Identification of Fusion Transcripts in Leukеmic Cells by Whole-Transcriptome Sequencing

Ikonnikova, A. Yu.; Ammour, Y. I.; Снежкина, А. В.; Krasnov, George S.; Kudryavtseva, Anna V.; Наседкина, Т. В.

doi:10.1134/s0026893318020048

Cited by 3 publications

(1 citation statement)

References 15 publications

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“…Specifically, in leukemias, PTMA has been reported in fusion with OAZ1 and CXCR4. LRRFIP1 has been implicated in 8p11 myeloproliferative syndrome through its fusion with FGFR1, in inflammatory myofibroblastic tumors with ALK and in atypical Spitz tumors with MET [27,[93][94][95][96].…”

Section: Discussionmentioning

confidence: 99%

Linking Gene Fusions to Bone Marrow Failure and Malignant Transformation in Dyskeratosis Congenita

Güllülü,

Mayer,

Toplek

2024

IJMS

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Dyskeratosis Congenita (DC) is a multisystem disorder intrinsically associated with telomere dysfunction, leading to bone marrow failure (BMF). Although the pathology of DC is largely driven by mutations in telomere-associated genes, the implications of gene fusions, which emerge due to telomere-induced genomic instability, remain unexplored. We meticulously analyzed gene fusions in RNA-Seq data from DC patients to provide deeper insights into DC’s progression. The most significant DC-specific gene fusions were subsequently put through in silico assessments to ascertain biophysical and structural attributes, including charge patterning, inherent disorder, and propensity for self-association. Selected candidates were then analyzed using deep learning-powered structural predictions and molecular dynamics simulations to gauge their potential for forming higher-order oligomers. Our exploration revealed that genes participating in fusion events play crucial roles in upholding genomic stability, facilitating hematopoiesis, and suppressing tumors. Notably, our analysis spotlighted a particularly disordered polyampholyte fusion protein that exhibits robust higher-order oligomerization dynamics. To conclude, this research underscores the potential significance of several high-confidence gene fusions in the progression of BMF in DC, particularly through the dysregulation of genomic stability, hematopoiesis, and tumor suppression. Additionally, we propose that these fusion proteins might hold a detrimental role, specifically in inducing proteotoxicity-driven hematopoietic disruptions.

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Section: Discussionmentioning

confidence: 99%

Linking Gene Fusions to Bone Marrow Failure and Malignant Transformation in Dyskeratosis Congenita

Güllülü,

Mayer,

Toplek

2024

IJMS

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A t(4;13)(q21;q14) translocation in B-cell chronic lymphocytic leukemia causing concomitant homozygous DLEU2/miR15a/miR16-1 and heterozygous ARHGAP24 deletions

et al. 2023

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Bioinformatic identification of differentially expressed genes associated with prognosis of locally advanced lymph node-positive prostate cancer

Kudryavtseva

Lukyanova

Kharitonov

et al. 2019

J. Bioinform. Comput. Biol.

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Prostate cancer (PCa) is one of the primary causes of cancer-related mortality in men worldwide. Patients with locally advanced PCa with metastases in regional lymph nodes are usually marked as a high-risk group. One of the chief concerns for this group is to make an informed decision about the necessity of conducting adjuvant androgen deprivation therapy after radical surgical treatment. During the oncogenic transformation and progression of the disease, the expression of many genes is altered. Some of these genes can serve as markers for diagnosis, predicting the prognosis or effectiveness of drug therapy, as well as possible therapeutic targets. We undertook bioinformatic analysis of the RNA-seq data deposited in The Cancer Genome Atlas consortium database to identify possible prognostic markers. We compared the groups with favorable and unfavorable prognosis for the cohort of patients with PCa showing lymph node metastasis (pT2N1M0, pT3N1M0, and pT4N1M0) and for the most common molecular type carrying the fusion transcript TMPRSS2-ERG. For the entire cohort, we revealed at least six potential markers (IDO1, UGT2B15, IFNG, MUC6, CXCL11, and GBP1). Most of these genes are involved in the positive regulation of immune response. For the TMPRSS2-ERG subtype, we also identified six genes, the expression of which may be associated with prognosis: TOB1, GALNT7, INAFM1, APELA, RAC3, and NNMT. The identified genes, after additional studies and validation in the extended cohort, could serve as a prognostic marker of locally advanced lymph node-positive PCa.

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Identification of Fusion Transcripts in Leukеmic Cells by Whole-Transcriptome Sequencing

Cited by 3 publications

References 15 publications

Linking Gene Fusions to Bone Marrow Failure and Malignant Transformation in Dyskeratosis Congenita

Linking Gene Fusions to Bone Marrow Failure and Malignant Transformation in Dyskeratosis Congenita

A t(4;13)(q21;q14) translocation in B-cell chronic lymphocytic leukemia causing concomitant homozygous DLEU2/miR15a/miR16-1 and heterozygous ARHGAP24 deletions

Bioinformatic identification of differentially expressed genes associated with prognosis of locally advanced lymph node-positive prostate cancer

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