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Qazi S, Jit BP, Das A, Karthikeyan M, Saxena A, Ray M, Singh AR, Raza K, Jayaram B, Sharma A. BESFA: bioinformatics based evolutionary, structural & functional analysis of prostrate, Placenta, Ovary, Testis, and Embryo (POTE) paralogs. Heliyon 2022; 8:e10476. [PMID: 36132183 PMCID: PMC9483601 DOI: 10.1016/j.heliyon.2022.e10476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/25/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
The POTE family comprises 14 paralogues and is primarily expressed in Prostrate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins' structure, function, and Adaptive Divergence. Our results suggest that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this study’s outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.
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Affiliation(s)
- Sahar Qazi
- Department of Biochemistry, All India Institute of Medical Sciences, Delhi 110029, India
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Bimal Prasad Jit
- Department of Biochemistry, All India Institute of Medical Sciences, Delhi 110029, India
| | - Abhishek Das
- Department of Biochemistry, All India Institute of Medical Sciences, Delhi 110029, India
| | - Muthukumarasamy Karthikeyan
- National Chemical Laboratory, Council of Scientific and Industrial Research (NCL-CSIR), Pune, Maharashtra, India
| | - Amit Saxena
- Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - M.D. Ray
- Dr. B.R.A Institute-Rotary Cancer Hospital, All India Institute of Medical Sciences, Delhi 110029, India
| | - Angel Rajan Singh
- Dr. B.R.A Institute-Rotary Cancer Hospital, All India Institute of Medical Sciences, Delhi 110029, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - B. Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Delhi, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Delhi 110029, India
- Corresponding author.
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Barger CJ, Zhang W, Sharma A, Chee L, James SR, Kufel CN, Miller A, Meza J, Drapkin R, Odunsi K, Klinkebiel D, Karpf AR. Expression of the POTE gene family in human ovarian cancer. Sci Rep 2018; 8:17136. [PMID: 30459449 PMCID: PMC6244393 DOI: 10.1038/s41598-018-35567-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/07/2018] [Indexed: 12/23/2022] Open
Abstract
The POTE family includes 14 genes in three phylogenetic groups. We determined POTE mRNA expression in normal tissues, epithelial ovarian and high-grade serous ovarian cancer (EOC, HGSC), and pan-cancer, and determined the relationship of POTE expression to ovarian cancer clinicopathology. Groups 1 & 2 POTEs showed testis-specific expression in normal tissues, consistent with assignment as cancer-testis antigens (CTAs), while Group 3 POTEs were expressed in several normal tissues, indicating they are not CTAs. Pan-POTE and individual POTEs showed significantly elevated expression in EOC and HGSC compared to normal controls. Pan-POTE correlated with increased stage, grade, and the HGSC subtype. Select individual POTEs showed increased expression in recurrent HGSC, and POTEE specifically associated with reduced HGSC OS. Consistent with tumors, EOC cell lines had significantly elevated Pan-POTE compared to OSE and FTE cells. Notably, Group 1 & 2 POTEs (POTEs A/B/B2/C/D), Group 3 POTE-actin genes (POTEs E/F/I/J/KP), and other Group 3 POTEs (POTEs G/H/M) show within-group correlated expression, and pan-cancer analyses of tumors and cell lines confirmed this relationship. Based on their restricted expression in normal tissues and increased expression and association with poor prognosis in ovarian cancer, POTEs are potential oncogenes and therapeutic targets in this malignancy.
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Affiliation(s)
- Carter J Barger
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Wa Zhang
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Ashok Sharma
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Linda Chee
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Smitha R James
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Christina N Kufel
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Austin Miller
- Department of Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Jane Meza
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, 68198-4375, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Kunle Odunsi
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - David Klinkebiel
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
- Department of Biochemistry, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Adam R Karpf
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA.
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA.
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research. Int J Mol Sci 2017; 18:ijms18040714. [PMID: 28350330 PMCID: PMC5412300 DOI: 10.3390/ijms18040714] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 12/27/2022] Open
Abstract
There have been tens of thousands of RNAs deposited in different databases that contain sequences of two genes and are coined chimeric RNAs, or chimeras. However, "chimeric RNA" has never been lucidly defined, partly because "gene" itself is still ill-defined and because the means of production for many RNAs is unclear. Since the number of putative chimeras is soaring, it is imperative to establish a pellucid definition for it, in order to differentiate chimeras from regular RNAs. Otherwise, not only will chimeric RNA studies be misled but also characterization of fusion genes and unannotated genes will be hindered. We propose that only those RNAs that are formed by joining two RNA transcripts together without a fusion gene as a genomic basis should be regarded as authentic chimeras, whereas those RNAs transcribed as, and cis-spliced from, single transcripts should not be deemed as chimeras. Many RNAs containing sequences of two neighboring genes may be transcribed via a readthrough mechanism, and thus are actually RNAs of unannotated genes or RNA variants of known genes, but not chimeras. In today's chimeric RNA research, there are still several key flaws, technical constraints and understudied tasks, which are also described in this perspective essay.
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Armanet N, Tosca L, Brisset S, Liehr T, Tachdjian G. Small Supernumerary Marker Chromosomes in Human Infertility. Cytogenet Genome Res 2015; 146:100-108. [PMID: 26398339 DOI: 10.1159/000438718] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2015] [Indexed: 11/19/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be unambiguously identified by banding cytogenetics. The objective of this study was to provide an overview of sSMC frequency and characterization in a context of infertility and to review the literature describing sSMC in relation with male and female infertility. Therefore, a systematic literature review on sSMC associated with infertility was conducted by means of a PubMed literature and a sSMC database (http://ssmc-tl.com/sSMC.html) search. A total of 234 patients with infertility were identified as carriers of sSMC. All chromosomes, except chromosomes 10, 19 and the X, were involved in sSMC, and in 72% the sSMC originated from acrocentric chromosomes. Euchromatic imbalances were caused by the presence of sSMC in 30% of the cases. Putative genes have been identified in only 1.2% of sSMC associated with infertility. The implication of sSMC in infertility could be due to a partial trisomy of some genes but also to mechanical effects perturbing meiosis. Further precise molecular and interphase-architecture studies on sSMC are needed in the future to characterize the relationship between this chromosomal anomaly and human infertility.
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Affiliation(s)
- Narjes Armanet
- Service d'Histologie, Embryologie et Cytogénétique, Hôpital Antoine Béclère, Hôpitaux Universitaires Paris-Sud, Clamart, France
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Redfield SM, Mao J, Zhu H, He Z, Zhang X, Bigler SA, Zhou X. The C-terminal common to group 3 POTES (CtG3P): a newly discovered nucleolar marker associated with malignant progression and metastasis. Am J Cancer Res 2013; 3:278-289. [PMID: 23841027 PMCID: PMC3696534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 05/31/2013] [Indexed: 06/02/2023] Open
Abstract
A gene family expressed in prostate, ovary, testis and placenta (POTEs) is newly defined and primate-specific. POTE genes have 13 paralogs, which are dispersed in 8 chromosomes and divided into three groups. The proteins encoded by these genes contain three domains: An N-terminal, ankyrin repeats and a C-terminus. Previous studies suggest that POTE proteins are localized in the inner aspect of cellular membrane and are considered as cancer-testis antigens, because they expressed widely in cancers, but in limited benign tissues. In this study, we will study the subcellular distribution of all POTE proteins and their associations with the progress and metastasis of malignancies. By performing Immunohistochemistry, Immunocytochemistry and immunofluorescence assay on tissue microarray slides containing tissues with different pathology and origins or on cell lines, we found that the epitopes of N- and C-terminals of all detected POTEs were widely expressed in benign and malignant tissues. Among these epitopes, C-terminal common to group 3 POTEs (CtG3P) was the only portion localized in nucleoli. The nucleolar IHC scores for CtG3P was lowest in benign tissues (4.47 ± 3.43), significantly higher in localized malignancies (5.32 ± 3.36, p = 3.63E-02), and highest in metastatic malignancies (7.90 ± 2.29, p = 8.13E-12). The CtG3P was better in differentiation of benign from malignant changes, and/or in differentiation of localized from metastatic cancers as compared with Ki-67 and AgNORs. In addition, transient transfection of siRNA against mRNA of group 3 POTEs influences the growth and survival of MCF-7 cells in vitro in a dose dependent manner.
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Affiliation(s)
- Samantha M Redfield
- Department of Pathology, University of Mississippi Medical Center2500 North State Street, MS 39216, USA
| | - Jinghe Mao
- Department of Biology, Tougaloo College500 West County Line Road, Tougaloo, MS 39157, USA
| | - He Zhu
- Department of Pathology, University of Mississippi Medical Center2500 North State Street, MS 39216, USA
| | - Zhi He
- Department of Pathology, University of Mississippi Medical Center2500 North State Street, MS 39216, USA
| | - Xu Zhang
- Center of biostatistics and Bioinformatics, University of Mississippi Medical Center2500 North State Street, MS 39216, USA
| | - Steven A Bigler
- Department of Pathology, Mississippi Baptist Medical Center1190 North State Street, Jackson, MS 39202, USA
| | - Xinchun Zhou
- Department of Pathology, University of Mississippi Medical Center2500 North State Street, MS 39216, USA
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Bera TK, Walker DA, Sherins RJ, Pastan I. POTE protein, a cancer-testis antigen, is highly expressed in spermatids in human testis and is associated with apoptotic cells. Biochem Biophys Res Commun 2012; 417:1271-4. [PMID: 22234308 DOI: 10.1016/j.bbrc.2011.12.125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 12/25/2011] [Indexed: 10/14/2022]
Abstract
The POTE gene family encodes very closely related proteins that are highly expressed in testis and in many cancers. Recent studies indicate that the POTE proteins have a pro-apoptotic function. To examine if POTE is associated with cells that are undergoing apoptosis in testis, we determined the cellular location of POTE and of Cleaved Caspase-3 in testicular tissues from 26 azoospermic men. We found intense expression of POTE in round spermatids that are undergoing apoptosis, which are positive for Cleaved Caspase-3. This study suggests POTE may have a role in apoptosis in the human testis.
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Affiliation(s)
- Tapan K Bera
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Guediche N, Tosca L, Kara Terki A, Bas C, Lecerf L, Young J, Briand-Suleau A, Tou B, Bouligand J, Brisset S, Misrahi M, Guiochon-Mantel A, Goossens M, Tachdjian G. Array comparative genomic hybridization analysis of small supernumerary marker chromosomes in human infertility. Reprod Biomed Online 2011; 24:72-82. [PMID: 22116069 DOI: 10.1016/j.rbmo.2011.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 11/16/2022]
Abstract
Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be unambiguously identified by conventional banding cytogenetics. This study describes four patients with sSMC in relation with infertility. Patient 1 had primary infertility. His brother, fertile, carried the same sSMC (patient 2). Patient 3 presented polycystic ovary syndrome and patient 4 primary ovarian insufficiency. Cytogenetic studies, array comparative genomic hybridization (CGH) and sperm analyses were compared with cases previously reported. sSMC corresponded to the 15q11.2 region (patients 1 and 2), the centromeric chromosome 15 region (patient 3) and the 21p11.2 region (patient 4). Array CGH showed 3.6-Mb gain for patients 1 and 2 and 0.266-Mb gain for patient 4. Sperm fluorescent in-situ hybridization analyses found ratios of 0.37 and 0.30 of sperm nuclei with sSMC(15) for patients 1 and 2, respectively (P < 0.001). An increase of sperm nuclei with disomy X, Y and 18 was noted for patient 1 compared with control and patient 2 (P < 0.001). Among the genes mapped in the unbalanced chromosomal regions, POTE B and BAGE are related to the testis and ovary, respectively. The implication of sSMC in infertility could be due to duplication, but also to mechanical effects perturbing meiosis.
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Affiliation(s)
- N Guediche
- Université Paris-Sud, Service d'Histologie Embryologie et Cytogénétique, APHP, Hôpital Antoine Béclère, Clamart 92141, France.
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Brun ME, Lana E, Rivals I, Lefranc G, Sarda P, Claustres M, Mégarbané A, De Sario A. Heterochromatic genes undergo epigenetic changes and escape silencing in immunodeficiency, centromeric instability, facial anomalies (ICF) syndrome. PLoS One 2011; 6:e19464. [PMID: 21559330 PMCID: PMC3084872 DOI: 10.1371/journal.pone.0019464] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 03/30/2011] [Indexed: 12/01/2022] Open
Abstract
Immunodeficiency, Centromeric Instability, Facial Anomalies (ICF) syndrome is a rare autosomal recessive disorder that is characterized by a marked immunodeficiency, severe hypomethylation of the classical satellites 2 and 3 associated with disruption of constitutive heterochromatin, and facial anomalies. Sixty percent of ICF patients have mutations in the DNMT3B (DNA methyltransferase 3B) gene, encoding a de novo DNA methyltransferase. In the present study, we have shown that, in ICF lymphoblasts and peripheral blood, juxtacentromeric heterochromatic genes undergo dramatic changes in DNA methylation, indicating that they are bona fide targets of the DNMT3B protein. DNA methylation in heterochromatic genes dropped from about 80% in normal cells to approximately 30% in ICF cells. Hypomethylation was observed in five ICF patients and was associated with activation of these silent genes. Although DNA hypomethylation occurred in all the analyzed heterochromatic genes and in all the ICF patients, gene expression was restricted to some genes, every patient having his own group of activated genes. Histone modifications were preserved in ICF patients. Heterochromatic genes were associated with histone modifications that are typical of inactive chromatin: they had low acetylation on H3 and H4 histones and were slightly enriched in H3K9Me(3), both in ICF and controls. This was also the case for those heterochromatic genes that escaped silencing. This finding suggests that gene activation was not generalized to all the cells, but rather was restricted to a clonal cell population that may contribute to the phenotypic variability observed in ICF syndrome. A slight increase in H3K27 monomethylation was observed both in heterochromatin and active euchromatin in ICF patients; however, no correlation between this modification and activation of heterochromatic genes was found.
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Affiliation(s)
| | - Erica Lana
- INSERM U827, Montpellier, France
- Université Montpellier 1, Montpellier, France
| | | | - Gérard Lefranc
- CNRS UPR 1142, Montpellier, France
- Université Montpellier 2, Montpellier, France
| | | | - Mireille Claustres
- INSERM U827, Montpellier, France
- Université Montpellier 1, Montpellier, France
- CHRU, Montpellier, France
| | - André Mégarbané
- Unité de Génétique Médicale and Laboratoire Associé INSERM à l’UMR S910, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
- Institut Jérôme Lejeune, Paris, France
| | - Albertina De Sario
- INSERM U827, Montpellier, France
- Université Montpellier 1, Montpellier, France
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Hermo L, Pelletier RM, Cyr DG, Smith CE. Surfing the wave, cycle, life history, and genes/proteins expressed by testicular germ cells. Part 4: intercellular bridges, mitochondria, nuclear envelope, apoptosis, ubiquitination, membrane/voltage-gated channels, methylation/acetylation, and transcription factors. Microsc Res Tech 2010; 73:364-408. [PMID: 19941288 DOI: 10.1002/jemt.20785] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As germ cells divide and differentiate from spermatogonia to spermatozoa, they share a number of structural and functional features that are common to all generations of germ cells and these features are discussed herein. Germ cells are linked to one another by large intercellular bridges which serve to move molecules and even large organelles from the cytoplasm of one cell to another. Mitochondria take on different shapes and features and topographical arrangements to accommodate their specific needs during spermatogenesis. The nuclear envelope and pore complex also undergo extensive modifications concomitant with the development of germ cell generations. Apoptosis is an event that is normally triggered by germ cells and involves many proteins. It occurs to limit the germ cell pool and acts as a quality control mechanism. The ubiquitin pathway comprises enzymes that ubiquitinate as well as deubiquitinate target proteins and this pathway is present and functional in germ cells. Germ cells express many proteins involved in water balance and pH control as well as voltage-gated ion channel movement. In the nucleus, proteins undergo epigenetic modifications which include methylation, acetylation, and phosphorylation, with each of these modifications signaling changes in chromatin structure. Germ cells contain specialized transcription complexes that coordinate the differentiation program of spermatogenesis, and there are many male germ cell-specific differences in the components of this machinery. All of the above features of germ cells will be discussed along with the specific proteins/genes and abnormalities to fertility related to each topic.
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Affiliation(s)
- Louis Hermo
- Department of Anatomy and Cell Biology, Faculty of Medicine, McGill University, 3640 University Street, Montreal, QC Canada H3A 2B2.
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Liu XF, Bera TK, Liu LJ, Pastan I. A primate-specific POTE-actin fusion protein plays a role in apoptosis. Apoptosis 2010; 14:1237-44. [PMID: 19669888 DOI: 10.1007/s10495-009-0392-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The primate-specific gene family, POTE, is expressed in many cancers but only in a limited number of normal tissues (testis, ovary, prostate). The 13 POTE paralogs are dispersed among 8 human chromosomes. They evolved by gene duplication and remodeling from an ancestral gene, Ankrd26, recently implicated in controlling body size and obesity. In addition, several POTE paralogs are fused to an actin retrogene producing POTE-actin fusion proteins. The biological function of the POTE genes is unknown, but their high expression in primary spermatocytes, some of which are undergoing apoptosis, suggests a role in inducing programmed cell death. We have chosen Hela cells as a model to study POTE function in human cancer, and have identified POTE-2alpha-actin as the major transcript and the protein it encodes in Hela cells. Transfection experiments show that both POTE-2alpha-actin and POTE-2gammaC are localized to actin filaments close to the inner plasma membrane. Transient expression of POTE-2alpha-actin or POTE-2gammaC induces apoptosis in Hela cells. Using wild-type and mutant mouse embryo cells, we find apoptosis induced by over-expression of POTE-2gammaC is decreased in Bak ( -/- ) or Bak ( -/- ) Bax ( -/- ) cells indicating POTE is acting through a mitochondrial pathway. Endogenous POTE-actin protein levels but not RNA levels increased in a time dependent manner by stimulation of death receptors with their cognate ligands. Our data indicates that the POTE gene family encodes a new family of proapoptotic proteins.
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Affiliation(s)
- Xiu Fen Liu
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA
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Hahn Y. Molecular evolution of TEPP protein genes in metazoans. Biochem Genet 2009; 47:651-64. [PMID: 19548082 DOI: 10.1007/s10528-009-9261-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 06/03/2009] [Indexed: 10/20/2022]
Abstract
TEPP is a gene expressed in human reproductive organs such as testis, prostate, and placenta. Here, identification and molecular evolutionary analysis of TEPP proteins in various metazoan animals including deuterostomes (chordates, hemichordates, and echinoderms), lophotrochozoans (mollusks and annelids), and cnidarians (sea anemone and coral) are reported. A multiple sequence alignment revealed two highly conserved regions in TEPP proteins that had no similarity to any other known domains or proteins. Genomic sequence analysis showed frequent shifting of the splice sites of intron 1 in mammalian TEPP genes. A comparison of the intron positions in the coding region showed that the exon/intron structure of the TEPP gene was established in an early metazoan ancestor and that independent loss of a single intron occurred in echinoderms and in vertebrates. The urochordate tunicate TEPP genes are intronless, possibly due to replacement of the original gene by a retrogene. No homolog was detected in birds, insects, nematodes, and teleost fishes despite the extensive sequence data of these species, implying that the TEPP gene might be lost in these lineages.
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Affiliation(s)
- Yoonsoo Hahn
- Department of Life Science (BK21 Program) and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Korea.
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Das S, Hahn Y, Walker DA, Nagata S, Willingham MC, Peehl DM, Bera TK, Lee B, Pastan I. Topology of NGEP, a prostate-specific cell:cell junction protein widely expressed in many cancers of different grade level. Cancer Res 2008; 68:6306-12. [PMID: 18676855 DOI: 10.1158/0008-5472.can-08-0870] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
New gene expressed in prostate (NGEP) is a prostate-specific polytopic membrane protein found at high concentrations at cell:cell contact regions. To determine if NGEP is a useful target for antibody-based therapy of prostate cancer, we performed an immunohistochemical analysis of 126 human prostate carcinoma samples using polyclonal anti-NGEP sera and found that 91% of the cancers express NGEP protein. To elucidate the topology of NGEP and guide the development of monoclonal antibodies (mAb) reacting with the extracellular regions of NGEP, a hemagglutinin epitope tag was inserted at several positions within the NGEP sequence. The tagged proteins were expressed in 293T cells and locations of the tags were determined by immunofluorescence in intact or permeabilized cells. The results indicate that NGEP contains eight transmembrane domains with both the NH(2) and COOH termini of NGEP located inside the cell. We produced mAb to three regions that are predicted to be intracellular based on the epitope tag data (amino acids 1-352, 441-501, and 868-933), and as predicted, the mAb only detected the protein in permeabilized cells. NGEP is a glycoprotein with predicted glycosylation sites at N809 and N824. When these residues were converted to glutamine, glycosylation was abolished, confirming that the residues are extracellular. Our findings on the expression and the orientation of the NGEP protein serve as an important framework for the development of mAb targeting the extracellular regions of NGEP that could be used for prostate cancer immunotherapy.
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Affiliation(s)
- Sudipto Das
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892-4264, USA
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