for: Opioid Use Disorder (OUD), Genome- wide association studies (GWAS); genetic variants; polymorphisms, restriction fragment length polymorphisms (RFLP); genomics, epigenetics, race, ethnic group, ethnicity, ancestry, Caucasian/ White, African American/Black, Hispanic, Asian, addictive behaviors, reward deficiency syndrome (RDS), mutation, insertion/deletion, and promotor region. RESULTS Many studies exclude non-White individuals. Studies that include diverse populations report ethnicity-specific frequencies of risk genes, with certain polymorphisms specifically associated with Caucasian and not African-American or Hispanic susceptibility to OUD or SUDs, and vice versa. CONCLUSION To adapt precision medicine-based addiction management in a blended society, we propose that ethnicity/ancestry-informed genetic variations must be analyzed to provide real precision- guided therapeutics with the intent to attenuate this uncontrollable fatal epidemic.
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Affiliation(s)
| | | | - Marjorie C. Gondré-Lewis
- Address correspondence to this author at the Department of Anatomy, Howard University College of Medicine, 520 W St NW, Washington DC 20059 USA; Tel/Fax: +1-202-806-5274; E-mail:
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Hishimoto A, Pletnikova O, Lang DL, Troncoso JC, Egan JM, Liu QR. Neurexin 3 transmembrane and soluble isoform expression and splicing haplotype are associated with neuron inflammasome and Alzheimer's disease. ALZHEIMERS RESEARCH & THERAPY 2019; 11:28. [PMID: 30902061 PMCID: PMC6429815 DOI: 10.1186/s13195-019-0475-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/17/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Synaptic damage precedes neuron death in Alzheimer's disease (AD). Neurexins, NRXN1, NRXN2, and NRXN3, are presynaptic adhesion molecules that specify neuron synapses and regulate neurotransmitter release. Neurexins and postsynaptic neuroligins interact with amyloid beta oligomer (AβO) deposits in damaged synapses. NRXN3 gene variants have been associated with autism, addiction, and schizophrenia, however, not fully investigated in Alzheimer's disease. In the present study, we investigated an AD association of a 3'-splicing allele of rs8019381 that produces altered expression of transmembrane or soluble NRXN3 isoforms. METHODS We carried out RT-PCR (reverse transcription polymerase chain reaction), PCR-RFLP (PCR and restriction fragment length polymorphism), Sanger sequencing, and in situ hybridization (ISH) assays for NRXN3 neuron expression and genotyping. Genetic associations were analyzed by χ2 tests, and ISH signals were analyzed by FISH v1.0 module of Indica Labs HALO software. RESULTS We previously identified a functional haplotype in the 3' region of neurexin 3 (NRXN3) gene that alters the expression ratios between NRXN3 transmembrane and soluble isoforms. In this study, we found that expression and ratio of transmembrane and soluble NRXN3 isoforms were reduced in AD postmortem brains and inversely correlated with inflammasome component NLRP3 in AD brain regions. The splicing haplotype related to the transmembrane and soluble NRXN3 expression was associated with AD samples with P = 6.3 × 10-5 (odds ratio = 2.48) and interacted with APOE genotypes. CONCLUSIONS We found that the SNP rs8019381 of NRXN3 that is located adjacent to splicing site #5 (SS#5) interacts with the APOE ε4 haplotype and alters NRXN3 transmembrane or soluble isoform expression in AD postmortem cortex. Dysregulation of presynaptic NRXN3 expression and splicing might increase neuron inflammation in AD brain.
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Affiliation(s)
- Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-Cho, Chuo-Ku, Kobe, 650-0017, Japan
| | - Olga Pletnikova
- Departments of Pathology, Neuropathology Division, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Doyle Lu Lang
- Lab of Clinical Investigation, NIA-NIH, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Juan C Troncoso
- Departments of Pathology, Neuropathology Division, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Josephine M Egan
- Lab of Clinical Investigation, NIA-NIH, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Qing-Rong Liu
- Lab of Clinical Investigation, NIA-NIH, 251 Bayview Blvd, Baltimore, MD, 21224, USA.
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Young A, Dandekar U, Pan C, Sader A, Zheng JJ, Lewis RA, Farber DB. GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism. PLoS One 2016; 11:e0162273. [PMID: 27607449 PMCID: PMC5015898 DOI: 10.1371/journal.pone.0162273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/21/2016] [Indexed: 11/18/2022] Open
Abstract
Ocular albinism type 1 (OA), caused by mutations in the OA1 gene, encodes a G-protein coupled receptor, OA1, localized in melanosomal membranes of the retinal pigment epithelium (RPE). This disorder is characterized by both RPE macro-melanosomes and abnormal decussation of ganglion cell axons at the brain's optic chiasm. We demonstrated previously that Oa1 specifically activates Gαi3, which also signals in the Oa1 transduction pathway that regulates melanosomal biogenesis. In this study, we screened the human Gαi3 gene, GNAI3, in DNA samples from 26 patients who had all clinical characteristics of OA but in whom a specific mutation in the OA1 gene had not been found, and in 6 normal control individuals. Using the Agilent HaloPlex Target Enrichment System and next-generation sequencing (NGS) on the Illumina MiSeq platform, we identified 518 variants after rigorous filtering. Many of these variants were corroborated by Sanger sequencing. Overall, 98.8% coverage of the GNAI3 gene was obtained by the HaloPlex amplicons. Of all variants, 6 non-synonymous and 3 synonymous were in exons, 41 in a non-coding exon embedded in the 3' untranslated region (UTR), 6 in the 5' UTR, and 462 in introns. These variants included novel SNVs, insertions, deletions, and a frameshift mutation. All were found in at least one patient but none in control samples. Using computational methods, we modeled the GNAI3 protein and its non-synonymous exonic mutations and determined that several of these may be the cause of disease in the patients studied. Thus, we have identified GNAI3 as a second gene possibly responsible for X-linked ocular albinism.
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Affiliation(s)
- Alejandra Young
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
- Molecular Biology Institute, UCLA, Los Angeles, CA, United States of America
| | - Uma Dandekar
- UCLA-GenoSeq Core, UCLA, Los Angeles, CA, United States of America
| | - Calvin Pan
- UCLA-GenoSeq Core, UCLA, Los Angeles, CA, United States of America
| | - Avery Sader
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
| | - Jie J. Zheng
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
| | - Richard A. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Debora B. Farber
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
- Molecular Biology Institute, UCLA, Los Angeles, CA, United States of America
- Brain Research Institute, UCLA, Los Angeles, CA, United States of America
- * E-mail:
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Zhong X, Drgonova J, Li CY, Uhl GR. Human cell adhesion molecules: annotated functional subtypes and overrepresentation of addiction-associated genes. Ann N Y Acad Sci 2015; 1349:83-95. [PMID: 25988664 DOI: 10.1111/nyas.12776] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Human cell adhesion molecules (CAMs) are essential for proper development, modulation, and maintenance of interactions between cells and cell-to-cell (and matrix-to-cell) communication about these interactions. Despite the differential functional significance of these roles, there have been surprisingly few systematic studies to enumerate the universe of CAMs and identify specific CAMs in distinct functions. In this paper, we update and review the set of human genes likely to encode CAMs with searches of databases, literature reviews, and annotations. We describe likely CAMs and functional subclasses, including CAMs that have a primary function in information exchange (iCAMs), CAMs involved in focal adhesions, CAM gene products that are preferentially involved with stereotyped and morphologically identifiable connections between cells (e.g., adherens junctions, gap junctions), and smaller numbers of CAM genes in other classes. We discuss a novel proposed mechanism involving selective anchoring of the constituents of iCAM-containing lipid rafts in zones of close neuronal apposition to membranes expressing iCAM binding partners. We also discuss data from genetic and genomic studies of addiction in humans and mouse models to highlight the ways in which CAM variation may contribute to a specific brain-based disorder such as addiction. Specific examples include changes in CAM mRNA splicing mediated by differences in the addiction-associated splicing regulator RBFOX1/A2BP1 and CAM expression in dopamine neurons.
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Affiliation(s)
- Xiaoming Zhong
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jana Drgonova
- Molecular Neurobiology, NIH-IRP (NIDA), Baltimore, Maryland
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - George R Uhl
- Molecular Neurobiology, NIH-IRP (NIDA), Baltimore, Maryland.,Research Office, New Mexico VA Health Care System, Albuquerque, New Mexico
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Uhl GR, Drgonova J. Cell adhesion molecules: druggable targets for modulating the connectome and brain disorders? Neuropsychopharmacology 2014; 39:235. [PMID: 24317312 PMCID: PMC3857667 DOI: 10.1038/npp.2013.240] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- George R Uhl
- Molecular Neurobiology Branch, NIH-IRP, NIDA, Baltimore, Maryland, USA,E-mail:
| | - Jana Drgonova
- Molecular Neurobiology Branch, NIH-IRP, NIDA, Baltimore, Maryland, USA
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Nguyen-Ngoc KV, Cheung KJ, Brenot A, Shamir ER, Gray RS, Hines WC, Yaswen P, Werb Z, Ewald AJ. ECM microenvironment regulates collective migration and local dissemination in normal and malignant mammary epithelium. Proc Natl Acad Sci U S A 2012; 109:E2595-604. [PMID: 22923691 PMCID: PMC3465416 DOI: 10.1073/pnas.1212834109] [Citation(s) in RCA: 310] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Breast cancer progression involves genetic changes and changes in the extracellular matrix (ECM). To test the importance of the ECM in tumor cell dissemination, we cultured epithelium from primary human breast carcinomas in different ECM gels. We used basement membrane gels to model the normal microenvironment and collagen I to model the stromal ECM. In basement membrane gels, malignant epithelium either was indolent or grew collectively, without protrusions. In collagen I, epithelium from the same tumor invaded with protrusions and disseminated cells. Importantly, collagen I induced a similar initial response of protrusions and dissemination in both normal and malignant mammary epithelium. However, dissemination of normal cells into collagen I was transient and ceased as laminin 111 localized to the basal surface, whereas dissemination of carcinoma cells was sustained throughout culture, and laminin 111 was not detected. Despite the large impact of ECM on migration strategy, transcriptome analysis of our 3D cultures revealed few ECM-dependent changes in RNA expression. However, we observed many differences between normal and malignant epithelium, including reduced expression of cell-adhesion genes in tumors. Therefore, we tested whether deletion of an adhesion gene could induce sustained dissemination of nontransformed cells into collagen I. We found that deletion of P-cadherin was sufficient for sustained dissemination, but exclusively into collagen I. Our data reveal that metastatic tumors preferentially disseminate in specific ECM microenvironments. Furthermore, these data suggest that breaks in the basement membrane could induce invasion and dissemination via the resulting direct contact between cancer cells and collagen I.
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Affiliation(s)
- Kim-Vy Nguyen-Ngoc
- Departments of Cell Biology and
- Oncology, Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Kevin J. Cheung
- Departments of Cell Biology and
- Oncology, Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Audrey Brenot
- Department of Anatomy, University of California, San Francisco, CA 94143; and
| | - Eliah R. Shamir
- Departments of Cell Biology and
- Oncology, Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ryan S. Gray
- Departments of Cell Biology and
- Oncology, Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - William C. Hines
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Paul Yaswen
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Zena Werb
- Department of Anatomy, University of California, San Francisco, CA 94143; and
| | - Andrew J. Ewald
- Departments of Cell Biology and
- Oncology, Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Anatomy, University of California, San Francisco, CA 94143; and
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Goel R, Muthusamy B, Pandey A, Prasad TSK. Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Mol Biotechnol 2011; 48:87-95. [PMID: 20927658 DOI: 10.1007/s12033-010-9336-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the recent years, research in molecular biotechnology has transformed from being small scale studies targeted at a single or a small set of molecule(s) into a combination of high throughput discovery platforms and extensive validations. Such a discovery platform provided an unbiased approach which resulted in the identification of several novel genetic and protein biomarkers. High throughput nature of these investigations coupled with higher sensitivity and specificity of Next Generation technologies provided qualitatively and quantitatively richer biological data. These developments have also revolutionized biological research and speed of data generation. However, it is becoming difficult for individual investigators to directly benefit from this data because they are not easily accessible. Data resources became necessary to assimilate, store and disseminate information that could allow future discoveries. We have developed two resources--Human Protein Reference Database (HPRD) and Human Proteinpedia, which integrate knowledge relevant to human proteins. A number of protein features including protein-protein interactions, post-translational modifications, subcellular localization, and tissue expression, which have been studied using different strategies were incorporated in these databases. Human Proteinpedia also provides a portal for community participation to annotate and share proteomic data and uses HPRD as the scaffold for data processing. Proteomic investigators can even share unpublished data in Human Proteinpedia, which provides a meaningful platform for data sharing. As proteomic information reflects a direct view of cellular systems, proteomics is expected to complement other areas of biology such as genomics, transcriptomics, molecular biology, cloning, and classical genetics in understanding the relationships among multiple facets of biological systems.
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Affiliation(s)
- Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
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Uhl GR, Drgon T, Johnson C, Ramoni MF, Behm FM, Rose JE. Genome-wide association for smoking cessation success in a trial of precessation nicotine replacement. Mol Med 2010; 16:513-26. [PMID: 20811658 PMCID: PMC2972392 DOI: 10.2119/molmed.2010.00052] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 08/23/2010] [Indexed: 02/06/2023] Open
Abstract
Abilities to successfully quit smoking display substantial evidence for heritability in classic and molecular genetic studies. Genome-wide association (GWA) studies have demonstrated single-nucleotide polymorphisms (SNPs) and haplotypes that distinguish successful quitters from individuals who were unable to quit smoking in clinical trial participants and in community samples. Many of the subjects in these clinical trial samples were aided by nicotine replacement therapy (NRT). We now report novel GWA results from participants in a clinical trial that sought dose/response relationships for "precessation" NRT. In this trial, 369 European-American smokers were randomized to 21 or 42 mg NRT, initiated 2 wks before target quit dates. Ten-week continuous smoking abstinence was assessed on the basis of self-reports and carbon monoxide levels. SNP genotyping used Affymetrix 6.0 arrays. GWA results for smoking cessation success provided no P value that reached "genome-wide" significance. Compared with chance, these results do identify (a) more clustering of nominally positive results within small genomic regions, (b) more overlap between these genomic regions and those identified in six prior successful smoking cessation GWA studies and (c) sets of genes that fall into gene ontology categories that appear to be biologically relevant. The 1,000 SNPs with the strongest associations form a plausible Bayesian network; no such network is formed by randomly selected sets of SNPs. The data provide independent support, based on individual genotyping, for many loci previously nominated on the basis of data from genotyping in pooled DNA samples. These results provide further support for the idea that aid for smoking cessation may be personalized on the basis of genetic predictors of outcome.
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Affiliation(s)
- George R Uhl
- Molecular Neurobiology Branch, National Institutes of Health Intramural Research Program, National Institute on Drug Abuse (NIH-IRP, NIDA), Baltimore, Maryland, United States of America
| | - Tomas Drgon
- Molecular Neurobiology Branch, National Institutes of Health Intramural Research Program, National Institute on Drug Abuse (NIH-IRP, NIDA), Baltimore, Maryland, United States of America
| | - Catherine Johnson
- Molecular Neurobiology Branch, National Institutes of Health Intramural Research Program, National Institute on Drug Abuse (NIH-IRP, NIDA), Baltimore, Maryland, United States of America
| | - Marco F Ramoni
- Children’s Hospital Informatics Program, Harvard–Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
| | - Frederique M Behm
- Department of Psychiatry and Center for Nicotine and Smoking Cessation Research, Duke University, Durham, North Carolina, United States of America
| | - Jed E Rose
- Department of Psychiatry and Center for Nicotine and Smoking Cessation Research, Duke University, Durham, North Carolina, United States of America
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Rodan AR, Rothenfluh A. The genetics of behavioral alcohol responses in Drosophila. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2010; 91:25-51. [PMID: 20813239 DOI: 10.1016/s0074-7742(10)91002-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Drosophila melanogaster is commonly found near rotting or fermenting fruit, reflected in its name pomace, or vinegar fly. In such environments, flies often encounter significant levels of ethanol. Three observations have made Drosophila a very promising model organism to understand the genetic contributions to the behavioral responses to alcohol. First, similar to higher vertebrates, flies show hyperactivation upon exposure to a low to medium dose of alcohol, while high doses can lead to sedation. In addition, when given a choice, flies will actually prefer alcohol-containing food over regular food. Second, the genes and biochemical pathways implicated in controlling these behavioral responses in flies are also participating in determining alcohol responses, and drinking behavior in mammals. Third, the fact that flies have been studied genetically for over one hundred years means that an exceptional repertoire of genetic tools are at our disposal. Here, we will review some of these tools and experimental approaches, survey the methods for, and measures after Drosophila ethanol exposure, and discuss the different molecular components and functional pathways involved in these behavioral responses to alcohol.
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Affiliation(s)
- Aylin R Rodan
- Division of Nephrology, Department of Psychiatry and Program in Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
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Gorlov IP, Byun J, Gorlova OY, Aparicio AM, Efstathiou E, Logothetis CJ. Candidate pathways and genes for prostate cancer: a meta-analysis of gene expression data. BMC Med Genomics 2009; 2:48. [PMID: 19653896 PMCID: PMC2731785 DOI: 10.1186/1755-8794-2-48] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 08/04/2009] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The genetic mechanisms of prostate tumorigenesis remain poorly understood, but with the advent of gene expression array capabilities, we can now produce a large amount of data that can be used to explore the molecular and genetic mechanisms of prostate tumorigenesis. METHODS We conducted a meta-analysis of gene expression data from 18 gene array datasets targeting transition from normal to localized prostate cancer and from localized to metastatic prostate cancer. We functionally annotated the top 500 differentially expressed genes and identified several candidate pathways associated with prostate tumorigeneses. RESULTS We found the top differentially expressed genes to be clustered in pathways involving integrin-based cell adhesion: integrin signaling, the actin cytoskeleton, cell death, and cell motility pathways. We also found integrins themselves to be downregulated in the transition from normal prostate tissue to primary localized prostate cancer. Based on the results of this study, we developed a collagen hypothesis of prostate tumorigenesis. According to this hypothesis, the initiating event in prostate tumorigenesis is the age-related decrease in the expression of collagen genes and other genes encoding integrin ligands. This concomitant depletion of integrin ligands leads to the accumulation of ligandless integrin and activation of integrin-associated cell death. To escape integrin-associated death, cells suppress the expression of integrins, which in turn alters the actin cytoskeleton, elevates cell motility and proliferation, and disorganizes prostate histology, contributing to the histologic progression of prostate cancer and its increased metastasizing potential. CONCLUSION The results of this study suggest that prostate tumor progression is associated with the suppression of integrin-based cell adhesion. Suppression of integrin expression driven by integrin-mediated cell death leads to increased cell proliferation and motility and increased tumor malignancy.
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Affiliation(s)
- Ivan P Gorlov
- Department of Genitourinary Medical Oncology, The University of Texas M, D, Anderson Cancer Center, Houston, TX, USA.
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Prasad TSK, Kandasamy K, Pandey A. Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol 2009; 577:67-79. [PMID: 19718509 DOI: 10.1007/978-1-60761-232-2_6] [Citation(s) in RCA: 226] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Although high-throughput technologies used in biology have resulted in the accumulation of vast amounts of data in the literature, it is becoming difficult for individual investigators to directly benefit from this data because they are not easily accessible. Databases have assumed a crucial role in assimilating and storing information that could enable future discoveries. To this end, our group has developed two resources - Human Protein Reference Database (HPRD) and Human Proteinpedia - that provide integrated information pertaining to human proteins. These databases contain information on a number of features of proteins that have been discovered using various experimental methods. Human Proteinpedia was developed as a portal for community participation to annotate and share proteomic data using HPRD as the scaffold. It allows proteomic investigators to even share unpublished data and provides an effective medium for data sharing. As proteomic information reflects a direct view of cellular systems, proteomics is expected to complement other areas of biology such as genomics, transcriptomics, classical genetics, and chemical genetics in understanding the relationships among genome, gene functions, and living systems.
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Johnson C, Drgon T, Liu QR, Zhang PW, Walther D, Li CY, Anthony JC, Ding Y, Eaton WW, Uhl GR. Genome wide association for substance dependence: convergent results from epidemiologic and research volunteer samples. BMC MEDICAL GENETICS 2008; 9:113. [PMID: 19094236 PMCID: PMC2637238 DOI: 10.1186/1471-2350-9-113] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 12/18/2008] [Indexed: 11/15/2022]
Abstract
Background Dependences on addictive substances are substantially-heritable complex disorders whose molecular genetic bases have been partially elucidated by studies that have largely focused on research volunteers, including those recruited in Baltimore. Maryland. Subjects recruited from the Baltimore site of the Epidemiological Catchment Area (ECA) study provide a potentially-useful comparison group for possible confounding features that might arise from selecting research volunteer samples of substance dependent and control individuals. We now report novel SNP (single nucleotide polymorphism) genome wide association (GWA) results for vulnerability to substance dependence in ECA participants, who were initially ascertained as members of a probability sample from Baltimore, and compare the results to those from ethnically-matched Baltimore research volunteers. Results We identify substantial overlap between the home address zip codes reported by members of these two samples. We find overlapping clusters of SNPs whose allele frequencies differ with nominal significance between substance dependent vs control individuals in both samples. These overlapping clusters of nominally-positive SNPs identify 172 genes in ways that are never found by chance in Monte Carlo simulation studies. Comparison with data from human expressed sequence tags suggests that these genes are expressed in brain, especially in hippocampus and amygdala, to extents that are greater than chance. Conclusion The convergent results from these probability sample and research volunteer sample datasets support prior genome wide association results. They fail to support the idea that large portions of the molecular genetic results for vulnerability to substance dependence derive from factors that are limited to research volunteers.
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Affiliation(s)
- Catherine Johnson
- Molecular Neurobiology Branch, NIH-IRP (NIDA), Suite 3510, 333 Cassell Drive Baltimore, Maryland 21224, USA.
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