Target amplicon exome-sequencing identifies promising diagnosis and prognostic markers involved in RTK-RAS and PI3K-AKT signaling as central oncopathways in primary central nervous system lymphoma

Abstract

Exome-sequencing for somatic mutation detection and copy number variation analysis are effective and valid methods for evaluating human cancers in current molecular medicine. We conducted target amplicon exome-sequencing analyses using PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Twenty-seven primary central nervous system lymphoma (PCNSL) specimens and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverages of the entire coding regions of 409 cancer-related genes. The average of the total numbers of somatic mutations including single-nucleotide variations and insertion/deletion mutations in each specimen was 13.3. Of these, the average of the ratios of nonsynonymous substitutions in each specimen was 74.8%. The most frequent mutations in 27 specimens were in PIM1, MYD88, CD79B, DST, IRF4, ERBB3, MYH11, DCC, and KMT2D. Furthermore, somatic mutations of MYH11 were related to poor prognoses in PCNSL patients. Copy number variations were also duplicated and/or deleted from deep-sequencing in segmental genomic islands. In addition to these prognostic marker candidates, analysis of RTK-RAS-MAPK signaling and the PTEN-PI3K-AKT proapoptotic pathway showed that somatic activations and aberrations, respectively, may be involved in a promising central oncopathway harboring mTOR, c-Myc, FOXO1, and p53. This study provides a foundation for molecular targeted therapies based on genome diagnostics and prognosis in PCNSL.

Mutation profiling of uterine cervical cancer patients treated with definitive radiotherapy

“…Lastly and unfortunately, we were not able to perform Sanger sequencing to validate or results due to insufficient amounts of FFPE samples. However, a previous study that analyzed FFPE-derived DNAs using analytical flow and variant calling cut-offs identical to those used in this study demonstrated that 100% of 11 randomly selected SNVs and five InDels identified by next-generation sequencing were validated by Sanger sequencing [24,25]. In addition, another study that analyzed FFPEderived DNAs using an identical analytical flow but with a lower variant frequency cut-off of 5% demonstrated that 93.7% (30/32) of SNVs in PIK3CA, KRAS, SMAD4, KMT2A, TET1, and NLRP1, which were identified by next-generation sequencing, were validated by Sanger sequencing [32].…”

“…Somatic mutations were identified as previously described, with minor modifications [24,25]. Briefly, data were analyzed using Torrent Suite version 5.0 (Thermo Fisher Scientific), which generated parsed barcoded reads, assessed read quality, performed trimming, and aligned base calls to the Genome Reference Consortium Human Build 37 (hg19) using the TMAP aligner (Torrent Mapping Alignment Program) to generate BAM (binary format) files.…”

<p>B7-H6 Promotes Cell Proliferation, Migration and Invasion of Non-Hodgkin Lymphoma via Ras/MEK/ERK Pathway Based on Quantitative Phosphoproteomics Data</p>

“…[19][20][21][22][23] Gene mutation in Ras, as well as changes in Ras signaling cascade have been detected in a variety of NHL, especially in chronic lymphocytic leukemia, T cell lymphoblastic leukemia/lymphoma, central nervous system lymphoma and cutaneous T cell lymphoma. [24][25][26][27] Since HIF-1 usually plays a role as a downstream effector of Ras signaling, 10,11 we selected Ras signaling pathway for validation. Our data demonstrated that the phosphorylation levels of MEK and ERK in Ras/MEK/ ERK pathway are regulated by B7-H6 upstream, indicating that B7-H6 facilitates cell proliferation, migration and invasion in NHL through Ras/MEK/ERK pathway.…”

miR-101, miR-548b, miR-554, and miR-1202 are reliable prognosis predictors of the miRNAs associated with cancer immunity in primary central nervous system lymphoma

“…Expression of miRNAs was clustered with Ward method using the JMP built-in modules (SAS Institute, Inc., Tokyo, Japan), as described [29].…”

“…The Kaplan-Meier method was used to estimate the survival distributions for each subgroup with the log-rank test among subgroups using the JMP built-in modules (SAS Institute Inc, Tokyo, Japan.) [29].…”