Biological roles of THRAP3, STMN1 and GNA13 in human blood cancer cells

Abstract

Blood cancers, such as diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma (BL) and acute myeloid leukemia (AML), are aggressive neoplasms that are characterized by undesired clinical courses with dismal survival rates. The objective of the current work is to study the expression THRAP3, STMN1 and GNA13 in DLBCL, BL and AML, and to investigate if these proteins are implicated in the prognosis and progression of the blood cancers. Isolation of normal blood cells was performed using lymphoprep coupled with gradient centrifugation and magnetic beads. Flow-cytometric analysis showed high quality of the isolated cells. Western blotting identified THRAP3, STMN1 and GNA13 to be overexpressed in the blood cancer cells but hardly detected in normal blood cells from healthy donors. Consistently, investigations performed using genotype-tissue expression (GTEx) and gene expression profiling interactive analysis (GEPIA) showed that the three proteins had higher mRNA expression in various cancers compared with matched normal tissues (p ≤ 0.01). Furthermore, the up-regulated transcript expression of these proteins was a feature of short overall survival (OS; p ≤ 0.02) in patients with the blood cancers. Interestingly, functional profiling using gProfiler and protein-protein interaction network analysis using STRING with cytoscape reported THRAP3 to be associated with cancer-dependent proliferation and survival pathways (corrected p ≤ 0.05) and to interact with proteins (p = 1 × 10^-16) implicated in tumourigenesis and chemotherapy resistance. Taken together, these findings indicated a possible implication of THRAP3, STMN1 and GNA13 in the progression and prognosis of the blood cancers. Additional work using clinical samples of the blood cancers is required to further investigate and validate the results reported here.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04093-5.

Keywords: Blood cancers; GNA13; STMN1; THRAP3.

Fig. 1

Diagram of pooling normal cells. This figure shows how the pooling of normal PBMCs samples (A) and normal B cells’ samples was performed (B)

Fig. 2

Flow-cytometric analysis of the isolation of PBMCs and B cells. Lymphoprep and gradient centrifugation were applied on blood samples from healthy donors to extract PBMCs (A and B). Next, B cells were isolated from PBMCs using CD19 magnetic beads (C and D). LP: lymphocytes population; GMP: granulocytes and monocytes population

Fig. 3

Protein expression of THRAP3, STMN1 and GNA13 in blood cancer cells and normal blood cells. Western blotting was employed to study the expression of THRAP3, STMN1 and GNA13 in DLBCL cells (OCI-LY3), BL cells (Daudi), AML cells (THP-1) and normal blood cells. Normal blood cells: #1 and #2 are pooled PBMC samples; #3, #4 and #5 are pooled B-cell samples

Fig. 4

Transcript expression of THRAP3, STMN1 and GNA13 in malignant lymphoid tissues (MLT) and matched normal tissues. The analysis was conducted using TCGA and GTEx data operated through GEPIA. THRAP3 and STMN1 returned p value ≤ 0.01, whereas GNA13 showed p value > 0.05

Fig. 5

Transcript expression of THRAP3 in solid malignancies and matched normal tissues. TCGA and GTEx data computed through GEPIA were used for the analysis. All results shown in this figure are reported with p ≤ 0.01. CHOL cholangiocarcinoma, PAAD pancreatic adenocarcinoma, THYM thymoma

Fig. 6

Transcript expression of STMN1 in solid neoplasms and matched normal tissues. TCGA and GTEx data computed through GEPIA were used for the analysis. All findings demonstrated in this figure are reported with p ≤ 0.01. BLCA bladder urothelial carcinoma, BRCA breast invasive carcinoma, COAD colon adenocarcinoma; LIHC liver hepatocellular carcinoma, PAAD pancreatic adenocarcinoma; SKCM skin cutaneous melanoma, STAD stomach adenocarcinoma, THYM thymoma

Fig. 7

Transcript expression of GNA13 in solid cancers and matched normal tissues. This analysis was done using TCGA and GTEx data through GEPIA. All comparisons presented in this figure are reported with p ≤ 0.01. CHOL cholangiocarcinoma, ESCA esophageal carcinoma, GBM glioblastoma multiforme, LAML acute myeloid leukemia, LGG brain lower grade glioma, PAAD pancreatic adenocarcinoma, SKCM skin cutaneous melanoma, STAD stomach adenocarcinoma

Fig. 8

Association of the transcript expression of THRAP3, STMN1 and GNA13 with short OS in the blood cancers. Two transcriptomics data sets from GEO (data set accession number: GSE181063 for DLBCL and BL) and from TCGA (name of data set: Acute Myeloid Leukemia (TCGA, NEJM 2013) for AML) were used for this analysis. DLBCL diffuse large B-cell lymphoma, BL Burkitt’s lymphoma, AML acute myeloid leukemia, OS overall survival, HR hazard ration

Fig. 9

Functional profiling of THRAP3 in blood cancer cells. Pearson score (correlation coefficient) and the transcriptomics data sets (GSE181063 and Acute Myeloid Leukemia (TCGA, NEJM 2013)) from GEO and TCGA were used to search for genes whose expression correlate with the transcript expression of THAP3 in DLBCL, BL and AML (A). Next, functional enrichment of the genes that correlated with THRAP3 expression in BL was performed using gProfiler (B). DLBCL diffuse large B-cell lymphoma; BL Burkitt’s lymphoma, AML acute myeloid leukemia

Fig. 10

Illustration of the genes that correlated with THRAP3 in BL and were assigned to the spliceosome pathway (KEGG; entry number: hsa03040). The genes that were color-highlighted are those that correlated with THRAP3 in BL. The color range is indicative of the correlation coefficient (Pearson score)

Fig. 11

Demonstration of the genes that correlated with THRAP3 in BL and were assigned to the B-cell receptor signaling pathway (KEGG; entry number: hsa04662). The genes that were color-highlighted are those that correlated with THRAP3 in BL. The color range is indicative of the correlation coefficient (Pearson score)

Fig. 12

Protein–protein interaction network analysis of THRAP3. STRING was used to search for THRAP3 interaction partners among the protein product of the genes that were found to correlate with THRAP3 in BL (data set GSE181063). Next, the PPIs network was visualized using Cytoscape (A). Functional profiling of the THRAP3 interactors (n = 43 proteins) was performed using STRING and showed in cord plot (B)