Mutational Landscape and Gene Expression Patterns in Adult Acute Myeloid Leukemias with Monosomy 7 as a Sole Abnormality
CANCER RESEARCH
Authors: Eisfeld, Ann-Kathrin; Kohlschmidt, Jessica; Mrozek, Krzysztof; Volinia, Stefano; Blachly, James S.; Nicolet, Deedra; Oakes, Christopher; Kroll, Karl; Orwick, Shelley; Carroll, Andrew J.; Stone, Richard M.; Byrd, John C.; de la Chapelle, Albert; Bloomfield, Clara D.
Abstract
Monosomy of chromosome 7 is the most frequent autosomal monosomy in acute myeloid leukemia (AML), where it associates with poor clinical outcomes. However, molecular features associated with this sole monosomy subtype (-7 AML), which may give insights into the basis for its poor prognosis, have not been characterized. In this study, we analyzed 36 cases of -7 AML for mutations in 81 leukemia/cancer-associated genes using a customized targeted next-generation sequencing panel (Miseq). Global gene and miRNA expression profiles were also determined using paired RNA and small RNA sequencing data. Notably, gene mutations were detected in all the major AML-associated functional groups, which include activated signaling, chromatin remodeling, cohesin complex, methylation, NPM1, spliceosome, transcription factors, and tumor suppressors. Gene mutations in the chromatin remodeling groups were relatively more frequent in patients <60 years of age, who also had less mutations in the methylation and spliceosome groups compared with patients >= 60 years of age. Novel recurrent mutational events in AML were identified in the SMARCA2 gene. In patients >= 60 years of age, the presence of spliceosome mutations associated with a lower complete remission rate ( P = 0.03). RNA sequencing revealed distinct gene and miRNA expression patterns between the sole - 7 and non -7 AML cases, with reduced expression, as expected, of many genes and miRNAs mapped to chromosome 7, and overexpression of ID1, MECOM, and PTPRM, among others. Overall, our findings illuminate a number of molecular features of the underlying aggressive pathobiology in -7 AML patients. (C) 2016 AACR.
Comprehensive tissue-specific gene set enrichment analysis and transcription factor analysis of breast cancer by integrating 14 gene expression datasets
ONCOTARGET
Authors: Li, Wen-Xing; He, Kan; Tang, Ling; Dai, Shao-Xing; Li, Gong-Hua; Lv, Wen-Wen; Guo, Yi-Cheng; An, San-Qi; Wu, Guo-Ying; Liu, Dahai; Huang, Jing-Fei
Abstract
Breast cancer is the most commonly diagnosed malignancy in women. Several key genes and pathways have been proven to correlate with breast cancer pathology. This study sought to explore the differences in key transcription factors (TFs), transcriptional regulation networks and dysregulated pathways in different tissues in breast cancer. We employed 14 breast cancer datasets from NCBI-GEO and performed an integrated analysis in three different tissues including breast, blood and saliva. The results showed that there were eight genes (CEBPD, EGR1, EGR2, EGR3, FOS, FOSB, ID1 and NFIL3) down-regulated in breast tissue but up-regulated in blood tissue. Furthermore, we identified several unreported tissue-specific TFs that may contribute to breast cancer, including ATOH8, DMRT2, TBX15 and ZNF367. The dysregulation of these TFs damaged lipid metabolism, development, cell adhesion, proliferation, differentiation and metastasis processes. Among these pathways, the breast tissue showed the most serious impairment and the blood tissue showed a relatively moderate damage, whereas the saliva tissue was almost unaffected. This study could be helpful for future biomarker discovery, drug design, and therapeutic and predictive applications in breast cancers.