Upregulation of long noncoding RNA Lnc‐IRF2‐3 and Lnc‐ZNF667‐AS1 is associated with poor survival in B‐chronic lymphocytic leukemia

El‐Khazragy, Nashwa; Esmaiel, Marwa A.; Mohamed, Mervat S.; Hassan, Nahla S.

doi:10.1111/ijlh.13167

Cited by 8 publications

(5 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several publications have already highlighted the differential patterns on transcriptomics and epigenomics layers ( 8 , 19 , 33–35 ) in these disease subgroups, hence suggesting the biological relevance of InterTADs. Focusing on the IG SHM status, we found genes that were targeted by more than one event, such as KCNJ2 ( 51 ) , CRY1 ( 51 ) , ZNF667-AS1 ( 52 ) , MYLK ( 51 ) , ZAP70 ( 53 ), all of which have been previously identified in previous reports. We also observed that events of inactive regions in U-CLL were enriched for binding sites of several TFs relevant to B cell/CLL biology, while also showing differential expression between the two groups, including the ATF5 ( 54 ), MYBL2 ( 55 ).…”

Section: Discussionsupporting

confidence: 57%

InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia

Tsagiopoulou¹,

Pechlivanis²,

Μανιού³

et al. 2022

NAR Genomics and Bioinformatics

View full text Add to dashboard Cite

The integration of multi-omics data can greatly facilitate the advancement of research in Life Sciences by highlighting new interactions. However, there is currently no widespread procedure for meaningful multi-omics data integration. Here, we present a robust framework, called InterTADs, for integrating multi-omics data derived from the same sample, and considering the chromatin configuration of the genome, i.e. the topologically associating domains (TADs). Following the integration process, statistical analysis highlights the differences between the groups of interest (normal versus cancer cells) relating to (i) independent and (ii) integrated events through TADs. Finally, enrichment analysis using KEGG database, Gene Ontology and transcription factor binding sites and visualization approaches are available. We applied InterTADs to multi-omics datasets from 135 patients with chronic lymphocytic leukemia (CLL) and found that the integration through TADs resulted in a dramatic reduction of heterogeneity compared to individual events. Significant differences for individual events and on TADs level were identified between patients differing in the somatic hypermutation status of the clonotypic immunoglobulin genes, the core biological stratifier in CLL, attesting to the biomedical relevance of InterTADs. In conclusion, our approach suggests a new perspective towards analyzing multi-omics data, by offering reasonable execution time, biological benchmarking and potentially contributing to pattern discovery through TADs.

show abstract

Section: Discussionsupporting

confidence: 57%

InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia

Tsagiopoulou¹,

Pechlivanis²,

Μανιού³

et al. 2022

NAR Genomics and Bioinformatics

View full text Add to dashboard Cite

show abstract

“… 18 Moreover, Lnc-IRF2-3 and Lnc-ZNF667-AS1 owned high specificity and sensitivity to distinguish B-chronic lymphocytic leukemia (B-CLL) between healthy controls and were potential prognostic indicators in B-CLL. 19 For RCC, quite a few lncRNAs have been identified to have involvement in diagnosis or prognosis. 20 Ellinger et al quantified the lnc-ZNF180-2 expression in patients with ccRCC and concluded it may be a useful prediction factor of ccRCC patients’ outcomes.…”

Section: Discussionmentioning

confidence: 99%

Aberration of lncRNA LINC00460 is a Promising Prognosis Factor and Associated with Progression of Clear Cell Renal Cell Carcinoma

Zhang¹,

Zhang²,

Niu³

et al. 2021

CMAR

View full text Add to dashboard Cite

Purpose Long noncoding RNAs have been studied more and more as potential prognostic markers. However, the prognostic of LINC00460 in clear cell renal cell carcinoma (ccRCC) has not been explored. In this study, the potential role of LINC00460 was investigated in ccRCC. Patients and Methods One hundred thirteen pairs of ccRCC tissues and para-normal tissues were collected. The expressions of LINC00460 in these tissues and ccRCC cells were evaluated via qRT-PCR. The prognostic value of LINC00460 was accessed with the use of Kaplan–Meier analysis and Cox proportional hazards model analysis. The influence of LINC00460 on ccRCC cell proliferation, migration, and invasion was determined via cell counting kit-8 (CCK-8) and Transwell assays. Results The results revealed that LINC00460 was significantly enhanced in ccRCC tissues, as well as in ccRCC cell lines. The overexpression of LINC00460 was significantly associated with lymph node metastasis and TNM stage, and lead to poor overall survival. Knockdown of LINC00460 reduces the cell ability of proliferation, migration, and invasion. LINC00460 could sponge to miR-149-5p. Conclusion LINC00460 may be developed as a prognostic biomarker and molecular therapy target for ccRCC.

show abstract

“…According to a recent study, the highest levels of Lnc-IRF2-3 and Lnc-ZNF667-AS1 were found in CLL patients with del17p and del11q, respectively. Of note, increased expression of these lncRNAs was associated with poor prognostic factors, including high levels of ZAP70 protein and un-mutant IGHV [ 113 ]. In contrast, lncRNA is associated with ZAP70 protein levels and un-mutant IGHV.…”

Section: Alterations In Lncrnas In Lymphoid Malignancymentioning

confidence: 99%

Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies

Baghdadi

Heidari

Zavvar

et al. 2023

ncRNA

View full text Add to dashboard Cite

Lymphoid cells play a critical role in the immune system, which includes three subgroups of T, B, and NK cells. Recognition of the complexity of the human genetics transcriptome in lymphopoiesis has revolutionized our understanding of the regulatory potential of RNA in normal lymphopoiesis and lymphoid malignancies. Long non-coding RNAs (lncRNAs) are a class of RNA molecules greater than 200 nucleotides in length. LncRNAs have recently attracted much attention due to their critical roles in various biological processes, including gene regulation, chromatin organization, and cell cycle control. LncRNAs can also be used for cell differentiation and cell fate, as their expression patterns are often specific to particular cell types or developmental stages. Additionally, lncRNAs have been implicated in lymphoid differentiation, such as regulating T-cell and B-cell development, and their expression has been linked to immune-associated diseases such as leukemia and lymphoma. In addition, lncRNAs have been investigated as potential biomarkers for diagnosis, prognosis, and therapeutic response to disease management. In this review, we provide an overview of the current knowledge about the regulatory role of lncRNAs in physiopathology processes during normal lymphopoiesis and lymphoid leukemia.

show abstract

Upregulation of long noncoding RNA Lnc‐IRF2‐3 and Lnc‐ZNF667‐AS1 is associated with poor survival in B‐chronic lymphocytic leukemia

Cited by 8 publications

References 26 publications

InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia

InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia

Aberration of lncRNA LINC00460 is a Promising Prognosis Factor and Associated with Progression of Clear Cell Renal Cell Carcinoma

Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies

Contact Info

Product

Resources

About