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Kreis J, Aybey B, Geist F, Brors B, Staub E. Stromal Signals Dominate Gene Expression Signature Scores That Aim to Describe Cancer Cell-intrinsic Stemness or Mesenchymality Characteristics. CANCER RESEARCH COMMUNICATIONS 2024; 4:516-529. [PMID: 38349551 PMCID: PMC10885853 DOI: 10.1158/2767-9764.crc-23-0383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/14/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Epithelial-to-mesenchymal transition (EMT) in cancer cells confers migratory abilities, a crucial aspect in the metastasis of tumors that frequently leads to death. In multiple studies, authors proposed gene expression signatures for EMT, stemness, or mesenchymality of tumors based on bulk tumor expression profiling. However, recent studies suggested that noncancerous cells from the microenvironment or macroenvironment heavily influence such signature profiles. Here, we strengthen these findings by investigating 11 published and frequently referenced gene expression signatures that were proposed to describe EMT-related (EMT, mesenchymal, or stemness) characteristics in various cancer types. By analyses of bulk, single-cell, and pseudobulk expression data, we show that the cell type composition of a tumor sample frequently dominates scores of these EMT-related signatures. A comprehensive, integrated analysis of bulk RNA sequencing (RNA-seq) and single-cell RNA-seq data shows that stromal cells, most often fibroblasts, are the main drivers of EMT-related signature scores. We call attention to the risk of false conclusions about tumor properties when interpreting EMT-related signatures, especially in a clinical setting: high patient scores of EMT-related signatures or calls of "stemness subtypes" often result from low cancer cell content in tumor biopsies rather than cancer cell-specific stemness or mesenchymal/EMT characteristics. SIGNIFICANCE Cancer self-renewal and migratory abilities are often characterized via gene module expression profiles, also called EMT or stemness gene expression signatures. Using published clinical tumor samples, cancer cell lines, and single cancer cells, we highlight the dominating influence of noncancer cells in low cancer cell content biopsies on their scores. We caution on their application for low cancer cell content clinical cancer samples with the intent to assign such characteristics or subtypes.
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Affiliation(s)
- Julian Kreis
- The healthcare business of Merck KGaA, Darmstadt, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Bogac Aybey
- The healthcare business of Merck KGaA, Darmstadt, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Felix Geist
- The healthcare business of Merck KGaA, Darmstadt, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
- Medical Faculty Heidelberg and Faculty of Biosciences, Heidelberg University, and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Eike Staub
- The healthcare business of Merck KGaA, Darmstadt, Germany
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Braune EB, Geist F, Tang X, Kalari K, Boughey J, Wang L, Leon-Ferre RA, D'Assoro AB, Ingle JN, Goetz MP, Kreis J, Wang K, Foukakis T, Seshire A, Wienke D, Lendahl U. Identification of a Notch transcriptomic signature for breast cancer. Breast Cancer Res 2024; 26:4. [PMID: 38172915 PMCID: PMC10765899 DOI: 10.1186/s13058-023-01757-7] [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: 07/07/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Dysregulated Notch signalling contributes to breast cancer development and progression, but validated tools to measure the level of Notch signalling in breast cancer subtypes and in response to systemic therapy are largely lacking. A transcriptomic signature of Notch signalling would be warranted, for example to monitor the effects of future Notch-targeting therapies and to learn whether altered Notch signalling is an off-target effect of current breast cancer therapies. In this report, we have established such a classifier. METHODS To generate the signature, we first identified Notch-regulated genes from six basal-like breast cancer cell lines subjected to elevated or reduced Notch signalling by culturing on immobilized Notch ligand Jagged1 or blockade of Notch by γ-secretase inhibitors, respectively. From this cadre of Notch-regulated genes, we developed candidate transcriptomic signatures that were trained on a breast cancer patient dataset (the TCGA-BRCA cohort) and a broader breast cancer cell line cohort and sought to validate in independent datasets. RESULTS An optimal 20-gene transcriptomic signature was selected. We validated the signature on two independent patient datasets (METABRIC and Oslo2), and it showed an improved coherence score and tumour specificity compared with previously published signatures. Furthermore, the signature score was particularly high for basal-like breast cancer, indicating an enhanced level of Notch signalling in this subtype. The signature score was increased after neoadjuvant treatment in the PROMIX and BEAUTY patient cohorts, and a lower signature score generally correlated with better clinical outcome. CONCLUSIONS The 20-gene transcriptional signature will be a valuable tool to evaluate the response of future Notch-targeting therapies for breast cancer, to learn about potential effects on Notch signalling from conventional breast cancer therapies and to better stratify patients for therapy considerations.
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Affiliation(s)
- Eike-Benjamin Braune
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Xiaojia Tang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Krishna Kalari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Judy Boughey
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | | | - James N Ingle
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | | | - Kang Wang
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Theodoros Foukakis
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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Aybey B, Zhao S, Brors B, Staub E. Immune cell type signature discovery and random forest classification for analysis of single cell gene expression datasets. Front Immunol 2023; 14:1194745. [PMID: 37609075 PMCID: PMC10441575 DOI: 10.3389/fimmu.2023.1194745] [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: 03/27/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
Background Robust immune cell gene expression signatures are central to the analysis of single cell studies. Nearly all known sets of immune cell signatures have been derived by making use of only single gene expression datasets. Utilizing the power of multiple integrated datasets could lead to high-quality immune cell signatures which could be used as superior inputs to machine learning-based cell type classification approaches. Results We established a novel workflow for the discovery of immune cell type signatures based primarily on gene-versus-gene expression similarity. It leverages multiple datasets, here seven single cell expression datasets from six different cancer types and resulted in eleven immune cell type-specific gene expression signatures. We used these to train random forest classifiers for immune cell type assignment for single-cell RNA-seq datasets. We obtained similar or better prediction results compared to commonly used methods for cell type assignment in independent benchmarking datasets. Our gene signature set yields higher prediction scores than other published immune cell type gene sets in random forest-based cell type classification. We further demonstrate how our approach helps to avoid bias in downstream statistical analyses by re-analysis of a published IFN stimulation experiment. Discussion and conclusion We demonstrated the quality of our immune cell signatures and their strong performance in a random forest-based cell typing approach. We argue that classifying cells based on our comparably slim sets of genes accompanied by a random forest-based approach not only matches or outperforms widely used published approaches. It also facilitates unbiased downstream statistical analyses of differential gene expression between cell types for significantly more genes compared to previous cell classification algorithms.
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Affiliation(s)
- Bogac Aybey
- Oncology Data Science, Merck Healthcare KGaA, Darmstadt, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sheng Zhao
- Oncology Data Science, Merck Healthcare KGaA, Darmstadt, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Eike Staub
- Oncology Data Science, Merck Healthcare KGaA, Darmstadt, Germany
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Kreis J, Nedić B, Mazur J, Urban M, Schelhorn SE, Grombacher T, Geist F, Brors B, Zühlsdorf M, Staub E. RosettaSX: Reliable gene expression signature scoring of cancer models and patients. Neoplasia 2021; 23:1069-1077. [PMID: 34583245 PMCID: PMC8479477 DOI: 10.1016/j.neo.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022]
Abstract
Gene expression signatures have proven their potential to characterize important cancer phenomena like oncogenic signaling pathway activities, cellular origins of tumors, or immune cell infiltration into tumor tissues. Large collections of expression signatures provide the basis for their application to data sets, but the applicability of each signature in a new experimental context must be reassessed. We apply a methodology that utilizes the previously developed concept of coherent expression of genes in signatures to identify translatable signatures before scoring their activity in single tumors. We present a web interface (www.rosettasx.com) that applies our methodology to expression data from the Cancer Cell Line Encyclopaedia and The Cancer Genome Atlas. Configurable heat maps visualize per-cancer signature scores for 293 hand-curated literature-derived gene sets representing a wide range of cancer-relevant transcriptional modules and phenomena. The platform allows users to complement heatmaps of signature scores with molecular information on SNVs, CNVs, gene expression, gene dependency, and protein abundance or to analyze own signatures. Clustered heatmaps and further plots to drill-down results support users in studying oncological processes in cancer subtypes, thereby providing a rich resource to explore how mechanisms of cancer interact with each other as demonstrated by exemplary analyses of 2 cancer types.
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Affiliation(s)
- Julian Kreis
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany; Faculty of Bioscience, University of Heidelberg, Heidelberg, Germany
| | - Boro Nedić
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Johanna Mazur
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Miriam Urban
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Sven-Eric Schelhorn
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Thomas Grombacher
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany
| | - Felix Geist
- Therapeutic Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Core Center, Heidelberg, Germany
| | - Michael Zühlsdorf
- Therapeutic Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Darmstadt, Germany
| | - Eike Staub
- Department of Translational Medicine, Oncology Bioinformatics, Merck KGaA, Darmstadt, Germany.
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Koras K, Juraeva D, Kreis J, Mazur J, Staub E, Szczurek E. Feature selection strategies for drug sensitivity prediction. Sci Rep 2020; 10:9377. [PMID: 32523056 PMCID: PMC7287073 DOI: 10.1038/s41598-020-65927-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/06/2020] [Indexed: 12/16/2022] Open
Abstract
Drug sensitivity prediction constitutes one of the main challenges in personalized medicine. Critically, the sensitivity of cancer cells to treatment depends on an unknown subset of a large number of biological features. Here, we compare standard, data-driven feature selection approaches to feature selection driven by prior knowledge of drug targets, target pathways, and gene expression signatures. We asses these methodologies on Genomics of Drug Sensitivity in Cancer (GDSC) dataset, evaluating 2484 unique models. For 23 drugs, better predictive performance is achieved when the features are selected according to prior knowledge of drug targets and pathways. The best correlation of observed and predicted response using the test set is achieved for Linifanib (r = 0.75). Extending the drug-dependent features with gene expression signatures yields the most predictive models for 60 drugs, with the best performing example of Dabrafenib. For many compounds, even a very small subset of drug-related features is highly predictive of drug sensitivity. Small feature sets selected using prior knowledge are more predictive for drugs targeting specific genes and pathways, while models with wider feature sets perform better for drugs affecting general cellular mechanisms. Appropriate feature selection strategies facilitate the development of interpretable models that are indicative for therapy design.
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Affiliation(s)
- Krzysztof Koras
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Dilafruz Juraeva
- Merck Healthcare KGaA, Translational Medicine, Department of Bioinformatics, Darmstadt, Germany
| | - Julian Kreis
- Merck Healthcare KGaA, Translational Medicine, Department of Bioinformatics, Darmstadt, Germany
| | - Johanna Mazur
- Merck Healthcare KGaA, Translational Medicine, Department of Bioinformatics, Darmstadt, Germany
| | - Eike Staub
- Merck Healthcare KGaA, Translational Medicine, Department of Bioinformatics, Darmstadt, Germany
| | - Ewa Szczurek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.
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Zhang Q, Green MD, Lang X, Lazarus J, Parsels JD, Wei S, Parsels LA, Shi J, Ramnath N, Wahl DR, Pasca di Magliano M, Frankel TL, Kryczek I, Lei YL, Lawrence TS, Zou W, Morgan MA. Inhibition of ATM Increases Interferon Signaling and Sensitizes Pancreatic Cancer to Immune Checkpoint Blockade Therapy. Cancer Res 2019; 79:3940-3951. [PMID: 31101760 PMCID: PMC6684166 DOI: 10.1158/0008-5472.can-19-0761] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 01/07/2023]
Abstract
Combinatorial strategies are needed to overcome the resistance of pancreatic cancer to immune checkpoint blockade (ICB). DNA damage activates the innate immune response and improves ICB efficacy. Because ATM is an apical kinase in the radiation-induced DNA damage response, we investigated the effects of ATM inhibition and radiation on pancreatic tumor immunogenicity. ATM was inhibited through pharmacologic and genetic strategies in human and murine pancreatic cancer models both in vitro and in vivo. Tumor immunogenicity was evaluated after ATM inhibition alone and in combination with radiation by assessing TBK1 and Type I interferon (T1IFN) signaling as well as tumor growth following PD-L1/PD-1 checkpoint inhibition. Inhibition of ATM increased tumoral T1IFN expression in a cGAS/STING-independent, but TBK1- and SRC-dependent, manner. The combination of ATM inhibition with radiation further enhanced TBK1 activity, T1IFN production, and antigen presentation. Furthermore, ATM silencing increased PD-L1 expression and increased the sensitivity of pancreatic tumors to PD-L1-blocking antibody in association with increased tumoral CD8+ T cells and established immune memory. In patient pancreatic tumors, low ATM expression inversely correlated with PD-L1 expression. Taken together, these results demonstrate that the efficacy of ICB in pancreatic cancer is enhanced by ATM inhibition and further potentiated by radiation as a function of increased tumoral immunogenicity, underscoring the potential of ATM inhibition in combination with ICB and radiation as an efficacious treatment strategy for pancreatic cancer. SIGNIFICANCE: This study demonstrates that ATM inhibition induces a T1IFN-mediated innate immune response in pancreatic cancer that is further enhanced by radiation and leads to increased sensitivity to anti-PD-L1 therapy.See related commentary by Gutiontov and Weichselbaum, p. 3815.
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Affiliation(s)
- Qiang Zhang
- Department of Radiation Oncology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Michael D Green
- Department of Radiation Oncology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Xueting Lang
- Department of Surgery, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Jenny Lazarus
- Department of Surgery, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Joshua D Parsels
- Department of Radiation Oncology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Shuang Wei
- Department of Surgery, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Leslie A Parsels
- Department of Radiation Oncology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Jiaqi Shi
- Department of Pathology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Nithya Ramnath
- Department of Medical Oncology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Daniel R Wahl
- Department of Radiation Oncology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Marina Pasca di Magliano
- Department of Surgery, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Timothy L Frankel
- Department of Surgery, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Ilona Kryczek
- Department of Surgery, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Yu L Lei
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
- Graduate Program in Immunology and Graduate Program in Cancer Biology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Weiping Zou
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
- Department of Surgery, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
- Department of Pathology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan
- Graduate Program in Immunology and Graduate Program in Cancer Biology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Meredith A Morgan
- Department of Radiation Oncology, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan.
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Robbins CJ, Bou-Dargham MJ, Sanchez K, Rosen MC, Sang QXA. Decoding Somatic Driver Gene Mutations and Affected Signaling Pathways in Human Medulloblastoma Subgroups. J Cancer 2018; 9:4596-4610. [PMID: 30588243 PMCID: PMC6299398 DOI: 10.7150/jca.27993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/08/2018] [Indexed: 01/02/2023] Open
Abstract
Medulloblastoma is the most common malignant pediatric brain tumor. Prior studies have concentrated their efforts studying the four molecular subgroups: SHH, Wnt, group 3, and group 4. SHH and Wnt are driven by their canonical pathways. Groups 3 and 4 are highly metastatic and associated with aberrations in epigenetic regulators. Recent developments in the field have revealed that these subgroups are not as homogenous as previously believed. The objective of this study is to investigate the involvement of somatic driver gene mutations in these medulloblastoma subgroups. We obtained medulloblastoma data from the Catalogue of Somatic Mutations in Cancer (COSMIC), which contains distinct samples that were not previously studied in a large cohort. We identified somatic driver gene mutations and the signaling pathways affected by these driver genes for medulloblastoma subgroups using bioinformatics tools. We have revealed novel infrequent drivers in these subgroups that contribute to our understanding of tumor heterogeneity in medulloblastoma. Normally SHH signaling is activated in the SHH subgroup, however, we determined gain-of-function mutations in ubiquitin ligase (CUL1) that inhibit Gli-mediated transcription. This suggests a potential hindrance in SHH signaling for some patients. For group 3, gain-of-function in the inhibitor of proinflammatory cytokines (HIVEP3) suggests an immunosuppressive phenotype and thus a more hostile tumor microenvironment. Surprisingly, group 4 tumors possess mutations that may prompt the activation of Wnt signaling through gain-of-function mutations in MUC16 and PCDH9. These infrequent mutations detected in this study could be due to subclonal or spatially restricted alterations. The investigation of aberrant driver gene mutations can lead to the identification of new drug targets and a greater understanding of human medulloblastoma heterogeneity.
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Affiliation(s)
- Charles J Robbins
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
| | - Mayassa J Bou-Dargham
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
| | - Kevin Sanchez
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
| | - Matthew C Rosen
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
| | - Qing-Xiang Amy Sang
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
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Oncogenic role of cytomegalovirus in medulloblastoma? Cancer Lett 2017; 408:55-59. [PMID: 28844716 DOI: 10.1016/j.canlet.2017.08.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/12/2017] [Accepted: 08/17/2017] [Indexed: 12/20/2022]
Abstract
Medulloblastoma is the most common solid tumor among children. Current therapeutic strategies for this malignancy include surgical resection, radiation therapy and chemotherapy. However, these treatments are accompanied with serious side effects such as neurological complications and psychosocial problems, due to the severity of treatment on the developing nervous system. To solve this problem, novel therapeutic approaches are currently being investigated. One of them is targeting human cytomegalovirus in medulloblastoma cancer cells. However, this approach is still under debate, since the presence of cytomegalovirus in medulloblastomas remains controversial. In this review, we discuss the current controversies on the role of cytomegalovirus in medulloblastoma oncogenesis and the potential of cytomegalovirus as a novel (immuno)therapeutic target.
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Conservation of immune gene signatures in solid tumors and prognostic implications. BMC Cancer 2016; 16:911. [PMID: 27871313 PMCID: PMC5118876 DOI: 10.1186/s12885-016-2948-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 11/03/2016] [Indexed: 12/20/2022] Open
Abstract
Background Tumor-infiltrating leukocytes can either limit cancer growth or facilitate its spread. Diagnostic strategies that comprehensively assess the functional complexity of tumor immune infiltrates could have wide-reaching clinical value. In previous work we identified distinct immune gene signatures in breast tumors that reflect the relative abundance of infiltrating immune cells and exhibited significant associations with patient outcomes. Here we hypothesized that immune gene signatures agnostic to tumor type can be identified by de novo discovery of gene clusters enriched for immunological functions and possessing internal correlation structure conserved across solid tumors from different anatomic sites. Methods We assembled microarray expression datasets encompassing 5,295 tumors of the breast, colon, lung, ovarian and prostate. Unsupervised clustering methods were used to determine number and composition of gene clusters within each dataset. Immune-enriched gene clusters (signatures) identified by gene ontology enrichment were analyzed for internal correlation structure and conservation across tumors then compared against expression profiles of: 1) flow-sorted leukocytes from peripheral blood and 2) >300 cancer cell lines from solid and hematologic cancers. Cox regression analysis was used to identify signatures with significant associations with clinical outcome. Results We identified nine distinct immune-enriched gene signatures conserved across all five tumor types. The signatures differentiated specific leukocyte lineages with moderate discernment overall, and naturally organized into six discrete groups indicative of admixed lineages. Moreover, seven of the signatures exhibit minimal and uncorrelated expression in cancer cell lines, suggesting that these signatures derive predominantly from infiltrating immune cells. All nine immune signatures achieved statistically significant associations with patient prognosis (p<0.05) in one or more tumor types with greatest significance observed in breast and skin cancers. Several signatures indicative of myeloid lineages exhibited poor outcome associations that were most apparent in brain and colon cancers. Conclusions These findings suggest that tumor infiltrating immune cells can be differentiated by immune-specific gene expression patterns that quantify the relative abundance of multiple immune infiltrates across a range of solid tumor types. That these markers of immune involvement are significantly associated with patient prognosis in diverse cancers suggests their clinical utility as pan-cancer markers of tumor behavior and immune responsiveness. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2948-z) contains supplementary material, which is available to authorized users.
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Characterization of human gene locus CYYR1: a complex multi-transcript system. Mol Biol Rep 2014; 41:6025-38. [PMID: 24981926 DOI: 10.1007/s11033-014-3480-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/17/2014] [Indexed: 01/19/2023]
Abstract
Cysteine/tyrosine-rich 1 (CYYR1) is a gene we previously identified on human chromosome 21 starting from an in-depth bioinformatics analysis of chromosome 21 segment 40/105 (21q21.3), where no coding region had previously been predicted. CYYR1 was initially characterized as a four-exon gene, whose brain-derived cDNA sequencing predicts a 154-amino acid product. In this study we provide, with in silico and in vitro analyses, the first detailed description of the human CYYR1 locus. The analysis of this locus revealed that it is composed of a multi-transcript system, which includes at least seven CYYR1 alternative spliced isoforms and a new CYYR1 antisense gene (named CYYR1-AS1). In particular, we cloned, for the first time, the following isoforms: CYYR1-1,2,3,4b and CYYR1-1,2,3b, which present a different 3' transcribed region, with a consequent different carboxy-terminus of the predicted proteins; CYYR1-1,2,4 lacks exon 3; CYYR1-1,2,2bis,3,4 presents an additional exon between exon 2 and exon 3; CYYR1-1b,2,3,4 presents a different 5' untranslated region when compared to CYYR1. The complexity of the locus is enriched by the presence of an antisense transcript. We have cloned a long transcript overlapping with CYYR1 as an antisense RNA, probably a non-coding RNA. Expression analysis performed in different normal tissues, tumour cell lines as well as in trisomy 21 and euploid fibroblasts has confirmed a quantitative and qualitative variability in the expression pattern of the multi-transcript locus, suggesting a possible role in complex diseases that should be further investigated.
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