1
|
Armaos A, Serra F, Núñez-Carpintero I, Seo JH, Baca SC, Gustincich S, Valencia A, Freedman ML, Cirillo D, Giambartolomei C, Tartaglia GG. The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer. Nat Commun 2023; 14:8084. [PMID: 38057321 PMCID: PMC10700545 DOI: 10.1038/s41467-023-43767-1] [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: 11/08/2022] [Accepted: 11/18/2023] [Indexed: 12/08/2023] Open
Abstract
We introduce Promoter-Enhancer-Guided Interaction Networks (PENGUIN), a method for studying protein-protein interaction (PPI) networks within enhancer-promoter interactions. PENGUIN integrates H3K27ac-HiChIP data with tissue-specific PPIs to define enhancer-promoter PPI networks (EPINs). We validated PENGUIN using cancer (LNCaP) and benign (LHSAR) prostate cell lines. Our analysis detected EPIN clusters enriched with the architectural protein CTCF, a regulator of enhancer-promoter interactions. CTCF presence was coupled with the prevalence of prostate cancer (PrCa) single nucleotide polymorphisms (SNPs) within the same EPIN clusters, suggesting functional implications in PrCa. Within the EPINs displaying enrichments in both CTCF and PrCa SNPs, we also show enrichment in oncogenes. We substantiated our identified SNPs through CRISPR/Cas9 knockout and RNAi screens experiments. Here we show that PENGUIN provides insights into the intricate interplay between enhancer-promoter interactions and PPI networks, which are crucial for identifying key genes and potential intervention targets. A dedicated server is available at https://penguin.life.bsc.es/ .
Collapse
Affiliation(s)
- Alexandros Armaos
- Istituto Italiano di Tecnologia, CHT@Erzelli, Via Enrico Melen 83, Building B, 7th floor, 16152, Genova, Italy
| | - François Serra
- Barcelona Supercomputing Center, Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Josep Carreras Leukaemia Research Institute, Ctra de Can Ruti, Camí de les Escoles, 08916, Badalona, Barcelona, Spain
| | | | - Ji-Heui Seo
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan C Baca
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Stefano Gustincich
- Istituto Italiano di Tecnologia, CHT@Erzelli, Via Enrico Melen 83, Building B, 7th floor, 16152, Genova, Italy
| | - Alfonso Valencia
- Barcelona Supercomputing Center, Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- ICREA - Institució Catalana de Recerca I Estudis Avançats, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Eli and Edythe L. Broad Institute, 415 Main St., Cambridge, MA, 02142, USA
| | - Davide Cirillo
- Barcelona Supercomputing Center, Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain.
| | - Claudia Giambartolomei
- Istituto Italiano di Tecnologia, CHT@Erzelli, Via Enrico Melen 83, Building B, 7th floor, 16152, Genova, Italy.
- Health Data Science Centre, Human Technopole, Milan, Italy.
| | - Gian Gaetano Tartaglia
- Istituto Italiano di Tecnologia, CHT@Erzelli, Via Enrico Melen 83, Building B, 7th floor, 16152, Genova, Italy.
- ICREA - Institució Catalana de Recerca I Estudis Avançats, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
- Istituto Italiano di Tecnologia, CNLS@Sapienza, Viale Regina Elena, 00161, Rome, Italy.
| |
Collapse
|
2
|
Ruggiero V, Fagioli C, de Pretis S, Di Carlo V, Landsberger N, Zacchetti D. Complex CDKL5 translational regulation and its potential role in CDKL5 deficiency disorder. Front Cell Neurosci 2023; 17:1231493. [PMID: 37964795 PMCID: PMC10642286 DOI: 10.3389/fncel.2023.1231493] [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: 05/31/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
CDKL5 is a kinase with relevant functions in correct neuronal development and in the shaping of synapses. A decrease in its expression or activity leads to a severe neurodevelopmental condition known as CDKL5 deficiency disorder (CDD). CDD arises from CDKL5 mutations that lie in the coding region of the gene. However, the identification of a SNP in the CDKL5 5'UTR in a patient with symptoms consistent with CDD, together with the complexity of the CDKL5 transcript leader, points toward a relevant translational regulation of CDKL5 expression with important consequences in physiological processes as well as in the pathogenesis of CDD. We performed a bioinformatics and molecular analysis of the 5'UTR of CDKL5 to identify translational regulatory features. We propose an important role for structural cis-acting elements, with the involvement of the eukaryotic translational initiation factor eIF4B. By evaluating both cap-dependent and cap-independent translation initiation, we suggest the presence of an IRES supporting the translation of CDKL5 mRNA and propose a pathogenic effect of the C>T -189 SNP in decreasing the translation of the downstream protein.
Collapse
Affiliation(s)
- Valeria Ruggiero
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Fagioli
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano de Pretis
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valerio Di Carlo
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Nicoletta Landsberger
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Daniele Zacchetti
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
3
|
Babina M, Franke K, Bal G. How "Neuronal" Are Human Skin Mast Cells? Int J Mol Sci 2022; 23:ijms231810871. [PMID: 36142795 PMCID: PMC9505265 DOI: 10.3390/ijms231810871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
Mast cells are evolutionarily old cells and the principal effectors in allergic responses and inflammation. They are seeded from the yolk sac during embryogenesis or are derived from hematopoietic progenitors and are therefore related to other leukocyte subsets, even though they form a separate clade in the hematopoietic system. Herein, we systematically bundle information from several recent high-throughput endeavors, especially those comparing MCs with other cell types, and combine such information with knowledge on the genes’ functions to reveal groups of neuronal markers specifically expressed by MCs. We focus on recent advances made regarding human tissue MCs, but also refer to studies in mice. In broad terms, genes hyper-expressed in MCs, but largely inactive in other myelocytes, can be classified into subcategories such as traffic/lysosomes (MLPH and RAB27B), the dopamine system (MAOB, DRD2, SLC6A3, and SLC18A2), Ca2+-related entities (CALB2), adhesion molecules (L1CAM and NTM) and, as an overall principle, the transcription factors and modulators of transcriptional activity (LMO4, PBX1, MEIS2, and EHMT2). Their function in MCs is generally unknown but may tentatively be deduced by comparison with other systems. MCs share functions with the nervous system, as they express typical neurotransmitters (histamine and serotonin) and a degranulation machinery that shares features with the neuronal apparatus at the synapse. Therefore, selective overlaps are plausible, and they further highlight the uniqueness of MCs within the myeloid system, as well as when compared with basophils. Apart from investigating their functional implications in MCs, a key question is whether their expression in the lineage is due to the specific reactivation of genes normally silenced in leukocytes or whether the genes are not switched off during mastocytic development from early progenitors.
Collapse
Affiliation(s)
- Magda Babina
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
- Correspondence:
| | - Kristin Franke
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Gürkan Bal
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
| |
Collapse
|
4
|
Poeta L, Padula A, Lioi MB, van Bokhoven H, Miano MG. Analysis of a Set of KDM5C Regulatory Genes Mutated in Neurodevelopmental Disorders Identifies Temporal Coexpression Brain Signatures. Genes (Basel) 2021; 12:genes12071088. [PMID: 34356104 PMCID: PMC8305412 DOI: 10.3390/genes12071088] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/22/2022] Open
Abstract
Dysregulation of transcriptional pathways is observed in multiple forms of neurodevelopmental disorders (NDDs), such as intellectual disability (ID), epilepsy and autism spectrum disorder (ASD). We previously demonstrated that the NDD genes encoding lysine-specific demethylase 5C (KDM5C) and its transcriptional regulators Aristaless related-homeobox (ARX), PHD Finger Protein 8 (PHF8) and Zinc Finger Protein 711 (ZNF711) are functionally connected. Here, we show their relation to each other with respect to the expression levels in human and mouse datasets and in vivo mouse analysis indicating that the coexpression of these syntenic X-chromosomal genes is temporally regulated in brain areas and cellular sub-types. In co-immunoprecipitation assays, we found that the homeotic transcription factor ARX interacts with the histone demethylase PHF8, indicating that this transcriptional axis is highly intersected. Furthermore, the functional impact of pathogenic mutations of ARX, KDM5C, PHF8 and ZNF711 was tested in lymphoblastoid cell lines (LCLs) derived from children with varying levels of syndromic ID establishing the direct correlation between defects in the KDM5C-H3K4me3 pathway and ID severity. These findings reveal novel insights into epigenetic processes underpinning NDD pathogenesis and provide new avenues for assessing developmental timing and critical windows for potential treatments.
Collapse
Affiliation(s)
- Loredana Poeta
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy;
- Department of Science, University of Basilicata, 85100 Potenza, Italy;
- Correspondence: (L.P.); (M.G.M.); Tel.: +39-(0)-816132261/445 (M.G.M.)
| | - Agnese Padula
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy;
| | | | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, 6525 GA Nijmegen, The Netherlands;
| | - Maria Giuseppina Miano
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy;
- Correspondence: (L.P.); (M.G.M.); Tel.: +39-(0)-816132261/445 (M.G.M.)
| |
Collapse
|
5
|
Mepyans M, Andrzejczuk L, Sosa J, Smith S, Herron S, DeRosa S, Slaugenhaupt SA, Misko A, Grishchuk Y, Kiselyov K. Early evidence of delayed oligodendrocyte maturation in the mouse model of mucolipidosis type IV. Dis Model Mech 2020; 13:dmm044230. [PMID: 32586947 PMCID: PMC7406328 DOI: 10.1242/dmm.044230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
Mucolipidosis type IV (MLIV) is a lysosomal disease caused by mutations in the MCOLN1 gene that encodes the endolysosomal transient receptor potential channel mucolipin-1, or TRPML1. MLIV results in developmental delay, motor and cognitive impairments, and vision loss. Brain abnormalities include thinning and malformation of the corpus callosum, white-matter abnormalities, accumulation of undegraded intracellular 'storage' material and cerebellar atrophy in older patients. Identification of the early events in the MLIV course is key to understanding the disease and deploying therapies. The Mcoln1-/- mouse model reproduces all major aspects of the human disease. We have previously reported hypomyelination in the MLIV mouse brain. Here, we investigated the onset of hypomyelination and compared oligodendrocyte maturation between the cortex/forebrain and cerebellum. We found significant delays in expression of mature oligodendrocyte markers Mag, Mbp and Mobp in the Mcoln1-/- cortex, manifesting as early as 10 days after birth and persisting later in life. Such delays were less pronounced in the cerebellum. Despite our previous finding of diminished accumulation of the ferritin-bound iron in the Mcoln1-/- brain, we report no significant changes in expression of the cytosolic iron reporters, suggesting that iron-handling deficits in MLIV occur in the lysosomes and do not involve broad iron deficiency. These data demonstrate very early deficits of oligodendrocyte maturation and critical regional differences in myelination between the forebrain and cerebellum in the mouse model of MLIV. Furthermore, they establish quantitative readouts of the MLIV impact on early brain development, useful to gauge efficacy in pre-clinical trials.
Collapse
Affiliation(s)
- Molly Mepyans
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Livia Andrzejczuk
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jahree Sosa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sierra Smith
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Shawn Herron
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Samantha DeRosa
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Susan A Slaugenhaupt
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Albert Misko
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Yulia Grishchuk
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Kirill Kiselyov
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| |
Collapse
|
6
|
Croci S, Carriero ML, Capitani K, Daga S, Donati F, Papa FT, Frullanti E, Lopergolo D, Lamacchia V, Tita R, Giliberti A, Benetti E, Niccheri F, Furini S, Lo Rizzo C, Conticello SG, Renieri A, Meloni I. AAV-mediated FOXG1 gene editing in human Rett primary cells. Eur J Hum Genet 2020; 28:1446-1458. [PMID: 32541681 PMCID: PMC7608362 DOI: 10.1038/s41431-020-0652-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 12/21/2022] Open
Abstract
Variations in the Forkhead Box G1 (FOXG1) gene cause FOXG1 syndrome spectrum, including the congenital variant of Rett syndrome, characterized by early onset of regression, Rett-like and jerky movements, and cortical visual impairment. Due to the largely unknown pathophysiological mechanisms downstream the impairment of this transcriptional regulator, a specific treatment is not yet available. Since both haploinsufficiency and hyper-expression of FOXG1 cause diseases in humans, we reasoned that adding a gene under nonnative regulatory sequences would be a risky strategy as opposed to a genome editing approach where the mutated gene is reversed into wild-type. Here, we demonstrate that an adeno-associated viruses (AAVs)-coupled CRISPR/Cas9 system is able to target and correct FOXG1 variants in patient-derived fibroblasts, induced Pluripotent Stem Cells (iPSCs) and iPSC-derived neurons. Variant-specific single-guide RNAs (sgRNAs) and donor DNAs have been selected and cloned together with a mCherry/EGFP reporter system. Specific sgRNA recognition sequences were inserted upstream and downstream Cas9 CDS to allow self-cleavage and inactivation. We demonstrated that AAV serotypes vary in transduction efficiency depending on the target cell type, the best being AAV9 in fibroblasts and iPSC-derived neurons, and AAV2 in iPSCs. Next-generation sequencing (NGS) of mCherry+/EGFP+ transfected cells demonstrated that the mutated alleles were repaired with high efficiency (20–35% reversion) and precision both in terms of allelic discrimination and off-target activity. The genome editing strategy tested in this study has proven to precisely repair FOXG1 and delivery through an AAV9-based system represents a step forward toward the development of a therapy for Rett syndrome.
Collapse
Affiliation(s)
| | | | - Katia Capitani
- Medical Genetics, University of Siena, Siena, Italy.,Molecular Mechanisms of Oncogenesis, ISPRO Core Research Laboratory (CRL), Firenze, Italy
| | - Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy
| | - Francesco Donati
- Medical Genetics, University of Siena, Siena, Italy.,Molecular Mechanisms of Oncogenesis, ISPRO Core Research Laboratory (CRL), Firenze, Italy
| | | | | | - Diego Lopergolo
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Vittoria Lamacchia
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Elisa Benetti
- Medical Genetics, University of Siena, Siena, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Niccheri
- Molecular Mechanisms of Oncogenesis, ISPRO Core Research Laboratory (CRL), Firenze, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Caterina Lo Rizzo
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy. .,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
| | | |
Collapse
|
7
|
Thodberg M, Thieffry A, Vitting-Seerup K, Andersson R, Sandelin A. CAGEfightR: analysis of 5'-end data using R/Bioconductor. BMC Bioinformatics 2019; 20:487. [PMID: 31585526 PMCID: PMC6778389 DOI: 10.1186/s12859-019-3029-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND 5'-end sequencing assays, and Cap Analysis of Gene Expression (CAGE) in particular, have been instrumental in studying transcriptional regulation. 5'-end methods provide genome-wide maps of transcription start sites (TSSs) with base pair resolution. Because active enhancers often feature bidirectional TSSs, such data can also be used to predict enhancer candidates. The current availability of mature and comprehensive computational tools for the analysis of 5'-end data is limited, preventing efficient analysis of new and existing 5'-end data. RESULTS We present CAGEfightR, a framework for analysis of CAGE and other 5'-end data implemented as an R/Bioconductor-package. CAGEfightR can import data from BigWig files and allows for fast and memory efficient prediction and analysis of TSSs and enhancers. Downstream analyses include quantification, normalization, annotation with transcript and gene models, TSS shape statistics, linking TSSs to enhancers via co-expression, identification of enhancer clusters, and genome-browser style visualization. While built to analyze CAGE data, we demonstrate the utility of CAGEfightR in analyzing nascent RNA 5'-data (PRO-Cap). CAGEfightR is implemented using standard Bioconductor classes, making it easy to learn, use and combine with other Bioconductor packages, for example popular differential expression tools such as limma, DESeq2 and edgeR. CONCLUSIONS CAGEfightR provides a single, scalable and easy-to-use framework for comprehensive downstream analysis of 5'-end data. CAGEfightR is designed to be interoperable with other Bioconductor packages, thereby unlocking hundreds of mature transcriptomic analysis tools for 5'-end data. CAGEfightR is freely available via Bioconductor: bioconductor.org/packages/CAGEfightR .
Collapse
Affiliation(s)
- Malte Thodberg
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.
| | - Axel Thieffry
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
| | - Kristoffer Vitting-Seerup
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
- Danish Cancer Society, Strandboulevarden 49 DK2100, Copenhagen Ø, Denmark
| | - Robin Andersson
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.
| |
Collapse
|
8
|
Takamochi K, Ohmiya H, Itoh M, Mogushi K, Saito T, Hara K, Mitani K, Kogo Y, Yamanaka Y, Kawai J, Hayashizaki Y, Oh S, Suzuki K, Kawaji H. Novel biomarkers that assist in accurate discrimination of squamous cell carcinoma from adenocarcinoma of the lung. BMC Cancer 2016; 16:760. [PMID: 27681076 PMCID: PMC5041559 DOI: 10.1186/s12885-016-2792-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 09/16/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. The most effective regimen in lung cancers is different between squamous cell carcinoma (SCC) and adenocarcinoma (AD). Therefore a precise diagnosis is crucial, but this has been difficult, particularly for poorly differentiated SCC (PDSCC) and AD without a lepidic growth component (non-lepidic AD). Biomarkers enabling a precise diagnosis are therefore urgently needed. METHODS Cap Analysis of Gene Expression (CAGE) is a method used to quantify promoter activities across the whole genome by determining the 5' ends of capped RNA molecules with next-generation sequencing. We performed CAGE on 97 frozen tissues from surgically resected lung cancers (22 SCC and 75 AD), and confirmed the findings by immunohistochemical analysis (IHC) in an independent group (29 SCC and 45 AD). RESULTS Using the genome-wide promoter activity profiles, we confirmed that the expression of known molecular markers used in IHC for SCC (CK5, CK6, p40 and desmoglein-3) and AD (TTF-1 and napsin A) were different between SCC and AD. We identified two novel marker candidates, SPATS2 for SCC and ST6GALNAC1 for AD, as showing comparable performance and complementary utility to the known markers in discriminating PDSCC and non-lepidic AD. We subsequently confirmed their utility at the protein level by IHC in an independent group. CONCLUSIONS We identified two genes, SPATS2 and ST6GALNAC1, as novel complemental biomarkers discriminating SCC and AD. These findings will contribute to a more accurate diagnosis of NSCLC, which is crucial for precision medicine for lung cancer.
Collapse
Affiliation(s)
- Kazuya Takamochi
- Department of General Thoracic Surgery, Juntendo University School of Medicine, 1-3, Hongo 3-chome, Bunkyo-ku, Tokyo, 113-8431, Japan.
| | - Hiroko Ohmiya
- Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, 230-0045, Yokohama, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Kaoru Mogushi
- Center for Genomic and Regenerative Medicine, Juntendo University School of Medicine, 1-3, Hongo 3-chome, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University School of Medicine, 1-3, Hongo 3-chome, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Kieko Hara
- Department of Human Pathology, Juntendo University School of Medicine, 1-3, Hongo 3-chome, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Keiko Mitani
- Department of Human Pathology, Juntendo University School of Medicine, 1-3, Hongo 3-chome, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Yasushi Kogo
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Yasunari Yamanaka
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Jun Kawai
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Shiaki Oh
- Department of General Thoracic Surgery, Juntendo University School of Medicine, 1-3, Hongo 3-chome, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Kenji Suzuki
- Department of General Thoracic Surgery, Juntendo University School of Medicine, 1-3, Hongo 3-chome, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Hideya Kawaji
- Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, 230-0045, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| |
Collapse
|
9
|
Characterisation of CDKL5 Transcript Isoforms in Human and Mouse. PLoS One 2016; 11:e0157758. [PMID: 27315173 PMCID: PMC4912119 DOI: 10.1371/journal.pone.0157758] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
Mutations in the X-linked Cyclin-Dependent Kinase-Like 5 gene (CDKL5) cause early onset infantile spasms and subsequent severe developmental delay in affected children. Deleterious mutations have been reported to occur throughout the CDKL5 coding region. Several studies point to a complex CDKL5 gene structure in terms of exon usage and transcript expression. Improvements in molecular diagnosis and more extensive research into the neurobiology of CDKL5 and pathophysiology of CDKL5 disorders necessitate an updated analysis of the gene. In this study, we have analysed human and mouse CDKL5 transcript patterns both bioinformatically and experimentally. We have characterised the predominant brain isoform of CDKL5, a 9.7 kb transcript comprised of 18 exons with a large 6.6 kb 3’-untranslated region (UTR), which we name hCDKL5_1. In addition we describe new exonic regions and a range of novel splice and UTR isoforms. This has enabled the description of an updated gene model in both species and a standardised nomenclature system for CDKL5 transcripts. Profiling revealed tissue- and brain development stage-specific differences in expression between transcript isoforms. These findings provide an essential backdrop for the diagnosis of CDKL5-related disorders, for investigations into the basic biology of this gene and its protein products, and for the rational design of gene-based and molecular therapies for these disorders.
Collapse
|
10
|
Gadalla KKE, Ross PD, Hector RD, Bahey NG, Bailey MES, Cobb SR. Gene therapy for Rett syndrome: prospects and challenges. FUTURE NEUROLOGY 2015. [DOI: 10.2217/fnl.15.29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rett syndrome (RTT) is a neurological disorder that affects females and is caused by loss-of-function mutations in the X-linked gene MECP2. Deletion of Mecp2 in mice results in a constellation of neurological features that resemble those seen in RTT patients. Experiments in mice have demonstrated that restoration of MeCP2, even at adult stages, reverses several aspects of the RTT-like pathology suggesting that the disorder may be inherently treatable. This has provided an impetus to explore several therapeutic approaches targeting RTT at the level of the gene, including gene therapy, activation of MECP2 on the inactive X chromosome and read-through and repair of RTT-causing mutations. Here, we review these different strategies and the challenges of gene-based approaches in RTT.
Collapse
Affiliation(s)
- Kamal KE Gadalla
- University of Glasgow, Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, Glasgow, UK
- Pharmacology Department, Faculty of Medicine, Tanta University, Egypt
| | - Paul D Ross
- University of Glasgow, Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, Glasgow, UK
| | - Ralph D Hector
- University of Glasgow, Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, Glasgow, UK
| | - Noha G Bahey
- University of Glasgow, Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, Glasgow, UK
- Histology Department, Faculty of Medicine, Tanta University, Egypt
| | - Mark ES Bailey
- School of Life Sciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Stuart R Cobb
- University of Glasgow, Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, Glasgow, UK
| |
Collapse
|