PLCB4 copy gain and PLCß4 overexpression in primary gastrointestinal stromal tumors: Integrative characterization of a lipid-catabolizing enzyme associated with worse disease-free survival

Abstract

To explore the implications of lipid catabolism-associated genes in gastrointestinal stromal tumors, we reappraised transcriptomic and genomic datasets and identified copy-gained and differentially upregulated PLCB4 gene associated with tumor progression. On full sections, PLCB4 mRNA abundance and PLCß4 immunoexpression were validated in 70 cases. On tissue microarrays, PLCB4 gene copies and PLCß4 immunoexpression were both informative in 350 cases with KIT/PDGFRA/BRAF genotypes noted in 213. In GIST48 cell line, we stably silenced PLCB4 and YAP1 to characterize their functional effects and regulatory link. Compared with normal tissue, PLCB4 mRNA abundance significantly increased across tumors of various risk levels (p<0.001), and was strongly correlated with immunoexpression level (p<0.001, r=0.468). Including polysomy (12.6%) and amplification (17.4%), PLCB4 copy gain was detected in 105 (30%) cases and significantly more frequent (p<0.001) in cases exhibiting higher PLCß4 immunoexpression (82/175). Copy gain and protein overexpression were modestly associated with unfavorable genotypes (both p<0.05), strongly associated with increased size, mitosis, and risk levels defined by both the NIH and NCCN schemes (all p<0.001), and univariately predictive of shorter disease-free survival (both p<0.0001). In PLCß4-overexpressing cases, PLCB4 copy gain still predicted worse prognosis (p<0.0001). In a multivariate comparison, both overexpression (p=0.007, hazard ratio: 2.454) and copy gain (p=0.031, hazard ratio: 1.892) exhibited independent impact. In vitro, YAP1 increased PLCB4 mRNA and protein expression, and both molecules significantly promoted cell proliferation. Being driven by copy gain or YAP1, PLCß4 is a novel overexpressed enzyme regulating lipid catabolism that promotes cell proliferation and independently confers a worse prognosis.

Positive Caricature Transcriptomic Effects Associated with Broad Genomic Aberrations in Colorectal Cancer

“…Six of the top ten Over-UpT genes in Chr20 have been involved in tumorigenesis based on overexpression, functional assays and clinical data: CSE1L 44 , 45 , POFUT1 54 , TPX2 55 RPN2 56 , PLCB4 57 , CPNE1 58 , 59 .…”

Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy

“…ADAMTS12 is a member of disintegrin and metalloproteinase with thrombospondin motifs family which is important in the turnover of extracellular matrix proteins in various tissues [ 56 ]. In contrast, PLCB4, a phospholipase Cβ, catalyzes the formation of 1,4,5-triphosphate and diacylglycerol form phosphatidylinositol 4,5-bisphosphate [ 57 , 58 ] and is involved in signaling pathways such as calcium signaling pathway [ 57 ] as well as lipid metabolism [ 58 , 59 ] and the novel lincRNA have no clear functions in skeletal muscle and warrant further investigation.…”

Overexpressed Fatty Acid Synthase in Gastrointestinal Stromal Tumors: Targeting a Progression-Associated Metabolic Driver Enhances the Antitumor Effect of Imatinib

“…There were 350 GISTs informative for FASN immunoexpression status (Table 1) with clinical followup data, which comprised 88 no-or very low-risk cases, 100 low-risk cases, 65 moderate-risk cases, and 97 high-risk cases based on NCCN guidelines and corresponded to 127 very low/low-risk cases, 110 intermediate-risk cases, and 113 high-risk cases according to the NIH risk scheme. Of these, 22 cases with wild-type KIT and PDGFRA genes exhibited neither a BRAF hotspot mutation nor aberrant loss of SDHA or SDHB (16). FASN-overexpressing GISTs were frequently nongastric (P ¼ 0.050) and were strongly associated with the presence of epithelioid cells, unfavorable KIT/PDGFR/ BRAF genotypes, and increasing tumor size, mitotic rate, and risk levels by both NCCN and NIH criteria (all P 0.005).…”

“…In GISTs, overexpressed FASN may serve as a poor prognosticator, and dual blockade of FASN and KIT emerges as a therapeutic strategy for imatinib-resistant cases. PDGFRA genes were screened for possible mutation in the BRAF hotspot exon 15 (16). The prognostically dichotomized grouping of genotypes is detailed in Supplementary Methods S2 and has been reported previously (13)(14)(15)(16).…”

“…FASN immunoexpression was recorded as the mean percentage of labeled cells in the tumoral cytoplasm, and overexpression was defined by 50% or more tumor cells with moderate or strong cytoplasmic staining. To screen for defects in the mitochondrial succinate dehydrogenase (SDH) complex, 22 GISTs without KIT or PDGFRA mutations in the TMA cohort were evaluated for immunoexpression of SDHA (1:750; Abcam) and SDHB (1:200; Abcam) on full sections (16).…”