scholarly journals Protein Structure Prediction and Bioinfamatic Analysis of Novel Fusion Gene IKZF1/Pfas in BPDCN

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 4319-4319
Author(s):  
Yin Le ◽  
Qian Yu ◽  
Hongkai Zhu ◽  
Yi Jiang ◽  
Zhihua Wang ◽  
...  

Abstract A novel fusion gene, IKAROS Family Zinc Finger 1 (IKZF1)/Phosphoribosylformylglycinamidine Synthase (PFAS), was identified in a patient diagnosed with Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN). Secondary protein structure analysis, 3D protein structure determination and domain analysis revealed loss of the ZnF-C2H2 domains of IKZF1 caused by premature translation termination at amino acid (AA) residue 55, which might cause dysfunction of IKZF1. Bioinformatic analysis was conducted using RNA-seq data for 37 BPDCN samples from the GSE database (GSE62014 and GSE89565) to elucidate the role of IKZF1 in BPDCN. WGCNA showed that IKZF1 expression could be used to categorize BPDCN samples into two distinct clusters (IKZF1 high and IKZF1 low). Differentially expressed genes (DEGs) were identified in these two subgroups and subjected to GO and KEGG analyses. Mitochondrial function-related pathways and ubiquitin-mediated proteolysis were the most enriched pathways in the GO and KEGG analyses, respectively. A PPI network of the DEGs was constructed, and 10 key genes were identified (CSTF2, SF3B1, U2AF2, HNRNPH1, SF3B3, SNRNP200, LSM2, SLU7, CPSF4 and UPF3B). Most of these genes are related to tumorigenesis, cancer metastasis, and hematopoietic malignancies. In conclusion, the novel IKZF1/PFAS fusion gene could cause dysfunction of the IKZF1. The bioinformatic analysis results emphasized the role of IKZF1 in BPDCN and identified 10 key genes closely related to IKZF1, most of which are tumorigenesis-related. Disclosures No relevant conflicts of interest to declare.

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 895
Author(s):  
Yue Yao ◽  
Heng Wee Tan ◽  
Zhan-Ling Liang ◽  
Gao-Qi Wu ◽  
Yan-Ming Xu ◽  
...  

Coilin is the main component of Cajal body (CB), a membraneless organelle that is involved in the biogenesis of ribonucleoproteins and telomerase, cell cycle, and cell growth. The disruption of CBs is linked to neurodegenerative diseases and potentially cancers. The coilin gene (COIL) contains two nonsynonymous SNPs: rs116022828 (E121K) and rs61731978 (V145I). Here, we investigated for the first time the functional impacts of these coilin SNPs on CB formation, coilin subcellular localization, microtubule formation, cell growth, and coilin expression and protein structure. We revealed that both E121K and V145I mutants could disrupt CB formation and result in various patterns of subcellular localization with survival motor neuron protein. Noteworthy, many of the E121K cells showed nucleolar coilin accumulation. The microtubule regrowth and cell cycle assays indicated that the E121K cells appeared to be trapped in the S and G2/M phases of cell cycle, resulting in reduced cell proliferation. In silico protein structure prediction suggested that the E121K mutation caused greater destabilization on the coilin structure than the V145I mutation. Additionally, clinical bioinformatic analysis indicated that coilin expression levels could be a risk factor for cancer, depending on the cancer types and races.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3666-3666 ◽  
Author(s):  
Ling Zhao ◽  
Lemlem Alemu ◽  
Jun Cheng ◽  
Tao Zhen ◽  
Alan D. Friedman ◽  
...  

Abstract Among acute myeloid leukemia (AML) with cytogenetic abnormalities, core binding factor (CBF) leukemia acounts for 20-30% of adult AML, and 20-30% of pediatric AML. The chromosome 16 inversion (inv(16)), which results in a fusion gene CBFB -MYH11 and an encoded chimeric protein CBFβ-SMMHC (core binding factor β - smooth muscle myosin heavy chain), is observed primarily in AML subtype M4Eo. Using Cbfb-MYH11 knock-in mouse models we previously demonstrated that CBFβ-SMMHC needs its C terminal domains for leukemogenesis (Kamikubo et al, Blood 121:638, 2013). In this study we generated a new CBFB-MYH11 knock-in mouse model to determine the role of the multimerization domain at the C terminus of CBFβ-SMMHC for hematopoietic defects and leukemogenesis. Previous studies have shown that the C-terminal 29-residue assembly competent domain (ACD) is essential for multimerization of SMMHC. Within ACD, clustered point mutations in helices D and E specifically disrupts multimerization of CBFβ-SMMHC without interfering with the repression function of CBFβ-SMMHC (Zhang et al., Oncogene 25:7289, 2006). Therefore, we generated knock-in mice expressing CBFβ-SMMHC with mutated helices D and E (mDE) to study the role of the multimerization domain in vivo. Heterozygous embryos (Cbfb+/mDE) were viable and showed no defects in fetal liver definitive hematopoiesis, while homozygous embryos (CbfbmDE/mDE) showed complete blockage of definitive hematopoiesis, hemorrhage in the central nervous system and midgestation lethality, similar to the phenotype in Cbfb+/MYH11 mice and the Cbfb or Runx1 null mice. This phenotype is also similar to that in the homozygous knockin embryos expressing C-terminally-deleted CBFβ-SMMHC (Kamikubo et al, Blood 121:638, 2013). The fetal liver of E12.5 CbfbmDE/mDE embryos gave no colonies while the fetal liver of Cbfb+/mDE mice generated similar number of colonies as the WT controls. We further looked at the peripheral blood of E10.5 CbfbmDE/mDE embryos and found that the primitive hematopoiesis was not affected, while E10.5 Cbfb+/MYH11 embryos showed a developmental delay at this stage. Analysis of peripheral blood showed decreased B cell population in young adult Cbfb+/mDE mice, while the myeloid compartment was unchanged. In aged mice (>12 months), however, there was an increase of immature myeloid cells in the peripheral blood. Importantly, there was no leukemia development in the Cbfb+/mDE mice one year after ENU treatment (to induce cooperating mutations), while Cbfb+/MYH11 micedied of leukemia within 2 months of ENU treatment. Notably bone marrow cells in the Cbfb+/mDE and Cbfb+/MYH11 mice expressed their respective fusion proteins at similar levels. Overall our data suggest that the C terminal multimerization domain is required for the defects in primitive and definitive hematopoiesis caused by CBFβ-SMMHC, and the domain is essential for leukemogenesis by CBFβ-SMMHC. Further mechanistic studies of this domain may lead to new drug targets for treating inv(16) leukemia. For this purpose we have performed gene expression profiling with microarray and RNA-seq technologies, comparing gene expression changes in adult bone marrow c-Kit+ cells as well as embryonic primitive blood cells from Cbfb+/mDE and Cbfb+/MYH11 mice. Preliminary analysis indicates that the gene expression profile of the hematopoietic cells from the Cbfb+/mDE mice was much similar to that of Cbfb+/+ than Cbfb+/MYH11 mice. Validation and pathway analysis of those differentially expressed genes are ongoing and the results will be presented at the annual meeting. Disclosures No relevant conflicts of interest to declare.


2011 ◽  
Vol 80 (2) ◽  
pp. 490-504 ◽  
Author(s):  
Julia Handl ◽  
Joshua Knowles ◽  
Robert Vernon ◽  
David Baker ◽  
Simon C. Lovell

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