Genetic lineages of undifferentiated-type gastric carcinomas analysed by unsupervised clustering of genomic DNA microarray data

Abstract

BackgroundIt is suspected that early gastric carcinoma (GC) is a dormant variant that rarely progresses to advanced GC. We demonstrated that the dormant and aggressive variants of tubular adenocarcinomas (TUBs) of the stomach are characterized by loss of MYC and gain of TP53 and gain of MYC and/or loss of TP53, respectively. The aim of this study is to determine whether this is also the case in undifferentiated-type GCs (UGCs) of different genetic lineages: one with a layered structure (LS+), derived from early signet ring cell carcinomas (SIGs), and the other, mostly poorly differentiated adenocarcinomas, without LS but with a minor tubular component (TC), dedifferentiated from TUBs (LS−/TC+).MethodsUsing 29 surgically resected stomachs with 9 intramucosal and 20 invasive UGCs (11 LS+ and 9 LS−/TC+), 63 genomic DNA samples of mucosal and invasive parts and corresponding reference DNAs were prepared from formalin-fixed, paraffin-embedded tissues with laser microdissection, and were subjected to array-based comparative genomic hybridization (aCGH), using 60K microarrays, and subsequent unsupervised, hierarchical clustering. Of 979 cancer-related genes assessed, we selected genes with mean copy numbers significantly different between the two major clusters.ResultsBased on similarity in genomic copy-number profile, the 63 samples were classified into two major clusters. Clusters A and B, which were rich in LS+ UGC and LS−/TC+ UGC, respectively, were discriminated on the basis of 40 genes. The aggressive pattern was more frequently detected in LS−/TC+ UGCs, (20/26; 77%), than in LS+UGCs (17/37; 46%; P = 0.0195), whereas no dormant pattern was detected in any of the UGC samples.ConclusionsIn contrast to TUBs, copy number alterations of MYC and TP53 exhibited an aggressive pattern in LS+ SIG at early and advanced stages, indicating that early LS+ UGCs inevitably progress to an advanced GC. Cluster B (enriched in LS−/TC+) exhibited more frequent gain of driver genes and a more frequent aggressive pattern than cluster A, suggesting potentially worse prognosis in UGCs of cluster B.

Gastric cancer and gene copy number variation: emerging cancer drivers for targeted therapy

“…85,86 Many studies reported that a significant increase in MYC copy number can be detected in the carcinogenic process of GC and in gastric cell lines. [87][88][89][90][91][92] The amplification of MYC has also been suggested with independent prognostic value on overall survival. 93 In addition, MYC CNVs has a tight connection with the clinicopathological features of GC.…”

Rapidly and Slowly Growing Lineages in Chromosomal Instability-Type Gland-Forming Gastric Carcinomas as Revealed by Multisampling Analysis of DNA Copy-Number Profile

“…Given that samples from the same tumor might share random generation of gene CNAs and tissue environmental selection, different parts of a tumor might have similar CNA profiles in the presence of a common carcinogenetic process [8, 9]. CNA profiles that have a low noise level could satisfy this internal standard.…”

“…For smaller gene numbers, the reproducibility of clustering analysis becomes lower, but gene size is larger. Thus, for determining optimal gene size and number, the clustering analysis was repeatedly performed using the Clustering 3.0 (v1.52) software and TreeView (v1.1.6r2) [8, 9]. The unsupervised clustering analysis was based on genomic copy-number profile resemblance, and complete linkage and uncentered correlation distance were applied.…”

“…In our previous studies, we applied genomic DNA copy-number alteration (CNA) profiling to precursor lesions as well as to early and advanced GC specimens, and classified GC samples using unsupervised hierarchical cluster analysis. Using this approach, we demonstrated that virtually all undifferentiated (diffuse) early GC cases were considered to become advanced [8] whereas around 20% of noninvasive (gland-forming) neoplasms were considered to eventually become invasive [9]. In this study, we utilized this approach on multiple samples from mucosal, extramucosal invasive, and metastatic lymph node lesions of individual tumor specimens to confirm the consistency of individual-specific changes, and examine the changes associated with tumor progression.…”

Progression Potential of Ductal Carcinoma in situ Assessed by Genomic Copy Number Profiling

“…Thus, the CNA profile of clinically detectable breast cancer may already include information enough for outcome prediction. In our previous gastric cancer studies, we classified the samples based on their CNA profiles using unsupervised hierarchical cluster analyses and demonstrated that nearly all early cancer of the undifferentiated type can become advanced [19], whereas approximately 80% of noninvasive neoplasms of the differentiated type showed a lineage distinct from advanced cancers [20]. …”