Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse
ONCOTARGET
Authors: Krzeminski, Patryk; Corchete, Luis A.; Garcia, Juan L.; Lopez-Corral, Lucia; Ferminan, Encarna; Garcia, Eva M.; Martin, Ana A.; Hernandez-Rivas, Jesus M.; Garcia-Sanz, Ramon; San Miguel, Jesus F.; Gutierrez, Norma C.
Abstract
Multiple myeloma (MM) remains incurable despite the introduction of novel agents, and a relapsing course is observed in most patients. Although the development of genomic technologies has greatly improved our understanding of MM pathogenesis, the mechanisms underlying relapse have been less thoroughly investigated. In this study, an integrative analysis of DNA copy number, DNA methylation and gene expression was conducted in matched diagnosis and relapse samples from MM patients. Overall, the acquisition of abnormalities at relapse was much more frequent than the loss of lesions present at diagnosis, and DNA losses were significantly more frequent in relapse than in diagnosis samples. Interestingly, copy number abnormalities involving more than 100 Mb of DNA at relapse significantly affect the gene expression of these samples, provoking a particular deregulation of the IL-8 pathway. On the other hand, no significant modifications of gene expression were observed in those samples with less than 100 Mb affected by chromosomal changes. Although several statistical approaches were used to identify genes whose abnormal expression at relapse was regulated by methylation, only two genes that were significantly deregulated in relapse samples (SORL1 and GLT1D1) showed a negative correlation between methylation and expression. Further analysis revealed that DNA methylation was involved in regulating SORL1 expression in MM. Finally, relevant changes in gene expression observed in relapse samples, such us downregulation of CD27 and P2RY8, were most likely not preceded by alterations in the corresponding DNA. Taken together, these results suggest that the genomic heterogeneity described at diagnosis remains at relapse.
Analysis of dementia-related gene variants in APOE epsilon 4 noncarrying Korean patients with early-onset Alzheimer's disease
NEUROBIOLOGY OF AGING
Authors: Park, Jong Eun; Kim, Hee Jin; Kim, Young-Eun; Jang, Hyemin; Cho, Soo Hyun; Kim, Seung Joo; Na, Duk L.; Won, Hong-Hee; Ki, Chang-Seok; Seo, Sang Won
Abstract
There is a genetic overlap among various neurodegenerative diseases that cause dementia. We analyzed dementia-related gene variants in 60 apolipoprotein E epsilon 4 non-carrying Korean patients with early-onset Alzheimer's disease. Thirty-one dementia-related genes were screened by exome sequencing. Among the 60 patients, three likely pathogenic variants (LPVs) and 1 variant of uncertain significance (VUS) were identified in PSEN1. In addition, two LPVs in TYROBP (c.141del) and PINK1 (c.1220G>A) and 17 VUS were found in other dementia-causing genes. Two variants in SORL1 and TREM2 were identified that were associated with Alzheimer's disease. In this study, we identified 5 (8.3%) LPVs and 18 (30%) VUSs in known dementia-related genes in apolipoprotein E epsilon 4 noncarrying Korean patients with early-onset Alzheimer's disease. (C) 2019 Elsevier Inc. All rights reserved.