Patched 1 and Patched 2 Redundancy Has a Key Role In
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Multivariate Meta-Analysis of Differential Principal Components Underlying Human Primed and Naive-Like Pluripotent States
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.20.347666; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. October 20, 2020 To: bioRxiv Multivariate Meta-Analysis of Differential Principal Components underlying Human Primed and Naive-like Pluripotent States Kory R. Johnson1*, Barbara S. Mallon2, Yang C. Fann1, and Kevin G. Chen2*, 1Intramural IT and Bioinformatics Program, 2NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA Keywords: human pluripotent stem cells; naive pluripotency, meta-analysis, principal component analysis, t-SNE, consensus clustering *Correspondence to: Dr. Kory R. Johnson ([email protected]) Dr. Kevin G. Chen ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.20.347666; this version posted October 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. ABSTRACT The ground or naive pluripotent state of human pluripotent stem cells (hPSCs), which was initially established in mouse embryonic stem cells (mESCs), is an emerging and tentative concept. To verify this important concept in hPSCs, we performed a multivariate meta-analysis of major hPSC datasets via the combined analytic powers of percentile normalization, principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and SC3 consensus clustering. -
Coincident Two Mutations and One Single Nucleotide Polymorphism of the PTCH1 Gene in a Family with Naevoid Basal Cell Carcinoma Syndrome
Letters to the Editor 635 Coincident Two Mutations and One Single Nucleotide Polymorphism of the PTCH1 Gene in a Family with Naevoid Basal Cell Carcinoma Syndrome Shoko Abe1, Kenji Kabashima1*, Jun-ichi Sakabe1, Takatoshi Shimauchi1, Zhang Yan2, Tetsuji Okamoto2 and Yoshiki Tokura1 1Department of Dermatology, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, and 2Department of Molecular Oral Medicine and Maxillofacial Surgery 1, Division of Frontier Medical Science, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan. E-mail: [email protected] Accepted May 7, 2008. Sir, at nucleotide position 667 within exon 3 and an intervening se- Naevoid basal cell carcinoma syndrome (NBCCS, OMIM quence (IVS)16 -3T > C, and a SNP; IVS10 -8T > C, were detected in all three cases. A deletion of AGAC causes a frameshift and a #109400), also called Gorlin’s syndrome, is an autosomal subsequent stop codon in exon 3, which prematurely truncates dominant disease that affects about 1 in 60,000 indivi- the protein (Fig. 1a). In addition, the IVS16 -3T > C could lead duals (1, 2). NBCCS is associated with various skeletal to an aberrant splicing and truncation of PTCH1 (10–12). and neurocutaneous abnormalities. Major manifestations To detect the expression level of PTCH1 protein in the skin, are multiple basal cell carcinomas (BCCs), odontogenic an immunohistochemical study was performed using goat poly- clonal anti-PTCH1 antibody (G-19; Santa Cruz Biotechnology, keratocysts, palmoplantar dyskeratotic pits and intra- Santa Cruz, CA, USA). Enzyme reactions were developed with cranial calcification (3). In addition, rib and vertebral conventional substrates for diamino-benzidine (Sigma, St Louis, malformations, epidermal cysts, macrocephaly, facial MO, USA) (13). -
Review of the Molecular Genetics of Basal Cell Carcinoma; Inherited Susceptibility, Somatic Mutations, and Targeted Therapeutics
cancers Review Review of the Molecular Genetics of Basal Cell Carcinoma; Inherited Susceptibility, Somatic Mutations, and Targeted Therapeutics James M. Kilgour , Justin L. Jia and Kavita Y. Sarin * Department of Dermatology, Stanford University School of Medcine, Stanford, CA 94305, USA; [email protected] (J.M.K.); [email protected] (J.L.J.) * Correspondence: [email protected] Simple Summary: Basal cell carcinoma is the most common human cancer worldwide. The molec- ular basis of BCC involves an interplay of inherited genetic susceptibility and somatic mutations, commonly induced by exposure to UV radiation. In this review, we outline the currently known germline and somatic mutations implicated in the pathogenesis of BCC with particular attention paid toward affected molecular pathways. We also discuss polymorphisms and associated phenotypic traits in addition to active areas of BCC research. We finally provide a brief overview of existing non-surgical treatments and emerging targeted therapeutics for BCC such as Hedgehog pathway inhibitors, immune modulators, and histone deacetylase inhibitors. Abstract: Basal cell carcinoma (BCC) is a significant public health concern, with more than 3 million cases occurring each year in the United States, and with an increasing incidence. The molecular basis of BCC is complex, involving an interplay of inherited genetic susceptibility, including single Citation: Kilgour, J.M.; Jia, J.L.; Sarin, nucleotide polymorphisms and genetic syndromes, and sporadic somatic mutations, often induced K.Y. Review of the Molecular Genetics of Basal Cell Carcinoma; by carcinogenic exposure to UV radiation. This review outlines the currently known germline and Inherited Susceptibility, Somatic somatic mutations implicated in the pathogenesis of BCC, including the key molecular pathways Mutations, and Targeted affected by these mutations, which drive oncogenesis. -
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Jägers and Roelink BMC Molecular and Cell Biology (2021) 22:22 BMC Molecular and https://doi.org/10.1186/s12860-021-00359-5 Cell Biology RESEARCH ARTICLE Open Access Association of Sonic Hedgehog with the extracellular matrix requires its zinc- coordination center Carina Jägers and Henk Roelink* Abstract Background: Sonic Hedgehog (Shh) has a catalytic cleft characteristic for zinc metallopeptidases and has significant sequence similarities with some bacterial peptidoglycan metallopeptidases defining a subgroup within the M15A family that, besides having the characteristic zinc coordination motif, can bind two calcium ions. Extracellular matrix (ECM) components in animals include heparan-sulfate proteoglycans, which are analogs of bacterial peptidoglycan and are involved in the extracellular distribution of Shh. Results: We found that the zinc-coordination center of Shh is required for its association to the ECM as well as for non-cell autonomous signaling. Association with the ECM requires the presence of at least 0.1 μM zinc and is prevented by mutations affecting critical conserved catalytical residues. Consistent with the presence of a conserved calcium binding domain, we find that extracellular calcium inhibits ECM association of Shh. Conclusions: Our results indicate that the putative intrinsic peptidase activity of Shh is required for non-cell autonomous signaling, possibly by enzymatically altering ECM characteristics. Keywords: Shh signaling, Zinc metallopeptidases, Extracellular matrix, BacHh Background rejected by demonstrating that mutation of a critical The Hedgehog (Hh) gene was first identified in the residue involved in catalysis (E177) did not impair the Drosophila melanogaster screen performed by Christiane ability of Shh to activate the Hh response [4], and conse- Nüsslein-Volhard and Eric Wieshaus in the late 1970s quently the zinc coordination center of Shh is often re- [1]. -
The Cell Adhesion Molecule CHL1 Interacts with Patched-1 to Regulate
© 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 2606-2619 doi:10.1242/jcs.194563 RESEARCH ARTICLE The cell adhesion molecule CHL1 interacts with patched-1 to regulate apoptosis during postnatal cerebellar development Jelena Katic1, Gabriele Loers1, Jelena Tosic1, Melitta Schachner2,3,4,* and Ralf Kleene1 ABSTRACT differentiated neural cells (Holm et al., 1996; Chen et al., 1999; The immunoglobulin superfamily adhesion molecule close homolog of Hillenbrand et al., 1999; Buhusi et al., 2003; Jakovcevski et al., L1 (CHL1) plays important roles during nervous system development. 2007, 2009; Katic et al., 2014). Moreover, CHL1 regulates Here, we identified the hedgehog receptor patched-1 (PTCH1) as a neuritogenesis through different mechanisms (Chen et al., 1999; novel CHL1-binding protein and showed that CHL1 interacts with Hillenbrand et al., 1999; Jakovcevski et al., 2007, 2009; Katic et al., the first extracellular loop of PTCH1 via its extracellular domain. 2014). In search for novel binding partners for CHL1, we found that trans Colocalization and co-immunoprecipitation of CHL1 with PTCH1 PTCH1 and CHL1 associate in a heterophilic -interaction. The suggest an association of CHL1 with this major component of the 12-pass transmembrane protein PTCH1 is a cognate receptor for the hedgehog signaling pathway. The trans-interaction of CHL1 with PTCH1 three mammalian hedgehog family members sonic hedgehog promotes neuronal survival in cultures of dissociated cerebellar granule (SHH), desert hedgehog (DHH) and indian hedgehog (IHH), cells and of organotypic cerebellar slices. An inhibitor of the PTCH1- which act as morphogens and function as signaling molecules by regulated hedgehog signal transducer, smoothened (SMO), and binding to PTCH1 (for reviews and references therein, see Jenkins, inhibitors of RhoA and Rho-associated kinase (ROCK) 1 and 2 2009; Robbins et al., 2012; Briscoe and Thérond, 2013). -
A New Trick for an Old Lipid Cholesterol Can Regulate the Hedgehog Signalling Pathway by Directly Binding to a Receptor on the Cell Surface
INSIGHT SIGNALLING A new trick for an old lipid Cholesterol can regulate the Hedgehog signalling pathway by directly binding to a receptor on the cell surface. HAYLEY SHARPE Hedgehog, a transmembrane protein called Related research article Luchetti G, Sircar Patched, and a transmembrane receptor protein R, Kong JH, Nachtergaele S, Sagner A, called Smoothened. In the absence of Hedge- Byrne EFX, Covey DF, Siebold C, Rohatgi R. hog, Patched inhibits Smoothened. However, when Hedgehog binds to Patched, this inhibi- 2016. Cholesterol activates the G-protein tion is blocked and Smoothened is able to acti- coupled receptor Smoothened to promote vate other Hedgehog pathway components morphogenetic signaling. eLife 5:e20304. inside the cell. It is thought that Patched and doi: 10.7554/eLife.20304 Smoothened communicate using a small mole- cule rather than by direct contact (Taipale et al., 2002), but it is not clear exactly how this works. Smoothened possesses two sites at which holesterol is a lipid molecule that is a small molecules are able to bind: one is in its vital component of all animal cell mem- transmembrane domain region and the other is C branes. It provides structural integrity, in its cysteine-rich domain on the external sur- which is needed for the membrane to be an face of the cell. A similar cysteine-rich domain is effective barrier, and is also required for the pro- found in several other proteins, where it is duction of hormones and vitamin D. These roles known to be able to bind to lipids (Bazan et al., mean the production and transport of choles- 2009). -
Atlas Journal
Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Solid Tumours Cancer-Prone Deep Insight Portal Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 12, Number 6, Nov-Dec 2008 Previous Issue / Next Issue Genes BCL8 (B-cell CLL/lymphoma 8) (15q11). Silvia Rasi, Gianluca Gaidano. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 781-784. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/BCL8ID781ch15q11.html CDC25A (Cell division cycle 25A) (3p21). Dipankar Ray, Hiroaki Kiyokawa. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 785-791. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/CDC25AID40004ch3p21.html CDC73 (cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)) (1q31.2). Leslie Farber, Bin Tean Teh. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 792-797. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/CDC73D181ch1q31.html EIF3C (eukaryotic translation initiation factor 3, subunit C) (16p11.2). Daniel R Scoles. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 798-802. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/EIF3CID44187ch16p11.html ELAC2 (elaC homolog 2 (E. coli)) (17p11.2). Yang Chen, Sean Tavtigian, Donna Shattuck. Atlas Genet Cytogenet Oncol Haematol 2008; 12 (6): 803-806. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/ELAC2ID40437ch17p11.html FOXM1 (forkhead box M1) (12p13). Jamila Laoukili, Monica Alvarez Fernandez, René H Medema. -
Underestimated PTCH1 Mutation Rate in Sporadic Keratocystic Odontogenic Tumors Q
Oral Oncology 51 (2015) 40–45 Contents lists available at ScienceDirect Oral Oncology journal homepage: www.elsevier.com/locate/oraloncology Underestimated PTCH1 mutation rate in sporadic keratocystic odontogenic tumors q Jiafei Qu a, Feiyan Yu a, Yingying Hong a, Yanyan Guo a, Lisha Sun b, Xuefen Li b, Jianyun Zhang a, ⇑ ⇑ Heyu Zhang b, Ruirui Shi b, Feng Chen b, , Tiejun Li a, a Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China b Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China article info summary Article history: Objectives: Keratocystic odontogenic tumors (KCOTs) are benign cystic lesions of the jaws that occur spo- Received 11 July 2014 radically in isolation or in association with nevoid basal cell carcinoma syndrome (NBCCS). The protein Received in revised form 29 August 2014 patched homolog 1 gene (PTCH1) is associated with NBCCS development and tumor genesis associated Accepted 26 September 2014 with this syndrome. However, previous studies have revealed that more than 85% of syndromic KCOTs Available online 18 November 2014 and less than 30% of sporadic KCOTs harbor PTCH1 mutations. The significantly lower PTCH1 mutation rates observed in sporadic KCOTs suggest that they serve a minor role in pathogenesis. We aimed to Keywords: discern the importance of PTCH1 mutations in sporadic KCOTs. PTCH1 Materials and methods: PTCH1 mutational analysis was performed with 19 new sporadic KCOT cases by Mutation Keratocystic odontogenic tumors direct sequencing of epithelial lining samples separated from fibrous capsules. Using this approach, we further reexamined 9 sporadic KCOTs that were previously reported to lack PTCH1 mutations by our group. -
Nevoid Basal Cell Carcinoma Syndrome and Non-Hodgkin's
Nevoid Basal Cell Carcinoma Syndrome and Non-Hodgkin’s Lymphoma CPT Beth A. Schulz-Butulis, MC, USAR, Fort Sam Houston, Texas MAJ Robert Gilson, MC, USAF, Fort Sam Houston, Texas MAJ Mary Farley, MC, USAR, Fort Sam Houston, Texas COL James H. Keeling, MC, USA, Fort Sam Houston, Texas Nevoid basal cell carcinoma syndrome (NBCCS) is a hereditary disorder with a predilection for nu- merous basal cell carcinomas in addition to odon- togenic keratocysts, palmoplantar pitting, and skeletal malformations. NBCCS has been associ- ated with a number of benign and malignant neo- plasms. We report the first case of NBCCS in as- sociation with non-Hodgkin’s lymphoma. evoid basal cell carcinoma syndrome (NBCCS), also known as basal cell nevus syn- drome, Gorlin syndrome, Gorlin-Goltz syn- N 1,2 drome, or fifth phacomatosis, is an autosomal dom- inant disease linked to chromosome 9q22.3-q31.3-5 It is a progressive degenerative multisystem disease FIGURE 1. The back of a patient shows multiple basal characterized by a predisposition to develop basal cell cell carcinomas. (Photograph courtesy of MAJ Thomas carcinomas (BCCs) of the skin, palmoplantar pitting, Hirota, MC, USA.) odontogenic keratocysts, bifid ribs, kyphoscoliosis, short fourth metacarpals, ocular abnormalities, calci- the first known report of non-Hodgkin’s lymphoma fied dural folds, endocrine abnormalities, and various associated with NBCCS. internal neoplasms.1,2 Internal neoplasms that have been reported in asso- Case Report ciation with NBCCS include medulloblastoma,6 cran- A 54-year-old white man presented with numerous iopharyngioma,7 meningioma,2 astrocytoma,8 oligo- basal cell cancers. -
Characterization of Two Patched Receptors for the Vertebrate Hedgehog Protein Family
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 13630–13634, November 1998 Cell Biology Characterization of two patched receptors for the vertebrate hedgehog protein family DAVID CARPENTER*, DONNA M. STONE†,JENNIFER BRUSH‡,ANNE RYAN§,MARK ARMANINI†,GRETCHEN FRANTZ§, ARNON ROSENTHAL†, AND FREDERIC J. DE SAUVAGE*¶ Departments of *Molecular Oncology, ‡Molecular Biology, §Pathology, and †Neuroscience, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080 Communicated by David V. Goeddel, Tularik, Inc., South San Francisco, CA, September 24, 1998 (received for review June 12, 1998) ABSTRACT The multitransmembrane protein Patched mammalian hedgehogs or whether ligand-specific components (PTCH) is the receptor for Sonic Hedgehog (Shh), a secreted exist. Interestingly, a second murine PTCH gene, PTCH2, was molecule implicated in the formation of embryonic structures isolated recently (25) but its function as a hedgehog receptor and in tumorigenesis. Current models suggest that binding of has not been established. To characterize PTCH2 and com- Shh to PTCH prevents the normal inhibition of the seven- pare it with PTCH with respect to the biological function of the transmembrane-protein Smoothened (SMO) by PTCH. Ac- various hedgehog family members, we isolated the human cording to this model, the inhibition of SMO signaling is PTCH2 gene. Binding analysis shows that both PTCH and relieved after mutational inactivation of PTCH in the basal PTCH2 bind to all three hedgehog ligands with similar affinity. cell nevus syndrome. Recently, PTCH2, a molecule with Furthermore PTCH2 interacts with SMO, suggesting that it sequence homology to PTCH, has been identified. To charac- can form a functional multicomponent hedgehog receptor terize both PTCH molecules with respect to the various complex similar to PTCH-SMO. -
Genetic Analysis of Gorlin Syndrome Using a Multiplex PCR Gene Panel, and Its Potential Clinical Utility for Liquid Biopsy
Genetic Analysis of Gorlin Syndrome Using a Multiplex PCR Gene Panel, and Its Potential Clinical Utility for Liquid Biopsy Yuriko Nakamura Tokyo Dental College: Tokyo Shika Daigaku Shoko Onodera Tokyo Dental College: Tokyo Shika Daigaku Kazuhiko Hashimoto Tokyo Dental College Ichikawa General Hospital: Tokyo Shika Daigaku Ichikawa Sogo Byoin Masayuki Takano Tokyo Dental College: Tokyo Shika Daigaku Akira Katakura Tokyo Dental College: Tokyo Shika Daigaku Takeshi Nomura Tokyo Dental College: Tokyo Shika Daigaku Toshifumi Azuma ( [email protected] ) Tokyo Dental College https://orcid.org/0000-0003-0673-3400 Research Keywords: Genetic testing, NGS panel, Genetic diagnosis, Pathogenic gene prediction, Liquid biopsy, Next- generation sequencing (NGS) Posted Date: July 13th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-676760/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract Background: Gorlin syndrome is an autosomal dominant, rare disease caused by mutations in PTCH1, PTCH2, and SUFU with various symptoms in multiple organs making early diagnosis challenging. In this study, we generated a Gorlin syndrome gene panel that could help to overcome the diculties in diagnosing Gorlin syndrome using a single test. Results: This gene panel is time- and cost-ecient and highly reliable with a high-quality score of 30, on- target ratio, and coverage depth, and could detect more mutations than whole-exome sequencing of the same patient. Although the current in silico prediction tools have a limited genetic database of gene mutations in rare hereditary diseases, ve prediction tools were used to identify pathological mutations. -
Interaction of the Primordial Germ Cell-Specific Protein C2EIP With
Zuo et al. Cell Death and Disease (2018) 9:497 DOI 10.1038/s41419-018-0557-2 Cell Death & Disease ARTICLE Open Access Interaction of the primordial germ cell- specific protein C2EIP with PTCH2 directs differentiation of embryonic stem cells via HH signaling activation Qisheng Zuo1,KaiJin1, Jiuzhou Song2, Yani Zhang1, Guohong Chen1 and Bichun Li1 Abstract Although many marker genes for germ cell differentiation have been identified, genes that specifically regulate primordial germ cell (PGC) generation are more difficult to determine. In the current study, we confirmed that C2EIP is a PGC marker gene that regulates differentiation by influencing the expression of pluripotency-associated genes such as Oct4 and Sox2. Knockout of C2EIP during embryonic development reduced PGC generation efficiency 1.5-fold, whereas C2EIP overexpression nearly doubled the generation efficiency both in vitro and in vivo. C2EIP encodes a cytoplasmic protein that interacted with PTCH2 at the intracellular membrane, promoted PTCH2 ubiquitination, activated the Hedgehog (HH) signaling pathway via competitive inhibition of the GPCR-like protein SMO, and positively regulated PGC generation. Activation and expression of C2EIP are regulated by the transcription factor STAT1, histone acetylation, and promoter methylation. Our data suggest that C2EIP is a novel, specific indicator of PGC generation whose gene product regulates embryonic stem cell differentiation by activating the HH signaling pathway fi 1234567890():,; 1234567890():,; via PTCH2 modi cation. Introduction re-programming them to differentiate into spermatogo- – Primordial germ cells (PGC) can be used for therapeutic nial stem cells (SSC)7 10. Moreover, RNAi-mediated purposes and genetic modification as an alternative to knockout of LIN28 downregulates expression of multi- + embryonic stem cells1,2.