Stakaitis, Rytis
Item type:Publication, preprint[2026][S1][N010,M001]; ; ; ; Cancer Cell International, 2026-02-2017 - conference paper[2025][T1e][N010][1]
; ; ; 17th International Conference of the Lithuanian Neuroscience Association „Brain Function, Dysfunction, and Translational Research“ : 28th November 2025, Kaunas, Lithuania, 2025-11-28, p. 50-50Glioblastoma (GB) are highly aggressive and genetically complex brain tumors that infiltrate surrounding brain tissue, making them extremely difficult to treat effectively. Recent research has revealed that m6A modification is abnormally activated in glioma, underscoring its key role in various processes of glioma development. m6A modifications in mRNA of glioma stem cells NCH421k (GSCs) and in glioblastoma tumor tissues were investigated using methylation-based RNA immunoprecipitation (MeRIP) and direct Nanopore RNA sequencing (dRNA-seq). Data analysis amongst GSCs demonstrated 740 hypermethylated and 830 hypomethylated genes after MeRIP-seq. dRNA-seq data presented 4,340 RRACH motifs associated with hyper-methylated up-regulated genes and 9,106 motifs associated with hyper-methylated down-regulated genes across samples taken from glioma patients. We identified eight statistically significant RRACH motifs across seven genes — AAACA|2129|OS9, AGACA|1210|PAGR1, GGACA|2173|OS9, GGACT|2187|TOB1, AAACC|3283|PIK3R2, GAACC|3068|GP1BB, GGACA|3110|RETREG1, and GGACT|3122|LUC7L3 — to narrow down potential gene candidates. Findings indicated that m6A in target motifs is modified approximately 3.4-fold more in LGG than in GB, distinguishing patient samples by pathology. Next, we found that global m6A methylation score was significantly lower in GB cluster compared to LGG cluster (p=0.0002). Furthermore, lower m6A methylation scores were associated with shorter survival in glioma patients (p=0.016) while the expression levels did not differ among m6A-based clusters (p=0.08) or in a Kaplan-Meier survival analysis (p=0.79). In summary, m6A modifications in mRNA may emerge as future-defining biomarkers capable of reshaping gliomas biology.
12 Item type:Publication, conference paper[2025][T1e][N010][1]; ; ; ; ; 17th International Conference of the Lithuanian Neuroscience Association „Brain Function, Dysfunction, and Translational Research“ : 28th November 2025, Kaunas, Lithuania, 2025-11-28, p. 34-34Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by the gradual loss of dopaminergic neurons in the substantia nigra. PD usually leads to hallmark motor symptoms such as bradykinesia and resting tremor. Although current therapies can alleviate symptoms, the disease remains incurable. MiRNAs derived from extracellular vesicles (EV-derived) have shown great potential as biomarkers for various diseases, including PD. Therefore, finding miRNA biomarkers could enable early disease detection and support personalised treatment strategies. We aimed yo profile EV-derived miRNAs in Parkinson’s disease patients and healthy controls using next-generation sequencing (NGS) to identify potential biomarkers for the disease. EV-derived miRNAs were isolated from the blood serum of five PD patients and five healthy controls. The samples were then subjected to NGS. Sequencing data were analysed using principal component analysis (PCA), DESeq2 for differential expression and KEGG pathway analysis. PCA revealed two distinct clusters corresponding to healthy controls and PD patients. Differential expression analysis using DESeq2 identified ten miRNAs significantly deregulated in PD patients compared to controls. KEGG pathway analysis showed that these miRNAs are involved in pathways, like PD, Alzheimer’s disease, dopaminergic synapse, MAPK signaling, suggesting potential links to molecular mechanisms underlying PD. We identified ten miRNAs as potential biomarkers for Parkinson’s disease. These miRNAs were found to be involved in neurodegeneration-related pathways, suggesting their possible role in PD pathogenesis. Further studies with larger sample sizes are required to validate these findings and better characterize the expression patterns of these miRNAs.
19 Item type:Publication, conference poster[2025][T2][N010][1]; ; ; Abstracts of papers presented at the EMBO Workshop: The epitranscriptome : EMBL Advanced Training Centre, 28 - 30 October 2025, 2025-10-28, p. 71-71Glioblastoma (GB) continue to be a devastating disease despite advances in treatment therapies. High invasiveness, intra-tumoral heterogeneity and poor prognosis are key barriers to successful GB treatment. The most prevalent m6A modification in RNA serves as a biomarker for cancer diseases. Recent findings implicate the valuable role of m6A modification in tumor progression and tumorigenesis of gliomas. We profiled m6A modifications within mRNA across glioma stem cells NCH421k (GSCs) using methylated RNA immunoprecipitation (MeRIP) technique and glioblastoma tumor tissues using direct Nanopore RNA sequencing (dRNA-seq). A total of 1,570 distinct differentially modified genes were found after MeRIP-seq data analysis of which 740 genes were hypermethylated, and 830 genes were hypomethylated in GSCs. Four-quadrant plot was produced to evaluate the distribution of differentially expressed mRNAs with statistically significant m6A modifications. After, dRNA-seq data showed 4,340 RRACH motifs linked to hyper-methylated upregulated genes and 9,106 linked to hyper-methylated downregulated genes across all patients’ samples. To find statistically significant 8 RRACH motifs through seven genes and narrow down the list we used logistic regression model and Chi-square test: AAACA|2129|OS9, AGACA|1210|PAGR1, GGACA|2173|OS9, GGACT|2187|TOB1, AAACC|3283|PIK3R2, GAACC|3068|GP1BB, GGACA|3110|RETREG1 and GGACT|3122|LUC7L3. Analysis showed that adenosine in selected motifs in LGG samples undergo modifications about 3.4 times more frequently compared to GB, and subsequent hierarchical clustering analysis classified patient samples according to pathology. Next, based on 8 RRACH motifs methylation we constructed total m6A methylation score which significantly differed between LGG and GB clusters (p=0.0002) being higher in LGG cluster. Low m6A methylation score was associated with a worse survival prognosis in glioma patients (p=0.016). The expression patterns of selected genes did not show any significant differences in m6A-based clusters (p=0.08), as well as the Kaplan-Meier survival analysis (p=0.79). To summarize, m6a modifications in mRNA can serve as potential biomarkers in gliomas.
17 Item type:Publication, conference paper[2025][T1e][N011,N010][1]; ; ; ; 1st International Vilnius Conference on Statistics and Its Applications : August 27-29, 2025, Vilnius, Lithuania : Abstract book / Editor: Jurgita Markevičiūtė, 2025-08-27, p. 58-58Gene expression is a quantitative estimate reflecting how much the information encoded in a gene is turned into a functional “outcome”, usually proteins or RNA molecules. Evaluation of gene expression levels can reveal peculiarities of cellular processes related with particular pathogenic mechanisms. The construction of biomarkers of certain diseases can be based on gene expression estimates. However, processing, analyzing and generalizing the gene expression data is challenging due to the inescapable variation of technical conditions in sophisticated biochemical process. It results in so called “batch effects” in estimates, when artifact differences appear not due to the sought genetic differences, but due to the variety of technical conditions. The normalization of gene expression levels is the solution and a crucial step in obtaining reliable results. The expression of so called „House-keeping“ genes, ensuring the basic functions of the cells can serve as normalizing values in such cases. We propose Principal Component Analysis [1] approach to concentrate the correlated variety of gene expression values into uncorrelated principal components. In that way variety of gene expression estimates concentrated in the same principal component as the ones from “House
- keeping” genes will be concerned as technical artifacts, while the others will reflect the sought epigenetic phenomena. The proposed method was used to validate expression levels of targeted gene set related to various complexity brain tumors. Data were collected by Oxford Nanopore [2] direct RNA Sequencing. Potential biomarker genes were identified as showing statistically different in Glioblastoma vs Low-grade-glioma cases.
14 Item type:Publication, research article[2025][S1][N010][16]; ; ; ; Molecular Medicine, 2025-05-17, vol. 31, no. 1, p. 1-16Background: Efforts to understand the interplay between m6A (N6-methyladenosine) modification and long noncoding RNAs (lncRNAs) in the pathogenesis of various diseases, including cancer, have recently attracted considerable attention. Methods: Herein, we profiled epitranscriptome-wide m6A modifications within lncRNAs at single m6A site resolution across different grades of gliomas (Glioblastomas (GB): n = 17, Low grade gliomas (LGG): n= 9) using direct RNA long-read sequencing. Results: Our analysis demonstrated that, 1) 98.5% of m6A-modified RRACH motifs were present within mRNA transcripts, while only 1.16% were conspicuous within lncRNAs. Importantly, LGGs exhibited a higher m6A abundance (23.73%) compared to the GB transcriptome (15.84%). 2) The m6A profiles of lncRNAs differed significantly between gliomas, with unsupervised cluster analysis revealing two clusters (C1, C2). LGG dispersed between C1 and C2 clusters while GB stayed mainly in C1. Clinical feature association analysis between m6A clusters showed the tendency of m6A to be associated with higher malignancy grade (p = 0.053), while significant association was observed with higher Ki-67 proliferation index (p = 0.04), and tumor location (p < 0.01). Specifically, brain tumors located in cerebellum (n = 3) were highly m6A modified on lncRNAs as compared to tumors in other locations (frontal lobe, n = 5, p = 0.003; frontotemporal lobe, n = 2, p = 0.08; occipital,n = 2, p = 0.038; parietal, n = 2, p = 0.007; temporal, n = 11, p < 0.001). Cox regression analysis showed that the status of lncRNAs m6A modifications had no significant value in predicting post-surgical survival time in our GB or LGG cohorts. The trend of higher lncRNA expression in m6A methylated group was observed for the majority of lncRNAs, while only MIR9-1HG (r = 0.439, p = 0.028) and ZFAS1 (r = 0.609, p < 0.05) m6A showed statistically significant positive correlations in gliomas. A high-resolution m6A study revealed that mRNA levels of m6A writers and erasers in gliomas do not reflect global m6A methylation. Conclusions: Overall, we provide evidence that m6A lncRNAs are strongly modulated in gliomas, representing biologically distinct subgroups. Ten novel differentially methylated lncRNAs were identified in gliomas, which might exert regulatory role in glioma cells. These findings may provide a basis for further deeper research on the role of m6A lncRNAs in gliomas.
23 2WOS© Citations 8 - conference paper[2024][T2][N010,N004][1]
; ; ; ; 1st Net4Brain Annual Meeting "Closing the translational gap in brain cancer treatment" : September 4th-6th, 2024 : Book of Abstracts / Editors: Barbara Breznik, Metka Novak, 2024-09-04, p. 49-49Interest in long-non-coding RNAs (lncRNAs) during oncogenesis is constantly increasing. lncRNA plays an important role in gene regulation via chromatin remodelling, RNA processing, transcriptional activation, in protein function and activity alteration via direct interaction with proteins etc. Recently developed methods for RNA chemical modification identification, promoted interest in human epitranscriptome. N6-methyladenosine (m6A) is the most prominent and widely studied RNA modification, which affects RNA stability, location, and translation. However, information on m6A effect to lncRNAs and other non-coding RNAs (ncRNAs) is lacking. Here we compare transcriptome wide m6A modifications of lncRNAs in human glioblastoma and healthy brain samples applying direct RNA sequencing method from Oxford Nanopore Technology (ONT dRNA-seq). The analysis of ONT dRNA-seq identified lncRNA targets that are differentially modified between glioblastoma and healthy human brain specimen. Previously reported glioma associated lncRNAs like NEAT1, SOX2-OT, SNGH6, OIP5-AS1, etc. in present study showed decreased levels of m6A modification in glioblastoma specimens compared to healthy brain samples indicating that m6A demethylation of lncRNAs transcripts might be characteristic during gliomagenesis.
13 Item type:Publication, research article[2024][S1][N010][18]; piRNAs are crucial for transposon silencing, germ cell maturation, and fertility in male mice. Here, we report on the genetic landscape of piRNA dysfunction in humans and present 39 infertile men carrying biallelic variants in 14 different piRNA pathway genes, including PIWIL1, GTSF1, GPAT2, MAEL, TDRD1, and DDX4. In some affected men, the testicular phenotypes differ from those of the respective knockout mice and range from complete germ cell loss to the production of a few morphologically abnormal sperm. A reduced number of pachytene piRNAs was detected in the testicular tissue of variant carriers, demonstrating impaired piRNA biogenesis. Furthermore, LINE1 expression in spermatogonia links impaired piRNA biogenesis to transposon de-silencing and serves to classify variants as functionally relevant. These results establish the disrupted piRNA pathway as a major cause of human spermatogenic failure and provide insights into transposon silencing in human male germ cells.
46WOS© Citations 44 Item type:Publication, conference poster[2024][T2][M001,N010][1]; ; ; FENS Forum 2024 : 25-29 June 2024, Vienna, Austria, 2024-06-25, p. 1-1Alterations of N6-methyladenosine (m6A) RNA modifications are responsible for a platter of structural and functional changes in healthy and cancerous cell states. Even though several studies have linked m6A to the onset and development of tumors, very few have examined transcriptome-wide m6A landscape of long non-coding RNAs (lncRNAs) in cancerous cells, including gliomas. This work aims to explore and elucidate lncRNA m6A alterations and expression in glioma stem cells, U87-MG cells and glioma patients. We utilized four cell lines (NCH421k, NCH644, NCH690, U-87 MG), along with 16 glioblastomas (GB) and 9 low grade (LGG) gliomas. m6A RNA modifications were detected using MeRIP-seq and dRNA-seq. First, we provided transcriptome-wide lncRNAs m6A peak distribution in GSCs. MERIP-seq analysis between U-87 MG and GSCs showed 76.4% overlap of lncRNAs m6A peaks, while 19.4% of peaks were exclusively identified in GSCs. Next, m6A was observed uniquely in GSCs for previously identified glioma-associated lncRNAs, including LINC000461, HOTTIP, CRNDE, TUG1, and XIST. Further, dRNA-seq transcript hierarchical clustering analysis revealed differentially expressed lncRNAs capable to separate LGG, GB, and GSCs (NEAT1, ANAPC1P2, CYTOR, ZNF8-ERVK3-1, MIR4435-2HG, LINC01116, and MIR222HG). Subsequently, PCA analysis based on lncRNA expression pattern identified clusters attributed to GSCs-GB and LGG. Additionally, we discovered that a set of lncRNAs were associated with stemness transcript activation in gliomas and worse patient survival (p<0.05). Our findings offer a foundation and understanding for further research on m6A modifications and expression patterns in the non-coding epitranscriptome of GSCs and glioma.
9 Item type:Publication, conference paper[2024][T1e][M001,N010][2]; ; International Health Sciences Conference for All (IHSC for All) "Precision Medicine" : Abstract book 2024 : [March 25-26, 2024, Kaunas] / Edited by Ignas Lapeikis, Livija Petrokaitė, 2024-04-16, p. 466-467Introduction The most aggressive glial tumor in the brain, glioblastoma (GBM), is incurable and resistant to current treatments. Treatment for GBM is extremely difficult because of tumor heterogeneity and resistance generated by glioma stem cells (GSCs). Aim To distinguish glioma stem cell specific lncRNAs associated with glioma malignancy.
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