WILMS TUMOR MUTATIONAL SUBCLASSES CONVERGE TO DRIVE CCND2 OVEREXPRESSION

Wilms tumor, the most common kidney cancer in pediatrics, arises from embryonic renal progenitors. Although many patients are cured with multimodal therapy, outcomes remain poor for those with high-risk features. Recent sequencing efforts have provided few biological or clinically actionable insights. Here, we performed DNA and RNA sequencing on 94 Wilms tumors to understand how Wilms tumor mutations transform the transcriptome to arrest differentiation and drive proliferation. We show that most Wilms tumor mutations fall into four classes, each with unique transcriptional signatures: microRNA processing, MYCN activation, chromatin remodeling, and kidney development. In particular, the microRNA processing enzyme DROSHA is one of the most commonly mutated genes in Wilms tumor. We show that DROSHA mutations impair pri-microRNA cleavage, de-repress microRNA target genes, halt differentiation, and overexpress cyclin D2 (CCND2). Several mutational classes converge to drive CCND2 overexpression, which could render them susceptible to cell-cycle inhibitors.

[1]  M. Malumbres,et al.  Mechanisms of Sensitivity and Resistance to CDK4/6 Inhibition. , 2020, Cancer cell.

[2]  Matthew D. Young,et al.  Embryonal precursors of Wilms tumor , 2019, Science.

[3]  Gennady Korotkevich,et al.  Fast gene set enrichment analysis , 2019, bioRxiv.

[4]  Y. Arai,et al.  Combined Genetic and Chromosomal Characterization of Wilms Tumors Identifies Chromosome 12 Gain as a Potential New Marker Predicting a Favorable Outcome12 , 2018, Neoplasia.

[5]  J. Mendell,et al.  Mutations in microRNA processing genes in Wilms tumors derepress the IGF2 regulator PLAG1 , 2018, Genes & development.

[6]  A. Ransick,et al.  Conserved and Divergent Features of Mesenchymal Progenitor Cell Types within the Cortical Nephrogenic Niche of the Human and Mouse Kidney. , 2018, Journal of the American Society of Nephrology : JASN.

[7]  C. Caldwell,et al.  Genomic Aberrations that Activate D-type Cyclins Are Associated with Enhanced Sensitivity to the CDK4 and CDK6 Inhibitor Abemaciclib. , 2017, Cancer cell.

[8]  Qing-Rong Chen,et al.  A Children's Oncology Group and TARGET Initiative Exploring the Genetic Landscape of Wilms Tumor , 2017, Nature Genetics.

[9]  Jeffrey T Leek,et al.  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown , 2016, Nature Protocols.

[10]  Masanori Kawano,et al.  c-Myc Represses Tumor-Suppressive microRNAs, let-7a, miR-16 and miR-29b, and Induces Cyclin D2-Mediated Cell Proliferation in Ewing’s Sarcoma Cell Line , 2015, PloS one.

[11]  D. Bartel,et al.  Predicting effective microRNA target sites in mammalian mRNAs , 2015, eLife.

[12]  Eckart Meese,et al.  Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors. , 2015, Cancer cell.

[13]  Richard A. Moore,et al.  Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors. , 2015, Cancer cell.

[14]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[15]  Dinesh Rakheja,et al.  Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours , 2014, Nature Communications.

[16]  P. Grundy,et al.  Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour , 2014, Nature Communications.

[17]  Hao Zhu,et al.  Lin28 sustains early renal progenitors and induces Wilms tumor , 2014, Genes & development.

[18]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[19]  Namshin Kim,et al.  Bioinformatics Interpretation of Exome Sequencing: Blood Cancer , 2013, Genomics & informatics.

[20]  E. Fridman,et al.  The isolation and characterization of renal cancer initiating cells from human Wilms' tumour xenografts unveils new therapeutic targets† , 2012, EMBO molecular medicine.

[21]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[22]  Mukesh Jain,et al.  NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data , 2012, PloS one.

[23]  L. Hawthorn,et al.  Analysis of Wilms Tumors Using SNP Mapping Array-Based Comparative Genomic Hybridization , 2011, PloS one.

[24]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[25]  Cole Trapnell,et al.  Improving RNA-Seq expression estimates by correcting for fragment bias , 2011, Genome Biology.

[26]  H. Clevers,et al.  Cyclin D2-cyclin-dependent kinase 4/6 is required for efficient proliferation and tumorigenesis following Apc loss. , 2010, Cancer research.

[27]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[28]  Derek Y. Chiang,et al.  MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.

[29]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[30]  Jared M Flatow,et al.  An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1 , 2009, Proceedings of the National Academy of Sciences.

[31]  A. Ashworth,et al.  Perilobar Nephrogenic Rests Are Nonobligate Molecular Genetic Precursor Lesions of Insulin-Like Growth Factor-II-Associated Wilms Tumors , 2008, Clinical Cancer Research.

[32]  Eric C. Lai,et al.  Biological principles of microRNA-mediated regulation: shared themes amid diversity , 2008, Nature Reviews Genetics.

[33]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  C. Junien,et al.  Frequent overexpression of cyclin D2/cyclin-dependent kinase 4 in Wilms' tumor. , 2005, Cancer letters.

[35]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[36]  N. Nowak,et al.  Molecular analysis of region t(5;6)(q21;q21) in Wilms tumor. , 2003, Cancer genetics and cytogenetics.

[37]  C. Junien,et al.  Profiling of differential gene expression in Wilms tumor by cDNA expression array , 2001, Pediatric Nephrology.

[38]  M. Eilers,et al.  Regulation of cyclin D2 gene expression by the Myc/Max/Mad network: Myc-dependent TRRAP recruitment and histone acetylation at the cyclin D2 promoter. , 2001, Genes & development.

[39]  M. Gessler,et al.  Gain of 1q is associated with adverse outcome in favorable histology Wilms' tumors. , 2001, The American journal of pathology.

[40]  D. Evans,et al.  Physical localisation of the breakpoints of a constitutional translocation t(5;6)(q21;q21) in a child with bilateral Wilms' tumour. , 1997, Journal of medical genetics.

[41]  WILMS' TUMOUR , 1972 .

[42]  J. Mesirov,et al.  The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.

[43]  Claude-Alain H. Roten,et al.  Theoretical and practical advances in genome halving , 2004 .