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Wesoly J, Pstrąg N, Derylo K, Michalec-Wawiórka B, Derebecka N, Nowicka H, Kajdasz A, Kluzek K, Srebniak M, Tchórzewski M, Kwias Z, Bluyssen H. Structural, topological, and functional characterization of transmembrane proteins TMEM213, 207, 116, 72 and 30B provides a potential link to ccRCC etiology. Am J Cancer Res 2023; 13:1863-1883. [PMID: 37293153 PMCID: PMC10244102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/02/2023] [Indexed: 06/10/2023] Open
Abstract
Due to their involvement in the development of various cancers Transmembrane Proteins (TMEMs) are the focus of many recent studies. Previously we reported TMEM de-regulation in clear cell Renal Cell Carcinoma (ccRCC) with TMEM213, 207, 116, 72 and 30B being among the most downregulated on mRNA level. TMEM down-regulation was also more pronounced in advanced ccRCC tumors and was potentially linked to clinical parameters such as: metastasis (TMEM72 and 116), Fuhrman grade (TMEM30B) and overall survival (TMEM30B). To further investigate these findings, first, we set off to prove experimentally that selected TMEMs are indeed membrane-bound as predicted in silico, we verified the presence of signaling peptides on their N-termini, orientation of TMEMs within the membrane and validated their predicted cellular localization. To investigate the potential role of selected TMEMs in cellular processes overexpression studies in HEK293 and HK-2 cell lines were carried out. Additionally, we tested TMEM isoform expression in ccRCC tumors, identified mutations in TMEM genes and examined chromosomal aberrations in their loci. We confirmed the membrane-bound status of all selected TMEMs, assigned TMEM213, and 207 to early endosomes, TMEM72 to early endosomes and plasma membrane, TMEM116 and 30B to the endoplasmic reticulum. The N-terminus of TMEM213 was found to be exposed to the cytoplasm, the C-terminus of TMEM207, 116 and 72 were directed toward the cytoplasm, and both termini of TMEM30B faced the cytoplasm. Interestingly, TMEM mutations and chromosomal aberrations were infrequent in ccRCC tumors, yet we identified potentially damaging mutations in TMEM213 and TMEM30B and found deletions in the TMEM30B locus in nearly 30% of the tumors. Overexpression studies suggested selected TMEMs may take part in carcinogenesis processes such as cell adhesion, regulation of epithelial cell proliferation, and regulation of adaptive immune response, which could indicate a link to the development and progression of ccRCC.
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Affiliation(s)
- Joanna Wesoly
- Laboratory of High Throughput Technologies, Adam Mickiewicz UniversityPoznan, Poland
| | - Natalia Pstrąg
- Laboratory of High Throughput Technologies, Adam Mickiewicz UniversityPoznan, Poland
| | - Kamil Derylo
- Department of Molecular Biology, Maria Curie-Sklodowska UniversityLublin, Poland
| | | | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Adam Mickiewicz UniversityPoznan, Poland
| | - Hanna Nowicka
- Laboratory of High Throughput Technologies, Adam Mickiewicz UniversityPoznan, Poland
| | - Arkadiusz Kajdasz
- Laboratory of Human Molecular Genetics, Adam Mickiewicz UniversityPoznan, Poland
| | - Katarzyna Kluzek
- Laboratory of Human Molecular Genetics, Adam Mickiewicz UniversityPoznan, Poland
| | | | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Sklodowska UniversityLublin, Poland
| | - Zbigniew Kwias
- Department of Urology and Urological Oncology, Poznan University of Medical SciencesPoznan, Poland
| | - Hans Bluyssen
- Laboratory of Human Molecular Genetics, Adam Mickiewicz UniversityPoznan, Poland
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Beasley HK, Rodman TA, Collins GV, Hinton A, Exil V. TMEM135 is a Novel Regulator of Mitochondrial Dynamics and Physiology with Implications for Human Health Conditions. Cells 2021; 10:cells10071750. [PMID: 34359920 PMCID: PMC8303332 DOI: 10.3390/cells10071750] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/16/2022] Open
Abstract
Transmembrane proteins (TMEMs) are integral proteins that span biological membranes. TMEMs function as cellular membrane gates by modifying their conformation to control the influx and efflux of signals and molecules. TMEMs also reside in and interact with the membranes of various intracellular organelles. Despite much knowledge about the biological importance of TMEMs, their role in metabolic regulation is poorly understood. This review highlights the role of a single TMEM, transmembrane protein 135 (TMEM135). TMEM135 is thought to regulate the balance between mitochondrial fusion and fission and plays a role in regulating lipid droplet formation/tethering, fatty acid metabolism, and peroxisomal function. This review highlights our current understanding of the various roles of TMEM135 in cellular processes, organelle function, calcium dynamics, and metabolism.
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Affiliation(s)
- Heather K. Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (H.K.B.); (T.A.R.)
| | - Taylor A. Rodman
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (H.K.B.); (T.A.R.)
| | - Greg V. Collins
- Fraternal Order of Eagles Diabetes Research Center, Iowa City, IA 52242, USA;
- Department of Pediatrics-Cardiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (H.K.B.); (T.A.R.)
- Correspondence: (A.H.J.); (V.E.)
| | - Vernat Exil
- Fraternal Order of Eagles Diabetes Research Center, Iowa City, IA 52242, USA;
- Department of Pediatrics-Cardiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Correspondence: (A.H.J.); (V.E.)
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Zhang H, Weström S, Kappelin P, Virtanen M, Vahlquist A, Törmä H. Exploration of novel candidate genes involved in epidermal keratinocyte differentiation and skin barrier repair in man. Differentiation 2021; 119:19-27. [PMID: 34029921 DOI: 10.1016/j.diff.2021.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/11/2021] [Accepted: 04/27/2021] [Indexed: 12/26/2022]
Abstract
A proper skin barrier function requires constant formation of stratum corneum, i.e. the outermost layer of epidermis composed of terminally differentiated keratinocytes. The complex process of converting proliferative basal keratinocytes into corneocytes relies on programmed changes in the activity of many well-established genes. Much remains however to be investigated about this process, e.g. in conjunction with epidermal barrier defects due to genetic errors as in ichthyosis. To this end, we re-analyzed two sets of microarray-data comparing altered gene expression in differentiated vs. proliferating keratinocytes and in the skin of patients with autosomal recessive congenital ichthyosis (ARCI) vs. healthy controls, respectively. We thus identified 24 genes to be upregulated in both sets of array and not previously associated with keratinocyte differentiation. For 10 of these genes (AKR1B10, BLNK, ENDOU, GCNT4, GLTP, RHCG, SLC15A1, TMEM45B, TMEM86A and VSNL1), qPCR analysis confirmed the array results and subsequent immunostainings of normal epidermis showed superficial expression of several of the proteins. Furthermore, induction of keratinocyte differentiation using phorbol esters (PMA) resulted in increased expression of eight of the genes, whereas siRNA silencing of PPARδ, a transcription factor supporting differentiation, had the opposite effect. In summary, our results identify ten new candidate genes seemingly involved in human epidermal keratinocyte differentiation and possibly important for epidermal repair in a genetic skin disease characterized by barrier failure.
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Affiliation(s)
- Hanqian Zhang
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Simone Weström
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Per Kappelin
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Marie Virtanen
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Anders Vahlquist
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Hans Törmä
- Department of Medical Sciences/Dermatology, Uppsala University, SE-751 85, Uppsala, Sweden.
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Hu Q, Wang G, Chen X, Zhang L, Zhao W, Jiang Y, Zhang C, Sun J, Xu H, Li H, Kong Q, Zhao J, Li X, Zhang X, Lv W, Liu Y, Yang G, Mu L, Wang J. Neural-specific distribution of transmembrane protein TMEM240 and formation of TMEM240-Body. Int J Biol Macromol 2020; 161:692-703. [PMID: 32535204 DOI: 10.1016/j.ijbiomac.2020.06.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/18/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
Abstract
Mutation in TMEM240 is suggested to cause SCA21, but the specific mechanism has not been clarified. The subcellular localization, specific biological function, and corresponding mechanism of action of TMEM240 have also not been delineated. In this study, the mRNA and protein expression of TMEM240 were assessed using qPCR and western blotting, respectively. Live cell imaging was used to establish the sub-cellular location of TMEM240, and electron microscopy was used to determine the morphology and distribution of TMEM240 in the cell. TMEM240 was specifically expressed in the neurons. Exogenous TMEM240 formed a multilayered cell structure, which we refer to as TMEM240-Body (T240-Body). T240-Body was separated and purified by centrifugation and filtration. An anchor protein His-tagged-GFP-BP on Ni-NTA agarose was used to pull down T240-GFP binding proteins. Both the N-terminal and the C-terminal of TMEM240 were confirmed to be inside the T240-Body. Co-localization experiments suggested that peroxisomes might contribute to T240-Body formation, and the two transmembrane regions of TMEM240 appear to be essential for formation of the T240-Body. Emerin protein contributed to formation of T240-Body when combined with TMEM240. Overall, this study provides new insights into TMEM240, which inform future research to further our understanding of its biological function.
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Affiliation(s)
- Qiongqiong Hu
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China; Department of Neurology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan 450007, China
| | - Guangyou Wang
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xin Chen
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Liulei Zhang
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Wei Zhao
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yan Jiang
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Chong Zhang
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jin Sun
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hao Xu
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hulun Li
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Qingfei Kong
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jiarui Zhao
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xinrong Li
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xiaoyu Zhang
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Weiqi Lv
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yumei Liu
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Gaiqing Yang
- Department of Neurology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan 450007, China
| | - Lili Mu
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China.
| | - Jinghua Wang
- Department of Neurobiology, Heilongjiang Provincial Key Laboratory of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China; Ministry of Education Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, Heilongjiang 150086, China.
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Zou J, Li Z, Deng H, Hao J, Ding R, Zhao M. TMEM213 as a novel prognostic and predictive biomarker for patients with lung adenocarcinoma after curative resection: a study based on bioinformatics analysis. J Thorac Dis 2019; 11:3399-3410. [PMID: 31559044 DOI: 10.21037/jtd.2019.08.01] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Background Lung cancer is the leading cause of cancer-related death worldwide. Few effective biomarkers for lung adenocarcinoma have been adapted for clinical practice to assist in prognosis evaluation and treatment plan implementation. Our study's goal was to find a new biological marker associated with the prognosis of lung adenocarcinoma after curative resection and the benefit of adjuvant chemotherapy (ACT). Methods Using the clinical information and RNA-Seq expression from The Cancer Genome Atlas (TCGA) database, prognostic genes were screened out and analyzed by Subpopulation Treatment Effect Pattern Plot (STEPP) in GSE42127 to filter out the drug-related gene. The relationship between the gene expression and clinicopathological parameters was assessed in the TCGA database. The prognostic significance was evaluated by Cox proportional hazards (PHs) regression analysis with 1,000 bootstrap replications. Gene set enrichment analysis (GSEA) was performed using high-throughput RNA sequencing data in TCGA and functional gene sets derived from the Molecular Signatures Database (MSigDB). Results A total of 297 prognostic genes were analyzed by STEPP in GSE42127. The results indicated a beneficial effect of adjuvant paclitaxel-carboplatin in patients with high TMEM213 expression. Its expression correlated with gender (P=0.013), and Kaplan-Meier analysis showed that patients with high TMEM213 expression had significantly longer overall survival (OS) (P=0.014, 0.027, and 0.000). Multivariate analysis showed TMEM213 to be an independent predictor for improved OS of patients (P=0.020), and the result was verified with the bootstrapping methodology and online "Kaplan-Meier Plotter" database analysis. Moreover, enriched pathway analysis indicated that TMEM213 expression was associated with the two gene sets of KEGG_DRUG_METABOLISM_CYTOCHROME_P450 and KEGG_ABC_TRANSPORTERS. Conclusions Based on bioinformatics analysis, we found that TMEM213 expression independently predicted better OS for lung adenocarcinoma. Patients in the high TMEM213 group appear to benefit more from adjuvant paclitaxel-carboplatin, but this needs further validation.
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Affiliation(s)
- Jiayun Zou
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang 110001, China.,Department of Oncology, Shengjing Hospital of China Medical University, Shenyang 110000, China
| | - Zhi Li
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang 110001, China
| | - Hao Deng
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Junli Hao
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang 110001, China
| | - Rui Ding
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang 110001, China
| | - Mingfang Zhao
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang 110001, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang 110001, China
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Tesei A, Cortesi M, Zamagni A, Arienti C, Pignatta S, Zanoni M, Paolillo M, Curti D, Rui M, Rossi D, Collina S. Sigma Receptors as Endoplasmic Reticulum Stress "Gatekeepers" and their Modulators as Emerging New Weapons in the Fight Against Cancer. Front Pharmacol 2018; 9:711. [PMID: 30042674 PMCID: PMC6048940 DOI: 10.3389/fphar.2018.00711] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Despite the interest aroused by sigma receptors (SRs) in the area of oncology, their role in tumor biology remains enigmatic. The predominant subcellular localization and main site of activity of SRs are the endoplasmic reticulum (ER). Current literature data, including recent findings on the sigma 2 receptor subtype (S2R) identity, suggest that SRs may play a role as ER stress gatekeepers. Although SR endogenous ligands are still unknown, a wide series of structurally unrelated compounds able to bind SRs have been identified. Currently, the identification of novel antiproliferative molecules acting via SR interaction is a challenging task for both academia and industry, as shown by the fact that novel anticancer drugs targeting SRs are in the preclinical-stage pipeline of pharmaceutical companies (i.e., Anavex Corp. and Accuronix). So far, no clinically available anticancer drugs targeting SRs are still available. The present review focuses literature advancements and provides a state-of-the-art overview of SRs, with emphasis on their involvement in cancer biology and on the role of SR modulators as anticancer agents. Findings from preclinical studies on novel anticancer drugs targeting SRs are presented in brief.
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Affiliation(s)
- Anna Tesei
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRCCS), Meldola, Italy
| | - Michela Cortesi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRCCS), Meldola, Italy
| | - Alice Zamagni
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRCCS), Meldola, Italy
| | - Chiara Arienti
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRCCS), Meldola, Italy
| | - Sara Pignatta
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRCCS), Meldola, Italy
| | - Michele Zanoni
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRCCS), Meldola, Italy
| | - Mayra Paolillo
- Pharmacology Section, Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Daniela Curti
- Laboratory of Cellular and Molecular Neuropharmacology, Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, Pavia, Italy
| | - Marta Rui
- Medicinal Chemistry and Pharmaceutical Technology Section, Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Daniela Rossi
- Medicinal Chemistry and Pharmaceutical Technology Section, Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Simona Collina
- Medicinal Chemistry and Pharmaceutical Technology Section, Department of Drug Sciences, University of Pavia, Pavia, Italy
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Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions. Nat Commun 2017; 8:15355. [PMID: 28513602 PMCID: PMC5442326 DOI: 10.1038/ncomms15355] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/23/2017] [Indexed: 12/13/2022] Open
Abstract
Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical families, G-quadruplexes and i-motifs, that have been a focus of intense research due to their potential biological impact in G- and C-rich DNA regions, respectively. High-resolution structures determined by solution-state nuclear magnetic resonance (NMR) spectroscopy demonstrate that AGCGA-quadruplexes comprise four 5′-AGCGA-3′ tracts and are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets, respectively. Residues in the core of the structure are connected with edge-type loops. Sequences of alternating 5′-AGCGA-3′ and 5′-GGG-3′ repeats could be expected to form G-quadruplexes, but are shown herein to form AGCGA-quadruplexes instead. Unique structural features of AGCGA-quadruplexes together with lower sensitivity to cation and pH variation imply their potential biological relevance in regulatory regions of genes responsible for basic cellular processes that are related to neurological disorders, cancer and abnormalities in bone and cartilage development. DNA tetrahelical structures such as G-quadruplexes are known to play important roles in DNA replication and repair. Here the authors present the structure of 5′-AGCGA-3′-quadruplexes enriched in genetic regulatory regions.
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Labonne JDJ, Lee KH, Iwase S, Kong IK, Diamond MP, Layman LC, Kim CH, Kim HG. An atypical 12q24.31 microdeletion implicates six genes including a histone demethylase KDM2B and a histone methyltransferase SETD1B in syndromic intellectual disability. Hum Genet 2016; 135:757-71. [PMID: 27106595 DOI: 10.1007/s00439-016-1668-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/31/2016] [Indexed: 12/22/2022]
Abstract
Microdeletion syndromes are frequent causes of neuropsychiatric disorders leading to intellectual disability as well as autistic features accompanied by epilepsy and craniofacial anomalies. From comparative deletion mapping of the smallest microdeletion to date at 12q24.31, found in a patient with overlapping clinical features of 12q24.31 microdeletion syndrome, we narrowed the putative critical region to 445 kb containing seven genes, one microRNA, and one non-coding RNA. Zebrafish in situ hybridization and comprehensive transcript analysis of annotated genes in the panels of human organ and brain suggest that these are all candidates for neurological phenotypes excluding the gene HPD. This is also corroborated by synteny analysis revealing the conservation of the order of these six candidate genes between humans and zebrafish. Among them, we propose histone demethylase KDM2B and histone methyltransferase SETD1B as the two most plausible candidate genes involved in intellectual disability, autism, epilepsy, and craniofacial anomalies. These two chromatin modifiers located approximately 224 kb apart were both commonly deleted in six patients, while two additional patients had either KDM2B or SETD1B deleted. The four additional candidate genes (ORAI1, MORN3, TMEM120B, RHOF), a microRNA MIR548AQ, and a non-coding RNA LINC01089 are localized between KDM2B and SETD1B. The 12q24.31 microdeletion syndrome with syndromic intellectual disability extends the growing list of microdeletion syndromes and underscores the causative roles of chromatin modifiers in cognitive and craniofacial development.
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Affiliation(s)
- Jonathan D J Labonne
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA
| | - Kang-Han Lee
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Il-Keun Kong
- Division of Applied Life Science (BK21plus), Department of Animal Science, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Gyeongsangnam-do, Korea
| | - Michael P Diamond
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA
- Neuroscience Program, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, 30912, USA.
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA.
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Wrzesiński T, Szelag M, Cieślikowski WA, Ida A, Giles R, Zodro E, Szumska J, Poźniak J, Kwias Z, Bluyssen HAR, Wesoly J. Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors. BMC Cancer 2015; 15:518. [PMID: 26169495 PMCID: PMC5015219 DOI: 10.1186/s12885-015-1530-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 07/01/2015] [Indexed: 11/24/2022] Open
Abstract
Background VHL inactivation is the most established molecular characteristic of clear cell renal cell carcinoma (ccRCC), with only a few additional genes implicated in development of this kidney tumor. In recently published ccRCC gene expression meta-analysis study we identified a number of deregulated genes with limited information available concerning their biological role, represented by gene transcripts belonging to transmembrane proteins family (TMEMs). TMEMs are predicted to be components of cellular membranes, such as mitochondrial membranes, ER, lysosomes and Golgi apparatus. Interestingly, the function of majority of TMEMs remains unclear. Here, we analyzed expression of ten TMEM genes in the context of ccRCC progression and development, and characterized these proteins bioinformatically. Methods The expression of ten TMEMs (RTP3, SLC35G2, TMEM30B, TMEM45A, TMEM45B, TMEM61, TMEM72, TMEM116, TMEM207 and TMEM213) was measured by qPCR. T-test, Pearson correlation, univariate and multivariate logistic and Cox regression were used in statistical analysis. The topology of studied proteins was predicted with Metaserver, together with PSORTII, Pfam and Localizome tools. Results We observed significant deregulation of expression of 10 analyzed TMEMs in ccRCC tumors. Cluster analysis of expression data suggested the down-regulation of all tested TMEMs to be a descriptor of the most advanced tumors. Logistic and Cox regression potentially linked TMEM expression to clinical parameters such as: metastasis, Fuhrman grade and overall survival. Topology predictions classified majority of analyzed TMEMs as type 3 and type 1 transmembrane proteins, with predicted localization mainly in ER. Conclusions The massive down-regulation of expression of TMEM family members suggests their importance in the pathogenesis of ccRCC and the bioinformatic analysis of TMEM topology implies a significant involvement of ER proteins in ccRCC pathology. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1530-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomasz Wrzesiński
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Malgorzata Szelag
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Wojciech A Cieślikowski
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland.
| | - Agnieszka Ida
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland.
| | - Rachel Giles
- Department of Nephrology and Hypertension, University Medical Center, Postbus 85500, 3508 GA, Utrecht, Netherlands.
| | - Elżbieta Zodro
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Joanna Szumska
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Joanna Poźniak
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Zbigniew Kwias
- Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland.
| | - Hans A R Bluyssen
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
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