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Cai H, Chen L, Yang S, Jiang R, Guo Y, He M, Luo Y, Hong G, Li H, Song K. Personalized differential expression analysis in triple-negative breast cancer. Brief Funct Genomics 2024; 23:495-506. [PMID: 38197537 DOI: 10.1093/bfgp/elad057] [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: 01/30/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024] Open
Abstract
Identification of individual-level differentially expressed genes (DEGs) is a pre-step for the analysis of disease-specific biological mechanisms and precision medicine. Previous algorithms cannot balance accuracy and sufficient statistical power. Herein, RankCompV2, designed for identifying population-level DEGs based on relative expression orderings, was adjusted to identify individual-level DEGs. Furthermore, an optimized version of individual-level RankCompV2, named as RankCompV2.1, was designed based on the assumption that the rank positions of genes and relative rank differences of gene pairs would influence the identification of individual-level DEGs. In comparison to other individualized analysis algorithms, RankCompV2.1 performed better on statistical power, computational efficiency, and acquired coequal accuracy in both simulation and real paired cancer-normal data from ten cancer types. Besides, single sample GSEA and Gene Set Variation Analysis analysis showed that pathways enriched with up-regulated and down-regulated genes presented higher and lower enrichment scores, respectively. Furthermore, we identified 16 genes that were universally deregulated in 966 triple-negative breast cancer (TNBC) samples and interacted with Food and Drug Administration (FDA)-approved drugs or antineoplastic agents, indicating notable therapeutic targets for TNBC. In addition, we also identified genes with highly variable deregulation status and used these genes to cluster TNBC samples into three subgroups with different prognoses. The subgroup with the poorest outcome was characterized by down-regulated immune-regulated pathways, signal transduction pathways, and apoptosis-related pathways. Protein-protein interaction network analysis revealed that OAS family genes may be promising drug targets to activate tumor immunity in this subgroup. In conclusion, RankCompV2.1 is capable of identifying individual-level DEGs with high accuracy and statistical power, analyzing mechanisms of carcinogenesis and exploring therapeutic strategy.
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Affiliation(s)
- Hao Cai
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Liangbo Chen
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Shuxin Yang
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, China
| | - Ronghong Jiang
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - You Guo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Ming He
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Yun Luo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Guini Hong
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Hongdong Li
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, China
| | - Kai Song
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
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2
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Anglada-Girotto M, Moakley DF, Zhang C, Miravet-Verde S, Califano A, Serrano L. Disentangling the splicing factor programs underlying complex molecular phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600051. [PMID: 38979366 PMCID: PMC11230296 DOI: 10.1101/2024.06.21.600051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The regulation of exon inclusion through alternative splicing tunes the cell's behavior by increasing the functional diversity of the transcriptome and the proteome. Splicing factors work in concert to generate gene isoform pools that contribute to cell phenotypes yet their activity is controlled by multiple regulatory and signaling layers. This hinders identification of functional, phenotype-specific splicing factors using traditional single-omic measurements, such as their mutational state or expression. To address this challenge, we propose repurposing the virtual inference of protein activity by enriched regulon analysis (VIPER) to measure splicing factor activity solely from their downstream exon transcriptomic inclusion signatures. This approach is effective in assessing the effect of co-occurring splicing factor perturbations, as well as their post-translational regulation. As proof of concept, we dissect recurrent splicing factor programs underlying tumorigenesis including aberrantly activated factors acting as oncogenes and inactivated ones acting as tumor suppressors, which are undetectable by more conventional methodologies. Activation and inactivation of these cancer splicing programs effectively stratifies overall survival, as well as cancer hallmarks such as proliferation and immune evasion. Altogether, repurposing network-based inference of protein activity for splicing factor networks distills common, functionally relevant splicing programs in otherwise heterogeneous molecular contexts.
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Affiliation(s)
- Miquel Anglada-Girotto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Daniel F. Moakley
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Center for Motor Neuron Biology and Disease, Columbia University, New York, USA 10032
| | - Chaolin Zhang
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Center for Motor Neuron Biology and Disease, Columbia University, New York, USA 10032
| | - Samuel Miravet-Verde
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Andrea Califano
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Chan Zuckerberg Biohub New York, New York, NY, USA
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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Lennartz M, Löhr N, Höflmayer D, Dwertmann Rico S, von Bargen C, Kind S, Reiswich V, Viehweger F, Lutz F, Bertram V, Fraune C, Gorbokon N, Weidemann S, Blessin NC, Hube-Magg C, Menz A, Schlichter R, Krech T, Hinsch A, Burandt E, Sauter G, Simon R, Kluth M, Marx AH, Lebok P, Dum D, Minner S, Jacobsen F, Clauditz TS, Bernreuther C, Steurer S. TRPS1 is a Highly Sensitive Marker for Breast Cancer: A Tissue Microarray Study Evaluating More Than 19,000 Tumors From 152 Different Tumor Entities. Am J Surg Pathol 2024; 48:637-651. [PMID: 38647255 PMCID: PMC11093513 DOI: 10.1097/pas.0000000000002213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Trichorhinophalangeal syndrome 1 (TRPS1) is a nuclear protein highly expressed in breast epithelial cells. TRPS1 immunohistochemistry (IHC) has been suggested as a breast cancer marker. To determine the diagnostic and prognostic utility of TRPS1 IHC, tissue microarrays containing 19,201 samples from 152 different tumor types and subtypes were analyzed. GATA3 IHC was performed in a previous study. TRPS1 staining was seen in 86 of 152 tumor categories with 36 containing at least one strongly positive case. TRPS1 staining predominated in various types of breast carcinomas (51%-100%), soft tissue tumors (up to 100%), salivary gland tumors (up to 46%), squamous cell carcinomas (up to 35%), and gynecological cancers (up to 40%). TRPS1 positivity occurred in 1.8% of 1083 urothelial neoplasms. In invasive breast carcinoma of no special type, low TRPS1 expression was linked to high grade ( P = 0.0547), high pT ( P < 0.0001), nodal metastasis ( P = 0.0571), loss of estrogen receptor and progesterone receptor expression ( P < 0.0001 each), and triple-negative status ( P < 0.0001) but was unrelated to patient survival ( P = 0.8016). In squamous cell carcinomas from 11 different sites, low TRPS1 expression was unrelated to tumor phenotype. Positivity for both TRPS1 and GATA3 occurred in 47.4% to 100% of breast cancers, up to 30% of salivary gland tumors, and 29 (0.3%) of 9835 tumors from 134 other cancer entities. TRPS1 IHC has high utility for the identification of cancers of breast (or salivary gland) origin, especially in combination with GATA3. The virtual absence of TRPS1 positivity in urothelial neoplasms is useful for the distinction of GATA3-positive urothelial carcinoma from breast cancer.
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Affiliation(s)
- Maximilian Lennartz
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Neele Löhr
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Doris Höflmayer
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Clara von Bargen
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Kind
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Viktor Reiswich
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Viehweger
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Lutz
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Veit Bertram
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Fraune
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Natalia Gorbokon
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sören Weidemann
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Niclas C. Blessin
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Hube-Magg
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Menz
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ria Schlichter
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Krech
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pathology, Clinical Center Osnabrueck, Osnabrueck, Germany
| | - Andrea Hinsch
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eike Burandt
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martina Kluth
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas H. Marx
- Department of Pathology, Academic Hospital Fuerth, Fuerth, Germany
| | - Patrick Lebok
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pathology, Clinical Center Osnabrueck, Osnabrueck, Germany
| | - David Dum
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Minner
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frank Jacobsen
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till S. Clauditz
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Bernreuther
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Steurer
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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4
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Tinholt M, Tekpli X, Torland LA, Tahiri A, Geisler J, Kristensen V, Sandset PM, Iversen N. The breast cancer coagulome in the tumor microenvironment and its role in prognosis and treatment response to chemotherapy. J Thromb Haemost 2024; 22:1319-1335. [PMID: 38237862 DOI: 10.1016/j.jtha.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/08/2023] [Accepted: 01/02/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND The procoagulant phenotype in cancer is linked to thrombosis, cancer progression, and immune response. A novel treatment that reduces the risk of both thrombosis and cancer progression without excess bleeding risk remains to be identified. OBJECTIVES Here, we aimed to broadly investigate the breast tumor coagulome and its relation to prognosis, treatment response to chemotherapy, and the tumor microenvironment. METHODS Key coagulation-related genes (n = 35) were studied in a Norwegian cohort with tumor (n = 134) and normal (n = 189) tissue and in the Cancer Genome Atlas (n = 1052) data set. We performed gene set variation analysis in the Norwegian cohort, and in the Cancer Genome Atlas cohort, associations with the tumor microenvironment and prognosis were evaluated. Analyses were performed with cBioPortal, Estimation of Stromal and Immune cells in Malignant Tumors Using Expression Data, Tumor Immune Estimation Resource, the integrated repository portal for tumor-immune system interactions, Tumor Immune Single-cell Hub 2, and the receiver operating characteristic plotter. Six independent breast cancer cohorts were used to study the tumor coagulome and treatment response to chemotherapy. RESULTS Twenty-two differentially expressed coagulation-related genes were identified in breast tumors. Several coagulome factors were correlated with tumor microenvironment characteristics and were expressed by nonmalignant cells in the tumor microenvironment. PLAT and F8 were independent predictors of better overall survival and progression-free survival, respectively. F12 and PLAU were predictors of worse progression-free survival. The PROCR-THBD-PLAT signature showed a promising predictive value (area under the curve, 0.75; 95% CI, 0.69-0.81; P = 3.6 × 10-17) for combination chemotherapy with fluorouracil, epirubicin, and cyclophosphamide. CONCLUSION The breast tumor coagulome showed potential in prediction of prognosis and chemotherapy response. Cells within the tumor microenvironment are sources of coagulome factors and may serve as therapeutic targets of coagulation factors.
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Affiliation(s)
- Mari Tinholt
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Department of Haematology, Oslo University Hospital, Oslo, Norway.
| | - Xavier Tekpli
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Lilly Anne Torland
- Department of Research and Innovation, Vestre Viken Hospital Trust, Drammen, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andliena Tahiri
- Department of Research and Innovation, Vestre Viken Hospital Trust, Drammen, Norway; Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital, Lørenskog, Norway
| | - Jürgen Geisler
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway; Institute of Clinical Medicine, University of Oslo, Campus Akershus University Hospital, Lørenskog, Norway
| | - Vessela Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Per Morten Sandset
- Department of Haematology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Research Institute of Internal Medicine, Oslo University Hospital, Norway
| | - Nina Iversen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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5
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Lai PM, Chan KM. Roles of Histone H2A Variants in Cancer Development, Prognosis, and Treatment. Int J Mol Sci 2024; 25:3144. [PMID: 38542118 PMCID: PMC10969971 DOI: 10.3390/ijms25063144] [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: 12/19/2023] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 07/16/2024] Open
Abstract
Histones are nuclear proteins essential for packaging genomic DNA and epigenetic gene regulation. Paralogs that can substitute core histones (H2A, H2B, H3, and H4), named histone variants, are constitutively expressed in a replication-independent manner throughout the cell cycle. With specific chaperones, they can be incorporated to chromatin to modify nucleosome stability by modulating interactions with nucleosomal DNA. This allows the regulation of essential fundamental cellular processes for instance, DNA damage repair, chromosomal segregation, and transcriptional regulation. Among all the histone families, histone H2A family has the largest number of histone variants reported to date. Each H2A variant has multiple functions apart from their primary role and some, even be further specialized to perform additional tasks in distinct lineages, such as testis specific shortH2A (sH2A). In the past decades, the discoveries of genetic alterations and mutations in genes encoding H2A variants in cancer had revealed variants' potentiality in driving carcinogenesis. In addition, there is growing evidence that H2A variants may act as novel prognostic indicators or biomarkers for both early cancer detection and therapeutic treatments. Nevertheless, no studies have ever concluded all identified variants in a single report. Here, in this review, we summarize the respective functions for all the 19 mammalian H2A variants and their roles in cancer biology whilst potentiality being used in clinical setting.
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Affiliation(s)
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China;
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6
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Kaczmarek K, Plage H, Furlano K, Hofbauer S, Weinberger S, Ralla B, Franz A, Fendler A, de Martino M, Roßner F, Schallenberg S, Elezkurtaj S, Kluth M, Lennartz M, Blessin NC, Marx AH, Samtleben H, Fisch M, Rink M, Slojewski M, Ecke T, Hallmann S, Koch S, Adamini N, Minner S, Simon R, Sauter G, Weischenfeldt J, Klatte T, Schlomm T, Horst D, Zecha H. Loss of Upk1a and Upk1b expression is linked to stage progression in urothelial carcinoma of the bladder. Int Urol Nephrol 2024; 56:499-508. [PMID: 37777995 PMCID: PMC10808463 DOI: 10.1007/s11255-023-03800-0] [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: 07/28/2023] [Accepted: 09/09/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Uroplakin-1a (Upk1a) and uroplakin-1b (Upk1b) have recently been identified as diagnostic markers for the distinction of urothelial carcinomas from other solid tumor entities. Both proteins play an important role in the stabilization and strengthening of epithelial cells that line the bladder. METHODS To evaluate the prognostic role of uroplakin expression in urothelial carcinomas, more than 2700 urothelial neoplasms were analyzed in a tissue microarray format by immunohistochemistry. To further assess the diagnostic role of uroplakin immunohistochemistry, results were compared with preexisting GATA3 data. RESULT The fraction of Upk1a/Upk1b positive cases decreased slightly from pTaG2 low-grade (88% positive for Upk1a/87% positive for Upk1b) and pTaG2 high-grade (92%/89%) to pTaG3 (83%/88%; p > 0.05) and was lower in muscle-invasive (pT2-4) carcinomas (42%/64%; p < 0.0001/p < 0.0001 for pTa vs. pT2-4). Within pT2-4 carcinomas, high expression of Upk1a and Upk1b was linked to nodal metastasis and lymphatic vessel infiltration (p < 0.05) but unrelated to patient outcome. There were significant associations between Upk1a, Upk1b and GATA3 immunostaining (p < 0.0001 each), but 11% of GATA3 negative cancers were Upk1a/b positive and 8% of Upk1a/b negative cancers were GATA3 positive. Absence of GATA3/Upk1a/b staining was significantly linked to poor patient survival in the subgroup of 126 pT4 carcinomas (p = 0.0004) but not in pT2 and pT3 cancers. CONCLUSIONS In summary, the results of our study demonstrate that Upk1a and/or Upk1b immunohistochemistry can complement GATA3 for the distinction of urothelial carcinomas. Furthermore, a progressive loss of Upk1a/b expression during stage progression and a prognostic role of the combination GATA3/Upk1a/Upk1b in pT4 carcinomas is evident.
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Affiliation(s)
- Krystian Kaczmarek
- Department of Urology and Urological Oncology, Pomeranian Medical University, Szczecin, Poland
| | - Henning Plage
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Kira Furlano
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sebastian Hofbauer
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sarah Weinberger
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Bernhard Ralla
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Antonia Franz
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Annika Fendler
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Michela de Martino
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Florian Roßner
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Simon Schallenberg
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sefer Elezkurtaj
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Maximilian Lennartz
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Niclas C Blessin
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Andreas H Marx
- Department of Pathology, Academic Hospital Fuerth, Fuerth, Germany
| | - Henrik Samtleben
- Department of Pathology, Academic Hospital Fuerth, Fuerth, Germany
| | - Margit Fisch
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Rink
- Department of Urology, Marienhospital Hamburg, Hamburg, Germany
| | - Marcin Slojewski
- Department of Urology and Urological Oncology, Pomeranian Medical University, Szczecin, Poland
| | - Thorsten Ecke
- Department of Urology, Helios Hospital Bad Saarow, Bad Saarow, Germany
| | - Steffen Hallmann
- Department of Urology, Helios Hospital Bad Saarow, Bad Saarow, Germany
| | - Stefan Koch
- Department of Pathology, Helios Hospital Bad Saarow, Bad Saarow, Germany
| | - Nico Adamini
- Department of Urology, Albertinen Hospital, Hamburg, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany.
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Joachim Weischenfeldt
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- Biotech Research & Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
- Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Tobias Klatte
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Thorsten Schlomm
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Henrik Zecha
- Department of Urology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- Department of Urology, Albertinen Hospital, Hamburg, Germany
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7
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Zhao Z, Jin T, Chen B, Dong Q, Liu M, Guo J, Song X, Li Y, Chen T, Han H, Liang H, Gu Y. Multi-omics integration analysis unveils heterogeneity in breast cancer at the individual level. Cell Cycle 2023; 22:2229-2244. [PMID: 37974462 PMCID: PMC10730166 DOI: 10.1080/15384101.2023.2281816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Identifying robust breast cancer subtypes will help to reveal the cancer heterogeneity. However, previous breast cancer subtypes were based on population-level quantitative gene expression, which is affected by batch effects and cannot be applied to individuals. We detected differential gene expression, genomic, and epigenomic alterations to identify driver differential expression at the individual level. The individual driver differential expression reflected the breast cancer patients' heterogeneity and revealed four subtypes. Mesenchymal subtype as the most aggressive subtype harbored deletion and downregulated expression of genes in chromosome 11q23 region. Specifically, silencing of the SDHD gene in 11q23 promoted the invasion and migration of breast cancer cells in vitro by the epithelial-mesenchymal transition. The immunologically hot subtype displayed an immune-hot microenvironment, including high T-cell infiltration and upregulated PD-1 and CTLA4. Luminal and genomic-unstable subtypes showed opposite macrophage polarization, which may be regulated by the ligand-receptor pairs of CD99. The integration of multi-omics data at the individual level provides a powerful framework for elucidating the heterogeneity of breast cancer.
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Affiliation(s)
- Zhangxiang Zhao
- The Sino-Russian Medical Research Center of Jinan University, The Institute of Chronic Disease of Jinan University, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Tongzhu Jin
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Bo Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qi Dong
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Mingyue Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiayu Guo
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Xiaoying Song
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yawei Li
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tingting Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Huiming Han
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haihai Liang
- The Sino-Russian Medical Research Center of Jinan University, The Institute of Chronic Disease of Jinan University, The First Affiliated Hospital of Jinan University, Guangzhou, China
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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8
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López-Guajardo A, Zafar A, Al Hennawi K, Rossi V, Alrwaili A, Medcalf JD, Dunning M, Nordgren N, Pettersson T, Estabrook ID, Hawkins RJ, Gad AKB. Regulation of cellular contractile force, shape and migration of fibroblasts by oncogenes and Histone deacetylase 6. Front Mol Biosci 2023; 10:1197814. [PMID: 37564130 PMCID: PMC10411354 DOI: 10.3389/fmolb.2023.1197814] [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: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
The capacity of cells to adhere to, exert forces upon and migrate through their surrounding environment governs tissue regeneration and cancer metastasis. The role of the physical contractile forces that cells exert in this process, and the underlying molecular mechanisms are not fully understood. We, therefore, aimed to clarify if the extracellular forces that cells exert on their environment and/or the intracellular forces that deform the cell nucleus, and the link between these forces, are defective in transformed and invasive fibroblasts, and to indicate the underlying molecular mechanism of control. Confocal, Epifluorescence and Traction force microscopy, followed by computational analysis, showed an increased maximum contractile force that cells apply on their environment and a decreased intracellular force on the cell nucleus in the invasive fibroblasts, as compared to normal control cells. Loss of HDAC6 activity by tubacin-treatment and siRNA-mediated HDAC6 knockdown also reversed the reduced size and more circular shape and defective migration of the transformed and invasive cells to normal. However, only tubacin-mediated, and not siRNA knockdown reversed the increased force of the invasive cells on their surrounding environment to normal, with no effects on nuclear forces. We observed that the forces on the environment and the nucleus were weakly positively correlated, with the exception of HDAC6 siRNA-treated cells, in which the correlation was weakly negative. The transformed and invasive fibroblasts showed an increased number and smaller cell-matrix adhesions than control, and neither tubacin-treatment, nor HDAC6 knockdown reversed this phenotype to normal, but instead increased it further. This highlights the possibility that the control of contractile force requires separate functions of HDAC6, than the control of cell adhesions, spreading and shape. These data are consistent with the possibility that defective force-transduction from the extracellular environment to the nucleus contributes to metastasis, via a mechanism that depends upon HDAC6. To our knowledge, our findings present the first correlation between the cellular forces that deforms the surrounding environment and the nucleus in fibroblasts, and it expands our understanding of how cells generate contractile forces that contribute to cell invasion and metastasis.
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Affiliation(s)
- Ana López-Guajardo
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Azeer Zafar
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Khairat Al Hennawi
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Valentina Rossi
- Immunology and Molecular Oncology Diagnostics, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - Abdulaziz Alrwaili
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Jessica D. Medcalf
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Mark Dunning
- Bioinformatics Core, The Medical School, The University of Sheffield, Sheffield, United Kingdom
| | - Niklas Nordgren
- Division Bioeconomy and Health, RISE Research Institutes of Sweden, Stockholm, Sweden
| | - Torbjörn Pettersson
- Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ian D. Estabrook
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
- Center for Advancing Electronics Dresden, Technische Universität Dresden, Dresden, Germany
| | - Rhoda J. Hawkins
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
- African Institute for Mathematical Sciences, Accra, Ghana
| | - Annica K. B. Gad
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
- Madeira Chemistry Research Centre, University of Madeira, Funchal, Portugal
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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9
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Kim HR, Warrington SJ, López-Guajardo A, Al Hennawi K, Cook SL, Griffith ZDJ, Symmes D, Zhang T, Qu Z, Xu Y, Chen R, Gad AKB. ALD-R491 regulates vimentin filament stability and solubility, cell contractile force, cell migration speed and directionality. Front Cell Dev Biol 2022; 10:926283. [PMID: 36483676 PMCID: PMC9723350 DOI: 10.3389/fcell.2022.926283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/07/2022] [Indexed: 08/12/2023] Open
Abstract
Metastasizing cells express the intermediate filament protein vimentin, which is used to diagnose invasive tumors in the clinic. However, the role of vimentin in cell motility, and if the assembly of non-filamentous variants of vimentin into filaments regulates cell migration remains unclear. We observed that the vimentin-targeting drug ALD-R491 increased the stability of vimentin filaments, by reducing filament assembly and/or disassembly. ALD-R491-treatment also resulted in more bundled and disorganized filaments and an increased pool of non-filamentous vimentin. This was accompanied by a reduction in size of cell-matrix adhesions and increased cellular contractile forces. Moreover, during cell migration, cells showed erratic formation of lamellipodia at the cell periphery, loss of coordinated cell movement, reduced cell migration speed, directionality and an elongated cell shape with long thin extensions at the rear that often detached. Taken together, these results indicate that the stability of vimentin filaments and the soluble pool of vimentin regulate the speed and directionality of cell migration and the capacity of cells to migrate in a mechanically cohesive manner. These observations suggest that the stability of vimentin filaments governs the adhesive, physical and migratory properties of cells, and expands our understanding of vimentin functions in health and disease, including cancer metastasis.
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Affiliation(s)
- Hyejeong Rosemary Kim
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | | | - Ana López-Guajardo
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Khairat Al Hennawi
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Sarah L. Cook
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Zak D. J. Griffith
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Deebie Symmes
- Aluda Pharmaceuticals, Inc., Menlo Park, CA, United States
| | - Tao Zhang
- Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, China
| | - Zhipeng Qu
- Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, China
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, China
| | - Ruihuan Chen
- Aluda Pharmaceuticals, Inc., Menlo Park, CA, United States
| | - Annica K. B. Gad
- Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
- Madeira Chemistry Research Centre, University of Madeira, Funchal, Portugal
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10
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Hyaluronan nanoscale clustering and Hyaluronan synthase 2 expression are linked to the invasion of child fibroblasts and infantile fibrosarcoma in vitro and in vivo. Sci Rep 2022; 12:19835. [PMID: 36400790 PMCID: PMC9674583 DOI: 10.1038/s41598-022-21952-4] [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: 02/26/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022] Open
Abstract
Infantile fibrosarcoma is a rare childhood tumour that originates in the fibrous connective tissue of the long bones for which there is an urgent need to identify novel therapeutic targets. This study aims to clarify the role of the extracellular matrix component hyaluronan in the invasion of child fibroblasts and Infantile fibrosarcoma into the surrounding environment. Using nanoscale super-resolution STED (Stimulated emission depletion) microscopy followed by computational image analysis, we observed, for the first time, that invasive child fibroblasts showed increased nanoscale clustering of hyaluronan at the cell periphery, as compared to control cells. Hyaluronan was not observed within focal adhesions. Bioinformatic analyses further revealed that the increased nanoscale hyaluronan clustering was accompanied by increased gene expression of Hyaluronan synthase 2, reduced expression of Hyaluronidase 2 and CD44, and no change of Hyaluronan synthase 1 and Hyaluronidases 1, 3, 4 or 5. We further observed that the expression of the Hyaluronan synthase 1, 2 and 3, and the Hyaluronidase 3 and 5 genes was linked to reduced life expectancy of fibrosarcoma patients. The invasive front of infantile fibrosarcoma tumours further showed increased levels of hyaluronan, as compared to the tumour centre. Taken together, our findings are consistent with the possibility that while Hyaluronan synthase 2 increases the levels, the Hyaluronidases 3 and 5 reduce the weight of hyaluronan, resulting in the nanoscale clustering of hyaluronan at the leading edge of cells, cell invasion and the spread of Infantile fibrosarcoma.
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11
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Cui J, Guo F, Yu Y, Ma Z, Hong Y, Su J, Ge Y. Development and validation of a prognostic 9-gene signature for colorectal cancer. Front Oncol 2022; 12:1009698. [DOI: 10.3389/fonc.2022.1009698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2022] Open
Abstract
IntroductionColorectal cancer (CRC) is one of the most prevalent cancers globally with a high mortality rate. Predicting prognosis using disease progression and cancer pathologic stage is insufficient, and a prognostic factor that can accurately evaluate patient prognosis needs to be developed. In this study, we aimed to infer a prognostic gene signature to identify a functional signature associated with the prognosis of CRC patients.MethodsFirst, we used univariate Cox regression, least absolute shrinkage and selection operator (lasso) regression, and multivariate Cox regression analyses to screen genes significantly associated with CRC patient prognosis, from colorectal cancer RNA sequencing data in The Cancer Genome Atlas (TCGA) database. We then calculated the risk score (RS) for each patient based on the expression of the nine candidate genes and developed a prognostic signature.ResultsBased on the optimal cut-off on the receiver operating characteristic (ROC) curve, patients were separated into high- and low-risk groups, and the difference in overall survival between the two groups was examined. Patients in the low-risk group had a better overall survival rate than those in the high-risk group. The results were validated using the GSE72970, GSE39582, and GSE17536 Gene Expression Omnibus (GEO) datasets, and the same conclusions were reached. ROC curve test of the RS signature also indicated that it had excellent accuracy. The RS signature was then compared with traditional clinical factors as a prognostic indicator, and we discovered that the RS signature had superior predictive ability.ConclusionThe RS signature developed in this study has excellent predictive power for the prognosis of patients with CRC and broad applicability as a prognostic indicator for patients.
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12
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Metastasising Fibroblasts Show an HDAC6-Dependent Increase in Migration Speed and Loss of Directionality Linked to Major Changes in the Vimentin Interactome. Int J Mol Sci 2022; 23:ijms23041961. [PMID: 35216078 PMCID: PMC8880509 DOI: 10.3390/ijms23041961] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/07/2023] Open
Abstract
Metastasising cells express the intermediate filament protein vimentin, which is used to diagnose invasive tumours in the clinic. We aimed to clarify how vimentin regulates the motility of metastasising fibroblasts. STED super-resolution microscopy, live-cell imaging and quantitative proteomics revealed that oncogene-expressing and metastasising fibroblasts show a less-elongated cell shape, reduced cell spreading, increased cell migration speed, reduced directionality, and stronger coupling between these migration parameters compared to normal control cells. In total, we identified and compared 555 proteins in the vimentin interactome. In metastasising cells, the levels of keratin 18 and Rab5C were increased, while those of actin and collagen were decreased. Inhibition of HDAC6 reversed the shape, spreading and migration phenotypes of metastasising cells back to normal. Inhibition of HDAC6 also decreased the levels of talin 1, tropomyosin, Rab GDI β, collagen and emilin 1 in the vimentin interactome, and partially reversed the nanoscale vimentin organisation in oncogene-expressing cells. These findings describe the changes in the vimentin interactome and nanoscale distribution that accompany the defective cell shape, spreading and migration of metastasising cells. These results support the hypothesis that oncogenes can act through HDAC6 to regulate the vimentin binding of the cytoskeletal and cell–extracellular matrix adhesion components that contribute to the defective motility of metastasising cells.
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13
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Cho-Clark MJ, Sukumar G, Vidal NM, Raiciulescu S, Oyola MG, Olsen C, Mariño-Ramírez L, Dalgard CL, Wu TJ. Comparative transcriptome analysis between patient and endometrial cancer cell lines to determine common signaling pathways and markers linked to cancer progression. Oncotarget 2021; 12:2500-2513. [PMID: 34966482 PMCID: PMC8711572 DOI: 10.18632/oncotarget.28161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/10/2021] [Indexed: 01/08/2023] Open
Abstract
The rising incidence and mortality of endometrial cancer (EC) in the United States calls for an improved understanding of the disease's progression. Current methodologies for diagnosis and treatment rely on the use of cell lines as models for tumor biology. However, due to inherent heterogeneity and differential growing environments between cell lines and tumors, these comparative studies have found little parallels in molecular signatures. As a consequence, the development and discovery of preclinical models and reliable drug targets are delayed. In this study, we established transcriptome parallels between cell lines and tumors from The Cancer Genome Atlas (TCGA) with the use of optimized normalization methods. We identified genes and signaling pathways associated with regulating the transformation and progression of EC. Specifically, the LXR/RXR activation, neuroprotective role for THOP1 in Alzheimer's disease, and glutamate receptor signaling pathways were observed to be mostly downregulated in advanced cancer stage. While some of these highlighted markers and signaling pathways are commonly found in the central nervous system (CNS), our results suggest a novel function of these genes in the periphery. Finally, our study underscores the value of implementing appropriate normalization methods in comparative studies to improve the identification of accurate and reliable markers.
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Affiliation(s)
- Madelaine J. Cho-Clark
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gauthaman Sukumar
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sorana Raiciulescu
- Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Mario G. Oyola
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Cara Olsen
- Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Leonardo Mariño-Ramírez
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20814, USA
| | - Clifton L. Dalgard
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - T. John Wu
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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14
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Priyadharshini V, Jiménez-Chobillon MA, de Graaf J, Porras Gutiérrez de Velasco R, Gratziou C, Ramírez-Jiménez F, Teran LM. Transcriptome Analysis Identifies Doublesex and Mab-3 Related Transcription Factor (DMRT3) in Nasal Polyp Epithelial Cells of Patients Suffering from Non-Steroidal Anti-Inflammatory Drug-Exacerbated Respiratory Disease (AERD). Biomolecules 2021; 11:biom11081092. [PMID: 34439758 PMCID: PMC8394795 DOI: 10.3390/biom11081092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/17/2021] [Accepted: 07/19/2021] [Indexed: 12/17/2022] Open
Abstract
Background: Aspirin-exacerbated respiratory disease (AERD) is a syndrome characterised by chronic rhinosinusitis, nasal polyps, asthma and aspirin intolerance. An imbalance of eicosanoid metabolism with anover-production of cysteinyl leukotrienes (CysLTs) has been associated with AERD. However, the precise mechanisms underlying AERD are unknown. Objective: To establish the transcriptome of the nasal polyp airway epithelial cells derived from AERD patients to discover gene expression patterns in this disease. Methods: Nasal airway epithelial cells were isolated from 12 AERD polyps and 8 AERD non-polyp nasal mucosa samples as controls from the same subjects. Utilising the Illumina HiSeq 2500 platform, RNA samples were sequenced. Potential gene candidate DMRT3 was selected from the differentially-expressed genes for validation. Results: Comparative transcriptome profiling of nasal epithelial cells was accomplished in AERD. A total of 20 genes had twofold mean regulation expression differences or greater. In addition, 8 genes were upregulated, including doublesex and mab-3 related transcription factor 3 (DMRT3), and 12 genes were downregulated. Differentially regulated genes comprised roles in inflammation, defence and immunity. Metabolic process and embryonic development pathways were significantly enriched. Enzyme-linked immune sorbent assay (ELISA) results of DMRT3 in AERD patients were significantly upregulated compared to controls (p = 0.03). Immunohistochemistry (IHC) of AERD nasal polyps localised DMRT3 and was predominantly released in the airway epithelia. Conclusion: Findings suggest that DMRT3 could be potentially involved in nasal polyp development in AERD patients. Furthermore, several genes are downregulated, hinting at the dedifferentiation phenomenon in AERD polyps. However, further studies are imperative to confirm the exact mechanism of polyp formation in AERD patients.
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Affiliation(s)
- V.S. Priyadharshini
- Instituto Nacional de EnfermedadesRespiratorias Ismael Cosío Villegas, Calz. de Tlalpan 4502, Belisario Domínguez Secc 16, Mexico City 14080, Mexico; (V.S.P.); (M.A.J.-C.); (F.R.-J.)
| | - Marcos Alejandro Jiménez-Chobillon
- Instituto Nacional de EnfermedadesRespiratorias Ismael Cosío Villegas, Calz. de Tlalpan 4502, Belisario Domínguez Secc 16, Mexico City 14080, Mexico; (V.S.P.); (M.A.J.-C.); (F.R.-J.)
| | - Jos de Graaf
- Translational Oncology at Johannes Gutenberg-University Medical Center gGmbH, D-55131 Mainz, Germany;
| | - Raúl Porras Gutiérrez de Velasco
- School of Medicine, Universidad Nacional Autónoma de México, Av. Universidad 3000, Circuito Exterior S/N. Delegación Coyoacán, Mexico City 04510, Mexico;
| | - Christina Gratziou
- Smoking Cessation Centre Pulmonary Department, Evgenidio Hospital, Athens University, 20 Papadiamantopoulou Street, 11528 Athens, Greece;
| | - Fernando Ramírez-Jiménez
- Instituto Nacional de EnfermedadesRespiratorias Ismael Cosío Villegas, Calz. de Tlalpan 4502, Belisario Domínguez Secc 16, Mexico City 14080, Mexico; (V.S.P.); (M.A.J.-C.); (F.R.-J.)
| | - Luis M. Teran
- Instituto Nacional de EnfermedadesRespiratorias Ismael Cosío Villegas, Calz. de Tlalpan 4502, Belisario Domínguez Secc 16, Mexico City 14080, Mexico; (V.S.P.); (M.A.J.-C.); (F.R.-J.)
- School of Medicine, Universidad Nacional Autónoma de México, Av. Universidad 3000, Circuito Exterior S/N. Delegación Coyoacán, Mexico City 04510, Mexico;
- Correspondence:
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15
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Pires JG, da Silva GF, Weyssow T, Conforte AJ, Pagnoncelli D, da Silva FAB, Carels N. Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy. Front Genet 2021; 12:624259. [PMID: 33679888 PMCID: PMC7935533 DOI: 10.3389/fgene.2021.624259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/22/2021] [Indexed: 12/24/2022] Open
Abstract
One aspect of personalized medicine is aiming at identifying specific targets for therapy considering the gene expression profile of each patient individually. The real-world implementation of this approach is better achieved by user-friendly bioinformatics systems for healthcare professionals. In this report, we present an online platform that endows users with an interface designed using MEAN stack supported by a Galaxy pipeline. This pipeline targets connection hubs in the subnetworks formed by the interactions between the proteins of genes that are up-regulated in tumors. This strategy has been proved to be suitable for the inhibition of tumor growth and metastasis in vitro. Therefore, Perl and Python scripts were enclosed in Galaxy for translating RNA-seq data into protein targets suitable for the chemotherapy of solid tumors. Consequently, we validated the process of target diagnosis by (i) reference to subnetwork entropy, (ii) the critical value of density probability of differential gene expression, and (iii) the inhibition of the most relevant targets according to TCGA and GDC data. Finally, the most relevant targets identified by the pipeline are stored in MongoDB and can be accessed through the aforementioned internet portal designed to be compatible with mobile or small devices through Angular libraries.
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Affiliation(s)
- Jorge Guerra Pires
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Gilberto Ferreira da Silva
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Thomas Weyssow
- Informatic Department, Free University of Brussels (ULB), Brussels, Belgium
| | - Alessandra Jordano Conforte
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil.,Laboratório de Modelagem Computacional de Sistemas Biológicos, Scientific Computing Program, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Fabricio Alves Barbosa da Silva
- Laboratório de Modelagem Computacional de Sistemas Biológicos, Scientific Computing Program, FIOCRUZ, Rio de Janeiro, Brazil
| | - Nicolas Carels
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
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Naydenov NG, Koblinski JE, Ivanov AI. Anillin is an emerging regulator of tumorigenesis, acting as a cortical cytoskeletal scaffold and a nuclear modulator of cancer cell differentiation. Cell Mol Life Sci 2021; 78:621-633. [PMID: 32880660 PMCID: PMC11072349 DOI: 10.1007/s00018-020-03605-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022]
Abstract
Remodeling of the intracellular cytoskeleton plays a key role in accelerating tumor growth and metastasis. Targeting different cytoskeletal elements is important for existing and future anticancer therapies. Anillin is a unique scaffolding protein that interacts with major cytoskeletal structures, e.g., actin filaments, microtubules and septin polymers. A well-studied function of this scaffolding protein is the regulation of cytokinesis at the completion of cell division. Emerging evidence suggest that anillin has other important activities in non-dividing cells, including control of intercellular adhesions and cell motility. Anillin is markedly overexpressed in different solid cancers and its high expression is commonly associated with poor prognosis of patient survival. This review article summarizes rapidly accumulating evidence that implicates anillin in the regulation of tumor growth and metastasis. We focus on molecular and cellular mechanisms of anillin-dependent tumorigenesis that include both canonical control of cytokinesis and novel poorly understood functions as a nuclear regulator of the transcriptional reprogramming and phenotypic plasticity of cancer cells.
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Affiliation(s)
- Nayden G Naydenov
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic Foundation, 9500 Euclid Avenue, NC22, Cleveland, OH, 44195, USA
| | - Jennifer E Koblinski
- Department of Pathology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Andrei I Ivanov
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic Foundation, 9500 Euclid Avenue, NC22, Cleveland, OH, 44195, USA.
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17
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Maharjan M, Tanvir RB, Chowdhury K, Duan W, Mondal AM. Computational identification of biomarker genes for lung cancer considering treatment and non-treatment studies. BMC Bioinformatics 2020; 21:218. [PMID: 33272232 PMCID: PMC7713218 DOI: 10.1186/s12859-020-3524-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Lung cancer is the number one cancer killer in the world with more than 142,670 deaths estimated in the United States alone in the year 2019. Consequently, there is an overreaching need to identify the key biomarkers for lung cancer. The aim of this study is to computationally identify biomarker genes for lung cancer that can aid in its diagnosis and treatment. The gene expression profiles of two different types of studies, namely non-treatment and treatment, are considered for discovering biomarker genes. In non-treatment studies healthy samples are control and cancer samples are cases. Whereas, in treatment studies, controls are cancer cell lines without treatment and cases are cancer cell lines with treatment. RESULTS The Differentially Expressed Genes (DEGs) for lung cancer were isolated from Gene Expression Omnibus (GEO) database using R software tool GEO2R. A total of 407 DEGs (254 upregulated and 153 downregulated) from non-treatment studies and 547 DEGs (133 upregulated and 414 downregulated) from treatment studies were isolated. Two Cytoscape apps, namely, CytoHubba and MCODE, were used for identifying biomarker genes from functional networks developed using DEG genes. This study discovered two distinct sets of biomarker genes - one from non-treatment studies and the other from treatment studies, each set containing 16 genes. Survival analysis results show that most non-treatment biomarker genes have prognostic capability by indicating low-expression groups have higher chance of survival compare to high-expression groups. Whereas, most treatment biomarkers have prognostic capability by indicating high-expression groups have higher chance of survival compare to low-expression groups. CONCLUSION A computational framework is developed to identify biomarker genes for lung cancer using gene expression profiles. Two different types of studies - non-treatment and treatment - are considered for experiment. Most of the biomarker genes from non-treatment studies are part of mitosis and play vital role in DNA repair and cell-cycle regulation. Whereas, most of the biomarker genes from treatment studies are associated to ubiquitination and cellular response to stress. This study discovered a list of biomarkers, which would help experimental scientists to design a lab experiment for further exploration of detail dynamics of lung cancer development.
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Affiliation(s)
- Mona Maharjan
- School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Raihanul Bari Tanvir
- School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Kamal Chowdhury
- School of Natural Sciences and Mathematics, Claflin University, Orangeburg, SC, USA
| | - Wenrui Duan
- Department of Human & Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Ananda Mohan Mondal
- School of Computing and Information Sciences, Florida International University, Miami, FL, USA.
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18
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Size-Exclusion Chromatography as a Technique for the Investigation of Novel Extracellular Vesicles in Cancer. Cancers (Basel) 2020; 12:cancers12113156. [PMID: 33121160 PMCID: PMC7693800 DOI: 10.3390/cancers12113156] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/06/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Extracellular vesicles (EVs) are small particles that are released by cancer cells, and they may hold vital information for researchers looking for early markers for diagnosis. Size-exclusion chromatography (SEC) is a classical technique that has become increasingly popular and can be used for rapid isolation and investigation of both their cargo and functionality. This systematic review highlights its main technical aspects, the type of materials involved and by covering the findings of the identified papers hopes to demonstrate the utility of this method in cancer research to date. Abstract Cancer cells release extracellular vesicles, which are a rich target for biomarker discovery and provide a promising mechanism for liquid biopsy. Size-exclusion chromatography (SEC) is an increasingly popular technique, which has been rediscovered for the purposes of extracellular vesicle (EV) isolation and purification from diverse biofluids. A systematic review was undertaken to identify all papers that described size exclusion as their primary EV isolation method in cancer research. In all, 37 papers were identified and discussed, which showcases the breadth of applications in which EVs can be utilised, from proteomics, to RNA, and through to functionality. A range of different methods are highlighted, with Sepharose-based techniques predominating. EVs isolated using SEC are able to identify cancer cells, highlight active pathways in tumourigenesis, clinically distinguish cohorts, and remain functionally active for further experiments.
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19
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Chen Y, Hesla AC, Lin Y, Ghaderi M, Liu M, Yang C, Zhang Y, Tsagkozis P, Larsson O, Haglund F. Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency. Mol Oncol 2020; 14:1101-1117. [PMID: 32115849 PMCID: PMC7191197 DOI: 10.1002/1878-0261.12655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 02/11/2020] [Accepted: 02/27/2020] [Indexed: 11/06/2022] Open
Abstract
Ewing sarcomas (ESs) are aggressive sarcomas driven by EWS fusion genes. We sought to investigate whether whole-transcriptome sequencing (RNA-seq) could be used to detect patterns associated with chemotherapy response or tumor progression after first-line treatment. Transcriptome sequencing (RNA-seq) of 13 ES cases was performed. Among the differentially expressed pathways, we identified IGF2 expression as a potential driver of chemotherapy response and progression. We investigated the effect of IGF2 on proliferation, radioresistance, apoptosis, and the transcriptome pattern in four ES cell lines and the effect of IGF2 expression in a validation series of 14 patients. Transcriptome analysis identified differentially expressed genes (adj. P < 0.005) and pathways associated with chemotherapy response (285 genes), short overall survival (662 genes), and progression after treatment (447 genes). Imprinting independent promoter P3-mediated IGF2 expression was identified in a subset of cases with aggressive clinical course. In ES cell lines, IGF2 induced proliferation, but promoted radioresistance only in CADO cells. High IGF2 expression was also significantly associated with shorter overall survival in patients with ES. Transcriptome analysis of the clinical samples and the cell lines revealed an IGF-dependent signature, potentially related to a stem cell-like phenotype. Transcriptome analysis is a potentially powerful complementary tool to predict the clinical behavior of ES and may be utilized for clinical trial stratification strategies and personalized oncology. Certain gene signatures, for example, IGF-related pathways, are coupled to biological functions that could be of clinical importance. Finally, our results indicate that IGF inhibition may be successful as a first-line therapy in conjunction with conventional radiochemotherapy for a subset of patients.
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Affiliation(s)
- Yi Chen
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Asle C Hesla
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Orthopedic Surgery, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Yingbo Lin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Mehran Ghaderi
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Mingzhi Liu
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Chen Yang
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Yifan Zhang
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Panagiotis Tsagkozis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Orthopedic Surgery, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Olle Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Pathology and Cytology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Felix Haglund
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Pathology and Cytology, Karolinska University Hospital Solna, Stockholm, Sweden
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20
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Kataka E, Zaucha J, Frishman G, Ruepp A, Frishman D. Edgetic perturbation signatures represent known and novel cancer biomarkers. Sci Rep 2020; 10:4350. [PMID: 32152446 PMCID: PMC7062722 DOI: 10.1038/s41598-020-61422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Isoform switching is a recently characterized hallmark of cancer, and often translates to the loss or gain of domains mediating protein interactions and thus, the re-wiring of the interactome. Recent computational tools leverage domain-domain interaction data to resolve the condition-specific interaction networks from RNA-Seq data accounting for the domain content of the primary transcripts expressed. Here, we used The Cancer Genome Atlas RNA-Seq datasets to generate 642 patient-specific pairs of interactomes corresponding to both the tumor and the healthy tissues across 13 cancer types. The comparison of these interactomes provided a list of patient-specific edgetic perturbations of the interactomes associated with the cancerous state. We found that among the identified perturbations, select sets are robustly shared between patients at the multi-cancer, cancer-specific and cancer sub-type specific levels. Interestingly, the majority of the alterations do not directly involve significantly mutated genes, nevertheless, they strongly correlate with patient survival. The findings (available at EdgeExplorer: “http://webclu.bio.wzw.tum.de/EdgeExplorer”) are a new source of potential biomarkers for classifying cancer types and the proteins we identified are potential anti-cancer therapy targets.
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Affiliation(s)
- Evans Kataka
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany
| | - Jan Zaucha
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany
| | - Goar Frishman
- Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Andreas Ruepp
- Institute of Experimental Genetics (IEG), Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany. .,Laboratory of Bioinformatics, RASA Research Center, St Petersburg State Polytechnic University, St Petersburg, 195251, Russia.
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21
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Fungal canker pathogens trigger carbon starvation by inhibiting carbon metabolism in poplar stems. Sci Rep 2019; 9:10111. [PMID: 31300723 PMCID: PMC6626041 DOI: 10.1038/s41598-019-46635-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
Carbon starvation is the current leading hypothesis of plant mortality mechanisms under drought stress; recently, it is also used to explain tree die-off in plant diseases. However, the molecular biology of the carbon starvation pathway is unclear. Here, using a punch inoculation system, we conducted transcriptome and physiological assays to investigate pathogen response in poplar stems at the early stages of Botryosphaeria and Valsa canker diseases. Transcriptome assays showed that the majority of differentially expressed genes (DEGs) in stem phloem and xylem, such as genes involved in carbon metabolism and transportation, aquaporin genes (in xylem) and genes related to the biosynthesis of secondary metabolites and the phenylpropanoid pathway (related to lignin synthesis), were downregulated at 7 days after inoculation (DAI). Results also showed that the expression of the majority of disease-resistance genes upregulated in poplar stems, which may be connected with the downregulation expression of the majority of WRKY family genes. Physiological assays showed that transpiration rate decreased but WUE (water use efficiency) increased the 3 and 7 DAI, while the net photosynthetic rate decreased at 11 DAI in Botryosphaeria infected poplars (ANOVA, P < 0.05). The NSC (non-structural carbohydrates) content assays showed that the soluble sugar content of stem phloem samples increased at 3, 7, and 11 DAI that might due to the impede of pathogen infection. However, soluble sugar content of stem xylem and root samples decreased at 11 DAI; in contrast, the starch content unchanged. Therefore, results revealed a chronological order of carbon related molecular and physiological performance: declination of genes involved in carbon and starch metabolism first (at least at 7 DAI), declination of assimilation and carbon reserve (at 11 DAI) second. Results implied a potential mechanism that affects the host carbon reserve, by directly inhibiting the expression of genes involved in carbon metabolism and transport.
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22
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Luo Z, Wang W, Li F, Songyang Z, Feng X, Xin C, Dai Z, Xiong Y. Pan-cancer analysis identifies telomerase-associated signatures and cancer subtypes. Mol Cancer 2019; 18:106. [PMID: 31179925 PMCID: PMC6556968 DOI: 10.1186/s12943-019-1035-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/29/2019] [Indexed: 01/09/2023] Open
Abstract
Background Cancer cells become immortalized through telomere maintenance mechanisms, such as telomerase reverse transcriptase (TERT) activation. In addition to maintaining telomere length, TERT activates manifold cell survival signaling pathways. However, telomerase-associated gene signatures in cancer remain elusive. Methods We performed a systematic analysis of TERT high (TERThigh) and low (TERTlow) cancers using multidimensional data from The Cancer Genome Atlas (TCGA). Multidimensional data were analyzed by propensity score matching weight algorithm. Coexpression networks were constructed by weight gene coexpression network analysis (WGCNA). Random forest classifiers were generated to identify cancer subtypes. Results The TERThigh-specific mRNA expression signature is associated with cell cycle-related coexpression modules across cancer types. Experimental screening of hub genes in the cell cycle module suggested TPX2 and EXO1 as potential regulators of telomerase activity and cell survival. MiRNA analysis revealed that the TERThigh-specific miR-17-92 cluster can target biological processes enriched in TERTlow cancer and that its expression is negatively correlated with the tumor/normal telomere length ratio. Intriguingly, TERThigh cancers tend to have mutations in extracellular matrix organization genes and amplify MAPK signaling. By mining the clinical actionable gene database, we uncovered a number of TERThigh-specific somatic mutations, amplifications and high expression genes containing therapeutic targets. Finally, a random forest classifier integrating telomerase-associated multi-omics signatures identifies two cancer subtypes showed profound differences in telomerase activity and patient survival. Conclusions In summary, our results depict a telomerase-associated molecular landscape in cancers and provide therapeutic opportunities for cancer treatment. Electronic supplementary material The online version of this article (10.1186/s12943-019-1035-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenhua Luo
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.,Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center and the Department of Pediatrics Cincinnati, Ohio, 45229, USA
| | - Weixu Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Feng Li
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Xuyang Feng
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, 45230, USA.,The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
| | - Changchang Xin
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zhiming Dai
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510006, China.
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
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23
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Condello V, Torregrossa L, Sartori C, Denaro M, Poma AM, Piaggi P, Valerio L, Materazzi G, Elisei R, Vitti P, Basolo F. mRNA and miRNA expression profiling of follicular variant of papillary thyroid carcinoma with and without distant metastases. Mol Cell Endocrinol 2019; 479:93-102. [PMID: 30261209 DOI: 10.1016/j.mce.2018.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 09/14/2018] [Accepted: 09/22/2018] [Indexed: 12/19/2022]
Abstract
Follicular Variant of Papillary Thyroid Carcinoma (FVPTC) is usually associated with a good outcome. Nevertheless, in rare cases, it develops distant metastases (1-9%). Our goal was to investigate whether mRNA and miRNA expression profiles may help distinguish between metastatic versus non-metastatic FVPTCs. Twenty-four primary FVPTCs, 12 metastatic and 12 non-metastatic, with similar clinicopathological features were selected and analyzed by nanoString nCounter technology using two distinct panels for expression analysis of 740 mRNA and 798 miRNAs. Data analysis was performed using the nanoString nSolver 3.0 software. Forty-seven mRNA and 35 miRNAs were differentially expressed between the two groups. Using these mRNA and miRNAs, metastatic and non-metastatic FVPTCs were clearly divided into two distinct clusters. Our results indicate that FVPTCs with metastatic abilities have different expression profiles compared to the non-metastatic. A prospective validation is needed to evaluate the usefulness of this molecular approach in the early identification of high-risk FVPTCs.
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Affiliation(s)
- Vincenzo Condello
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, via Savi 10, 56126, Pisa, Italy
| | - Liborio Torregrossa
- Division of Surgical Pathology, University Hospital of Pisa, via Paradisa 2, 56124, Pisa, Italy
| | - Chiara Sartori
- Division of Surgical Pathology, University Hospital of Pisa, via Paradisa 2, 56124, Pisa, Italy
| | - Maria Denaro
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, via Savi 10, 56126, Pisa, Italy
| | - Anello Marcello Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, via Savi 10, 56126, Pisa, Italy
| | - Paolo Piaggi
- National Institute of Diabetes and Digestive and Kidney Disease, Phoenix, AZ, USA
| | - Laura Valerio
- Department of Clinical and Experimental Medicine (Endocrine Unit), University Hospital of Pisa, via Paradisa 2, 56124, Pisa, Italy
| | - Gabriele Materazzi
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, via Savi 10, 56126, Pisa, Italy
| | - Rossella Elisei
- Department of Clinical and Experimental Medicine (Endocrine Unit), University Hospital of Pisa, via Paradisa 2, 56124, Pisa, Italy
| | - Paolo Vitti
- Department of Clinical and Experimental Medicine (Endocrine Unit), University Hospital of Pisa, via Paradisa 2, 56124, Pisa, Italy
| | - Fulvio Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University Hospital of Pisa, via Savi 10, 56126, Pisa, Italy.
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24
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Mishra A, Sriram H, Chandarana P, Tanavde V, Kumar RV, Gopinath A, Govindarajan R, Ramaswamy S, Sadasivam S. Decreased expression of cell adhesion genes in cancer stem-like cells isolated from primary oral squamous cell carcinomas. Tumour Biol 2018; 40:1010428318780859. [PMID: 29888653 DOI: 10.1177/1010428318780859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The goal of this study was to isolate cancer stem-like cells marked by high expression of CD44, a putative cancer stem cell marker, from primary oral squamous cell carcinomas and identify distinctive gene expression patterns in these cells. From 1 October 2013 to 4 September 2015, 76 stage III-IV primary oral squamous cell carcinoma of the gingivobuccal sulcus were resected. In all, 13 tumours were analysed by immunohistochemistry to visualise CD44-expressing cells. Expression of CD44 within The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma RNA-sequencing data was also assessed. Seventy resected tumours were dissociated into single cells and stained with antibodies to CD44 as well as CD45 and CD31 (together referred as Lineage/Lin). From 45 of these, CD44+Lin- and CD44-Lin- subpopulations were successfully isolated using fluorescence-activated cell sorting, and good-quality RNA was obtained from 14 such sorted pairs. Libraries from five pairs were sequenced and the results analysed using bioinformatics tools. Reverse transcription quantitative polymerase chain reaction was performed to experimentally validate the differential expression of selected candidate genes identified from the transcriptome sequencing in the same 5 and an additional 9 tumours. CD44 was expressed on the surface of poorly differentiated tumour cells, and within the The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma samples, its messenger RNA levels were higher in tumours compared to normal. Transcriptomics revealed that 102 genes were upregulated and 85 genes were downregulated in CD44+Lin- compared to CD44-Lin- cells in at least 3 of the 5 tumours sequenced. The upregulated genes included those involved in immune regulation, while the downregulated genes were enriched for genes involved in cell adhesion. Decreased expression of PCDH18, MGP, SPARCL1 and KRTDAP was confirmed by reverse transcription quantitative polymerase chain reaction. Lower expression of the cell-cell adhesion molecule PCDH18 correlated with poorer overall survival in the The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma data highlighting it as a potential negative prognostic factor in this cancer.
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Affiliation(s)
- Amrendra Mishra
- 1 Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, UAS-GKVK Campus, Bengaluru, India
- 2 Hannover Biomedical Research School, Hannover Medical School, Hannover, Germany
| | - Harshini Sriram
- 1 Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, UAS-GKVK Campus, Bengaluru, India
| | | | - Vivek Tanavde
- 3 iBioAnalysis Pvt. Ltd., Ahmedabad, India
- 4 Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
- 5 Bioinformatics Institute, Agency for Science Technology and Research (A*STAR), Singapore
| | - Rekha V Kumar
- 6 Kidwai Memorial Institute of Oncology, Bengaluru, India
| | | | | | - S Ramaswamy
- 1 Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, UAS-GKVK Campus, Bengaluru, India
| | - Subhashini Sadasivam
- 1 Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences, UAS-GKVK Campus, Bengaluru, India
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25
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Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia. Oncotarget 2018; 9:19730-19744. [PMID: 29731978 PMCID: PMC5929421 DOI: 10.18632/oncotarget.24808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/24/2018] [Indexed: 11/25/2022] Open
Abstract
In tumor tissues, hypoxia is a commonly observed feature resulting from rapidly proliferating cancer cells outgrowing their surrounding vasculature network. Transformed cancer cells are known to exhibit phenotypic alterations, enabling continuous proliferation despite a limited oxygen supply. The four-step isogenic BJ cell model enables studies of defined steps of tumorigenesis: the normal, immortalized, transformed, and metastasizing stages. By transcriptome profiling under atmospheric and moderate hypoxic (3% O2) conditions, we observed that despite being highly similar, the four cell lines of the BJ model responded strikingly different to hypoxia. Besides corroborating many of the known responses to hypoxia, we demonstrate that the transcriptome adaptation to moderate hypoxia resembles the process of malignant transformation. The transformed cells displayed a distinct capability of metabolic switching, reflected in reversed gene expression patterns for several genes involved in oxidative phosphorylation and glycolytic pathways. By profiling the stage-specific responses to hypoxia, we identified ASS1 as a potential prognostic marker in hypoxic tumors. This study demonstrates the usefulness of the BJ cell model for highlighting the interconnection of pathways involved in malignant transformation and hypoxic response.
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26
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O'Hagan S, Wright Muelas M, Day PJ, Lundberg E, Kell DB. GeneGini: Assessment via the Gini Coefficient of Reference "Housekeeping" Genes and Diverse Human Transporter Expression Profiles. Cell Syst 2018; 6:230-244.e1. [PMID: 29428416 PMCID: PMC5840522 DOI: 10.1016/j.cels.2018.01.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/26/2017] [Accepted: 12/30/2017] [Indexed: 01/13/2023]
Abstract
The expression levels of SLC or ABC membrane transporter transcripts typically differ 100- to 10,000-fold between different tissues. The Gini coefficient characterizes such inequalities and here is used to describe the distribution of the expression of each transporter among different human tissues and cell lines. Many transporters exhibit extremely high Gini coefficients even for common substrates, indicating considerable specialization consistent with divergent evolution. The expression profiles of SLC transporters in different cell lines behave similarly, although Gini coefficients for ABC transporters tend to be larger in cell lines than in tissues, implying selection. Transporter genes are significantly more heterogeneously expressed than the members of most non-transporter gene classes. Transcripts with the stablest expression have a low Gini index and often differ significantly from the "housekeeping" genes commonly used for normalization in transcriptomics/qPCR studies. PCBP1 has a low Gini coefficient, is reasonably expressed, and is an excellent novel reference gene. The approach, referred to as GeneGini, provides rapid and simple characterization of expression-profile distributions and improved normalization of genome-wide expression-profiling data.
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Affiliation(s)
- Steve O'Hagan
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK
| | - Marina Wright Muelas
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK
| | - Philip J Day
- The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK; Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Emma Lundberg
- Science for Life Laboratory, Royal Institute of Technology (KTH), SE-17121 Solna, Sweden.
| | - Douglas B Kell
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK.
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27
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Li QL, Lei PJ, Zhao QY, Li L, Wei G, Wu M. Epigenomic analysis in a cell-based model reveals the roles of H3K9me3 in breast cancer transformation. Epigenomics 2017; 9:1077-1092. [DOI: 10.2217/epi-2016-0183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aim: Epigenetic marks are critical regulators of chromatin and gene activity. Their roles in normal physiology and disease states, including cancer development, still remain elusive. Herein, the epigenomic change of H3K9me3, as well as its potential impacts on gene activity and genome stability, was investigated in an in vitro breast cancer transformation model. Methods: The global H3K9me3 level was studied with western blotting. The distribution of H3K9me3 on chromatin and gene expression was studied with ChIP-Seq and RNA-Seq, respectively. Results: The global H3K9me3 level decreases during transformation and its distribution on chromatin is reprogrammed. By combining with TCGA data, we identified 67 candidate oncogenes, among which five genes are totally novel. Our analysis further links H3K9me3 with transposon activity, and suggests H3K9me3 reduction increases the cell’s sensitivity to DNA damage reagents. Conclusion: H3K9me3 reduction is possibly related with breast cancer transformation by regulating gene expression and chromatin stability during transformation.
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Affiliation(s)
- Qing-Lan Li
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Pin-Ji Lei
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Quan-Yi Zhao
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Lianyun Li
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute of Computational Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min Wu
- Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Department of Biochemistry & Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
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28
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Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes AN, Liu EM, Liu D, Sboner A, Tamayo P, Rickman DS, Rubin MA, Khurana E. Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome Biol 2017; 18:141. [PMID: 28750683 PMCID: PMC5530464 DOI: 10.1186/s13059-017-1266-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/27/2017] [Indexed: 11/22/2022] Open
Abstract
We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity based regulatory network. Integration of multi-omics data from 521 prostate tumor samples indicated a stronger regulatory impact of structural variants, as they affect more transcription factor hubs in the tissue-specific network. Moreover, crosstalk between transcription factor hub expression modulated by structural variants and methylation levels likely leads to the differential expression of target genes. We report known prostate tumor regulatory drivers and nominate novel transcription factors (ERF, CREB3L1, and POU2F2), which are supported by functional validation.
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Affiliation(s)
- Priyanka Dhingra
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Alexander Martinez-Fundichely
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Adeline Berger
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
- Cancer Program, The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - Andre Neil Forbes
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Eric Minwei Liu
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Deli Liu
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Department of Urology, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Andrea Sboner
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA
| | - Pablo Tamayo
- Cancer Program, The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - David S Rickman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA.
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA.
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Ekta Khurana
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA.
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA.
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA.
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Terriac E, Coceano G, Mavajian Z, Hageman TAG, Christ AF, Testa I, Lautenschläger F, Gad AKB. Vimentin Levels and Serine 71 Phosphorylation in the Control of Cell-Matrix Adhesions, Migration Speed, and Shape of Transformed Human Fibroblasts. Cells 2017; 6:cells6010002. [PMID: 28117759 PMCID: PMC5371867 DOI: 10.3390/cells6010002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
Metastasizing tumor cells show increased expression of the intermediate filament (IF) protein vimentin, which has been used to diagnose invasive tumors for decades. Recent observations indicate that vimentin is not only a passive marker for carcinoma, but may also induce tumor cell invasion. To clarify how vimentin IFs control cell adhesions and migration, we analyzed the nanoscale (30-50 nm) spatial organization of vimentin IFs and cell-matrix adhesions in metastatic fibroblast cells, using three-color stimulated emission depletion (STED) microscopy. We also studied whether wild-type and phospho-deficient or -mimicking mutants of vimentin changed the size and lifetime of focal adhesions (FAs), cell shape, and cell migration, using live-cell total internal reflection imaging and confocal microscopy. We observed that vimentin exists in fragments of different lengths. Short fragments were mostly the size of a unit-length filament and were mainly localized close to small cell-matrix adhesions. Long vimentin filaments were found in the proximity of large FAs. Vimentin expression in these cells caused a reduction in FAs size and an elongated cell shape, but did not affect FA lifetime, or the speed or directionality of cell migration. Expression of a phospho-mimicking mutant (S71D) of vimentin increased the speed of cell migration. Taken together, our results suggest that in highly migratory, transformed mesenchymal cells, vimentin levels control the cell shape and FA size, but not cell migration, which instead is linked to the phosphorylation status of S71 vimentin. These observations are consistent with the possibility that not only levels, but also the assembly status of vimentin control cell migration.
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Affiliation(s)
- Emmanuel Terriac
- Department of Physics, University of the Saarland, 66123 Saarbrücken, Germany.
- INM - Leibniz Institute for New Materials, 66123 Saarbrücken, Germany.
| | - Giovanna Coceano
- Department of Applied Physics, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.
| | - Zahra Mavajian
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, 171 65 Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | | | - Andreas F Christ
- Department of Physics, University of the Saarland, 66123 Saarbrücken, Germany.
| | - Ilaria Testa
- Department of Applied Physics, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.
| | - Franziska Lautenschläger
- Department of Physics, University of the Saarland, 66123 Saarbrücken, Germany.
- INM - Leibniz Institute for New Materials, 66123 Saarbrücken, Germany.
| | - Annica K B Gad
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, 171 65 Stockholm, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.
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30
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Zhao QY, Lei PJ, Zhang X, Zheng JY, Wang HY, Zhao J, Li YM, Ye M, Li L, Wei G, Wu M. Global histone modification profiling reveals the epigenomic dynamics during malignant transformation in a four-stage breast cancer model. Clin Epigenetics 2016; 8:34. [PMID: 27034728 PMCID: PMC4815258 DOI: 10.1186/s13148-016-0201-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/21/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epigenetic regulation has emerged to be the critical steps for tumorigenesis and metastasis. Multiple histone methyltransferase and demethylase have been implicated as tumor suppressors or oncogenes recently. But the key epigenomic events in cancer cell transformation still remain poorly understood. METHODS A breast cancer transformation model was established via stably expressing three oncogenes in primary breast epithelial cells. Chromatin immunoprecipitation followed by the next-generation sequencing of histone methylations was performed to determine epigenetic events during transformation. Western blot, quantitative RT-PCR, and immunostaining were used to determine gene expression in cells and tissues. RESULTS Histones H3K9me2 and me3, two repressive marks of transcription, decrease in in vitro breast cancer cell model and in vivo clinical tissues. A survey of enzymes related with H3K9 methylation indicated that KDM3A/JMJD1A, a demethylase for H3K9me1 and me2, gradually increases during cancer transformation and is elevated in patient tissues. KDM3A/JMJD1A deficiency impairs the growth of tumors in nude mice and transformed cell lines. Genome-wide ChIP-seq analysis reveals that the boundaries of decreased H3K9me2 large organized chromatin K9 modifications (LOCKs) are enriched with cancer-related genes, such as MYC and PAX3. Further studies show that KDM3A/JMJD1A directly binds to these oncogenes and regulates their transcription by removing H3K9me2 mark. CONCLUSIONS Our study demonstrates reduction of histones H3K9 me2 and me3, and elevation of KDM3A/JMJD1A as important events for breast cancer, and illustrates the dynamic epigenomic mechanisms during breast cancer transformation.
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Affiliation(s)
- Quan-Yi Zhao
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei China
| | - Pin-Ji Lei
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei China
| | - Xiaoran Zhang
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Jun-Yi Zheng
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei China
| | - Hui-Yi Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei China
| | - Jiao Zhao
- Division of Gastroenterology, Department of Geriatrics, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430072 China
| | - Yi-Ming Li
- Division of Gastroenterology, Department of Geriatrics, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430072 China
| | - Mei Ye
- Division of Gastroenterology, Department of Geriatrics, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430072 China
| | - Lianyun Li
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei China
| | - Gang Wei
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Min Wu
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei China
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Tattoli I, Killackey SA, Foerster EG, Molinaro R, Maisonneuve C, Rahman MA, Winer S, Winer DA, Streutker CJ, Philpott DJ, Girardin SE. NLRX1 Acts as an Epithelial-Intrinsic Tumor Suppressor through the Modulation of TNF-Mediated Proliferation. Cell Rep 2016; 14:2576-86. [PMID: 26971996 DOI: 10.1016/j.celrep.2016.02.065] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/08/2016] [Accepted: 02/22/2016] [Indexed: 01/10/2023] Open
Abstract
The mitochondrial Nod-like receptor protein NLRX1 protects against colorectal tumorigenesis through mechanisms that remain unclear. Using mice with an intestinal epithelial cells (IEC)-specific deletion of Nlrx1, we find that NLRX1 provides an IEC-intrinsic protection against colitis-associated carcinogenesis in the colon. These Nlrx1 mutant mice have increased expression of Tnf, Egf, and Tgfb1, three factors essential for wound healing, as well as increased epithelial proliferation during the epithelial regeneration phase following injury triggered by dextran sodium sulfate. In primary intestinal organoids lacking Nlrx1, stimulation with TNF resulted in exacerbated proliferation and expression of the intestinal stem cell markers Olfm4 and Myb. This hyper-proliferation response was associated with increased activation of Akt and NF-κB pathways in response to TNF stimulation. Together, these results identify NLRX1 as a suppressor of colonic tumorigenesis that acts by controlling epithelial proliferation in the intestine during the regeneration phase following mucosal injury.
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Affiliation(s)
- Ivan Tattoli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, M5S 1A8 Toronto, Canada; Department of Immunology, University of Toronto, M5S 1A8 Toronto, Canada
| | - Samuel A Killackey
- Department of Laboratory Medicine and Pathobiology, University of Toronto, M5S 1A8 Toronto, Canada
| | | | - Raphael Molinaro
- Department of Laboratory Medicine and Pathobiology, University of Toronto, M5S 1A8 Toronto, Canada
| | | | - Muhammed A Rahman
- Department of Laboratory Medicine and Pathobiology, University of Toronto, M5S 1A8 Toronto, Canada; Department of Immunology, University of Toronto, M5S 1A8 Toronto, Canada
| | - Shawn Winer
- Department of Pathology, Toronto General Hospital, University of Toronto, M5S 1A8 Toronto, Canada
| | - Daniel A Winer
- Department of Pathology, Toronto General Hospital, University of Toronto, M5S 1A8 Toronto, Canada
| | - Catherine J Streutker
- Department of Laboratory Medicine and Pathobiology, University of Toronto, M5S 1A8 Toronto, Canada; Saint Michael's Hospital, University of Toronto, M5S 1A8 Toronto, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, M5S 1A8 Toronto, Canada
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, M5S 1A8 Toronto, Canada.
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32
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Bloomfield M, Duesberg P. Karyotype alteration generates the neoplastic phenotypes of SV40-infected human and rodent cells. Mol Cytogenet 2015; 8:79. [PMID: 26500699 PMCID: PMC4618876 DOI: 10.1186/s13039-015-0183-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 09/28/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Despite over 50 years of research, it remains unclear how the DNA tumor viruses SV40 and Polyoma cause cancers. Prevailing theories hold that virus-coded Tumor (T)-antigens cause cancer by inactivating cellular tumor suppressor genes. But these theories don't explain four characteristics of viral carcinogenesis: (1) less than one in 10,000 infected cells become cancer cells, (2) cancers have complex individual phenotypes and transcriptomes, (3) recurrent tumors without viral DNA and proteins, (4) preneoplastic aneuploidies and immortal neoplastic clones with individual karyotypes. RESULTS As an alternative theory we propose that viral carcinogenesis is a form of speciation, initiated by virus-induced aneuploidy. Since aneuploidy destabilizes the karyotype by unbalancing thousands of genes it catalyzes chain reactions of karyotypic and transcriptomic evolutions. Eventually rare karyotypes evolve that encode cancer-specific autonomy of growth. The low probability of forming new autonomous cancer-species by random karyotypic and transcriptomic variations predicts individual and clonal cancers. Although cancer karyotypes are congenitally aneuploid and thus variable, they are stabilized or immortalized by selections for variants with cancer-specific autonomy. Owing to these inherent variations cancer karyotypes are heterogeneous within clonal margins. To test this theory we analyzed karyotypes and phenotypes of SV40-infected human, rat and mouse cells developing into neoplastic clones. In all three systems we found (1) preneoplastic aneuploidies, (2) neoplastic clones with individual clonal but flexible karyotypes and phenotypes, which arose from less than one in 10,000 infected cells, survived over 200 generations, but were either T-antigen positive or negative, (3) spontaneous and drug-induced variations of neoplastic phenotypes correlating 1-to-1 with karyotypic variations. CONCLUSIONS Since all 14 virus-induced neoplastic clones tested contained individual clonal karyotypes and phenotypes, we conclude that these karyotypes have generated and since maintained these neoplastic clones. Thus SV40 causes cancer indirectly, like carcinogens, by inducing aneuploidy from which new cancer-specific karyotypes evolve automatically at low rates. This theory explains the (1) low probability of carcinogenesis per virus-infected cell, (2) the individuality and clonal flexibility of cancer karyotypes, (3) recurrence of neoplasias without viral T-antigens, and (4) the individual clonal karyotypes, transcriptomes and immortality of virus-induced neoplasias - all unexplained by current viral theories.
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Affiliation(s)
- Mathew Bloomfield
- Department of Molecular and Cell Biology, Donner Laboratory, University of California at Berkeley, Berkeley, CA USA
| | - Peter Duesberg
- Department of Molecular and Cell Biology, Donner Laboratory, University of California at Berkeley, Berkeley, CA USA
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33
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Gara SK, Wang Y, Patel D, Liu-Chittenden Y, Jain M, Boufraqech M, Zhang L, Meltzer PS, Kebebew E. Integrated genome-wide analysis of genomic changes and gene regulation in human adrenocortical tissue samples. Nucleic Acids Res 2015; 43:9327-39. [PMID: 26446994 PMCID: PMC4627080 DOI: 10.1093/nar/gkv908] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/29/2015] [Indexed: 01/08/2023] Open
Abstract
To gain insight into the pathogenesis of adrenocortical carcinoma (ACC) and whether there is progression from normal-to-adenoma-to-carcinoma, we performed genome-wide gene expression, gene methylation, microRNA expression and comparative genomic hybridization (CGH) analysis in human adrenocortical tissue (normal, adrenocortical adenomas and ACC) samples. A pairwise comparison of normal, adrenocortical adenomas and ACC gene expression profiles with more than four-fold expression differences and an adjusted P-value < 0.05 revealed no major differences in normal versus adrenocortical adenoma whereas there are 808 and 1085, respectively, dysregulated genes between ACC versus adrenocortical adenoma and ACC versus normal. The majority of the dysregulated genes in ACC were downregulated. By integrating the CGH, gene methylation and expression profiles of potential miRNAs with the gene expression of dysregulated genes, we found that there are higher alterations in ACC versus normal compared to ACC versus adrenocortical adenoma. Importantly, we identified several novel molecular pathways that are associated with dysregulated genes and further experimentally validated that oncostatin m signaling induces caspase 3 dependent apoptosis and suppresses cell proliferation. Finally, we propose that there is higher number of genomic changes from normal-to-adenoma-to-carcinoma and identified oncostatin m signaling as a plausible druggable pathway for therapeutics.
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Affiliation(s)
- Sudheer Kumar Gara
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yonghong Wang
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dhaval Patel
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Liu-Chittenden
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meenu Jain
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myriem Boufraqech
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa Zhang
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul S Meltzer
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Electron Kebebew
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer. PLoS One 2015; 10:e0133449. [PMID: 26237329 PMCID: PMC4523174 DOI: 10.1371/journal.pone.0133449] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/25/2015] [Indexed: 11/19/2022] Open
Abstract
To better understand prostate function and disease, it is important to define and explore the molecular constituents that signify the prostate gland. The aim of this study was to define the prostate specific transcriptome and proteome, in comparison to 26 other human tissues. Deep sequencing of mRNA (RNA-seq) and immunohistochemistry-based protein profiling were combined to identify prostate specific gene expression patterns and to explore tissue biomarkers for potential clinical use in prostate cancer diagnostics. We identified 203 genes with elevated expression in the prostate, 22 of which showed more than five-fold higher expression levels compared to all other tissue types. In addition to previously well-known proteins we identified two poorly characterized proteins, TMEM79 and ACOXL, with potential to differentiate between benign and cancerous prostatic glands in tissue biopsies. In conclusion, we have applied a genome-wide analysis to identify the prostate specific proteome using transcriptomics and antibody-based protein profiling to identify genes with elevated expression in the prostate. Our data provides a starting point for further functional studies to explore the molecular repertoire of normal and diseased prostate including potential prostate cancer markers such as TMEM79 and ACOXL.
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35
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Chen H, Lin F, Xing K, He X. The reverse evolution from multicellularity to unicellularity during carcinogenesis. Nat Commun 2015; 6:6367. [PMID: 25751731 DOI: 10.1038/ncomms7367] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 01/22/2015] [Indexed: 12/21/2022] Open
Abstract
Theoretical reasoning suggests that cancer may result from a knockdown of the genetic constraints that evolved for the maintenance of metazoan multicellularity. By characterizing the whole-life history of a xenograft tumour, here we show that metastasis is driven by positive selection for general loss-of-function mutations on multicellularity-related genes. Expression analyses reveal mainly downregulation of multicellularity-related genes and an evolving expression profile towards that of embryonic stem cells, the cell type resembling unicellular life in its capacity of unlimited clonal proliferation. Also, the emergence of metazoan multicellularity ~600 Myr ago is accompanied by an elevated birth rate of cancer genes, and there are more loss-of-function tumour suppressors than activated oncogenes in a typical tumour. These data collectively suggest that cancer represents a loss-of-function-driven reverse evolution back to the unicellular 'ground state'. This cancer evolution model may account for inter-/intratumoural genetic heterogeneity, could explain distant-organ metastases and hold implications for cancer therapy.
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Affiliation(s)
- Han Chen
- Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China
| | - Fangqin Lin
- Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China
| | - Ke Xing
- 1] Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China [2] Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xionglei He
- 1] Key Laboratory of Gene Engineering of Ministry of Education, Cooperative Innovation Center for High Performance Computing, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, China [2] Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou 510275, China
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36
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Uhlen M. Integrating omics to study human biology and disease. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.1723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Soares F, Tattoli I, Rahman MA, Robertson SJ, Belcheva A, Liu D, Streutker C, Winer S, Winer DA, Martin A, Philpott DJ, Arnoult D, Girardin SE. The mitochondrial protein NLRX1 controls the balance between extrinsic and intrinsic apoptosis. J Biol Chem 2014; 289:19317-30. [PMID: 24867956 PMCID: PMC4094044 DOI: 10.1074/jbc.m114.550111] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NLRX1 is a mitochondrial Nod-like receptor (NLR) protein whose function remains enigmatic. Here, we observed that NLRX1 expression was glucose-regulated and blunted by SV40 transformation. In transformed but not primary murine embryonic fibroblasts, NLRX1 expression mediated resistance to an extrinsic apoptotic signal, whereas conferring susceptibility to intrinsic apoptotic signals, such as glycolysis inhibition, increased cytosolic calcium and endoplasmic reticulum stress. In a murine model of colorectal cancer induced by azoxymethane, NLRX1-/- mice developed fewer tumors than wild type mice. In contrast, in a colitis-associated cancer model combining azoxymethane and dextran sulfate sodium, NLRX1-/- mice developed a more severe pathology likely due to the increased sensitivity to dextran sulfate sodium colitis. Together, these results identify NLRX1 as a critical mitochondrial protein implicated in the regulation of apoptosis in cancer cells. The unique capacity of NLRX1 to regulate the cellular sensitivity toward intrinsic versus extrinsic apoptotic signals suggests a critical role for this protein in numerous physiological processes and pathological conditions.
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Affiliation(s)
- Fraser Soares
- From the Departments of Laboratory Medicine and Pathobiology and
| | - Ivan Tattoli
- From the Departments of Laboratory Medicine and Pathobiology and Immunology
| | - Muhammed A Rahman
- From the Departments of Laboratory Medicine and Pathobiology and Immunology
| | | | | | - Daniel Liu
- From the Departments of Laboratory Medicine and Pathobiology and
| | - Catherine Streutker
- From the Departments of Laboratory Medicine and Pathobiology and Saint Michael's Hospital, and
| | - Shawn Winer
- Department of Pathology, Toronto General Hospital, University of Toronto, Toronto M6G 2T6, Canada and
| | - Daniel A Winer
- Department of Pathology, Toronto General Hospital, University of Toronto, Toronto M6G 2T6, Canada and
| | | | | | - Damien Arnoult
- INSERM U1014, Hôpital Paul Brousse, Bâtiment Lavoisier, 14 avenue Paul Vaillant Couturier, 94807 Villejuif Cedex, France
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38
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Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
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Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
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39
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Singh S, Carpenter AE, Genovesio A. Increasing the Content of High-Content Screening: An Overview. ACTA ACUST UNITED AC 2014; 19:640-50. [PMID: 24710339 PMCID: PMC4230961 DOI: 10.1177/1087057114528537] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/31/2013] [Indexed: 01/17/2023]
Abstract
Target-based high-throughput screening (HTS) has recently been critiqued for its relatively poor yield compared to phenotypic screening approaches. One type of phenotypic screening, image-based high-content screening (HCS), has been seen as particularly promising. In this article, we assess whether HCS is as high content as it can be. We analyze HCS publications and find that although the number of HCS experiments published each year continues to grow steadily, the information content lags behind. We find that a majority of high-content screens published so far (60−80%) made use of only one or two image-based features measured from each sample and disregarded the distribution of those features among each cell population. We discuss several potential explanations, focusing on the hypothesis that data analysis traditions are to blame. This includes practical problems related to managing large and multidimensional HCS data sets as well as the adoption of assay quality statistics from HTS to HCS. Both may have led to the simplification or systematic rejection of assays carrying complex and valuable phenotypic information. We predict that advanced data analysis methods that enable full multiparametric data to be harvested for entire cell populations will enable HCS to finally reach its potential.
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Affiliation(s)
- Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Auguste Genovesio
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA École Normale Supérieure, 45, Rue d'Ulm, 75005 Paris
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40
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Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma. Proc Natl Acad Sci U S A 2014; 111:E866-75. [PMID: 24550497 DOI: 10.1073/pnas.1319196111] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Several common oncogenic pathways have been implicated in the emergence of renowned metabolic features in cancer, which in turn are deemed essential for cancer proliferation and survival. However, the extent to which different cancers coordinate their metabolism to meet these requirements is largely unexplored. Here we show that even in the heterogeneity of metabolic regulation a distinct signature encompassed most cancers. On the other hand, clear cell renal cell carcinoma (ccRCC) strongly deviated in terms of metabolic gene expression changes, showing widespread down-regulation. We observed a metabolic shift that associates differential regulation of enzymes in one-carbon metabolism with high tumor stage and poor clinical outcome. A significant yet limited set of metabolic genes that explained the partial divergence of ccRCC metabolism correlated with loss of von Hippel-Lindau tumor suppressor (VHL) and a potential activation of signal transducer and activator of transcription 1. Further network-dependent analyses revealed unique defects in nucleotide, one-carbon, and glycerophospholipid metabolism at the transcript and protein level, which contrasts findings in other tumors. Notably, this behavior is recapitulated by recurrent loss of heterozygosity in multiple metabolic genes adjacent to VHL. This study therefore shows how loss of heterozygosity, hallmarked by VHL deletion in ccRCC, may uniquely shape tumor metabolism.
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Oncogenes induce a vimentin filament collapse mediated by HDAC6 that is linked to cell stiffness. Proc Natl Acad Sci U S A 2014; 111:1515-20. [PMID: 24474778 DOI: 10.1073/pnas.1300238111] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oncogenes deregulate fundamental cellular functions, which can lead to development of tumors, tumor-cell invasion, and metastasis. As the mechanical properties of cells govern cell motility, we hypothesized that oncogenes promote cell invasion by inducing cytoskeletal changes that increase cellular stiffness. We show that the oncogenes simian virus 40 large T antigen, c-Myc, and cyclin E induce spatial reorganization of the vimentin intermediate filament network in cells. At the cellular level, this reorganization manifests as increased width of vimentin fibers and the collapse of the vimentin network. At nanoscale resolution, the organization of vimentin fibers in these oncogene-expressing cells was more entangled, with increased width of the fibers compared with control cells. Expression of these oncogenes also resulted in up-regulation of the tubulin deacetylase histone deacetylase 6 (HDAC6) and altered spatial distribution of acetylated microtubules. This oncogene expression also induced increases in cellular stiffness and promoted the invasive capacity of the cells. Importantly, HDAC6 was required and sufficient for the structural collapse of the vimentin filament network, and was required for increased cellular stiffness of the oncogene-expressing cells. Taken together, these data are consistent with the possibility that oncogenes can induce cellular stiffness via an HDAC6-induced reorganization of the vimentin intermediate filament network.
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