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Taylor MA, Kandyba E, Halliwill K, Delrosario R, Khoroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam SR, Mirzoeva OK, Akhurst RJ, Balmain A. Stem-cell states converge in multistage cutaneous squamous cell carcinoma development. Science 2024; 384:eadi7453. [PMID: 38815020 DOI: 10.1126/science.adi7453] [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: 05/15/2023] [Accepted: 04/05/2024] [Indexed: 06/01/2024]
Abstract
Stem cells play a critical role in cancer development by contributing to cell heterogeneity, lineage plasticity, and drug resistance. We created gene expression networks from hundreds of mouse tissue samples (both normal and tumor) and integrated these with lineage tracing and single-cell RNA-seq, to identify convergence of cell states in premalignant tumor cells expressing markers of lineage plasticity and drug resistance. Two of these cell states representing multilineage plasticity or proliferation were inversely correlated, suggesting a mutually exclusive relationship. Treatment of carcinomas in vivo with chemotherapy repressed the proliferative state and activated multilineage plasticity whereas inhibition of differentiation repressed plasticity and potentiated responses to cell cycle inhibitors. Manipulation of this cell state transition point may provide a source of potential combinatorial targets for cancer therapy.
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Affiliation(s)
- Mark A Taylor
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Clinical Research Centre, Medical University of Bialystok, Bialystok 15-089, Poland
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kyle Halliwill
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- AbbVie, South San Francisco, CA 94080, USA
| | - Reyno Delrosario
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matvei Khoroshkin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Hani Goodarzi
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94518, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94518, USA
- Arc Institute, Palo Alto, CA 94304, USA
| | - David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94518, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA 94518, USA
| | - Yun Rose Li
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Cancer Genetics & Epigenetics, City of Hope National Medical Center, Duarte, CA 91010, USA
- Division of Quantitative Medicine & Systems Biology, Translational Genomics Research Institute, Phoenix, CA 85004, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Saumya R Bollam
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 94518, USA
| | - Olga K Mirzoeva
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rosemary J Akhurst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94518, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94518, USA
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Mendiburu‐Eliçabe M, García‐Sancha N, Corchado‐Cobos R, Martínez‐López A, Chang H, Hua Mao J, Blanco‐Gómez A, García‐Casas A, Castellanos‐Martín A, Salvador N, Jiménez‐Navas A, Pérez‐Baena MJ, Sánchez‐Martín MA, Abad‐Hernández MDM, Carmen SD, Claros‐Ampuero J, Cruz‐Hernández JJ, Rodríguez‐Sánchez CA, García‐Cenador MB, García‐Criado FJ, Vicente RS, Castillo‐Lluva S, Pérez‐Losada J. NCAPH drives breast cancer progression and identifies a gene signature that predicts luminal a tumour recurrence. Clin Transl Med 2024; 14:e1554. [PMID: 38344872 PMCID: PMC10859882 DOI: 10.1002/ctm2.1554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/01/2024] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Luminal A tumours generally have a favourable prognosis but possess the highest 10-year recurrence risk among breast cancers. Additionally, a quarter of the recurrence cases occur within 5 years post-diagnosis. Identifying such patients is crucial as long-term relapsers could benefit from extended hormone therapy, while early relapsers might require more aggressive treatment. METHODS We conducted a study to explore non-structural chromosome maintenance condensin I complex subunit H's (NCAPH) role in luminal A breast cancer pathogenesis, both in vitro and in vivo, aiming to identify an intratumoural gene expression signature, with a focus on elevated NCAPH levels, as a potential marker for unfavourable progression. Our analysis included transgenic mouse models overexpressing NCAPH and a genetically diverse mouse cohort generated by backcrossing. A least absolute shrinkage and selection operator (LASSO) multivariate regression analysis was performed on transcripts associated with elevated intratumoural NCAPH levels. RESULTS We found that NCAPH contributes to adverse luminal A breast cancer progression. The intratumoural gene expression signature associated with elevated NCAPH levels emerged as a potential risk identifier. Transgenic mice overexpressing NCAPH developed breast tumours with extended latency, and in Mouse Mammary Tumor Virus (MMTV)-NCAPHErbB2 double-transgenic mice, luminal tumours showed increased aggressiveness. High intratumoural Ncaph levels correlated with worse breast cancer outcome and subpar chemotherapy response. A 10-gene risk score, termed Gene Signature for Luminal A 10 (GSLA10), was derived from the LASSO analysis, correlating with adverse luminal A breast cancer progression. CONCLUSIONS The GSLA10 signature outperformed the Oncotype DX signature in discerning tumours with unfavourable outcomes, previously categorised as luminal A by Prediction Analysis of Microarray 50 (PAM50) across three independent human cohorts. This new signature holds promise for identifying luminal A tumour patients with adverse prognosis, aiding in the development of personalised treatment strategies to significantly improve patient outcomes.
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Mendiburu-Eliçabe M, García-Sancha N, Corchado-Cobos R, Martínez-López A, Chang H, Mao JH, Blanco-Gómez A, García-Casas A, Castellanos-Martín A, Salvador N, Jiménez-Navas A, Pérez-Baena MJ, Sánchez-Martín MA, Abad-Hernández MDM, Del Carmen S, Claros-Ampuero J, Cruz-Hernández JJ, Rodríguez-Sánchez CA, García-Cenador MB, García-Criado FJ, Vicente RS, Castillo-Lluva S, Pérez-Losada J. NCAPH Drives Breast Cancer Progression and Identifies a Gene Signature that Predicts Luminal A Tumor Recurrence. RESEARCH SQUARE 2023:rs.3.rs-3231230. [PMID: 37886490 PMCID: PMC10602143 DOI: 10.21203/rs.3.rs-3231230/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Despite their generally favorable prognosis, luminal A tumors paradoxically pose the highest ten-year recurrence risk among breast cancers. From those that relapse, a quarter of them do it within five years after diagnosis. Identifying such patients is crucial, as long-term relapsers could benefit from extended hormone therapy, whereas early relapsers may require aggressive treatment. In this study, we demonstrate that NCAPH plays a role in the pathogenesis of luminal A breast cancer, contributing to its adverse progression in vitro and in vivo. Furthermore, we reveal that a signature of intratumoral gene expression, associated with elevated levels of NCAPH, serves as a potential marker to identify patients facing unfavorable progression of luminal A breast cancer. Indeed, transgenic mice overexpressing NCAPH generated breast tumors with long latency, and in MMTV-NCAPH/ErbB2+ double-transgenic mice, the luminal tumors formed were more aggressive. In addition, high intratumoral levels of Ncaph were associated with worse breast cancer evolution and poor response to chemotherapy in a cohort of genetically heterogeneous transgenic mice generated by backcrossing. In this cohort of mice, we identified a series of transcripts associated with elevated intratumoral levels of NCAPH, which were linked to adverse progression of breast cancer in both mice and humans. Utilizing the Least Absolute Shrinkage and Selection Operator (LASSO) multivariate regression analysis on this series of transcripts, we derived a ten-gene risk score. This score is defined by a gene signature (termed Gene Signature for Luminal A 10 or GSLA10) that correlates with unfavorable progression of luminal A breast cancer. The GSLA10 signature surpassed the Oncotype DX signature in discerning tumors with unfavorable outcomes (previously categorized as Luminal A by PAM50) across three independent human cohorts. This GSLA10 signature aids in identifying patients with Luminal A tumors displaying adverse prognosis, who could potentially benefit from personalized treatment strategies.
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Affiliation(s)
- Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Angélica Martínez-López
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Ana García-Casas
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Andrés Castellanos-Martín
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Nélida Salvador
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Alejandro Jiménez-Navas
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Manuel Jesús Pérez-Baena
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Manuel Adolfo Sánchez-Martín
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Servicio de Transgénesis, Plataforma Nucleus, Universidad de Salamanca, Salamanca, Spain
| | - María Del Mar Abad-Hernández
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
- Servicio de Anatomía Patológica, Hospital Universitario de Salamanca, Spain
| | - Sofía Del Carmen
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
- Servicio de Anatomía Patológica, Hospital Universitario de Salamanca, Spain
| | - Juncal Claros-Ampuero
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Juan Jesús Cruz-Hernández
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - César Augusto Rodríguez-Sánchez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - María Begoña García-Cenador
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Cirugía, Universidad de Salamanca, Salamanca, Spain
| | - Francisco Javier García-Criado
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Cirugía, Universidad de Salamanca, Salamanca, Spain
| | | | - Sonia Castillo-Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Jesús Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
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Gómez-Vecino A, Corchado-Cobos R, Blanco-Gómez A, García-Sancha N, Castillo-Lluva S, Martín-García A, Mendiburu-Eliçabe M, Prieto C, Ruiz-Pinto S, Pita G, Velasco-Ruiz A, Patino-Alonso C, Galindo-Villardón P, Vera-Pedrosa ML, Jalife J, Mao JH, Macías de Plasencia G, Castellanos-Martín A, Sáez-Freire MDM, Fraile-Martín S, Rodrigues-Teixeira T, García-Macías C, Galvis-Jiménez JM, García-Sánchez A, Isidoro-García M, Fuentes M, García-Cenador MB, García-Criado FJ, García-Hernández JL, Hernández-García MÁ, Cruz-Hernández JJ, Rodríguez-Sánchez CA, García-Sancho AM, Pérez-López E, Pérez-Martínez A, Gutiérrez-Larraya F, Cartón AJ, García-Sáenz JÁ, Patiño-García A, Martín M, Alonso-Gordoa T, Vulsteke C, Croes L, Hatse S, Van Brussel T, Lambrechts D, Wildiers H, Chang H, Holgado-Madruga M, González-Neira A, Sánchez PL, Pérez Losada J. Intermediate Molecular Phenotypes to Identify Genetic Markers of Anthracycline-Induced Cardiotoxicity Risk. Cells 2023; 12:1956. [PMID: 37566035 PMCID: PMC10417374 DOI: 10.3390/cells12151956] [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: 04/17/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Cardiotoxicity due to anthracyclines (CDA) affects cancer patients, but we cannot predict who may suffer from this complication. CDA is a complex trait with a polygenic component that is mainly unidentified. We propose that levels of intermediate molecular phenotypes (IMPs) in the myocardium associated with histopathological damage could explain CDA susceptibility, so variants of genes encoding these IMPs could identify patients susceptible to this complication. Thus, a genetically heterogeneous cohort of mice (n = 165) generated by backcrossing were treated with doxorubicin and docetaxel. We quantified heart fibrosis using an Ariol slide scanner and intramyocardial levels of IMPs using multiplex bead arrays and QPCR. We identified quantitative trait loci linked to IMPs (ipQTLs) and cdaQTLs via linkage analysis. In three cancer patient cohorts, CDA was quantified using echocardiography or Cardiac Magnetic Resonance. CDA behaves as a complex trait in the mouse cohort. IMP levels in the myocardium were associated with CDA. ipQTLs integrated into genetic models with cdaQTLs account for more CDA phenotypic variation than that explained by cda-QTLs alone. Allelic forms of genes encoding IMPs associated with CDA in mice, including AKT1, MAPK14, MAPK8, STAT3, CAS3, and TP53, are genetic determinants of CDA in patients. Two genetic risk scores for pediatric patients (n = 71) and women with breast cancer (n = 420) were generated using machine-learning Least Absolute Shrinkage and Selection Operator (LASSO) regression. Thus, IMPs associated with heart damage identify genetic markers of CDA risk, thereby allowing more personalized patient management.
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Affiliation(s)
- Aurora Gómez-Vecino
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Sonia Castillo-Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain;
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), 24040 Madrid, Spain
| | - Ana Martín-García
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Cardiología, Hospital Universitario de Salamanca, Universidad de Salamanca (CIBER.CV), 37007 Salamanca, Spain
| | - Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Carlos Prieto
- Servicio de Bioinformática, Nucleus, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Sara Ruiz-Pinto
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (S.R.-P.); (G.P.); (A.V.-R.)
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (S.R.-P.); (G.P.); (A.V.-R.)
| | - Alejandro Velasco-Ruiz
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (S.R.-P.); (G.P.); (A.V.-R.)
| | - Carmen Patino-Alonso
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Estadística, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Purificación Galindo-Villardón
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Estadística, Universidad de Salamanca, 37007 Salamanca, Spain
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Estudios e Investigaciones Estadísticas, Campus Gustavo Galindo, Km. 30.5 Via Perimetral, Guayaquil P.O. Box 09-01-5863, Ecuador
| | | | - José Jalife
- Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, 28029 Madrid, Spain; (M.L.V.-P.); (J.J.)
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 92720, USA
| | - Guillermo Macías de Plasencia
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Cardiología, Hospital Universitario de Salamanca, Universidad de Salamanca (CIBER.CV), 37007 Salamanca, Spain
| | - Andrés Castellanos-Martín
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - María del Mar Sáez-Freire
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | - Susana Fraile-Martín
- Servicio de Patología Molecular Comparada, Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca, 37007 Salamanca, Spain; (S.F.-M.); (T.R.-T.); (C.G.-M.)
| | - Telmo Rodrigues-Teixeira
- Servicio de Patología Molecular Comparada, Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca, 37007 Salamanca, Spain; (S.F.-M.); (T.R.-T.); (C.G.-M.)
| | - Carmen García-Macías
- Servicio de Patología Molecular Comparada, Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca, 37007 Salamanca, Spain; (S.F.-M.); (T.R.-T.); (C.G.-M.)
| | - Julie Milena Galvis-Jiménez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Instituto Nacional de Cancerología de Colombia, Bogotá 111511-110411001, Colombia
| | - Asunción García-Sánchez
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Bioquímica Clínica, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - María Isidoro-García
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Bioquímica Clínica, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Manuel Fuentes
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
- Unidad de Proteómica y Servicio General de Citometría de Flujo, Nucleus, Universidad de Salamanca, 37007 Salamanca, Spain
| | - María Begoña García-Cenador
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Cirugía, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Francisco Javier García-Criado
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Cirugía, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Juan Luis García-Hernández
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
| | | | - Juan Jesús Cruz-Hernández
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - César Augusto Rodríguez-Sánchez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
- Servicio de Oncología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Alejandro Martín García-Sancho
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Hematología, Hospital Universitario de Salamanca, CIBERONC, 37007 Salamanca, Spain;
| | - Estefanía Pérez-López
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Servicio de Hematología, Hospital Universitario de Salamanca, CIBERONC, 37007 Salamanca, Spain;
| | - Antonio Pérez-Martínez
- Department of Paediatric Hemato-Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | - Federico Gutiérrez-Larraya
- Department of Paediatric Cardiology, Hospital Universitario La Paz, 28046 Madrid, Spain; (F.G.-L.); (A.J.C.)
| | - Antonio J. Cartón
- Department of Paediatric Cardiology, Hospital Universitario La Paz, 28046 Madrid, Spain; (F.G.-L.); (A.J.C.)
| | - José Ángel García-Sáenz
- Medical Oncology Service, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - Ana Patiño-García
- Department of Pediatrics, Solid Tumor Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, IdisNA, 31008 Pamplona, Spain;
| | - Miguel Martín
- Department of Medicine, Gregorio Marañón Health Research Institute (IISGM), Centro de Investigación Biomédica en Red Oncológica (CIBERONC), Universidad Complutense, 28007 Madrid, Spain;
| | - Teresa Alonso-Gordoa
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain;
| | - Christof Vulsteke
- Department of Molecular Imaging, Pathology, Radiotherapy and Oncology (MIPRO), Center for Oncological Research (CORE), Antwerp University, 2610 Antwerp, Belgium; (C.V.); (L.C.)
- Department of Oncology, Integrated Cancer Center in Ghent, AZ Maria Middelares, 9000 Ghent, Belgium
| | - Lieselot Croes
- Department of Molecular Imaging, Pathology, Radiotherapy and Oncology (MIPRO), Center for Oncological Research (CORE), Antwerp University, 2610 Antwerp, Belgium; (C.V.); (L.C.)
- Department of Oncology, Integrated Cancer Center in Ghent, AZ Maria Middelares, 9000 Ghent, Belgium
| | - Sigrid Hatse
- Laboratory of Experimental Oncology (LEO), Department of Oncology, Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium;
| | - Thomas Van Brussel
- VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium; (T.V.B.); (D.L.)
- Laboratory of Translational Genetics, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, 3000 Leuven, Belgium; (T.V.B.); (D.L.)
- Laboratory of Translational Genetics, Department of Human Genetics, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Hans Wildiers
- Department of General Medical Oncology and Multidisciplinary Breast Unit, Leuven Cancer Institute, and Laboratory of Experimental Oncology (LEO), Department of Oncology, Leuven Cancer Institute and University Hospital Leuven, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium;
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 92720, USA
| | - Marina Holgado-Madruga
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
- Instituto de Neurociencias de Castilla y León (INCyL), 37007 Salamanca, Spain
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (S.R.-P.); (G.P.); (A.V.-R.)
| | - Pedro L. Sánchez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Servicio de Cardiología, Hospital Universitario de Salamanca, Universidad de Salamanca (CIBER.CV), 37007 Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Jesús Pérez Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain; (A.G.-V.); (R.C.-C.); (A.B.-G.); (N.G.-S.); (M.M.-E.); (A.C.-M.); (M.d.M.S.-F.); (J.M.G.-J.); (M.F.); (J.L.G.-H.); (J.J.C.-H.); (C.A.R.-S.); (A.M.G.-S.); (E.P.-L.)
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain; (A.M.-G.); (C.P.-A.); (P.G.-V.); (G.M.d.P.); (A.G.-S.); (M.I.-G.); (M.B.G.-C.); (F.J.G.-C.)
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5
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Mao X, Cai Y, Long S, Perez-Losada J, Mao JH, Chang H. Pan-cancer evaluation of clinical value of mitotic network activity index (MNAI) and its predictive value for immunotherapy. Front Oncol 2023; 13:1178568. [PMID: 37456231 PMCID: PMC10349373 DOI: 10.3389/fonc.2023.1178568] [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: 03/03/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Increased mitotic activity is associated with the genesis and aggressiveness of many cancers. To assess the clinical value of mitotic activity as prognostic biomarker, we performed a pan-cancer study on the mitotic network activity index (MNAI) constructed based on 54-gene mitotic apparatus network. Our pan-cancer assessment on TCGA (33 tumor types, 10,061 patients) and validation on other publicly available cohorts (23 tumor types, 9,209 patients) confirmed the significant association of MNAI with overall survival, progression-free survival, and other prognostic endpoints in multiple cancer types, including lower-grade gliomas (LGG), breast invasive carcinoma (BRCA), as well as many others. We also showed significant association between MNAI and genetic instability, which provides a biological explanation of its prognostic impact at pan-cancer landscape. Our association analysis revealed that patients with high MNAI benefitted more from anti-PD-1 and Anti-CTLA-4 treatment. In addition, we demonstrated that multimodal integration of MNAI and the AI-empowered Cellular Morphometric Subtypes (CMS) significantly improved the predictive power of prognosis compared to using MNAI and CMS alone. Our results suggest that MNAI can be used as a potential prognostic biomarker for different tumor types toward different clinical endpoints, and multimodal integration of MNAI and CMS exceeds individual biomarker for precision prognosis.
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Affiliation(s)
- Xuanyu Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yimeng Cai
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Sarah Long
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jesus Perez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, Spain
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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6
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Taylor MA, Kandyba E, Halliwill K, Delrosario R, Koroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam S, Mirzoeva O, Akhurst RJ, Balmain A. Gene networks reveal stem-cell state convergence during preneoplasia and progression to malignancy in multistage skin carcinogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539863. [PMID: 37215032 PMCID: PMC10197547 DOI: 10.1101/2023.05.08.539863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Adult mammalian stem cells play critical roles in normal tissue homeostasis, as well as in tumor development, by contributing to cell heterogeneity, plasticity, and development of drug resistance. The relationship between different types of normal and cancer stem cells is highly controversial and poorly understood. Here, we carried out gene expression network analysis of normal and tumor samples from genetically heterogeneous mice to create network metagenes for visualization of stem-cell networks, rather than individual stem-cell markers, at the single-cell level during multistage carcinogenesis. We combined this approach with lineage tracing and single-cell RNASeq of stem cells and their progeny, identifying a previously unrecognized hierarchy in which Lgr6+ stem cells from tumors generate progeny that express a range of other stem-cell markers including Sox2, Pitx1, Foxa1, Klf5, and Cd44. Our data identify a convergence of multiple stem-cell and tumor-suppressor pathways in benign tumor cells expressing markers of lineage plasticity and oxidative stress. This same single-cell population expresses network metagenes corresponding to markers of cancer drug resistance in human tumors of the skin, lung and prostate. Treatment of mouse squamous carcinomas in vivo with the chemotherapeutic cis-platin resulted in elevated expression of the genes that mark this cell population. Our data have allowed us to create a simplified model of multistage carcinogenesis that identifies distinct stem-cell states at different stages of tumor progression, thereby identifying networks involved in lineage plasticity, drug resistance, and immune surveillance, providing a rich source of potential targets for cancer therapy.
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Affiliation(s)
- Mark A. Taylor
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Kyle Halliwill
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Reyno Delrosario
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Matvei Koroshkin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Hani Goodarzi
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Yun Rose Li
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Saumya Bollam
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Olga Mirzoeva
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Rosemary J. Akhurst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco; San Francisco, 94158, USA
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7
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Xie Y, Kuang W, Wang D, Yuan K, Yang P. Expanding role of CXCR2 and therapeutic potential of CXCR2 antagonists in inflammatory diseases and cancers. Eur J Med Chem 2023; 250:115175. [PMID: 36780833 DOI: 10.1016/j.ejmech.2023.115175] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023]
Abstract
C-X-C motif chemokine receptor 2 (CXCR2) is G protein-coupled receptor (GPCR) and plays important roles in various inflammatory diseases and cancers, including chronic obstructive pulmonary disease (COPD), atherosclerosis, asthma, and pancreatic cancer. Upregulation of CXCR2 is closely associated with the migration of neutrophils and monocytes. To date, many small-molecule CXCR2 antagonists have entered clinical trials, showing favorable safety and therapeutic effects. Hence, we provide an overview containing the discovery history, protein structure, signaling pathways, biological functions, structure-activity relationships and clinical significance of CXCR2 antagonists in inflammatory diseases and cancers. According to the latest development and recent clinical progress of CXCR2 small molecule antagonists, we speculated that CXCR2 can be used as a biomarker and a new target for diabetes and that CXCR2 antagonists may also attenuate lung injury in coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Yishi Xie
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
| | - Wenbin Kuang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
| | - Dawei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China.
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8
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Wong CT, Oh DH. Vitamin D Receptor Promotes Global Nucleotide Excision Repair by Facilitating XPC Dissociation from Damaged DNA. J Invest Dermatol 2021; 141:1656-1663. [PMID: 33524369 DOI: 10.1016/j.jid.2020.11.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022]
Abstract
Vitamin D receptor (VDR) is important for normal DNA repair, although the mechanism by which it acts is unclear. After focal UV irradiation to create subnuclear spots of DNA damage, epidermal keratinocytes from VDR-null mice as well as human epidermal keratinocytes depleted of VDR with small interfering RNA removed pyrimidine-pyrimidone (6-4) photoproducts more slowly than control cells. Costaining with antibodies to XPC, the DNA damage recognition sensor that initiates nucleotide excision repair, showed that XPC rapidly accumulated at spots of damage and gradually faded in control human keratinocytes. In VDR-depleted keratinocytes, XPC associated with DNA damage with comparable efficiency; however, XPC's dissociation dynamics were altered so that significantly more XPC was bound and retained over time than in control cells. The XPF endonuclease, which acts subsequently in nucleotide excision repair, bound and dissociated with comparable kinetics in control and VDR-depleted cells, but the extent of binding was reduced in the latter. These results as well as kinetic modeling of the data suggest that VDR's importance in the repair of UV-induced DNA damage is mediated in part by its ability to facilitate the dissociation of XPC from damaged DNA for the normal recruitment and assembly of other repair proteins to proceed.
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Affiliation(s)
- Christian T Wong
- Dermatology Research Unit, San Francisco VA Health Care System, San Francisco, California, USA; Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Dennis H Oh
- Dermatology Research Unit, San Francisco VA Health Care System, San Francisco, California, USA; Department of Dermatology, University of California San Francisco, San Francisco, California, USA.
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9
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Kobia FM, Preusse K, Dai Q, Weaver N, Hass MR, Chaturvedi P, Stein SJ, Pear WS, Yuan Z, Kovall RA, Kuang Y, Eafergen N, Sprinzak D, Gebelein B, Brunskill EW, Kopan R. Notch dimerization and gene dosage are important for normal heart development, intestinal stem cell maintenance, and splenic marginal zone B-cell homeostasis during mite infestation. PLoS Biol 2020; 18:e3000850. [PMID: 33017398 PMCID: PMC7561103 DOI: 10.1371/journal.pbio.3000850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/15/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022] Open
Abstract
Cooperative DNA binding is a key feature of transcriptional regulation. Here we examined the role of cooperativity in Notch signaling by CRISPR-mediated engineering of mice in which neither Notch1 nor Notch2 can homo- or heterodimerize, essential for cooperative binding to sequence-paired sites (SPS) located near many Notch-regulated genes. Although most known Notch-dependent phenotypes were unaffected in Notch1/2 dimer-deficient mice, a subset of tissues proved highly sensitive to loss of cooperativity. These phenotypes include heart development, compromised viability in combination with low gene dose, and the gut, developing ulcerative colitis in response to 1% dextran sulfate sodium (DSS). The most striking phenotypes-gender imbalance and splenic marginal zone B-cell lymphoma-emerged in combination with gene dose reduction or when challenged by chronic fur mite infestation. This study highlights the role of the environment in malignancy and colitis and is consistent with Notch-dependent anti-parasite immune responses being compromised in Notch dimer-deficient animals.
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Affiliation(s)
- Francis M. Kobia
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kristina Preusse
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Quanhui Dai
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Nicholas Weaver
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Matthew R. Hass
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Praneet Chaturvedi
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sarah J. Stein
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Warren S. Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Rhett A. Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Yi Kuang
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Natanel Eafergen
- School of Neurobiology, Biochemistry, and Biophysics, The George S. Wise Faculty of Life Sciences Tel Aviv University, Tel Aviv, Israel
| | - David Sprinzak
- School of Neurobiology, Biochemistry, and Biophysics, The George S. Wise Faculty of Life Sciences Tel Aviv University, Tel Aviv, Israel
| | - Brian Gebelein
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Eric W. Brunskill
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Raphael Kopan
- Division of Developmental Biology, Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
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Zieman AG, Coulombe PA. Pathophysiology of pachyonychia congenita-associated palmoplantar keratoderma: new insights into skin epithelial homeostasis and avenues for treatment. Br J Dermatol 2020; 182:564-573. [PMID: 31021398 PMCID: PMC6814456 DOI: 10.1111/bjd.18033] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Pachyonychia congenita (PC), a rare genodermatosis, primarily affects ectoderm-derived epithelial appendages and typically includes oral leukokeratosis, nail dystrophy and very painful palmoplantar keratoderma (PPK). PC dramatically impacts quality of life although it does not affect lifespan. PC can arise from mutations in any of the wound-repair-associated keratin genes KRT6A, KRT6B, KRT6C, KRT16 or KRT17. There is no cure for this condition, and current treatment options for PC symptoms are limited and palliative in nature. OBJECTIVES This review focuses on recent progress made towards understanding the pathophysiology of PPK lesions, the most prevalent and debilitating of all PC symptoms. METHODS We reviewed the relevant literature with a particular focus on the Krt16 null mouse, which spontaneously develops footpad lesions that mimic several aspects of PC-associated PPK. RESULTS There are three main stages of progression of PPK-like lesions in Krt16 null mice. Ahead of lesion onset, keratinocytes in the palmoplantar (footpad) skin exhibit specific defects in terminal differentiation, including loss of Krt9 expression. At the time of PPK onset, there is elevated oxidative stress and hypoactive Keap1-Nrf2 signalling. During active PPK, there is a profound defect in the ability of the epidermis to maintain or return to normal homeostasis. CONCLUSIONS The progress made suggests new avenues to explore for the treatment of PC-based PPK and deepens our understanding of the mechanisms controlling skin tissue homeostasis. What's already known about this topic? Pachyonychia congenita (PC) is a rare genodermatosis caused by mutations in KRT6A, KRT6B, KRT6C, KRT16 and KRT17, which are normally expressed in skin appendages and induced following injury. Individuals with PC present with multiple clinical symptoms that usually include thickened and dystrophic nails, palmoplantar keratoderma (PPK), glandular cysts and oral leukokeratosis. The study of PC pathophysiology is made challenging because of its low incidence and high complexity. There is no cure or effective treatment for PC. What does this study add? This text reviews recent progress made when studying the pathophysiology of PPK associated with PC. This recent progress points to new possibilities for devising effective therapeutics that may complement current palliative strategies.
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Affiliation(s)
- A. G. Zieman
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - P. A. Coulombe
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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11
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Bikle DD. The Vitamin D Receptor as Tumor Suppressor in Skin. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1268:285-306. [PMID: 32918224 DOI: 10.1007/978-3-030-46227-7_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cutaneous malignancies including melanomas and keratinocyte carcinomas (KC) are the most common types of cancer, occurring at a rate of over one million per year in the United States. KC, which include both basal cell carcinomas and squamous cell carcinomas, are substantially more common than melanomas and form the subject of this chapter. Ultraviolet radiation (UVR), both UVB and UVA, as occurs with sunlight exposure is generally regarded as causal for these malignancies, but UVB is also required for vitamin D synthesis in the skin. Keratinocytes are the major cell in the epidermis. These cells not only produce vitamin D but contain the enzymatic machinery to metabolize vitamin D to its active metabolite, 1,25(OH)2D, and express the receptor for this metabolite, the vitamin D receptor (VDR). This allows the cell to respond to the 1,25(OH)2D that it produces. Based on our own data and that reported in the literature, we conclude that vitamin D signaling in the skin suppresses UVR-induced epidermal tumor formation. In this chapter we focus on four mechanisms by which vitamin D signaling suppresses tumor formation. They are inhibition of proliferation/stimulation of differentiation with discussion of the roles of hedgehog, Wnt/β-catenin, and hyaluronan/CD44 pathways in mediating vitamin D regulation of proliferation/differentiation, regulation of the balance between oncogenic and tumor suppressor long noncoding RNAs, immune regulation, and promotion of DNA damage repair (DDR).
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Affiliation(s)
- Daniel D Bikle
- Medicine and Dermatology, VA Medical Center and University of California, San Francisco, San Francisco, CA, USA.
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12
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Elimination of KLK5 inhibits early skin tumorigenesis by reducing epidermal proteolysis and reinforcing epidermal microstructure. Biochim Biophys Acta Mol Basis Dis 2019; 1865:165520. [DOI: 10.1016/j.bbadis.2019.07.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/13/2019] [Accepted: 07/27/2019] [Indexed: 01/10/2023]
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13
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Niche-Specific Factors Dynamically Regulate Sebaceous Gland Stem Cells in the Skin. Dev Cell 2019; 51:326-340.e4. [PMID: 31564613 DOI: 10.1016/j.devcel.2019.08.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/22/2019] [Accepted: 08/23/2019] [Indexed: 12/22/2022]
Abstract
Oil-secreting sebaceous glands (SGs) are critical for proper skin function; however, it remains unclear how different factors act together to modulate SG stem cells. Here, we provide functional evidence that each SG lobe is serviced by its own dedicated stem cell population. Upon ablating Notch signaling in different skin subcompartments, we find that this pathway exerts dual counteracting effects on SGs. Suppressing Notch in SG progenitors traps them in a hybrid state where stem and differentiation features become intermingled. In contrast, ablating Notch outside of the SG stem cell compartment indirectly drives SG expansion. Finally, we report that a K14:K5→K14:K79 keratin shift occurs during SG differentiation. Deleting K79 destabilizes K14 in sebocytes, and attenuates SGs and eyelid meibomian glands, leading to corneal ulceration. Altogether, our findings demonstrate that SGs integrate diverse signals from different niches and suggest that mutations incurred within one stem cell compartment can indirectly influence another.
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Vitamin D receptor expression and serum 25(OH)D concentration inversely associates with burden of neurofibromas. Eur J Cancer Prev 2019; 28:220-224. [PMID: 30299316 DOI: 10.1097/cej.0000000000000467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vitamin D and its receptor may play a role in preventing tumor development and progression. As such antineoplastic effects are expected to be weak and to act over long periods, conditions with increased tumor incidence, such as the neurofibromatosis type 1 (NF1), provide suitable study models. We previously found an inverse correlation of serum 25(OH)D concentration with number of neurofibromas in NF1. Here we aim to further explore the role of the vitamin D receptor. A total of 141 adult NF1 patients were included in the study. For 101 of them, serum vitamin 25(OH)D data were available. From 87 patients, blood samples were obtained in PaxGene tubes containing a reagent to stabilize RNA immediately. mRNA of the vitamin D receptor (VDR) gene (coding for the vitamin D receptor) was measured by means of RT-PCR. Correlation of laboratory data with NF1-related tumors was statistically evaluated. Vitamin D receptor in NF1-tumors was examined by means of immunohistochemistry using an antibody against the vitamin D1 receptor. The number of dermal neurofibromas was significantly inversely correlated with VDR mRNA level and with serum 25(OH)D concentration in NF1 patients. In contrast, plexiform neurofibroma and malignant peripheral nerve sheath tumor did not correlate with these two parameters. Immunostaining did not detect vitamin D receptor in NF1-tumors. Both vitamin D and its receptor may play a role in suppressing the development of neurofibromas. Sustaining 25(OH)D at an adequate level may contribute to controlling neurofibromas and possibly also other tumors. This is especially important for individuals with lower expression of VDR.
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15
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Luckett-Chastain LR, Gipson JR, Gillaspy AF, Gallucci RM. Transcriptional profiling of irritant contact dermatitis (ICD) in a mouse model identifies specific patterns of gene expression and immune-regulation. Toxicology 2018; 410:1-9. [DOI: 10.1016/j.tox.2018.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/07/2018] [Accepted: 08/27/2018] [Indexed: 12/16/2022]
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16
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Jeong Ha S, Song KM, Lee J, Ho Kim Y, Hyouck Lee N, Eon Kim Y, Lee S, Keun Jung S. Preventive effect of Curcuma zedoaria
extract on UVB-induced skin inflammation and photoaging. J Food Biochem 2018. [DOI: 10.1111/jfbc.12598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Su Jeong Ha
- Division of Strategic Food Research; Korea Food Research Institute; Wanju-gun Republic of Korea
- Department of Agricultural Biotechnology; Seoul National University; Seoul Republic of Korea
| | - Kyung-Mo Song
- Division of Strategic Food Research; Korea Food Research Institute; Wanju-gun Republic of Korea
| | - Jangho Lee
- Division of Strategic Food Research; Korea Food Research Institute; Wanju-gun Republic of Korea
- Food Biotechnology Program; Korea University of Science and Technology; Daejeon Republic of Korea
| | - Young Ho Kim
- Division of Strategic Food Research; Korea Food Research Institute; Wanju-gun Republic of Korea
| | - Nam Hyouck Lee
- Division of Strategic Food Research; Korea Food Research Institute; Wanju-gun Republic of Korea
| | - Young Eon Kim
- Division of Strategic Food Research; Korea Food Research Institute; Wanju-gun Republic of Korea
| | - Sooyeun Lee
- College of Pharmacy; Keimyung University; Daegu Republic of Korea
| | - Sung Keun Jung
- Division of Strategic Food Research; Korea Food Research Institute; Wanju-gun Republic of Korea
- School of Food Science and Biotechnology; Kyungpook National University; Daegu Republic of Korea
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Morales-Prieto N, Ruiz-Laguna J, Sheehan D, Abril N. Transcriptome signatures of p,p´-DDE-induced liver damage in Mus spretus mice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:150-167. [PMID: 29554563 DOI: 10.1016/j.envpol.2018.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/19/2018] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
The use of DDT (1,1,1-trichloro-2,2-bis(p-chlorophenyl) ethane) in some countries, although regulated, is contributing to an increased worldwide risk of exposure to this organochlorine pesticide or its derivative p,p'-DDE [1,1-dichloro-2,2-bis(p-chlorophenyl) ethylene]. Many studies have associated p,p'-DDE exposure to type 2 diabetes, obesity and alterations of the reproductive system, but their molecular mechanisms of toxicity remain poorly understood. We have addressed this issue by using commercial microarrays based on probes for the entire Mus musculus genome to determine the hepatic transcriptional signatures of p,p'-DDE in the phylogenetically close mouse species Mus spretus. High-stringency hybridization conditions and analysis assured reliable results, which were also verified, in part, by qRT-PCR, immunoblotting and/or enzymatic activity. Our data linked 198 deregulated genes to mitochondrial dysfunction and perturbations of central signaling pathways (kinases, lipids, and retinoic acid) leading to enhanced lipogenesis and aerobic glycolysis, inflammation, cell proliferation and testosterone catabolism and excretion. Alterations of transcript levels of genes encoding enzymes involved in testosterone catabolism and excretion would explain the relationships established between p,p´-DDE exposure and reproductive disorders, obesity and diabetes. Further studies will help to fully understand the molecular basis of p,p´-DDE molecular toxicity in liver and reproductive organs, to identify effective exposure biomarkers and perhaps to design efficient p,p'-DDE exposure counteractive strategies.
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Affiliation(s)
- Noelia Morales-Prieto
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - Julia Ruiz-Laguna
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - David Sheehan
- College of Arts and Science, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Nieves Abril
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain.
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18
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Lander JM, Supp DM, He H, Martin LJ, Chen X, Weirauch MT, Boyce ST, Kopan R. Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers. PLoS One 2017; 12:e0184500. [PMID: 28953906 PMCID: PMC5617145 DOI: 10.1371/journal.pone.0184500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/24/2017] [Indexed: 01/12/2023] Open
Abstract
To identify putative gene regulatory regions that respond to epidermal injury, we mapped chromatin dynamics in a stratified human epidermis during barrier maturation and disruption. Engineered skin substitutes (ESS) cultured at the air-liquid interface were used as a model of developing human epidermis with incomplete barrier formation. The epidermal barrier stabilized following engraftment onto immunocompromised mice, and was compromised again upon injury. Modified formaldehyde-assisted isolation of regulatory elements (FAIRE) was used to identify accessible genomic regions characteristic of monolayer keratinocytes, ESS in vitro, grafted ESS, and tape-stripped ESS graft. We mapped differentiation- and maturation-associated changes in transcription factor binding sites enriched at each stage and observed overrepresentation of AP-1 gene family motifs in barrier-deficient samples. Transcription of TSLP, an important effector of immunological memory in response to allergen exposure, was dramatically elevated in our barrier-deficient samples. We identified dynamic DNA elements that correlated with TSLP induction and may contain enhancers that regulate TSLP. Two dynamic regions were located near the TSLP promoter and overlapped with allergy-associated SNPs rs17551370 and rs2289877, strongly implicating these loci in the regulation of TSLP expression in allergic disease. Additional dynamic chromatin regions ~250kb upstream of the TSLP promoter were found to be in high linkage disequilibrium with allergic disease SNPs. Taken together, these results define dynamic chromatin accessibility changes during epidermal development and dysfunction.
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Affiliation(s)
- Julie M. Lander
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Dorothy M. Supp
- Research Department, Shriners Hospitals for Children, Cincinnati, Ohio, United States of America
- Department of Surgery, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Hua He
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Lisa J. Martin
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Steven T. Boyce
- Research Department, Shriners Hospitals for Children, Cincinnati, Ohio, United States of America
- Department of Surgery, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Raphael Kopan
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- * E-mail:
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19
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Huang PY, Kandyba E, Jabouille A, Sjolund J, Kumar A, Halliwill K, McCreery M, DelRosario R, Kang HC, Wong CE, Seibler J, Beuger V, Pellegrino M, Sciambi A, Eastburn DJ, Balmain A. Lgr6 is a stem cell marker in mouse skin squamous cell carcinoma. Nat Genet 2017; 49:1624-1632. [PMID: 28945253 PMCID: PMC5662105 DOI: 10.1038/ng.3957] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022]
Abstract
The G-protein-coupled receptors Lgr4/5/6 are Wnt signalling mediators, but their functions in squamous carcinomas (SCCs) are unclear. Using lineage tracing in Lgr5-EGFP-CreERT2- and Lgr6-EGFP-CreERT2- Rosa26/Tomato reporter mice, we demonstrate that Lgr6, but not Lgr5, acts as an epithelial stem cell marker in vivo in SCCs. We identify, by single molecule in situ hybridisation and cell sorting, rare Lgr6-positive cells in immortalised keratinocytes, and show that their frequency increases in advanced SCCs. Lgr6 expression is enriched in cells with stem cell characteristics, and Lgr6 downregulation in vivo causes increased epidermal proliferation, with expanded lineage tracing from Lgr6+ epidermal stem cells. Surprisingly, Lgr6 germline knockout mice are predisposed to SCC development, by a mechanism that includes compensatory upregulation of Lgr5. These data provide a model for human patients with germline loss of function mutations in WNT pathway genes RSPO1 or LGR4, who show increased susceptibility to squamous tumour development.
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Affiliation(s)
- Phillips Y Huang
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, San Francisco, California, USA.,Genome Institute of Singapore, Singapore
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, San Francisco, California, USA
| | - Arnaud Jabouille
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, San Francisco, California, USA
| | - Jonas Sjolund
- Division of Translational Cancer Research, University of Lund, Lund, Sweden
| | - Atul Kumar
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, San Francisco, California, USA
| | - Kyle Halliwill
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, San Francisco, California, USA
| | - Melissa McCreery
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, San Francisco, California, USA
| | - Reyno DelRosario
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, San Francisco, California, USA
| | | | | | | | | | | | - Adam Sciambi
- Mission Bio, Inc., San Francisco, California, USA
| | | | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, San Francisco, California, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
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20
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Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and genetic inflammation networks in major human diseases. MOLECULAR BIOSYSTEMS 2017; 12:2318-41. [PMID: 27303926 DOI: 10.1039/c6mb00240d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It has been well-recognized that inflammation alongside tissue repair and damage maintaining tissue homeostasis determines the initiation and progression of complex diseases. Albeit with the accomplishment of having captured the most critical inflammation-involved molecules, genetic susceptibilities, epigenetic factors, and environmental factors, our schemata on the role of inflammation in complex diseases remain largely patchy, in part due to the success of reductionism in terms of research methodology per se. Omics data alongside the advances in data integration technologies have enabled reconstruction of molecular and genetic inflammation networks which shed light on the underlying pathophysiology of complex diseases or clinical conditions. Given the proven beneficial role of anti-inflammation in coronary heart disease as well as other complex diseases and immunotherapy as a revolutionary transition in oncology, it becomes timely to review our current understanding of the molecular and genetic inflammation networks underlying major human diseases. In this review, we first briefly discuss the complexity of infectious diseases and then highlight recently uncovered molecular and genetic inflammation networks in other major human diseases including obesity, type II diabetes, coronary heart disease, late onset Alzheimer's disease, Parkinson's disease, and sporadic cancer. The commonality and specificity of these molecular networks are addressed in the context of genetics based on genome-wide association study (GWAS). The double-sword role of inflammation, such as how the aberrant type 1 and/or type 2 immunity leads to chronic and severe clinical conditions, remains open in terms of the inflammasome and the core inflammatome network features. Increasingly available large Omics and clinical data in tandem with systems biology approaches have offered an exciting yet challenging opportunity toward reconstruction of more comprehensive and dynamic molecular and genetic inflammation networks, which hold great promise in transiting network snapshots to video-style multi-scale interplays of disease mechanisms, in turn leading to effective clinical intervention.
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Affiliation(s)
- Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Camil E Sayegh
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Armand-Frappier, Laval, Quebec H7V 4A7, Canada
| | - I-Ming Wang
- Informatics and Analysis, Merck Research Laboratories, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90025, USA.
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
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21
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Sarig R, Tzahor E. The cancer paradigms of mammalian regeneration: can mammals regenerate as amphibians? Carcinogenesis 2017; 38:359-366. [DOI: 10.1093/carcin/bgw103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023] Open
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22
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McCreery MQ, Balmain A. Chemical Carcinogenesis Models of Cancer: Back to the Future. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2017. [DOI: 10.1146/annurev-cancerbio-050216-122002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over a century has elapsed since the first demonstration that exposure to chemicals in coal tar can cause cancer in animals. These observations provided an essential causal mechanistic link between environmental chemicals and increased risk of cancer in human populations. Mouse models of chemical carcinogenesis have since led to the concept of multistage tumor development through distinct stages of initiation, promotion, and progression and identified many of the genetic and biological events involved in these processes. Recent breakthroughs in DNA sequencing have now given us tools to dissect complete tumor genome architectures and revealed that chemically induced cancers in the mouse carry a high point mutation load and mutation signatures that reflect the causative agent used for tumor induction. Chemical carcinogenesis models may therefore provide a route to identify the causes of mutation signatures found in human cancers and further inform studies of therapeutic drug resistance and responses to immunotherapy, which are dependent on mutation load and genetic heterogeneity.
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Affiliation(s)
- Melissa Q. McCreery
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California 94115;,
| | - Allan Balmain
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California 94115;,
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Maia Campos PMBG, G Mercurio D, O Melo M, Closs-Gonthier B. Cichorium intybus root extract: A "vitamin D-like" active ingredient to improve skin barrier function. J DERMATOL TREAT 2017; 28:78-81. [PMID: 27161285 DOI: 10.1080/09546634.2016.1178695] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/09/2016] [Indexed: 12/26/2022]
Abstract
During the aging process, the human skin suffers many alterations including dryness, skin barrier function damage. The skin barrier function is important to the prevention of skin alterations and maintenance of homeostasis. So, the objective of this study was to assess the clinical efficacy on skin barrier function of Cichorium intybus root extract in cosmetic formulations with or without UV filters. Fifty women, aged between 45 and 60 years, were divided into two groups. One group received vehicle formulations containing UV filters, and the other group received formulations without UV filters. Both groups received a formulation containing the extract and the vehicle. The formulations were applied twice daily to the upper arms after washing with sodium lauryl sulphate. Transepidermal water loss (TEWL) and skin microrelief were evaluated before and after a 14- and 28-day period of treatment. The control regions and regions where the vehicles were applied showed an increase in the TEWL. For the formulations containing the extract, decreased TEWL and improved microrelief were observed when compared to the vehicle and control areas after a 28-day period. In conclusion, Cichorium intybus root extract showed protective and restructuring effects on the skin and stands out as an innovative ingredient to improve skin barrier function.
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Affiliation(s)
- P M B G Maia Campos
- a NEATEC, Faculty of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Ribeirao Preto , Brazil
| | - D G Mercurio
- a NEATEC, Faculty of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Ribeirao Preto , Brazil
| | - M O Melo
- a NEATEC, Faculty of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Ribeirao Preto , Brazil
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24
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Halliwill KD, Quigley DA, Kang HC, Del Rosario R, Ginzinger D, Balmain A. Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer. Genome Med 2016; 8:83. [PMID: 27506198 PMCID: PMC4977876 DOI: 10.1186/s13073-016-0334-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/11/2016] [Indexed: 01/01/2023] Open
Abstract
Background Body mass index (BMI) has been implicated as a primary factor influencing cancer development. However, understanding the relationship between these two complex traits has been confounded by both environmental and genetic heterogeneity. Methods In order to gain insight into the genetic factors linking BMI and cancer, we performed chemical carcinogenesis on a genetically heterogeneous cohort of interspecific backcross mice ((Mus Spretus × FVB/N) F1 × FVB/N). Using this cohort, we performed quantitative trait loci (QTL) analysis to identify regions linked to BMI. We then performed an integrated analysis incorporating gene expression, sequence comparison between strains, and gene expression network analysis to identify candidate genes influencing both tumor development and BMI. Results Analysis of QTL linked to tumorigenesis and BMI identified several loci associated with both phenotypes. Exploring these loci in greater detail revealed a novel relationship between the Pannexin 3 gene (Panx3) and both BMI and tumorigenesis. Panx3 is positively associated with BMI and is strongly tied to a lipid metabolism gene expression network. Pre-treatment Panx3 gene expression levels in normal skin are associated with tumor susceptibility and inhibition of Panx function strongly influences inflammation. Conclusions These studies have identified several genetic loci that influence both BMI and carcinogenesis and implicate Panx3 as a candidate gene that links these phenotypes through its effects on inflammation and lipid metabolism. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0334-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyle D Halliwill
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Hio Chung Kang
- Invitae Corporation, 458 Brannan St, San Francisco, CA, 94107, USA
| | - Reyno Del Rosario
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - David Ginzinger
- Thermo Fisher Scientific, 5791 Van Allen Way, Carlsbad, CA, 92008, USA
| | - Allan Balmain
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA. .,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
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25
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Quigley DA, Kandyba E, Huang P, Halliwill KD, Sjölund J, Pelorosso F, Wong CE, Hirst GL, Wu D, Delrosario R, Kumar A, Balmain A. Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer. Cell Rep 2016; 16:1153-1165. [PMID: 27425619 DOI: 10.1016/j.celrep.2016.06.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/16/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022] Open
Abstract
Inherited germline polymorphisms can cause gene expression levels in normal tissues to differ substantially between individuals. We present an analysis of the genetic architecture of normal adult skin from 470 genetically unique mice, demonstrating the effect of germline variants, skin tissue location, and perturbation by exogenous inflammation or tumorigenesis on gene signaling pathways. Gene networks related to specific cell types and signaling pathways, including sonic hedgehog (Shh), Wnt, Lgr family stem cell markers, and keratins, differed at these tissue sites, suggesting mechanisms for the differential susceptibility of dorsal and tail skin to development of skin diseases and tumorigenesis. The Pten tumor suppressor gene network is rewired in premalignant tumors compared to normal tissue, but this response to perturbation is lost during malignant progression. We present a software package for expression quantitative trait loci (eQTL) network analysis and demonstrate how network analysis of whole tissues provides insights into interactions between cell compartments and signaling molecules.
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Affiliation(s)
- David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo 0310, Norway; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo 0313, Norway; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Phillips Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome Building, Singapore 138672, Singapore
| | - Kyle D Halliwill
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonas Sjölund
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 22381 Lund, Sweden
| | - Facundo Pelorosso
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, 9(th) Floor, Ciudad Autónoma de Buenos Aires 1121, Argentina
| | - Christine E Wong
- Institute of Surgical Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Reyno Delrosario
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atul Kumar
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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26
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Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, A. Dane M, Esch A, Feiler HS, Wang NJ, Hardwicke MA, Laquerre S, Jackson J, W. Wood K, Weber B, Spellman PT, Aparicio S, Wooster R, Caldas C, Gray JW. Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer. Breast Cancer Res 2016; 18:70. [PMID: 27368372 PMCID: PMC4930593 DOI: 10.1186/s13058-016-0728-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 06/07/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND High mitotic activity is associated with the genesis and progression of many cancers. Small molecule inhibitors of mitotic apparatus proteins are now being developed and evaluated clinically as anticancer agents. With clinical trials of several of these experimental compounds underway, it is important to understand the molecular mechanisms that determine high mitotic activity, identify tumor subtypes that carry molecular aberrations that confer high mitotic activity, and to develop molecular markers that distinguish which tumors will be most responsive to mitotic apparatus inhibitors. METHODS We identified a coordinately regulated mitotic apparatus network by analyzing gene expression profiles for 53 malignant and non-malignant human breast cancer cell lines and two separate primary breast tumor datasets. We defined the mitotic network activity index (MNAI) as the sum of the transcriptional levels of the 54 coordinately regulated mitotic apparatus genes. The effect of those genes on cell growth was evaluated by small interfering RNA (siRNA). RESULTS High MNAI was enriched in basal-like breast tumors and was associated with reduced survival duration and preferential sensitivity to inhibitors of the mitotic apparatus proteins, polo-like kinase, centromere associated protein E and aurora kinase designated GSK462364, GSK923295 and GSK1070916, respectively. Co-amplification of regions of chromosomes 8q24, 10p15-p12, 12p13, and 17q24-q25 was associated with the transcriptional upregulation of this network of 54 mitotic apparatus genes, and we identify transcription factors that localize to these regions and putatively regulate mitotic activity. Knockdown of the mitotic network by siRNA identified 22 genes that might be considered as additional therapeutic targets for this clinically relevant patient subgroup. CONCLUSIONS We define a molecular signature which may guide therapeutic approaches for tumors with high mitotic network activity.
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Affiliation(s)
- Zhi Hu
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Jian-Hua Mao
- />Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94127 USA
| | - Christina Curtis
- />Department of Medicine, Division of Oncology and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Ge Huang
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Shenda Gu
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Laura Heiser
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Marc E. Lenburg
- />Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02215 USA
| | - James E. Korkola
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Nora Bayani
- />Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94127 USA
| | | | - Jose A. Seoane
- />Department of Medicine, Division of Oncology and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Mark A. Dane
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Amanda Esch
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Heidi S. Feiler
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Nicholas J. Wang
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | | | | | | | | | | | - Paul T. Spellman
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
| | - Samuel Aparicio
- />Molecular Oncology, BC Cancer Research Centre, Vancouver, Canada
| | | | - Carlos Caldas
- />Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Joe W. Gray
- />Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, 3303 SW Bond Ave., CH13B, Portland, OR 97239 USA
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Rittié L, Tejasvi T, Harms PW, Xing X, Nair RP, Gudjonsson JE, Swindell WR, Elder JT. Sebaceous Gland Atrophy in Psoriasis: An Explanation for Psoriatic Alopecia? J Invest Dermatol 2016; 136:1792-1800. [PMID: 27312025 DOI: 10.1016/j.jid.2016.05.113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 05/20/2016] [Accepted: 05/30/2016] [Indexed: 12/17/2022]
Abstract
In a transcriptome study of lesional psoriatic skin (PP) versus normal skin, we found a coexpressed gene module (N5) enriched 11.5-fold for lipid biosynthetic genes. We also observed fewer visible hairs in PP skin, compared with uninvolved nonlesional psoriatic skin or normal skin (P < 0.0001). To ask whether these findings might be due to abnormalities of the pilosebaceous unit, we carried out three-dimensional morphometric analysis of paired PP and nonlesional psoriatic skin biopsies. Sebaceous glands were markedly atrophic in PP versus nonlesional psoriatic skin (91% average reduction in volume, P = 0.031). Module N5 genes were strongly downregulated in PP versus normal skin (fold change < 0.25, 44.4-fold) and strongly upregulated in sebaceous hyperplasia (fold change > 4, 54.1-fold). The intersection of PP-downregulated and sebaceous hyperplasia-upregulated gene lists generated a gene expression signature consisting solely of module N5 genes, whose expression in PP versus normal skin was inversely correlated with the signature of IL17-stimulated keratinocytes. Despite loss of visible hairs, morphometry identified elongated follicles in PP versus nonlesional psoriatic skin (average 1.7 vs. 1.2 μm, P = 0.020). These results document sebaceous gland atrophy in nonscalp psoriasis, identify a cytokine-regulated set of sebaceous gland signature genes, and suggest that loss of visible hair in PP skin may result from abnormal sebaceous gland function.
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Affiliation(s)
- Laure Rittié
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Paul W Harms
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - William R Swindell
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA.
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28
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Kim JS, Jung M, Yoo J, Choi EH, Park BC, Kim MH, Hong SP. Protective Effect of Topical Vitamin D3 against Photocarcinogenesis in a Murine Model. Ann Dermatol 2016; 28:304-13. [PMID: 27274628 PMCID: PMC4884706 DOI: 10.5021/ad.2016.28.3.304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/10/2015] [Accepted: 07/23/2015] [Indexed: 12/26/2022] Open
Abstract
Background Although the incidence of non-melanoma skin cancer is increasing, there are no effective practical preventive measures other than avoiding sun exposure. Objective To elucidate the protective effect of topical application of biologically active vitamin D3 (calcitriol) on skin cancer development caused by exposure to ultraviolet (UV). Methods Groups of hairless mice were topically treated with either calcitriol or vehicle immediately after exposure to UVB and UVA three times weekly for the initial 20 weeks, and without UV exposure in the following 6 weeks. Tumor number was counted and biopsies were done for histopathologic analysis. The changes of cyclobutane pyrimidine dimer (CPD) were evaluated 1 hour and 11 hours after short term of UV exposure and application of calcitriol. For safety evaluation, blood test and body weights were evaluated at 23rd and 25th week. Results Total tumor count and number of tumors less than 3 mm in size tended to be fewer in calcitriol group, and tumors more than 3 mm in size showed significantly lower tumor formation rate in calcitriol group. Single application of calcitriol reduced CPD at 1 hour and 11 hours after UV exposure. Histopathologic analysis showed tumors with lower grade malignancy in calcitriol group which suggested a delay in tumor progression. However, serum levels of calcium and phosphate in calcitriol group were above normal range, and weight loss was found. Conclusion Topical calcitriol may suppress the formation and progression of UV-induced non-melanoma skin cancer by enhancing the repair mechanism of UV damage.
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Affiliation(s)
- Ji Seok Kim
- Department of Dermatology, Dankook University College of Medicine, Cheonan, Korea
| | - Minyoung Jung
- Department of Dermatology, Dankook University College of Medicine, Cheonan, Korea
| | - Jiyeon Yoo
- Department of Dermatology, Dankook University College of Medicine, Cheonan, Korea
| | - Eung Ho Choi
- Department of Dermatology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Byung Cheol Park
- Department of Dermatology, Dankook University College of Medicine, Cheonan, Korea
| | - Myung Hwa Kim
- Department of Dermatology, Dankook University College of Medicine, Cheonan, Korea
| | - Seung Phil Hong
- Department of Dermatology, Dankook University College of Medicine, Cheonan, Korea
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29
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Kumar V, Bouameur JE, Bär J, Rice RH, Hornig-Do HT, Roop DR, Schwarz N, Brodesser S, Thiering S, Leube RE, Wiesner RJ, Vijayaraj P, Brazel CB, Heller S, Binder H, Löffler-Wirth H, Seibel P, Magin TM. A keratin scaffold regulates epidermal barrier formation, mitochondrial lipid composition, and activity. J Cell Biol 2016; 211:1057-75. [PMID: 26644517 PMCID: PMC4674273 DOI: 10.1083/jcb.201404147] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Epidermal keratin filaments are important components and organizers of the cornified envelope and regulate mitochondrial metabolism by modulating their membrane composition. Keratin intermediate filaments (KIFs) protect the epidermis against mechanical force, support strong adhesion, help barrier formation, and regulate growth. The mechanisms by which type I and II keratins contribute to these functions remain incompletely understood. Here, we report that mice lacking all type I or type II keratins display severe barrier defects and fragile skin, leading to perinatal mortality with full penetrance. Comparative proteomics of cornified envelopes (CEs) from prenatal KtyI−/− and KtyII−/−K8 mice demonstrates that absence of KIF causes dysregulation of many CE constituents, including downregulation of desmoglein 1. Despite persistence of loricrin expression and upregulation of many Nrf2 targets, including CE components Sprr2d and Sprr2h, extensive barrier defects persist, identifying keratins as essential CE scaffolds. Furthermore, we show that KIFs control mitochondrial lipid composition and activity in a cell-intrinsic manner. Therefore, our study explains the complexity of keratinopathies accompanied by barrier disorders by linking keratin scaffolds to mitochondria, adhesion, and CE formation.
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Affiliation(s)
- Vinod Kumar
- Translational Centre for Regenerative Medicine Leipzig, University of Leipzig, 04103 Leipzig, Germany Institute of Biology, Division of Cell and Developmental Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Jamal-Eddine Bouameur
- Translational Centre for Regenerative Medicine Leipzig, University of Leipzig, 04103 Leipzig, Germany Institute of Biology, Division of Cell and Developmental Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Janina Bär
- Translational Centre for Regenerative Medicine Leipzig, University of Leipzig, 04103 Leipzig, Germany Institute of Biology, Division of Cell and Developmental Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Robert H Rice
- Department of Environmental Toxicology, University of California, Davis, Davis, CA 95616
| | - Hue-Tran Hornig-Do
- Center for Physiology and Pathophysiology, Institute for Vegetative Physiology, University of Cologne, 50931 Cologne, Germany
| | - Dennis R Roop
- Department of Dermatology, University of Colorado, Denver, CO 80045 Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado, Denver, CO 80045
| | - Nicole Schwarz
- Institute of Molecular and Cellular Anatomy, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany
| | - Susanne Brodesser
- Center for Physiology and Pathophysiology, Institute for Vegetative Physiology, University of Cologne, 50931 Cologne, Germany Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Medical Faculty, University of Cologne, 50931 Cologne, Germany Center for Molecular Medicine Cologne, 50931 Cologne, Germany
| | - Sören Thiering
- Translational Centre for Regenerative Medicine Leipzig, University of Leipzig, 04103 Leipzig, Germany Institute of Biology, Division of Cell and Developmental Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Rudolf E Leube
- Institute of Molecular and Cellular Anatomy, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany
| | - Rudolf J Wiesner
- Center for Physiology and Pathophysiology, Institute for Vegetative Physiology, University of Cologne, 50931 Cologne, Germany Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Medical Faculty, University of Cologne, 50931 Cologne, Germany Center for Molecular Medicine Cologne, 50931 Cologne, Germany
| | | | - Christina B Brazel
- Translational Centre for Regenerative Medicine Leipzig, University of Leipzig, 04103 Leipzig, Germany Institute of Biology, Division of Cell and Developmental Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Sandra Heller
- Center for Biotechnology and Biomedicine, 04103 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Henry Löffler-Wirth
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Peter Seibel
- Center for Biotechnology and Biomedicine, 04103 Leipzig, Germany
| | - Thomas M Magin
- Translational Centre for Regenerative Medicine Leipzig, University of Leipzig, 04103 Leipzig, Germany Institute of Biology, Division of Cell and Developmental Biology, University of Leipzig, 04103 Leipzig, Germany
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Barcellos-Hoff MH, Mao JH. HZE Radiation Non-Targeted Effects on the Microenvironment That Mediate Mammary Carcinogenesis. Front Oncol 2016; 6:57. [PMID: 27014632 PMCID: PMC4786544 DOI: 10.3389/fonc.2016.00057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/28/2016] [Indexed: 01/06/2023] Open
Abstract
Clear mechanistic understanding of the biological processes elicited by radiation that increase cancer risk can be used to inform prediction of health consequences of medical uses, such as radiotherapy, or occupational exposures, such as those of astronauts during deep space travel. Here, we review the current concepts of carcinogenesis as a multicellular process during which transformed cells escape normal tissue controls, including the immune system, and establish a tumor microenvironment. We discuss the contribution of two broad classes of radiation effects that may increase cancer: radiation targeted effects that occur as a result of direct energy deposition, e.g., DNA damage, and non-targeted effects (NTE) that result from changes in cell signaling, e.g., genomic instability. It is unknown whether the potentially greater carcinogenic effect of high Z and energy (HZE) particle radiation is a function of the relative contribution or extent of NTE or due to unique NTE. We addressed this problem using a radiation/genetic mammary chimera mouse model of breast cancer. Our experiments suggest that NTE promote more aggressive cancers, as evidenced by increased growth rate, transcriptomic signatures, and metastasis, and that HZE particle NTE are more effective than reference γ-radiation. Emerging evidence suggest that HZE irradiation dampens antitumor immunity. These studies raise concern that HZE radiation exposure not only increases the likelihood of developing cancer but also could promote progression to more aggressive cancer with a greater risk of mortality.
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Affiliation(s)
| | - Jian-Hua Mao
- Lawrence Berkeley National Laboratory , Berkeley, CA , USA
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31
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Kemp CJ. Animal Models of Chemical Carcinogenesis: Driving Breakthroughs in Cancer Research for 100 Years. Cold Spring Harb Protoc 2015; 2015:865-74. [PMID: 26430259 PMCID: PMC4949043 DOI: 10.1101/pdb.top069906] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The identification of carcinogens in the workplace, diet, and environment through chemical carcinogenesis studies in animals has directly contributed to a reduction of cancer burden in the human population. Reduced exposure to these carcinogens through lifestyle changes, government regulation, or change in industry practices has reduced cancer incidence in exposed populations. In addition to providing the first experimental evidence for cancer's relationship to chemical and radiation exposure, animal models of environmentally induced cancer have and will continue to provide important insight into the causes, mechanisms, and conceptual frameworks of cancer. More recently, combining chemical carcinogens with genetically engineered mouse models has emerged as an invaluable approach to study the complex interaction between genotype and environment that contributes to cancer development. In the future, animal models of environmentally induced cancer are likely to provide insight into areas such as the epigenetic basis of cancer, genetic modifiers of cancer susceptibility, the systems biology of cancer, inflammation and cancer, and cancer prevention.
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Affiliation(s)
- Christopher J Kemp
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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Abstract
BACKGROUND Gene expression microarrays measure the levels of messenger ribonucleic acid (mRNA) in a sample using probe sequences that hybridize with transcribed regions. These probe sequences are designed using a reference genome for the relevant species. However, most model organisms and all humans have genomes that deviate from their reference. These variations, which include single nucleotide polymorphisms, insertions of additional nucleotides, and nucleotide deletions, can affect the microarray's performance. Genetic experiments comparing individuals bearing different population-associated single nucleotide polymorphisms that intersect microarray probes are therefore subject to systemic bias, as the reduction in binding efficiency due to a technical artifact is confounded with genetic differences between parental strains. This problem has been recognized for some time, and earlier methods of compensation have attempted to identify probes affected by genome variants using statistical models. These methods may require replicate microarray measurement of gene expression in the relevant tissue in inbred parental samples, which are not always available in model organisms and are never available in humans. RESULTS By using sequence information for the genomes of organisms under investigation, potentially problematic probes can now be identified a priori. However, there is no published software tool that makes it easy to eliminate these probes from an annotation. I present equalizer, a software package that uses genome variant data to modify annotation files for the commonly used Affymetrix IVT and Gene/Exon platforms. These files can be used by any microarray normalization method for subsequent analysis. I demonstrate how use of equalizer on experiments mapping germline influence on gene expression in a genetic cross between two divergent mouse species and in human samples significantly reduces probe hybridization-induced bias, reducing false positive and false negative findings. CONCLUSIONS The equalizer package reduces probe hybridization bias from experiments performed on the Affymetrix microarray platform, allowing accurate assessment of germline influence on gene expression.
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Affiliation(s)
- David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, 94158, USA.
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Liu Z, Brunskill E, Varnum-Finney B, Zhang C, Zhang A, Jay PY, Bernstein I, Morimoto M, Kopan R. The intracellular domains of Notch1 and Notch2 are functionally equivalent during development and carcinogenesis. Development 2015; 142:2452-63. [PMID: 26062937 DOI: 10.1242/dev.125492] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/02/2015] [Indexed: 12/26/2022]
Abstract
Although Notch1 and Notch2 are closely related paralogs and function through the same canonical signaling pathway, they contribute to different outcomes in some cell and disease contexts. To understand the basis for these differences, we examined in detail mice in which the Notch intracellular domains (N1ICD and N2ICD) were swapped. Our data indicate that strength (defined here as the ultimate number of intracellular domain molecules reaching the nucleus, integrating ligand-mediated release and nuclear translocation) and duration (half-life of NICD-RBPjk-MAML-DNA complexes, integrating cooperativity and stability dependent on shared sequence elements) are the factors that underlie many of the differences between Notch1 and Notch2 in all the contexts we examined, including T-cell development, skin differentiation and carcinogenesis, the inner ear, the lung and the retina. We were able to show that phenotypes in the heart, endothelium, and marginal zone B cells are attributed to haploinsufficiency but not to intracellular domain composition. Tissue-specific differences in NICD stability were most likely caused by alternative scissile bond choices by tissue-specific γ-secretase complexes following the intracellular domain swap. Reinterpretation of clinical findings based on our analyses suggests that differences in outcome segregating with Notch1 or Notch2 are likely to reflect outcomes dependent on the overall strength of Notch signals.
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Affiliation(s)
- Zhenyi Liu
- SAGE Labs, A Horizon Discovery Group Company, St Louis, MO 63146, USA
| | - Eric Brunskill
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Barbara Varnum-Finney
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chi Zhang
- Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Andrew Zhang
- University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Patrick Y Jay
- Departments of Pediatrics and Genetics, Washington University, St Louis, MO 63110, USA
| | - Irv Bernstein
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Mitsuru Morimoto
- Lung Development and Regeneration, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Raphael Kopan
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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Chen J, Hackett CS, Zhang S, Song YK, Bell RJA, Molinaro AM, Quigley DA, Balmain A, Song JS, Costello JF, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA. The genetics of splicing in neuroblastoma. Cancer Discov 2015; 5:380-95. [PMID: 25637275 PMCID: PMC4390477 DOI: 10.1158/2159-8290.cd-14-0892] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/26/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Regulation of mRNA splicing, a critical and tightly regulated cellular function, underlies the majority of proteomic diversity and is frequently disrupted in disease. Using an integrative genomics approach, we combined both genomic data and exon-level transcriptome data in two somatic tissues (cerebella and peripheral ganglia) from a transgenic mouse model of neuroblastoma, a tumor that arises from the peripheral neural crest. Here, we describe splicing quantitative trait loci associated with differential splicing across the genome that we use to identify genes with previously unknown functions within the splicing pathway and to define de novo intronic splicing motifs that influence splicing from hundreds of bases away. Our results show that these splicing motifs represent sites for functional recurrent mutations and highlight novel candidate genes in human cancers, including childhood neuroblastoma. SIGNIFICANCE Somatic mutations with predictable downstream effects are largely relegated to coding regions, which comprise less than 2% of the human genome. Using an unbiased in vivo analysis of a mouse model of neuroblastoma, we have identified intronic splicing motifs that translate into sites for recurrent somatic mutations in human cancers.
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Affiliation(s)
- Justin Chen
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California. Department of Neurology, University of California, San Francisco, San Francisco, California. Department of Neurosurgery, University of California, San Francisco, San Francisco, California
| | - Christopher S Hackett
- Department of Neurology, University of California, San Francisco, San Francisco, California. Department of Neurosurgery, University of California, San Francisco, San Francisco, California
| | - Shile Zhang
- Program in Bioinformatics, Boston University, Boston, Massachusetts. Oncogenomics Section, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Young K Song
- Oncogenomics Section, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Robert J A Bell
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Annette M Molinaro
- Department of Neurology, University of California, San Francisco, San Francisco, California. Department of Neurosurgery, University of California, San Francisco, San Francisco, California. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California. Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California. Institute for Cancer Research, Oslo, Norway
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Jun S Song
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California. Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, Illinois. Department of Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois
| | - Joseph F Costello
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - W Clay Gustafson
- Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Terry Van Dyke
- Mouse Cancer Genetics Program, Center for Advanced Preclinical Research, National Cancer Institute, Frederick, Maryland
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California. Department of Dermatology, University of California, San Francisco, San Francisco, California. Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California
| | - Javed Khan
- Oncogenomics Section, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - William A Weiss
- Department of Neurology, University of California, San Francisco, San Francisco, California. Department of Neurosurgery, University of California, San Francisco, San Francisco, California. Department of Pediatrics, University of California, San Francisco, San Francisco, California.
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Letteboer TGW, Benzinou M, Merrick CB, Quigley DA, Zhau K, Kim IJ, To MD, Jablons DM, van Amstel JKP, Westermann CJJ, Giraud S, Dupuis-Girod S, Lesca G, Berg JH, Balmain A, Akhurst RJ. Genetic variation in the functional ENG allele inherited from the non-affected parent associates with presence of pulmonary arteriovenous malformation in hereditary hemorrhagic telangiectasia 1 (HHT1) and may influence expression of PTPN14. Front Genet 2015; 6:67. [PMID: 25815003 PMCID: PMC4357294 DOI: 10.3389/fgene.2015.00067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/09/2015] [Indexed: 01/09/2023] Open
Abstract
HHT shows clinical variability within and between families. Organ site and prevalence of arteriovenous malformations (AVMs) depend on the HHT causative gene and on environmental and genetic modifiers. We tested whether variation in the functional ENG allele, inherited from the unaffected parent, alters risk for pulmonary AVM in HHT1 mutation carriers who are ENG haploinsufficient. Genetic association was found between rs10987746 of the wild type ENG allele and presence of pulmonary AVM [relative risk = 1.3 (1.0018-1.7424)]. The rs10987746-C at-risk allele associated with lower expression of ENG RNA in a panel of human lymphoblastoid cell lines (P = 0.004). Moreover, in angiogenically active human lung adenocarcinoma tissue, but not in uninvolved quiescent lung, rs10987746-C was correlated with expression of PTPN14 (P = 0.004), another modifier of HHT. Quantitative TAQMAN expression analysis in a panel of normal lung tissues from 69 genetically heterogeneous inter-specific backcross mice, demonstrated strong correlation between expression levels of Eng, Acvrl1, and Ptpn14 (r2 = 0.75-0.9, P < 1 × 10(-12)), further suggesting a direct or indirect interaction between these three genes in lung in vivo. Our data indicate that genetic variation within the single functional ENG gene influences quantitative and/or qualitative differences in ENG expression that contribute to risk of pulmonary AVM in HHT1, and provide correlative support for PTPN14 involvement in endoglin/ALK1 lung biology in vivo. PTPN14 has been shown to be a negative regulator of Yap/Taz signaling, which is implicated in mechanotransduction, providing a possible molecular link between endoglin/ALK1 signaling and mechanical stress. EMILIN2, which showed suggestive genetic association with pulmonary AVM, is also reported to interact with Taz in angiogenesis. Elucidation of the molecular mechanisms regulating these interactions in endothelial cells may ultimately provide more rational choices for HHT therapy.
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Affiliation(s)
- Tom G W Letteboer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco San Francisco, CA, USA ; Department of Medical Genetics, University Medical Centre Utrecht Utrecht, Netherlands
| | - Michael Benzinou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco San Francisco, CA, USA
| | - Christopher B Merrick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco San Francisco, CA, USA ; Department of Clinical Genetics, University of Dundee Dundee, UK
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco San Francisco, CA, USA
| | - Kechen Zhau
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco San Francisco, CA, USA
| | - Il-Jin Kim
- Department of Surgery, University of California, San Francisco San Francisco, CA, USA
| | - Minh D To
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco San Francisco, CA, USA ; Department of Surgery, University of California, San Francisco San Francisco, CA, USA
| | - David M Jablons
- Department of Surgery, University of California, San Francisco San Francisco, CA, USA
| | | | | | - Sophie Giraud
- Department of Medical Genetics, Lyon University Hospital Lyon, France
| | | | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital Lyon, France
| | - Jonathan H Berg
- Department of Clinical Genetics, University of Dundee Dundee, UK
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco San Francisco, CA, USA ; Department of Biochemistry and Biophysics, University of California, San Francisco San Francisco, CA, USA ; Institute of Human Genetics, University of California, San Francisco San Francisco, CA, USA
| | - Rosemary J Akhurst
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco San Francisco, CA, USA ; Institute of Human Genetics, University of California, San Francisco San Francisco, CA, USA ; Department of Anatomy, University of California, San Francisco San Francisco, CA, USA
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Zhu J, Xiong G, Fu H, Evers BM, Zhou BP, Xu R. Chaperone Hsp47 Drives Malignant Growth and Invasion by Modulating an ECM Gene Network. Cancer Res 2015; 75:1580-91. [PMID: 25744716 DOI: 10.1158/0008-5472.can-14-1027] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 01/21/2015] [Indexed: 01/08/2023]
Abstract
The extracellular matrix (ECM) is a determining factor in the tumor microenvironment that restrains or promotes malignant growth. In this report, we show how the molecular chaperone protein Hsp47 functions as a nodal hub in regulating an ECM gene transcription network. A transcription network analysis showed that Hsp47 expression was activated during breast cancer development and progression. Hsp47 silencing reprogrammed human breast cancer cells to form growth-arrested and/or noninvasive structures in 3D cultures, and to limit tumor growth in xenograft assays by reducing deposition of collagen and fibronectin. Coexpression network analysis also showed that levels of microRNA(miR)-29b and -29c were inversely correlated with expression of Hsp47 and ECM network genes in human breast cancer tissues. We found that miR-29 repressed expression of Hsp47 along with multiple ECM network genes. Ectopic expression of miR-29b suppressed malignant phenotypes of breast cancer cells in 3D culture. Clinically, increased expression of Hsp47 and reduced levels of miR-29b and -29c were associated with poor survival outcomes in breast cancer patients. Our results show that Hsp47 is regulated by miR-29 during breast cancer development and progression, and that increased Hsp47 expression promotes cancer progression in part by enhancing deposition of ECM proteins.
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Affiliation(s)
- Jieqing Zhu
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky
| | - Gaofeng Xiong
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky
| | - Hanjiang Fu
- Beijing Institute of Radiation Medicine, Beijing, People's Republic of China
| | - B Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Surgery, University of Kentucky, Lexington, Kentucky
| | - Binhua P Zhou
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky
| | - Ren Xu
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky.
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Expression quantitative trait loci and receptor pharmacology implicate Arg1 and the GABA-A receptor as therapeutic targets in neuroblastoma. Cell Rep 2014; 9:1034-46. [PMID: 25437558 DOI: 10.1016/j.celrep.2014.09.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 08/14/2014] [Accepted: 09/25/2014] [Indexed: 02/05/2023] Open
Abstract
The development of targeted therapeutics for neuroblastoma, the third most common tumor in children, has been limited by a poor understanding of growth signaling mechanisms unique to the peripheral nerve precursors from which tumors arise. In this study, we combined genetics with gene-expression analysis in the peripheral sympathetic nervous system to implicate arginase 1 and GABA signaling in tumor formation in vivo. In human neuroblastoma cells, either blockade of ARG1 or benzodiazepine-mediated activation of GABA-A receptors induced apoptosis and inhibited mitogenic signaling through AKT and MAPK. These results suggest that ARG1 and GABA influence both neural development and neuroblastoma and that benzodiazepines in clinical use may have potential applications for neuroblastoma therapy.
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38
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Refining the role for adult stem cells as cancer cells of origin. Trends Cell Biol 2014; 25:11-20. [PMID: 25242116 DOI: 10.1016/j.tcb.2014.08.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/22/2014] [Accepted: 08/25/2014] [Indexed: 12/17/2022]
Abstract
Significant progress has been made to identify the cells at the foundation of tumorigenesis, the cancer cell of origin (CCO). The majority of data points towards resident adult stem cells (ASCs) or primitive progenitors as the CCO for those cancers studied, highlighting the importance of stem cells not only as propagators but also as initiators of cancer. Recent data suggest tumor initiation at the CCOs can be regulated through both intrinsic and extrinsic signals and that the identity of the CCOs and their propensity to initiate tumorigenesis is context dependent. In this review, we summarize some of the recent findings regarding CCOs and solid tumor initiation and highlight its relation with bona fide human cancer.
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39
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Huang PY, Balmain A. Modeling cutaneous squamous carcinoma development in the mouse. Cold Spring Harb Perspect Med 2014; 4:a013623. [PMID: 25183851 DOI: 10.1101/cshperspect.a013623] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cutaneous squamous cell carcinoma (SCC) is one of the most common cancers in Caucasian populations and is associated with a significant risk of morbidity and mortality. The classic mouse model for studying SCC involves two-stage chemical carcinogenesis, which has been instrumental in the evolution of the concept of multistage carcinogenesis, as widely applied to both human and mouse cancers. Much is now known about the sequence of biological and genetic events that occur in this skin carcinogenesis model and the factors that can influence the course of tumor development, such as perturbations in the oncogene/tumor-suppressor signaling pathways involved, the nature of the target cell that acquires the first genetic hit, and the role of inflammation. Increasingly, studies of tumor-initiating cells, malignant progression, and metastasis in mouse skin cancer models will have the potential to inform future approaches to treatment and chemoprevention of human squamous malignancies.
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Affiliation(s)
- Phillips Y Huang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158
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40
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Abstract
Psoriasis is a chronic inflammatory skin disease driven by aberrant signals from the immune system. In this issue Li et al. present the first large RNA-seq analysis of gene expression in normal skin and psoriasis lesions, providing a more comprehensive view of mRNA expression than earlier microarray studies. This study’s size enables gene co-expression analysis, a method illustrating which pathways are altered by the presence of disease.
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41
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Lee SM, Bishop KA, Goellner JJ, O'Brien CA, Pike JW. Mouse and human BAC transgenes recapitulate tissue-specific expression of the vitamin D receptor in mice and rescue the VDR-null phenotype. Endocrinology 2014; 155:2064-76. [PMID: 24693968 PMCID: PMC4020932 DOI: 10.1210/en.2014-1107] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological actions of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) are mediated by the vitamin D receptor (VDR), which is expressed in numerous target tissues in a cell type-selective manner. Recent studies using genomic analyses and recombineered bacterial artificial chromosomes (BACs) have defined the specific features of mouse and human VDR gene loci in vitro. In the current study, we introduced recombineered mouse and human VDR BACs as transgenes into mice and explored their expression capabilities in vivo. Individual transgenic mouse strains selectively expressed BAC-derived mouse or human VDR proteins in appropriate vitamin D target tissues, thereby recapitulating the tissue-specific expression of endogenous mouse VDR. The mouse VDR transgene was also regulated by 1,25(OH)2D3 and dibutyryl-cAMP. When crossed into a VDR-null mouse background, both transgenes restored wild-type basal as well as 1,25(OH)2D3-inducible gene expression patterns in the appropriate tissues. This maneuver resulted in the complete rescue of the aberrant phenotype noted in the VDR-null mouse, including systemic features associated with altered calcium and phosphorus homeostasis and disrupted production of parathyroid hormone and fibroblast growth factor 23, and abnormalities associated with the skeleton, kidney, parathyroid gland, and the skin. This study suggests that both mouse and human VDR transgenes are capable of recapitulating basal and regulated expression of the VDR in the appropriate mouse tissues and restore 1,25(OH)2D3 function. These results provide a baseline for further dissection of mechanisms integral to mouse and human VDR gene expression and offer the potential to explore the consequence of selective mutations in VDR proteins in vivo.
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Affiliation(s)
- Seong Min Lee
- Department of Biochemistry (S.M.L., K.A.B., J.W.P.), University of Wisconsin-Madison, Madison, Wisconsin 53706; and University of Arkansas for Medical Sciences (J.J.G., C.A.O.), Little Rock, Arkansas 72205
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Kristensen VN, Lingjærde OC, Russnes HG, Vollan HKM, Frigessi A, Børresen-Dale AL. Principles and methods of integrative genomic analyses in cancer. Nat Rev Cancer 2014; 14:299-313. [PMID: 24759209 DOI: 10.1038/nrc3721] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Combined analyses of molecular data, such as DNA copy-number alteration, mRNA and protein expression, point to biological functions and molecular pathways being deregulated in multiple cancers. Genomic, metabolomic and clinical data from various solid cancers and model systems are emerging and can be used to identify novel patient subgroups for tailored therapy and monitoring. The integrative genomics methodologies that are used to interpret these data require expertise in different disciplines, such as biology, medicine, mathematics, statistics and bioinformatics, and they can seem daunting. The objectives, methods and computational tools of integrative genomics that are available to date are reviewed here, as is their implementation in cancer research.
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Affiliation(s)
- Vessela N Kristensen
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, 1478 Ahus, Norway
| | - Ole Christian Lingjærde
- 1] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [2] Division for Biomedical Informatics, Department of Computer Science, University of Oslo, 0316 Oslo, Norway
| | - Hege G Russnes
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Pathology, Oslo University Hospital, 0450 Oslo, Norway
| | - Hans Kristian M Vollan
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, 0450 Oslo, Norway
| | - Arnoldo Frigessi
- 1] Statistics for Innovation, Norwegian Computing Center, 0314 Oslo, Norway. [2] Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Anne-Lise Børresen-Dale
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
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Identification of Hipk2 as an essential regulator of white fat development. Proc Natl Acad Sci U S A 2014; 111:7373-8. [PMID: 24785298 DOI: 10.1073/pnas.1322275111] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Homeodomain-interacting protein kinase 2 (Hipk2) has previously been implicated in the control of several transcription factors involved in embryonic development, apoptosis, cell proliferation, and tumor development, but very little is understood about the exact mechanisms through which Hipk2 influences these processes. Analysis of gene expression in normal tissues from genetically heterogeneous mouse or human populations can reveal network motifs associated with the structural or functional components of the tissue, and may predict roles for genes of unknown function. Here we have applied this network strategy to uncover a role for the Hipk2 gene in the transcriptional system controlling adipogenesis. Both in vitro and in vivo models were used to show that knockdown or loss of Hipk2 specifically inhibits white adipose cell differentiation and tissue development. In addition, loss of Hipk2 leads to induction of pockets of multilocular brown fat-like cells in remaining white adipose depots, which express markers of brown and beige fat such as uncoupling protein 1 and transmembrane protein 26. These changes are accompanied by increased insulin sensitivity in Hipk2 knockout mice and reduced high-fat diet-induced weight gain, highlighting a potential role for this kinase in diseases such as diabetes and obesity. Our study underscores the versatility and power of a readily available tissue, such as skin, for network modeling of systemic transcriptional programs involved in multiple pathways, including lipid metabolism and adipogenesis.
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Nakata S, Phillips E, Goidts V. Emerging role for leucine-rich repeat-containing G-protein-coupled receptors LGR5 and LGR4 in cancer stem cells. Cancer Manag Res 2014; 6:171-80. [PMID: 24711713 PMCID: PMC3969255 DOI: 10.2147/cmar.s57846] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The concept of cancer stem cells has gained considerable interest in the last few decades, partly because of their potential implication in therapy resistance. However, the lack of specific cellular surface markers for these cells has impeded their isolation, making the characterization of this cellular subpopulation technically challenging. Recent studies have indicated that leucine-rich repeat-containing G-protein-coupled receptor 4 and 5 (LGR4 and LGR5) expression in multiple organs may represent a global marker of adult stem cells. This review aims to give an overview of LGR4 and LGR5 as cancer stem cell markers and their function in development.
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Affiliation(s)
- Susumu Nakata
- Division of Oncological Pathology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Emma Phillips
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Violaine Goidts
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
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Xu J, Weng Z, Arumugam A, Tang X, Chaudhary SC, Li C, Christiano AM, Elmets CA, Bickers DR, Athar M. Hair follicle disruption facilitates pathogenesis to UVB-induced cutaneous inflammation and basal cell carcinoma development in Ptch(+/-) mice. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1529-40. [PMID: 24631180 DOI: 10.1016/j.ajpath.2014.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 12/23/2013] [Accepted: 01/23/2014] [Indexed: 01/01/2023]
Abstract
Hairless mice carrying homozygous mutations in hairless gene manifest rudimentary hair follicles (HFs), epidermal cysts, hairless phenotype, and enhanced susceptibility to squamous cell carcinomas. However, their susceptibility to basal cell carcinomas (BCCs), a neoplasm considered originated from HF-localized stem cells, is unknown. To demonstrate the role of HFs in BCC development, we bred Ptch(+/-)/C57BL6 with SKH-1 hairless mice, followed by brother-sister cross to get F2 homozygous mutant (hairless) or wild-type (haired) mice. UVB-induced inflammation was less pronounced in shaved haired than in hairless mice. In hairless mice, inflammatory infiltrate was found around the rudimentary HFs and epidermal cysts. Expression of epidermal IL1f6, S100a8, vitamin D receptor, repetin, and major histocompatibility complex II, biomarkers depicting susceptibility to cutaneous inflammation, was also higher. In these animals, HF disruption altered susceptibility to UVB-induced BCCs. Tumor onset in hairless mice was 10 weeks earlier than in haired littermates. The incidence of BCCs was significantly higher in hairless than in haired animals; however, the magnitude of sonic hedgehog signaling did not differ significantly. Overall, 100% of hairless mice developed >12 tumors per mouse after 32 weeks of UVB therapy, whereas haired mice developed fewer than three tumors per mouse after 44 weeks of long-term UVB irradiation. Tumors in hairless mice were more aggressive than in haired littermates and manifested decreased E-cadherin and enhanced mesenchymal proteins. These data provide novel evidence that disruption of HFs in Ptch(+/-) mice enhances cutaneous susceptibility to inflammation and BCCs.
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Affiliation(s)
- Jianmin Xu
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhiping Weng
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Aadithya Arumugam
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Xiuwei Tang
- Department of Dermatology, Columbia University, New York, New York
| | - Sandeep C Chaudhary
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Changzhao Li
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Craig A Elmets
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - David R Bickers
- Department of Dermatology, Columbia University, New York, New York
| | - Mohammad Athar
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, Alabama.
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Barcellos-Hoff MH, Adams C, Balmain A, Costes SV, Demaria S, Illa-Bochaca I, Mao JH, Ouyang H, Sebastiano C, Tang J. Systems biology perspectives on the carcinogenic potential of radiation. JOURNAL OF RADIATION RESEARCH 2014; 55. [PMCID: PMC3941546 DOI: 10.1093/jrr/rrt211] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
This review focuses on recent experimental and modeling studies that attempt to define the physiological context in which high linear energy transfer (LET) radiation increases epithelial cancer risk and the efficiency with which it does so. Radiation carcinogenesis is a two-compartment problem: ionizing radiation can alter genomic sequence as a result of damage due to targeted effects (TE) from the interaction of energy and DNA; it can also alter phenotype and multicellular interactions that contribute to cancer by poorly understood non-targeted effects (NTE). Rather than being secondary to DNA damage and mutations that can initiate cancer, radiation NTE create the critical context in which to promote cancer. Systems biology modeling using comprehensive experimental data that integrates different levels of biological organization and time-scales is a means of identifying the key processes underlying the carcinogenic potential of high-LET radiation. We hypothesize that inflammation is a key process, and thus cancer susceptibility will depend on specific genetic predisposition to the type and duration of this response. Systems genetics using novel mouse models can be used to identify such determinants of susceptibility to cancer in radiation sensitive tissues following high-LET radiation. Improved understanding of radiation carcinogenesis achieved by defining the relative contribution of NTE carcinogenic effects and identifying the genetic determinants of the high-LET cancer susceptibility will help reduce uncertainties in radiation risk assessment.
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Affiliation(s)
- Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
- Corresponding author. Department of Radiation Oncology, New York University School of Medicine, 450 East 29th Street, New York, NY 10016, USA. Tel: +1-212-263-3021;
| | - Cassandra Adams
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 Third Street, San Francisco, CA 94158, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 Third Street, San Francisco, CA 94158, USA
| | - Sylvain V. Costes
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS977, Berkeley CA 94720, USA
| | - Sandra Demaria
- Department of Pathology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
| | - Irineu Illa-Bochaca
- Department of Radiation Oncology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
| | - Jian Hua Mao
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS977, Berkeley CA 94720, USA
| | - Haoxu Ouyang
- Department of Radiation Oncology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
| | - Christopher Sebastiano
- Department of Pathology, New York University School of Medicine, 566 First Avenue, New York, NY 10016, USA
| | - Jonathan Tang
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS977, Berkeley CA 94720, USA
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Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, Ding J, Stuart PE, Xing X, Kochkodan JJ, Voorhees JJ, Kang HM, Nair RP, Abecasis GR, Elder JT. Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms. J Invest Dermatol 2014; 134:1828-1838. [PMID: 24441097 PMCID: PMC4057954 DOI: 10.1038/jid.2014.28] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/27/2013] [Accepted: 12/09/2013] [Indexed: 02/08/2023]
Abstract
To increase our understanding of psoriasis, we utilized RNA-seq to assay the transcriptomes of lesional psoriatic and normal skin. We sequenced polyadenylated RNA-derived cDNAs from 92 psoriatic and 82 normal punch biopsies, generating an average of ~38 million single-end 80-bp reads per sample. Comparison of 42 samples examined by both RNA-seq and microarray revealed marked differences in sensitivity, with transcripts identified only by RNA-seq having much lower expression than those also identified by microarray. RNA-seq identified many more differentially expressed transcripts enriched in immune system processes. Weighted gene co-expression network analysis (WGCNA) revealed multiple modules of coordinately expressed epidermal differentiation genes, overlapping significantly with genes regulated by the long non-coding RNA TINCR, its target gene, staufen-1 (STAU1), the p63 target gene ZNF750, and its target KLF4. Other coordinately expressed modules were enriched for lymphoid and/or myeloid signature transcripts and genes induced by IL-17 in keratinocytes. Dermally-expressed genes were significantly down-regulated in psoriatic biopsies, most likely due to expansion of the epidermal compartment. These results demonstrate the power of WGCNA to elucidate gene regulatory circuits in psoriasis, and emphasize the influence of tissue architecture in both differential expression and co-expression analysis.
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Affiliation(s)
- Bingshan Li
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - William R Swindell
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew Johnston
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jun Ding
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA; Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - James J Kochkodan
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Hyun M Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, USA.
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48
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Stacey SN, Sulem P, Gudbjartsson DF, Jonasdottir A, Thorleifsson G, Gudjonsson SA, Masson G, Gudmundsson J, Sigurgeirsson B, Benediktsdottir KR, Thorisdottir K, Ragnarsson R, Fuentelsaz V, Corredera C, Grasa M, Planelles D, Sanmartin O, Rudnai P, Gurzau E, Koppova K, Hemminki K, Nexø BA, Tjønneland A, Overvad K, Johannsdottir H, Helgadottir HT, Thorsteinsdottir U, Kong A, Vogel U, Kumar R, Nagore E, Mayordomo JI, Rafnar T, Olafsson JH, Stefansson K. Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma. Hum Mol Genet 2014; 23:3045-53. [PMID: 24403052 PMCID: PMC4014188 DOI: 10.1093/hmg/ddt671] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
To search for new sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conducted a genome-wide association study of 38.5 million single nucleotide polymorphisms (SNPs) and small indels identified through whole-genome sequencing of 2230 Icelanders. We imputed genotypes for 4208 BCC patients and 109 408 controls using Illumina SNP chip typing data, carried out association tests and replicated the findings in independent population samples. We found new BCC susceptibility loci at TGM3 (rs214782[G], P = 5.5 × 10−17, OR = 1.29) and RGS22 (rs7006527[C], P = 8.7 × 10−13, OR = 0.77). TGM3 encodes transglutaminase type 3, which plays a key role in production of the cornified envelope during epidermal differentiation.
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Affiliation(s)
- Simon N Stacey
- deCODE Genetics/AMGEN, Sturlugata 8, 101 Reykjavik, Iceland
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49
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Beyond expectations: novel insights into epidermal keratin function and regulation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 311:265-306. [PMID: 24952920 DOI: 10.1016/b978-0-12-800179-0.00007-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The epidermis is a stratified epithelium that relies on its cytoskeleton and cell junctions to protect the body against mechanical injury, dehydration, and infections. Keratin intermediate filament proteins are involved in many of these functions by forming cell-specific cytoskeletal scaffolds crucial for the maintenance of cell and tissue integrity. In response to various stresses, the expression and organization of keratins are altered at transcriptional and posttranslational levels to restore tissue homeostasis. Failure to restore tissue homeostasis in the presence of keratin gene mutations results in acute and chronic skin disorders for which currently no rational therapies are available. Here, we review the recent progress on the role of keratins in cytoarchitecture, adhesion, signaling, and inflammation. By focusing on epidermal keratins, we illustrate the contribution of keratin isotypes to differentiated epithelial functions.
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50
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Faraji F, Hu Y, Wu G, Goldberger NE, Walker RC, Zhang J, Hunter KW. An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease. Genome Res 2013; 24:227-40. [PMID: 24322557 PMCID: PMC3912413 DOI: 10.1101/gr.166223.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Metastasis is the result of stochastic genomic and epigenetic events leading to gene expression profiles that drive tumor dissemination. Here we exploit the principle that metastatic propensity is modified by the genetic background to generate prognostic gene expression signatures that illuminate regulators of metastasis. We also identify multiple microRNAs whose germline variation is causally linked to tumor progression and metastasis. We employ network analysis of global gene expression profiles in tumors derived from a panel of recombinant inbred mice to identify a network of co-expressed genes centered on Cnot2 that predicts metastasis-free survival. Modulating Cnot2 expression changes tumor cell metastatic potential in vivo, supporting a functional role for Cnot2 in metastasis. Small RNA sequencing of the same tumor set revealed a negative correlation between expression of the Mir216/217 cluster and tumor progression. Expression quantitative trait locus analysis (eQTL) identified cis-eQTLs at the Mir216/217 locus, indicating that differences in expression may be inherited. Ectopic expression of Mir216/217 in tumor cells suppressed metastasis in vivo. Finally, small RNA sequencing and mRNA expression profiling data were integrated to reveal that miR-3470a/b target a high proportion of network transcripts. In vivo analysis of Mir3470a/b demonstrated that both promote metastasis. Moreover, Mir3470b is a likely regulator of the Cnot2 network as its overexpression down-regulated expression of network hub genes and enhanced metastasis in vivo, phenocopying Cnot2 knockdown. The resulting data from this strategy identify Cnot2 as a novel regulator of metastasis and demonstrate the power of our systems-level approach in identifying modifiers of metastasis.
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Affiliation(s)
- Farhoud Faraji
- Metastasis Susceptibility Section, Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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