Biology subjects

Mamedov, I.

Publications and source records attributed to Mamedov, I..

3 recordsLinked to original sources

bioRxiv2026

Retrotransposon Activity in Chronic Lymphocytic Leukemia: Associations with RNA Splicing and TP53 Dysfunction

Retroelements (RE), particularly autonomous Long Interspersed Element-1 (LINE-1), function as potent drivers of genomic instability in various malignancies. While normally silenced by epigenetic mechanisms, their reactivation in cancer cells can drive tumor evolution. TP53 is known to repress LINE-1 transcription; however, the consequences of TP53 dysfunction on retrotransposition and transcriptional activity in chronic lymphocytic leukemia (CLL) remain unknown. To investigate the relationship between TP53 status, LINE-1 retrotranspositional potential, and transcriptomic alterations, we utilized a multi-omics approach, combining a highly sensitive NGS protocol for detecting novel LINE-1 insertions with transcriptomic profiling of transposable elements and protein-coding genes. We applied these methods to a cohort of CLL patients stratified by the presence or absence of TP53 clonal evolution and to CLL-derived cell lines MEC1 and HG3, including CRISPR/Cas9-engineered TP53 mutants. Genomic analysis revealed no evidence of widespread somatic retrotransposition, suggesting that CLL exhibits resistance against de novo LINE-1 insertions. Conversely, transcriptomic profiling uncovered distinct transposon expression signatures aligned with patterns of TP53 mutation status evolution. Notably, differentially expressed genes were significantly enriched in the RNA splicing pathway, indicating that while LINE-1 elements remain largely constrained at the genomic level, their transcriptomic activity may influence cellular rewiring, affecting patterns of TP53 mutation clonal evolution. Based on these results, we argue that the pathogenic contribution of retroelements in CLL lies in transcriptomic dysregulation and splicing alterations, rather than in direct DNA damage caused by LINE-1 insertions.

cancer biology↗

bioRxiv2023

Mobile retroelements induced by hypomethylating agents are restricted to transpose in myeloid malignancies

Retroelements (RE) present in the human genome are silenced via multiple mechanisms, including DNA methylation, to prevent their potentially mutagenic effect. RE activity, demonstrated by their expression and somatic retrotransposition events, is deregulated in multiple tumor types but not in leukemia. We hypothesized that treatment with hypomethylating agents (HMA), commonly used in myelodysplastic syndromes and acute myeloid leukemia, could lead to increased RE activity and somatic retrotranspositions, and contribute to disease progression. We induced expression of ORF1p protein encoded by long interspersed nuclear element-1 (L1) after 72h treatment with HMA in DAMI and HL-60 cell lines. ORF1p was predominantly localized in the cytoplasm, as evidenced by fluorescent microscopy of the DAMI cell line. To study whether long-term HMA therapy may induce somatic retrotranspositions, we (i) treated both cell lines for four weeks, (ii) analyzed a cohort of 17 MDS patients before and on treatment with HMA. Using a previously established sensitive NGS-based method, no RE events were identified. To conclude, we show that although HMA induces the expression of L1-encoded proteins in tumor myeloid cell lines, de novo somatic retrotransposition events do not arise during the long-term treatment of MDS patients and myeloid cell lines with these agents.

cancer biology↗

bioRxiv2021

The use of non-functional clonotypes as a natural spike-in for multiplex PCR bias correction in immune receptor repertoire profiling

High-throughput sequencing of adaptive immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful TCR/BCR repertoire reconstruction and analysis methods have been developed in the past decade. However, detecting and correcting the discrepancy between real and experimentally observed lymphocyte clone frequencies is still challenging. Here we discovered a hallmark anomaly in the ratio between read count and clone count-based frequencies of non-functional clonotypes in multiplex PCR-based immune repertoires. Calculating this anomaly, we formulated a quantitative measure of V- and J-genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on the OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: Immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5 RACE (Rapid Amplification of cDNA Ends)-based and multiplex PCR-based approaches and compared with a biological spike-in-based method for PCR bias evaluation. The developed approach can increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.

immunology↗