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Sonnert ND, Rosen CE, Ghazi AR, Franzosa EA, Duncan-Lowey B, González-Hernández JA, Huck JD, Yang Y, Dai Y, Rice TA, Nguyen MT, Song D, Cao Y, Martin AL, Bielecka AA, Fischer S, Guan C, Oh J, Huttenhower C, Ring AM, Palm NW. A host-microbiota interactome reveals extensive transkingdom connectivity. Nature 2024; 628:171-179. [PMID: 38509360 DOI: 10.1038/s41586-024-07162-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 02/05/2024] [Indexed: 03/22/2024]
Abstract
The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown1-3. Classical pathogens often invade host tissues and modulate immune responses through interactions with human extracellular and secreted proteins (the 'exoproteome'). Commensal microorganisms may also facilitate niche colonization and shape host biology by engaging host exoproteins; however, direct exoproteome-microbiota interactions remain largely unexplored. Here we developed and validated a novel technology, BASEHIT, that enables proteome-scale assessment of human exoproteome-microbiome interactions. Using BASEHIT, we interrogated more than 1.7 million potential interactions between 519 human-associated bacterial strains from diverse phylogenies and tissues of origin and 3,324 human exoproteins. The resulting interactome revealed an extensive network of transkingdom connectivity consisting of thousands of previously undescribed host-microorganism interactions involving 383 strains and 651 host proteins. Specific binding patterns within this network implied underlying biological logic; for example, conspecific strains exhibited shared exoprotein-binding patterns, and individual tissue isolates uniquely bound tissue-specific exoproteins. Furthermore, we observed dozens of unique and often strain-specific interactions with potential roles in niche colonization, tissue remodelling and immunomodulation, and found that strains with differing host interaction profiles had divergent interactions with host cells in vitro and effects on the host immune system in vivo. Overall, these studies expose a previously unexplored landscape of molecular-level host-microbiota interactions that may underlie causal effects of indigenous microorganisms on human health and disease.
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Affiliation(s)
- Nicole D Sonnert
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Connor E Rosen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew R Ghazi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - John D Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yi Yang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tyler A Rice
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mytien T Nguyen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Deguang Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yiyun Cao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anjelica L Martin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Agata A Bielecka
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Suzanne Fischer
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron M Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
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2
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Huber LT, Kraus JM, Ezić J, Wanli A, Groth M, Laban S, Hoffmann TK, Wollenberg B, Kestler HA, Brunner C. Liquid biopsy: an examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for predictive molecular tumor markers. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:422-446. [PMID: 37455825 PMCID: PMC10344902 DOI: 10.37349/etat.2023.00143] [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: 11/16/2022] [Accepted: 03/01/2023] [Indexed: 07/18/2023] Open
Abstract
Aim Recently, a tumor cell-platelet interaction was identified in different tumor entities, resulting in a transfer of tumor-derived RNA into platelets, named further "tumor-educated platelets (TEP)". The present pilot study aims to investigate whether such a tumor-platelet transfer of RNA occurs also in patients suffering from head and neck squamous cell carcinoma (HNSCC). Methods Sequencing analysis of RNA derived from platelets of tumor patients (TPs) and healthy donors (HDs) were performed. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used for verification of differentially expressed genes in platelets from TPs and HDs in a second cohort of patients and HDs. Data were analyzed by applying bioinformatic tools. Results Sequencing of RNA derived from the tumor as well as from platelets of TPs and HDs revealed 426 significantly differentially existing RNA, at which 406 RNA were more and 20 RNA less abundant in platelets from TPs in comparison to that of HDs. In TPs' platelets, abundantly existing RNA coding for 49 genes were detected, characteristically expressed in epithelial cells and RNA, the products of which are involved in tumor progression. Applying bioinformatic tools and verification on a second TP/HD cohort, collagen type I alpha 1 chain (COL1A1) and zinc finger protein 750 (ZNF750) were identified as the strongest potentially platelet-RNA-sequencing (RNA-seq)-based biomarkers for HNSCC. Conclusions These results indicate a transfer of tumor-derived messenger RNA (mRNA) into platelets of HNSCC patients. Therefore, analyses of a patient's platelet RNA could be an efficient option for liquid biopsy in order to diagnose HNSCC or to monitor tumorigenesis as well as therapeutic responses at any time and in real time.
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Affiliation(s)
- Lisa T. Huber
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Jasmin Ezić
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Amin Wanli
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Marco Groth
- Leibniz Institute of Aging – Fritz Lipmann Institute, CF DNA sequencing, 07745 Jena, Germany
| | - Simon Laban
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Thomas K. Hoffmann
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Barbara Wollenberg
- Clinic for Otorhinolaryngology, Head and Neck Surgery, Technical University of Munich, 80333 Munich, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
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3
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Torres-Sánchez M, Wilkinson M, Gower DJ, Creevey CJ, San Mauro D. Insights into the skin of caecilian amphibians from gene expression profiles. BMC Genomics 2020; 21:515. [PMID: 32718305 PMCID: PMC7385959 DOI: 10.1186/s12864-020-06881-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background Gene expression profiles can provide insights into the molecular machinery behind tissue functions and, in turn, can further our understanding of environmental responses, and developmental and evolutionary processes. During vertebrate evolution, the skin has played a crucial role, displaying a wide diversity of essential functions. To unravel the molecular basis of skin specialisations and adaptations, we compared gene expression in the skin with eight other tissues in a phylogenetically and ecologically diverse species sample of one of the most neglected vertebrate groups, the caecilian amphibians (order Gymnophiona). Results The skin of the five studied caecilian species showed a distinct gene expression profile reflecting its developmental origin and showing similarities to other epithelial tissues. We identified 59 sequences with conserved enhanced expression in the skin that might be associated with caecilian dermal specialisations. Some of the up-regulated genes shared expression patterns with human skin and potentially are involved in skin functions across vertebrates. Variation trends in gene expression were detected between mid and posterior body skin suggesting different functions between body regions. Several candidate biologically active peptides were also annotated. Conclusions Our study provides the first atlas of differentially expressed sequences in caecilian tissues and a baseline to explore the molecular basis of the skin functions in caecilian amphibians, and more broadly in vertebrates.
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Affiliation(s)
- María Torres-Sánchez
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain. .,Present address: Department of Biology, University of Florida, Gainesville, Florida, 32611, USA.
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Christopher J Creevey
- Institute for Global Food Security, Queen's University Belfast, University Road, Belfast, Northern Ireland, BT7 1NN, UK
| | - Diego San Mauro
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain
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Alibardi L. Immunohistochemical localization of a proto‐cadherin fat tumour‐suppressor homolog in the regenerating tail of lizard suggests a role in apical growth control. ACTA ZOOL-STOCKHOLM 2019. [DOI: 10.1111/azo.12290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab Padova, Department of Biology University of Bologna Bologna Italy
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Dang TT, Westcott JM, Maine EA, Kanchwala M, Xing C, Pearson GW. ΔNp63α induces the expression of FAT2 and Slug to promote tumor invasion. Oncotarget 2017; 7:28592-611. [PMID: 27081041 PMCID: PMC5053748 DOI: 10.18632/oncotarget.8696] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/28/2016] [Indexed: 01/29/2023] Open
Abstract
Tumor invasion can be induced by changes in gene expression that alter cell phenotype. The transcription factor ΔNp63α promotes basal-like breast cancer (BLBC) migration by inducing the expression of the mesenchymal genes Slug and Axl, which confers cells with a hybrid epithelial/mesenchymal state. However, the extent of the ΔNp63α regulated genes that support invasive behavior is not known. Here, using gene expression analysis, ChIP-seq, and functional testing, we find that ΔNp63α promotes BLBC motility by inducing the expression of the atypical cadherin FAT2, the vesicular binding protein SNCA, the carbonic anhydrase CA12, the lipid binding protein CPNE8 and the kinase NEK1, along with Slug and Axl. Notably, lung squamous cell carcinoma migration also required ΔNp63α dependent FAT2 and Slug expression, demonstrating that ΔNp63α promotes migration in multiple tumor types by inducing mesenchymal and non-mesenchymal genes. ΔNp63α activation of FAT2 and Slug influenced E-cadherin localization to cell-cell contacts, which can restrict spontaneous cell movement. Moreover, live-imaging of spheroids in organotypic culture demonstrated that ΔNp63α, FAT2 and Slug were essential for the extension of cellular protrusions that initiate collective invasion. Importantly, ΔNp63α is co-expressed with FAT2 and Slug in patient tumors and the elevated expression of ΔNp63α, FAT2 and Slug correlated with poor patient outcome. Together, these results reveal how ΔNp63α promotes cell migration by directly inducing the expression of a cohort of genes with distinct cellular functions and suggest that FAT2 is a new regulator of collective invasion that may influence patient outcome.
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Affiliation(s)
- Tuyen T Dang
- Harold C. Simmons Cancer Center, University of Texas, Southwestern Medical Center, Dallas, TX 75390-8807, USA
| | - Jill M Westcott
- Harold C. Simmons Cancer Center, University of Texas, Southwestern Medical Center, Dallas, TX 75390-8807, USA
| | - Erin A Maine
- Harold C. Simmons Cancer Center, University of Texas, Southwestern Medical Center, Dallas, TX 75390-8807, USA
| | - Mohammed Kanchwala
- McDermott Center for Human Growth and Disease, University of Texas, Southwestern Medical Center, Dallas, TX 75390-8807, USA
| | - Chao Xing
- McDermott Center for Human Growth and Disease, University of Texas, Southwestern Medical Center, Dallas, TX 75390-8807, USA
| | - Gray W Pearson
- Harold C. Simmons Cancer Center, University of Texas, Southwestern Medical Center, Dallas, TX 75390-8807, USA.,Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, TX 75390-8807, USA
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Cohen AS, Khalil FK, Welsh EA, Schabath MB, Enkemann SA, Davis A, Zhou JM, Boulware DC, Kim J, Haura EB, Morse DL. Cell-surface marker discovery for lung cancer. Oncotarget 2017; 8:113373-113402. [PMID: 29371917 PMCID: PMC5768334 DOI: 10.18632/oncotarget.23009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/11/2017] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths in the United States. Novel lung cancer targeted therapeutic and molecular imaging agents are needed to improve outcomes and enable personalized care. Since these agents typically cannot cross the plasma membrane while carrying cytotoxic payload or imaging contrast, discovery of cell-surface targets is a necessary initial step. Herein, we report the discovery and characterization of lung cancer cell-surface markers for use in development of targeted agents. To identify putative cell-surface markers, existing microarray gene expression data from patient specimens were analyzed to select markers with differential expression in lung cancer compared to normal lung. Greater than 200 putative cell-surface markers were identified as being overexpressed in lung cancers. Ten cell-surface markers (CA9, CA12, CXorf61, DSG3, FAT2, GPR87, KISS1R, LYPD3, SLC7A11 and TMPRSS4) were selected based on differential mRNA expression in lung tumors vs. non-neoplastic lung samples and other normal tissues, and other considerations involving known biology and targeting moieties. Protein expression was confirmed by immunohistochemistry (IHC) staining and scoring of patient tumor and normal tissue samples. As further validation, marker expression was determined in lung cancer cell lines using microarray data and Kaplan–Meier survival analyses were performed for each of the markers using patient clinical data. High expression for six of the markers (CA9, CA12, CXorf61, GPR87, LYPD3, and SLC7A11) was significantly associated with worse survival. These markers should be useful for the development of novel targeted imaging probes or therapeutics for use in personalized care of lung cancer patients.
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Affiliation(s)
- Allison S Cohen
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Farah K Khalil
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric A Welsh
- Biomedical Informatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Steven A Enkemann
- Molecular Genomics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Andrea Davis
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jun-Min Zhou
- Biostatistics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David C Boulware
- Biostatistics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jongphil Kim
- Department of Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Oncologic Sciences, College of Medicine, University of South Florida, Tampa, FL, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - David L Morse
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Oncologic Sciences, College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Physics, College of Arts and Sciences, University of South Florida, Tampa, FL, USA
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Li Y, Kang K, Krahn JM, Croutwater N, Lee K, Umbach DM, Li L. A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data. BMC Genomics 2017; 18:508. [PMID: 28673244 PMCID: PMC5496318 DOI: 10.1186/s12864-017-3906-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/27/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The Cancer Genome Atlas (TCGA) has generated comprehensive molecular profiles. We aim to identify a set of genes whose expression patterns can distinguish diverse tumor types. Those features may serve as biomarkers for tumor diagnosis and drug development. METHODS Using RNA-seq expression data, we undertook a pan-cancer classification of 9,096 TCGA tumor samples representing 31 tumor types. We randomly assigned 75% of samples into training and 25% into testing, proportionally allocating samples from each tumor type. RESULTS We could correctly classify more than 90% of the test set samples. Accuracies were high for all but three of the 31 tumor types, in particular, for READ (rectum adenocarcinoma) which was largely indistinguishable from COAD (colon adenocarcinoma). We also carried out pan-cancer classification, separately for males and females, on 23 sex non-specific tumor types (those unrelated to reproductive organs). Results from these gender-specific analyses largely recapitulated results when gender was ignored. Remarkably, more than 80% of the 100 most discriminative genes selected from each gender separately overlapped. Genes that were differentially expressed between genders included BNC1, FAT2, FOXA1, and HOXA11. FOXA1 has been shown to play a role for sexual dimorphism in liver cancer. The differentially discriminative genes we identified might be important for the gender differences in tumor incidence and survival. CONCLUSIONS We were able to identify many sets of 20 genes that could correctly classify more than 90% of the samples from 31 different tumor types using TCGA RNA-seq data. This accuracy is remarkable given the number of the tumor types and the total number of samples involved. We achieved similar results when we analyzed 23 non-sex-specific tumor types separately for males and females. We regard the frequency with which a gene appeared in those sets as measuring its importance for tumor classification. One third of the 50 most frequently appearing genes were pseudogenes; the degree of enrichment may be indicative of their importance in tumor classification. Lastly, we identified a few genes that might play a role in sexual dimorphism in certain cancers.
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Affiliation(s)
- Yuanyuan Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, 27709, USA
| | - Kai Kang
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, 27709, USA
| | - Juno M Krahn
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Durham, NC, 27709, USA
| | - Nicole Croutwater
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, 27709, USA
| | - Kevin Lee
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, 27709, USA
| | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, 27709, USA
| | - Leping Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, 27709, USA.
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Ahmed AF, de Bock CE, Lincz LF, Pundavela J, Zouikr I, Sontag E, Hondermarck H, Thorne RF. FAT1 cadherin acts upstream of Hippo signalling through TAZ to regulate neuronal differentiation. Cell Mol Life Sci 2015; 72:4653-69. [PMID: 26104008 PMCID: PMC11113810 DOI: 10.1007/s00018-015-1955-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 12/19/2022]
Abstract
The Hippo pathway is emerging as a critical nexus that balances self-renewal of progenitors against differentiation; however, upstream elements in vertebrate Hippo signalling are poorly understood. High expression of Fat1 cadherin within the developing neuroepithelium and the manifestation of severe neurological phenotypes in Fat1-knockout mice suggest roles in neurogenesis. Using the SH-SY5Y model of neuronal differentiation and employing gene silencing techniques, we show that FAT1 acts to control neurite outgrowth, also driving cells towards terminal differentiation via inhibitory effects on proliferation. FAT1 actions were shown to be mediated through Hippo signalling where it activated core Hippo kinase components and antagonised functions of the Hippo effector TAZ. Suppression of FAT1 promoted the nucleocytoplasmic shuttling of TAZ leading to enhanced transcription of the Hippo target gene CTGF together with accompanying increases in nuclear levels of Smad3. Silencing of TAZ reversed the effects of FAT1 depletion thus connecting inactivation of TAZ-TGFbeta signalling with Hippo signalling mediated through FAT1. These findings establish FAT1 as a new upstream Hippo element regulating early stages of differentiation in neuronal cells.
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Affiliation(s)
- Abdulrzag F Ahmed
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Charles E de Bock
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Lisa F Lincz
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
- Hunter Haematology Research Group, Calvary Mater Newcastle Hospital, Waratah, NSW, 2298, Australia
| | - Jay Pundavela
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Ihssane Zouikr
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Estelle Sontag
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Priority Research Centre for Translational Neuroscience and Mental Health, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Rick F Thorne
- Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, 2258, Australia.
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Yadav DS, Chattopadhyay I, Verma A, Devi TR, Singh LC, Sharma JD, Kataki AC, Saxena S, Kapur S. A pilot study evaluating genetic alterations that drive tobacco- and betel quid-associated oral cancer in Northeast India. Tumour Biol 2014; 35:9317-30. [PMID: 24943687 DOI: 10.1007/s13277-014-2222-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 06/10/2014] [Indexed: 12/19/2022] Open
Abstract
The susceptibility of an individual to oral cancer is mediated by genetic factors and carcinogen-exposure behaviors such as betel quid chewing, tobacco use, and alcohol consumption. This pilot study was aimed to identify the genetic alteration in 100 bp upstream and downstream flanking regions in addition to the exonic regions of 169 cancer-associated genes by using Next Generation sequencing with aim to elucidate the molecular pathogenesis of tobacco- and betel quid-associated oral cancer of Northeast India. To understand the role of chemical compounds present in tobacco and betel quid associated with the progression of oral cancer, single nucleotide polymorphisms (SNPs) and insertion and deletion (Indels) found in this study were analyzed for their association with chemical compounds found in tobacco and betel quid using Comparative Toxogenomic Database. Genes (AR, BRCA1, IL8, and TP53) with novel SNP were found to be associated with arecoline which is the major component of areca nut. Genes (BARD1, BRCA2, CCND2, IGF1R, MSH6, and RASSF1) with novel deletion and genes (APC, BRMS1, CDK2AP1, CDKN2B, GAS1, IGF1R, and RB1) with novel insertion were found to be associated with aflatoxin B1 which is produced by fermented areca nut. Genes (ADH6, APC, AR, BARD1, BRMS1, CDKN1A, E2F1, FGFR4, FLNC, HRAS, IGF1R, IL12B, IL8, NBL1, STAT5B, and TP53) with novel SNP were found to be associated with aflatoxin B1. Genes (ATM, BRCA1, CDKN1A, EGFR, IL8, and TP53) with novel SNP were found to be associated with tobacco specific nitrosamines.
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Affiliation(s)
- Dhirendra Singh Yadav
- National Institute of Pathology, Indian Council of Medical Research, Room No 206, Safdarjung Hospital Campus, New Delhi, 110029, India,
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Sadeqzadeh E, de Bock CE, Thorne RF. Sleeping giants: emerging roles for the fat cadherins in health and disease. Med Res Rev 2013; 34:190-221. [PMID: 23720094 DOI: 10.1002/med.21286] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The vertebrate Fat cadherins comprise a small gene family of four members, Fat1-Fat4, all closely related in structure to Drosophila ft and ft2. Over the past decade, knock-out mouse studies, genetic manipulation, and large sequencing projects has aided our understanding of the function of vertebrate Fat cadherins in tissue development and disease. The majority of studies of this family have focused on Fat1, with evidence now showing it can bind enable (ENA)/Vasodilator-stimulated phosphoprotein (VASP), β-catenin and Atrophin proteins to influence cell polarity and motility; HOMER-1 and HOMER-3 proteins to regulate actin accumulation in neuronal synapses; and scribble to influence the Hippo signaling pathway. Fat2 and Fat3 can regulate cell migration in a tissue specific manner and Fat4 appears to influence both planar cell polarity and Hippo signaling recapitulating the activity of Drosophila ft. Knowledge about the exact downstream signaling pathways activated by each family member remains in its infancy, but it is becoming clearer that they have tissue specific and redundant roles in development and may be lost or gained in cancer. In this review, we summarize the recent progress on understanding the role of the Fat cadherin family, integrating the current knowledge of molecular interactions and tissue distributions, together with the accumulating evidence of their changed expression in human disease. The latter is now beginning to promote interest in these molecules as both biomarkers and new targets for therapeutic intervention.
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Affiliation(s)
- Elham Sadeqzadeh
- Cancer Research Unit, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, 2308, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
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Voutsadakis IA, Cairoli A. A critical review of the molecular pathophysiology of lenalidomide sensitivity in 5q − myelodysplastic syndromes. Leuk Lymphoma 2011; 53:779-88. [DOI: 10.3109/10428194.2011.623255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Knockdown of Fat2 by siRNA inhibits the migration of human squamous carcinoma cells. J Dermatol Sci 2008; 51:207-10. [DOI: 10.1016/j.jdermsci.2008.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 04/14/2008] [Accepted: 04/16/2008] [Indexed: 11/21/2022]
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