title: Expression profiling stratifies mesothelioma tumors and signifies deregulation of spindle checkpoint pathway and microtubule network with therapeutic implications.
abstract: BACKGROUND
  Malignant pleural mesothelioma (MPM) is a lethal neoplasm exhibiting resistance to most treatment regimens and requires effective therapeutic options. Though an effective strategy in many cancer, targeted therapy is relatively unexplored in MPM because the therapeutically important oncogenic pathways and networks in MPM are largely unknown.
  
  
  METHODS
  We carried out gene expression microarray profiling of 53 surgically resected MPMs tumors along with paired normal tissue. We also carried out whole transcriptomic sequence (RNA-seq) analysis on eight tumor specimens. Taqman-based quantitative Reverse-transcription polymerase chain reaction (qRT-PCR), western analysis and immunohistochemistry (IHC) analysis of mitotic arrest deficient-like 1 (MAD2L1) was carried out on tissue specimens. Cell viability assays of MPM cell lines were carried out to assess sensitivity to specific small molecule inhibitors.
  
  
  RESULTS
  Bioinformatics analysis of the microarray data followed by pathway analysis revealed that the mitotic spindle assembly checkpoint (MSAC) pathway was most significantly altered in MPM tumors with upregulation of 18 component genes, including MAD2L1 gene. We validated the microarray data for MAD2L1 expression using quantitative qRT-PCR and western blot analysis on tissue lysates. Additionally, we analyzed expression of the MAD2L1 protein by IHC using an independent tissue microarray set of 80 MPM tissue samples. Robust clustering of gene expression data revealed three novel subgroups of tumors, with unique expression profiles, and showed differential expression of MSAC pathway genes. Network analysis of the microarray data showed the cytoskeleton/spindle microtubules network was the second-most significantly affected network. We also demonstrate that a nontaxane small molecule inhibitor, epothilone B, targeting the microtubules have great efficacy in decreasing viability of 14 MPM cell lines.
  
  
  CONCLUSIONS
  Overall, our findings show that MPM tumors have significant deregulation of the MSAC pathway and the microtubule network, it can be classified into three novel molecular subgroups of potential therapeutic importance and epothilone B is a promising therapeutic agent for MPM.
authors.affiliation: Department of Translational Molecular Pathology.
authors.forename: M B
authors.initials: MB
authors.lastname: Suraokar
authors.affiliation: Department of Pathology.
authors.forename: M I
authors.initials: MI
authors.lastname: Nunez
authors.affiliation: Department of Bioinformatics and Computational Biology.
authors.forename: L
authors.initials: L
authors.lastname: Diao
authors.affiliation: Department of Translational Molecular Pathology.
authors.forename: C W
authors.initials: CW
authors.lastname: Chow
authors.affiliation: Department of Pathology.
authors.forename: D
authors.initials: D
authors.lastname: Kim
authors.affiliation: Department of Thoracic/Head and Neck Medical Oncology.
authors.forename: C
authors.initials: C
authors.lastname: Behrens
authors.affiliation: Department of Biostatistics.
authors.forename: H
authors.initials: H
authors.lastname: Lin
authors.affiliation: Department of Pathology.
authors.forename: S
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Pathology.
authors.forename: G
authors.initials: G
authors.lastname: Raso
authors.affiliation: Department of Pathology.
authors.forename: C
authors.initials: C
authors.lastname: Moran
authors.affiliation: Department of Thoracic and Cardiovascular Surgery.
authors.forename: D
authors.initials: D
authors.lastname: Rice
authors.affiliation: Department of Thoracic and Cardiovascular Surgery.
authors.forename: R
authors.initials: R
authors.lastname: Mehran
authors.affiliation: Department of Biostatistics.
authors.forename: J J
authors.initials: JJ
authors.lastname: Lee
authors.affiliation: Department of Cardiothoracic Surgery, New York University School of Medicine, New York, USA.
authors.forename: H I
authors.initials: HI
authors.lastname: Pass
authors.affiliation: Department of Bioinformatics and Computational Biology.
authors.forename: J
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Bioinformatics and Computational Biology.
authors.forename: A A
authors.initials: AA
authors.lastname: Momin
authors.affiliation: Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston.
authors.forename: B P
authors.initials: BP
authors.lastname: James
authors.affiliation: Department of Pathology Department of Thoracic/Head and Neck Medical Oncology.
authors.forename: A
authors.initials: A
authors.lastname: Corvalan
authors.affiliation: Department of Bioinformatics and Computational Biology.
authors.forename: K
authors.initials: K
authors.lastname: Coombes
authors.affiliation: Department of Thoracic/Head and Neck Medical Oncology.
authors.forename: A
authors.initials: A
authors.lastname: Tsao
authors.affiliation: Department of Translational Molecular Pathology Department of Thoracic/Head and Neck Medical Oncology iiwistuba@mdanderson.org.
authors.forename: I I
authors.initials: II
authors.lastname: Wistuba
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D000970:Antineoplastic Agents / Q000494:pharmacology; D015153:Blotting, Western; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D004252:DNA Mutational Analysis; D034261:Epothilones / Q000494:pharmacology; D020869:Gene Expression Profiling; D006801:Humans; D007150:Immunohistochemistry; D008175:Lung Neoplasms / Q000235:genetics*; D059566:M Phase Cell Cycle Checkpoints / Q000235:genetics*; D008654:Mesothelioma / Q000235:genetics*; D000086002:Mesothelioma, Malignant; D008870:Microtubules / Q000473:pathology*; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010997:Pleural Neoplasms / Q000235:genetics* / Q000473:pathology; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D046888:Tissue Array Analysis; D059467:Transcriptome; D050257:Tubulin Modulators / Q000494:pharmacology
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D000970:Antineoplastic Agents; D018797:Cell Cycle Proteins; D034261:Epothilones; C470309:MAD2L1BP protein, human; D009687:Nuclear Proteins; D050257:Tubulin Modulators; C093788:epothilone B
keywords: MAD2L1; epothilone B; mesothelioma; microarray; network; therapeutics