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Ma W, Hu J. Downregulated CDH3 is correlated with a better prognosis for LUAD and decreases proliferation and migration of lung cancer cells. Genes Genomics 2024; 46:713-731. [PMID: 38064156 DOI: 10.1007/s13258-023-01476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/05/2023] [Indexed: 05/19/2024]
Abstract
BACKGROUND CDH3 is a glycoprotein with a single-span transmembrane domain that mediates cell-to-cell adhesion. Abnormal expression of CDH3 is associated with a poor prognosis in patients with breast, thyroid, colorectal carcinomas and glioblastoma. Soluble CDH3 in pleural effusions can be used as a marker for real-time monitoring of resistance to first- and second-generation EGFR-TKIs. The CDH3 mechanism underlying lung adenocarcinomas (LUADs) has not been established. OBJECTIVE This study analyzed the correlation between CDH3 expression and lung cancer prognosis and the effect of down-regulation CDH3 expression on the proliferation and migration of lung cancer cells. METHODS CDH3 expression was studied using the Oncomine, TIMER, PanglaoDB, and GEPIA databases. The effect of CDH3 on clinical prognosis was assessed with GEPIA, the PrognoScan database, and Kaplan-Meier plotter. The relationship between CDH3 to immune infiltrating cells was explored using TIMER and TISIDB. The function of CDH3 in lung cancer cell lines was determined by CCK-8 and wound healing assays in vitro. Furthermore, RNA sequencing was used to identify key signaling pathways and differentially-expressed genes. RESULTS LUAD tissues had higher CDH3 expression compared with normal tissues and were associated with worse overall survival in patients with LUAD. CDH3 expression had positive associations with infiltration of CD4 + T cells, Tregs and exhausted T cells, but negative associations with infiltration of B cells in patients with LUAD. CCK-8 and wound healing assays revealed that downregulation of CDH3 inhibited the proliferation and migration of cells. KEGG analysis revealed that the TGF-beta signaling pathways were demonstrated to be enriched pathways for genes negatively regulated by knockdown of CDH3. CONCLUSION CDH3 expression affects proliferation and migration of lung cancer cells and might serve as a potential prognostic marker in LUAD patients.
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Affiliation(s)
- Wanru Ma
- Department of Blood Transfusion, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 Da Hua Road, Dong Dan, Beijing, 100730, People's Republic of China
| | - Junhua Hu
- Department of Blood Transfusion, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, No. 1 Da Hua Road, Dong Dan, Beijing, 100730, People's Republic of China.
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Horsthemke M, Arnaud CA, Hanley PJ. Are the class 18 myosins Myo18A and Myo18B specialist sarcomeric proteins? Front Physiol 2024; 15:1401717. [PMID: 38784114 PMCID: PMC11112018 DOI: 10.3389/fphys.2024.1401717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Initially, the two members of class 18 myosins, Myo18A and Myo18B, appeared to exhibit highly divergent functions, complicating the assignment of class-specific functions. However, the identification of a striated muscle-specific isoform of Myo18A, Myo18Aγ, suggests that class 18 myosins may have evolved to complement the functions of conventional class 2 myosins in sarcomeres. Indeed, both genes, Myo18a and Myo18b, are predominantly expressed in the heart and somites, precursors of skeletal muscle, of developing mouse embryos. Genetic deletion of either gene in mice is embryonic lethal and is associated with the disorganization of cardiac sarcomeres. Moreover, Myo18Aγ and Myo18B localize to sarcomeric A-bands, albeit the motor (head) domains of these unconventional myosins have been both deduced and biochemically demonstrated to exhibit negligible ATPase activity, a hallmark of motor proteins. Instead, Myo18Aγ and Myo18B presumably coassemble with thick filaments and provide structural integrity and/or internal resistance through interactions with F-actin and/or other proteins. In addition, Myo18Aγ and Myo18B may play distinct roles in the assembly of myofibrils, which may arise from actin stress fibers containing the α-isoform of Myo18A, Myo18Aα. The β-isoform of Myo18A, Myo18Aβ, is similar to Myo18Aα, except that it lacks the N-terminal extension, and may serve as a negative regulator through heterodimerization with either Myo18Aα or Myo18Aγ. In this review, we contend that Myo18Aγ and Myo18B are essential for myofibril structure and function in striated muscle cells, while α- and β-isoforms of Myo18A play diverse roles in nonmuscle cells.
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Affiliation(s)
- Markus Horsthemke
- IMM Institute for Molecular Medicine, HMU Health and Medical University Potsdam, Potsdam, Germany
| | - Charles-Adrien Arnaud
- IMM Institute for Molecular Medicine, HMU Health and Medical University Potsdam, Potsdam, Germany
- Department of Medicine, Science Faculty, MSB Medical School Berlin, Berlin, Germany
| | - Peter J. Hanley
- IMM Institute for Molecular Medicine, HMU Health and Medical University Potsdam, Potsdam, Germany
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Zou T, Sethi R, Wang J, Budak G, Chandran U, John I, Watters R, Weiss K. Whole genome sequencing for metastatic mutational burden in extraskeletal myxoid chondrosarcoma. FRONTIERS IN MOLECULAR MEDICINE 2023; 3:1152550. [PMID: 39086683 PMCID: PMC11285543 DOI: 10.3389/fmmed.2023.1152550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/28/2023] [Indexed: 08/02/2024]
Abstract
Extraskeletal myxoid chondrosarcoma (EMC) is an ultra-rare cancer that makes up less than 3% of all soft tissue sarcomas. It most often arises in the soft tissues of the proximal limbs and has a higher incidence in males. Though EMC has a good prognosis, it has an indolent course with high rates of local recurrence as well as metastasis to the lungs. EMC is characterized in 70% of cases by an EWS1-NR4A3 translocation, leading to constitutive expression of NR4A3. Structural variants (SVs) in EMC, especially large-scale genomic alterations, have not been well studied and studies are severely limited by sample size. In this study, we describe Whole Genome Sequencing (WGS) of a rare case of matched EMC primary tumor, lung metastasis, and pelvic metastasis to identify genomic alterations. We examined somatic variants, copy number variants (CNVs), and larger scale SVs such as translocations and breakend points. While the primary tumor and lung metastasis had similar somatic variations and CNVs, the pelvic metastasis had more unique SVs with especially increased mutational burden of SVs in chromosome 2. This suggests that different molecular drivers appear in more advanced, relapsing EMC compared with the primary tumor and early lung metastasis. Genomic studies such as ours may identify novel molecular complexities in rare cancers that may be leveraged for therapeutic strategies and precision medicine.
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Affiliation(s)
- Trudy Zou
- Musculoskeletal Oncology Laboratory, Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Rahil Sethi
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jiefei Wang
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Gungor Budak
- Seven Bridges, Inc., Cambridge, MA, United States
| | - Uma Chandran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ivy John
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Rebecca Watters
- Musculoskeletal Oncology Laboratory, Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Kurt Weiss
- Musculoskeletal Oncology Laboratory, Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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Abstract
Radiotherapy-induced second malignant neoplasms (SMNs) are a severe late complication in pediatric cancer survivors. Germline mutations in tumor suppressor genes contribute to SMNs; however, the most relevant germline variants mediating susceptibility are not fully defined. The authors performed matched whole-exome sequencing analyses of germline and tumor DNA from 4 pediatric solid tumor survivors who subsequently developed radiation-associated SMNs. Pathogenic and predicted deleterious germline variants were identified for each patient and validated with Sanger sequencing. These germline variants were compared with germline variants in a cohort of 59 pediatric patients diagnosed with primary sarcomas. Pathway analysis was performed to test for similarities in the germline variant profiles between individuals diagnosed with SMNs or primary sarcomas. One index patient was found to have a pathogenic germline monoallelic mutation in the MUTYH gene, which encodes the base excision repair enzyme adenine DNA glycosylase. This specific germline mutation is associated with a form of familial adenomatous polyposis, a new diagnosis in the patient. Germline-level genetic similarity exists between SMN-developing patients and patients developing primary sarcomas, with relevant genes involved in signal transduction and DNA repair mechanisms. The authors identify a germline MUTYH mutation in a pediatric cancer survivor developing an SMN. Germline mutations involving specific pathways such as base excision repair may identify individuals at risk for developing SMNs. The composition of germline variants in individual patients may enable estimates of patient-specific risk for developing SMNs. The authors anticipate that further analyses of germline genomes and epigenomes will reveal diverse genes and mechanisms influencing cancer risk.
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5
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Malik A, Afaq S, Alwabli AS, Al-ghmady K. Networking of predicted post-translational modification (PTM) sites in human EGFR. Bioinformation 2019; 15:448-456. [PMID: 31485130 PMCID: PMC6704328 DOI: 10.6026/97320630015448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 06/06/2019] [Indexed: 11/23/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) binds to EGF activating tyrosine phosphorylation through receptor dimerization prompting uncontrolled multiplication. Domain organization, secondary structure combinations in motifs and interactome define such transitory changes responsible for the multi-functionality of human EGFR. We report the predicted phosphorylation sites on Ser, Thr and Tyr residues in addition to 74 auto-phosphorylation sites on Tyr in human EGFR. These data suggest a complex interplay between phosphorylation types for modification resulting in the modulation of human EGFR functionality. It is of further interest in future to thoroughly understand the associated data to clarify the various roles played by post translational modifications (PTM) in human EGFR.
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Affiliation(s)
- Arshi Malik
- Department of Clinical Biochemistry, College of Medicine, King Khalid University, Abha Kingdom of Saudi Arabia-61421
| | - Sarah Afaq
- Department of Clinical Biochemistry, College of Medicine, King Khalid University, Abha Kingdom of Saudi Arabia-61421
| | - Afaf S Alwabli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Khalid Al-ghmady
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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6
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Berradi H, Kaanane H, El Kadmiri N, Nadifi S. Concomitance of EGFR mutations and ALK rearrangement in patients with Lung Cancer. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Labrecque MP, Takhar MK, Nason R, Santacruz S, Tam KJ, Massah S, Haegert A, Bell RH, Altamirano-Dimas M, Collins CC, Lee FJS, Prefontaine GG, Cox ME, Beischlag TV. The retinoblastoma protein regulates hypoxia-inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. Oncotarget 2018; 7:24284-302. [PMID: 27015368 PMCID: PMC5029701 DOI: 10.18632/oncotarget.8301] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/04/2016] [Indexed: 12/14/2022] Open
Abstract
Loss of tumor suppressor proteins, such as the retinoblastoma protein (Rb), results in tumor progression and metastasis. Metastasis is facilitated by low oxygen availability within the tumor that is detected by hypoxia inducible factors (HIFs). The HIF1 complex, HIF1α and dimerization partner the aryl hydrocarbon receptor nuclear translocator (ARNT), is the master regulator of the hypoxic response. Previously, we demonstrated that Rb represses the transcriptional response to hypoxia by virtue of its association with HIF1. In this report, we further characterized the role Rb plays in mediating hypoxia-regulated genetic programs by stably ablating Rb expression with retrovirally-introduced short hairpin RNA in LNCaP and 22Rv1 human prostate cancer cells. DNA microarray analysis revealed that loss of Rb in conjunction with hypoxia leads to aberrant expression of hypoxia-regulated genetic programs that increase cell invasion and promote neuroendocrine differentiation. For the first time, we have established a direct link between hypoxic tumor environments, Rb inactivation and progression to late stage metastatic neuroendocrine prostate cancer. Understanding the molecular pathways responsible for progression of benign prostate tumors to metastasized and lethal forms will aid in the development of more effective prostate cancer therapies.
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Affiliation(s)
- Mark P Labrecque
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mandeep K Takhar
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Rebecca Nason
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Stephanie Santacruz
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kevin J Tam
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shabnam Massah
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anne Haegert
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert H Bell
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Manuel Altamirano-Dimas
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin C Collins
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Frank J S Lee
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gratien G Prefontaine
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael E Cox
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Timothy V Beischlag
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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8
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Ren L, Mendoza A, Zhu J, Briggs JW, Halsey C, Hong ES, Burkett SS, Morrow J, Lizardo MM, Osborne T, Li SQ, Luu HH, Meltzer P, Khanna C. Characterization of the metastatic phenotype of a panel of established osteosarcoma cells. Oncotarget 2016; 6:29469-81. [PMID: 26320182 PMCID: PMC4745740 DOI: 10.18632/oncotarget.5177] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/25/2015] [Indexed: 11/25/2022] Open
Abstract
Osteosarcoma (OS) is the most common bone tumor in pediatric patients. Metastasis is a major cause of mortality and morbidity. The rarity of this disease coupled with the challenges of drug development for metastatic cancers have slowed the delivery of improvements in long-term outcomes for these patients. In this study, we collected 18 OS cell lines, confirmed their expression of bone markers and complex karyotypes, and characterized their in vivo tumorgenicity and metastatic potential. Since prior reports included conflicting descriptions of the metastatic and in vivo phenotypes of these models, there was a need for a comparative assessment of metastatic phenotypes using identical procedures in the hands of a single investigative group. We expect that this single characterization will accelerate the study of this metastatic cancer. Using these models we evaluated the expression of six previously reported metastasis-related OS genes. Ezrin was the only gene consistently differentially expressed in all the pairs of high/low metatstatic OS cells. We then used a subtractive gene expression approach of the high and low human metastatic cells to identify novel genes that may be involved in OS metastasis. PHLDA1 (pleckstrin homology-like domain, family A) was identified as one of the genes more highly expressed in the high metastatic compared to low metastatic cells. Knocking down PHLDA1 with siRNA or shRNA resulted in down regulation of the activities of MAPKs (ERK1/2), c-Jun N-terminal kinases (JNK), and p38 mitogen-activated protein kinases (MAPKs). Reducing the expression of PHLDA1 also delayed OS metastasis progression in mouse xenograft models.
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Affiliation(s)
- Ling Ren
- Molecular Oncology Section - Metastasis Biology Group, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Arnulfo Mendoza
- Molecular Oncology Section - Metastasis Biology Group, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Jack Zhu
- Genetic Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Joseph W Briggs
- Molecular Oncology Section - Metastasis Biology Group, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Charles Halsey
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Ellen S Hong
- Molecular Oncology Section - Metastasis Biology Group, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Sandra S Burkett
- Comparative Molecular Cytogenetics Core Facility, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - James Morrow
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michael M Lizardo
- Molecular Oncology Section - Metastasis Biology Group, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Tanasa Osborne
- National Institute of Environmental Health, Research Triangle Park, North Carolina, USA
| | - Samuel Q Li
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Hue H Luu
- Department of Orthopedic Surgery & Rehabilitation Medicine, University of Chicago, Medicine & Biological Sciences, Chicago, USA
| | - Paul Meltzer
- Genetic Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Chand Khanna
- Molecular Oncology Section - Metastasis Biology Group, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
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9
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Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 2015; 160:1246-60. [PMID: 25748654 PMCID: PMC4380877 DOI: 10.1016/j.cell.2015.02.038] [Citation(s) in RCA: 614] [Impact Index Per Article: 68.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 02/03/2015] [Accepted: 02/18/2015] [Indexed: 12/14/2022]
Abstract
Genetic screens are powerful tools for identifying genes responsible for diverse phenotypes. Here we describe a genome-wide CRISPR/Cas9-mediated loss-of-function screen in tumor growth and metastasis. We mutagenized a non-metastatic mouse cancer cell line using a genome-scale library with 67,405 single-guide RNAs (sgRNAs). The mutant cell pool rapidly generates metastases when transplanted into immunocompromised mice. Enriched sgRNAs in lung metastases and late-stage primary tumors were found to target a small set of genes, suggesting that specific loss-of-function mutations drive tumor growth and metastasis. Individual sgRNAs and a small pool of 624 sgRNAs targeting the top-scoring genes from the primary screen dramatically accelerate metastasis. In all of these experiments, the effect of mutations on primary tumor growth positively correlates with the development of metastases. Our study demonstrates Cas9-based screening as a robust method to systematically assay gene phenotypes in cancer evolution in vivo.
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Affiliation(s)
- Sidi Chen
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Neville E Sanjana
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kaijie Zheng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Ophir Shalem
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Kyungheon Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xi Shi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - David A Scott
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Jun Song
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jen Q Pan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Phillip A Sharp
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Lee BY, Lee KN, Lee T, Park JH, Kim SM, Lee HS, Chung DS, Shim HS, Lee HK, Kim H. Bovine Genome-wide Association Study for Genetic Elements to Resist the Infection of Foot-and-mouth Disease in the Field. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:166-70. [PMID: 25557811 PMCID: PMC4283160 DOI: 10.5713/ajas.14.0383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 08/06/2014] [Accepted: 08/21/2014] [Indexed: 12/29/2022]
Abstract
Foot-and-mouth disease (FMD) is a highly contagious disease affecting cloven-hoofed animals and causes severe economic loss and devastating effect on international trade of animal or animal products. Since FMD outbreaks have recently occurred in some Asian countries, it is important to understand the relationship between diverse immunogenomic structures of host animals and the immunity to foot-and-mouth disease virus (FMDV). We performed genome wide association study based on high-density bovine single nucleotide polymorphism (SNP) chip for identifying FMD resistant loci in Holstein cattle. Among 624532 SNP after quality control, we found that 11 SNPs on 3 chromosomes (chr17, 22, and 15) were significantly associated with the trait at the p.adjust <0.05 after PERMORY test. Most significantly associated SNPs were located on chromosome 17, around the genes Myosin XVIIIB and Seizure related 6 homolog (mouse)-like, which were associated with lung cancer. Based on the known function of the genes nearby the significant SNPs, the FMD resistant animals might have ability to improve their innate immune response to FMDV infection.
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Affiliation(s)
- Bo-Young Lee
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Kwang-Nyeong Lee
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Taeheon Lee
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Jong-Hyeon Park
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Su-Mi Kim
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Hyang-Sim Lee
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Dong-Su Chung
- Gangwon Veterinary Service Laboratory, Chuncheon 220-822, Korea
| | | | - Hak-Kyo Lee
- Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea
| | - Heebal Kim
- Foot-and-Mouth Disease Division, Animal and Plant Quarantine Agency, Anyang 430-757, Korea
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11
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Abstract
The control of cellular growth and proliferation is key to the maintenance of homeostasis. Survival, proliferation, and arrest are regulated, in part, by Growth Arrest Specific 6 (Gas6) through binding to members of the TAM receptor tyrosine kinase family. Activation of the TAM receptors leads to downstream signaling through common kinases, but the exact mechanism within each cellular context varies and remains to be completely elucidated. Deregulation of the TAM family, due to its central role in mediating cellular proliferation, has been implicated in multiple diseases. Axl was cloned as the first TAM receptor in a search for genes involved in the progression of chronic to acute-phase leukemia, and has since been established as playing a critical role in the progression of cancer. The oncogenic nature of Axl is demonstrated through its activation of signaling pathways involved in proliferation, migration, inhibition of apoptosis, and therapeutic resistance. Despite its recent discovery, significant progress has been made in the development of effective clinical therapeutics targeting Axl. In order to accurately define the role of Axl in normal and diseased processes, it must be analyzed in a cell type-specific context.
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12
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A TRIP230-retinoblastoma protein complex regulates hypoxia-inducible factor-1α-mediated transcription and cancer cell invasion. PLoS One 2014; 9:e99214. [PMID: 24919196 PMCID: PMC4053355 DOI: 10.1371/journal.pone.0099214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/12/2014] [Indexed: 12/15/2022] Open
Abstract
Localized hypoxia in solid tumors activates transcriptional programs that promote the metastatic transformation of cells. Like hypoxia-inducible hyper-vascularization, loss of the retinoblastoma protein (Rb) is a trait common to advanced stages of tumor progression in many metastatic cancers. However, no link between the role of Rb and hypoxia-driven metastatic processes has been established. We demonstrated that Rb is a key mediator of the hypoxic response mediated by HIF1α/β, the master regulator of the hypoxia response, and its essential co-activator, the thyroid hormone receptor/retinoblastoma-interacting protein (TRIP230). Furthermore, loss of Rb unmasks the full co-activation potential of TRIP230. Using small inhibitory RNA approaches in vivo, we established that Rb attenuates the normal physiological response to hypoxia by HIF1α. Notably, loss of Rb results in hypoxia-dependent biochemical changes that promote acquisition of an invasive phenotype in MCF7 breast cancer cells. In addition, Rb is present in HIF1α-ARNT/HIF1β transcriptional complexes associated with TRIP230 as determined by co-immuno-precipitation, GST-pull-down and ChIP assays. These results demonstrate that Rb is a negative modulator of hypoxia-regulated transcription by virtue of its direct effects on the HIF1 complex. This work represents the first link between the functional ablation of Rb in tumor cells and HIF1α-dependent transcriptional activation and invasion.
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13
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Hernández M, Almeida TA. Is there any association between nek3 and cancers with frequent 13q14 deletion? Cancer Invest 2007; 24:682-8. [PMID: 17118778 DOI: 10.1080/07357900600981364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromosomal region 13q14 is frequently deleted in prostate cancer. nek3, a protein kinase related gene, is located on this region. Analysis of the coding region of nek3 showed an A insertion/deletion polymorphism in a stretch of adenines at the end of exon 9, with 2 alleles showing either 7 or 8 adenines. In addition we found a variant human NEK3 transcript, which lacks the entire exon 10 due to alternative splicing. The frequency of A8 allele is statistically higher in prostate cancer samples (p < 0.001) than normal controls, indicating that tumor samples preferentially express a full length protein. On the contrary, normal samples have a higher frequency for the A7 allele, expressing preferentially a shorter protein. To test if this association is a common feature in cancers with frequent 13q14 alterations, we analyzed cell lines established from oral, lung, and hepatocellular cancers. An association between nek3 A insertion/deletion polymorphism and cancers with alterations at 13q14 is observed.
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Affiliation(s)
- M Hernández
- Universidad de La Laguna, Facultad de Biología, Departamento de Genética, Tenerife, Islas Canarias, Spain
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Zhang J, Zhu ZG, Ji J, Yuan F, Yu YY, Liu BY, Lin YZ. Transcription factor Sp1 expression in gastric cancer and its relationship to long-term prognosis. World J Gastroenterol 2005; 11:2213-7. [PMID: 15818728 PMCID: PMC4305801 DOI: 10.3748/wjg.v11.i15.2213] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To explore the expression of Sp1 in gastric carcinoma as well as its association with other clinicopathologic features, and to evaluate the role of Sp1 as a prognostic indicator of gastric carcinoma.
METHODS: By using immunohistochemistry, we examined the Sp1 expression patterns in 65 cases of human gastric cancer, and 40 normal gastric mucosa specimens. Simultaneously, the correlation between Sp1 expression and clinical outcome or clinicopathologic features was investigated.
RESULTS: The percentage of Sp1 expression was 12.5% (5/40) in normal gastric mucosa, and the Sp1 protein was mainly expressed in the nuclei of cells located in the mucous neck region. In sharp contrast, strong Sp1 expression was detected in tumor cells, whereas no or faint Sp1 staining was detected in stromal cells and normal glandular cells surrounding the tumors. The expression rate of Sp1 in gastric cancer lesions was 53.85% (35/65). The medium survival duration in patients who had a tumor with negative, weak and strong Sp1 expressions was 1700, 1560 and 1026 d, respectively (P<0.05). Sp1 protein expression was closely related to the depth of tumor infiltration (χ2 = 13.223, P<0.01) and TNM stage (χ2 = 11.009, P<0.05), but had no relationship with the number of lymph nodes and Lauren’s classification (P>0.05). Cox regression model for multivariate analysis revealed that high Sp1 expression (P<0.05) and advanced stage (P<0.01) were independent predictors of poor survival.
CONCLUSION: Normal and malignant gastric tissues have unique Sp1 expression patterns. Sp1 might serve as an independent prognostic factor, by influencing the tumor infiltration and progression.
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Affiliation(s)
- Jun Zhang
- Department of Surgery, Rui Jin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Second Medical University, Shanghai 200025, China.
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15
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Garnis C, Buys TPH, Lam WL. Genetic alteration and gene expression modulation during cancer progression. Mol Cancer 2004; 3:9. [PMID: 15035667 PMCID: PMC408463 DOI: 10.1186/1476-4598-3-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 03/22/2004] [Indexed: 02/06/2023] Open
Abstract
Cancer progresses through a series of histopathological stages. Progression is thought to be driven by the accumulation of genetic alterations and consequently gene expression pattern changes. The identification of genes and pathways involved will not only enhance our understanding of the biology of this process, it will also provide new targets for early diagnosis and facilitate treatment design. Genomic approaches have proven to be effective in detecting chromosomal alterations and identifying genes disrupted in cancer. Gene expression profiling has led to the subclassification of tumors. In this article, we will describe the current technologies used in cancer gene discovery, the model systems used to validate the significance of the genes and pathways, and some of the genes and pathways implicated in the progression of preneoplastic and early stage cancer.
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Affiliation(s)
- Cathie Garnis
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre; 601 West 10th Ave, Vancouver, BC, Canada V5Z 1L3
| | - Timon PH Buys
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre; 601 West 10th Ave, Vancouver, BC, Canada V5Z 1L3
| | - Wan L Lam
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre; 601 West 10th Ave, Vancouver, BC, Canada V5Z 1L3
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Yokota J, Kohno T. Molecular footprints of human lung cancer progression. Cancer Sci 2004; 95:197-204. [PMID: 15016317 PMCID: PMC11159118 DOI: 10.1111/j.1349-7006.2004.tb02203.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Revised: 01/07/2004] [Accepted: 01/09/2004] [Indexed: 02/04/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death in the world. To understand the molecular processes and pathways of, and contributing factors to lung cancer progression, genetic alterations in various progression stages of lung cancer cells have been studied, since these alterations can be regarded as molecular footprints representing the individual processes of multistage lung carcinogenesis. The results indicate that defects in both the p53 and RB/p16 pathways are essential for the malignant transformation of lung epithelial cells. Several other genes, such as K-ras, PTEN and MYO18B, are genetically altered less frequently than p53 and RB/p16 in lung cancer cells, suggesting that alterations in these genes are associated with further malignant progression or unique phenotypes in a subset of lung cancer cells. However, it is still unclear what genes control the metastatic potential of lung cancer cells. Further analyses of molecular footprints in lung cancer cells, in particular in the cells of metastatic sites, will give us valuable information to fully understand the process of lung cancer progression, and to find novel ways of controlling it. Molecular footprints at the sites of p53 mutations and p16 deletions further indicate that DNA repair activities for G:C to T:A transversion and non-homologous end-joining of DNA double-strand breaks play important roles in the accumulation of genetic alterations in lung cancer cells. Thus, identification of environmental as well as genetic factors inducing or suppressing the occurrence of such alterations would be a clue to find novel ways of lung cancer prevention.
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Affiliation(s)
- Jun Yokota
- Biology Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
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