Tagged: RNA

Trending with Impact: RNA Modification Regulatory Proteins in Melanoma

Researchers analyzed various publicly available datasets and identified two RNA modification regulatory proteins that are not only overexpressed in melanoma, but necessary for melanoma growth.

Malignant melanoma under the microscope.
Malignant melanoma under the microscope.

The Trending with Impact series highlights Oncotarget publications attracting higher visibility among readers around the world online, in the news, and on social media—beyond normal readership levels. Look for future science news about the latest trending publications here, and at Oncotarget.com.

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After melanoma of the skin metastasizes, it commonly becomes very difficult for doctors to treat. This is due to melanoma’s problematic tendency to acquire resistance to therapeutic interventions. Despite the development of many new targeted interventions and immunotherapies, five-year survival rates for patients with melanoma continue to be less than 10% for patients with lymph node metastasis and less than 5% for patients with distant metastasis.

“As the number of potential therapeutic DNA targets dwindle, many researchers are turning to RNA to tackle the problem.”

In 2018, researchers from Yale University School of Medicine and the University of Alabama at Birmingham in the United States set their focus on analyzing RNA alterations in melanoma, in hopes of identifying new, and more effective, therapeutic targets. Their research paper was published by Oncotarget in 2019, and entitled: “Dissecting the role of RNA modification regulatory proteins in melanoma.” 

“Many studies have shown that these RNA modifications play crucial role in melanoma growth and metastasis [5859]. They are also involved in drug resistance mechanism.”

The Study

“Since RNA is a key molecule that drives every cellular process, their deregulation is present in nearly all human disease and play a causative role.” 

The researchers explain that alterations among RNAs may arise due to altered activity or expression of the enzymes/proteins which are involved in the modification process. In this study, the team used multiple publicly available bioinformatics platforms to, first, analyze RNA alterations in melanoma samples, and then, to comprehensively analyze RNA modification regulatory proteins among melanoma samples. The publicly available datasets included: The Cancer Genome AtlasThe Human Protein AtlasOncomine, and the UALCAN database.

“Our study started with the analysis of various genetic alterations (amplifications, mutations/deletion) as well as RNA overexpression of these RNA modification regulatory proteins in The Cancer Genome Atlas melanoma database.”

Based on their analyses of these databases, reverse transcription quantitative PCR, soft-agar assays, validation by shRNA-mediated knockdown, and statistical analysis, the team identified what they believe are the most relevant RNA modifying proteins that play a crucial role in the development of melanoma. They found that METTL4 and DNMT3A RNA-modifying enzymes/proteins are both necessary for melanoma growth and overexpressed in melanoma.

“Based on this we infer that the upregulated expression of RNA modification regulatory proteins METTL4 and DNMT3A play a key role in melanoma initiation or progression.” 

Conclusion

The researchers explained that their studies served the duel purpose of improving their understanding of novel pathways that cause melanoma to become untreatable, and also paving the way “to develop new, effective and sustainable therapeutic tools for optimal drug selection and treatment.”

“Additional future studies are needed to fully determine the role of these RNA modification regulatory proteins in melanoma tumor growth and progression (e.g., metastasis).”

Click here to read the full scientific study, published by Oncotarget

Oncotarget is a unique platform designed to house scientific studies in a journal format that is available for anyone to read—without a paywall making access more difficult. This means information that has the potential to benefit our societies from the inside out can be shared with friends, neighbors, colleagues, and other researchers, far and wide.

For media inquiries, please contact media@impactjournals.com.

Trending with Impact: RNA-Seq Analyses Show Targets in B-cell Lymphoma

“The current study is the first of its kind, wherein comprehensive transcriptome analysis using RNA-Seq was performed in Notch2 depleted B-cell lymphoma cells.”

Malignant effusion cytology: microscopic image of diffuse large B-cell lymphoma, a type of non Hodgkin lymphoma.
Malignant effusion cytology: microscopic image of diffuse large B-cell lymphoma, a type of non Hodgkin lymphoma.

The Trending with Impact series highlights Oncotarget publications attracting higher visibility among readers around the world online, in the news, and on social media—beyond normal readership levels. Look for future science news and articles about the latest trending publications here, and at Oncotarget.com.

Listen to an audio version of this article

Splenic marginal zone lymphoma (SMZL) is a rare subtype of non-Hodgkin lymphoma that comprises approximately 10% of all lymphoma cases. Marginal zone lymphomas (MZL) originate from B memory lymphocytes (B-cells) in the marginal zone of secondary lymphoid follicles within the spleen, bone marrow, and blood.

Due to the rarity of SMZL, no randomized trials have yet been reported—only retrospective studies and some prospective studies have been conducted. The irregularity of frequency and the indolent nature of this disease makes SMZL a challenge for doctors to determine a standardized care or treatment plan other than intervention by splenectomy.

Bringing with it great potential, researchers have found that a pivotal gene is mutated in SMZL: the Notch2 gene. The abnormal signaling and increased expression in Notch2 has been observed in a number of cancers, including MZL, chronic lymphocytic leukemia, breast cancer, non-small cell lung cancer, pancreatic cancer, hepatocellular carcinoma, colorectal cancer, bladder cancer, medulloblastoma, and glioblastoma.

“A wide range of Notch2 mutations have been identified with relevance to different cancers, but the role of Notch2 and its downstream pathways in development of B-cell lymphoma has not been comprehensively studied to date.”

Researchers from the School of Biotechnology and Genetic Engineering at Bharathiar University in Coimbatore, India, conducted a study of RNA sequencing analyses to reveal the differentially expressed genes and pathways as Notch2 targets in B-cell lymphoma.

Whole Transcriptome Analysis

The researchers in this study explain that transcriptome analysis and RNA sequencing (RNA-Seq) provided them the opportunity to deeply and unbiasedly screen for the molecular changes that occur in Notch2 deregulated B-cells and to identify the genes and pathways downstream from it as potential targets.

“RNA-Seq is a more sensitive technology than expression profiling analysis using arrays, due to their low sensitivity and cross-hybridization of probes and targets [34]. “

In order to deregulate, or knockdown, Notch2 expression, the researchers employed short, or small, hairpin RNAs (shRNAs). shRNAs are artificially created RNA molecules that can be used to silence target gene expression (Notch2, in this case) via RNA interference.

“To determine the efficacy of Notch2-shRNA in reducing the intracellular levels of Notch2, we treated A549 (lung cancer) and SSK-41 cells (B-cell lymphoma) with viral supernatants of two different shRNA constructs in a lentiviral vector targeting Notch2.” 

“The current study is the first of its kind, wherein comprehensive transcriptome analysis using RNA-Seq was performed in Notch2 depleted B-cell lymphoma cells.”

The Study

 “In the present study, whole transcriptome analysis was performed in B-cells, where Notch2 expression is knocked down using Notch2-shRNA and compared with control scramble-shRNA treated cells.”

In their first step, the researchers identified a total of 15,083 differentially expressed genes and 1067 differentially expressed transcripts in control and Notch2-shRNA treated samples. They used a condition tree, correlation matrix, and principal component analysis test to measure significant reproducibility, similarity, and distance between the treated and untreated group. 

In their second step, a gene enrichment analysis was performed in the differentially expressed genes using the DAVID tool. This resulted in the identification of 208 unique gene ontology (GO) categories and pathways.

Results

“Among the 208 GO categories, 31 pathways were significantly enriched in biological processes (BP), 3 pathways were significantly enriched in cellular components (CC) and 18 pathways were significantly enriched in molecular functions (MF).”

The researchers state that the significantly enriched terms they found could help with further understanding which differentially expressed genes and differentially expressed transcripts play causative roles in the onset of B-cell lymphoma.

“The RNA-Seq and bioinformatics technology revealed notable information regarding gene expression at the transcriptome level and identified multiple significant molecular pathways in response to knockdown of Notch2.”

Figure 9: Pathway analysis. Gene regulatory network analysis for DEGs upon Notch2 knockdown were predicted by Pathreg algorithm and visualized in Cytoscape v2.8.2. Predicted pathways are depicted as rounded rectangles, where shades in red correspond to upregulated genes and shades in green correspond to downregulated genes.
Figure 9: Pathway analysis. Gene regulatory network analysis for differentially expressed genes upon Notch2 knockdown were predicted by Pathreg algorithm and visualized in Cytoscape v2.8.2. Predicted pathways are depicted as rounded rectangles, where shades in red correspond to upregulated genes and shades in green correspond to downregulated genes.

“The results of our gene network analysis suggest that, knockdown of Notch2 modulates multiple important cellular pathways, including immune-related pathways, apoptotic related pathway, PI3K/AKT, BCR, mTOR, VEGF, Wnt and Ca2+ signaling pathways.”

Conclusion

The authors note that the NF-kB signaling pathway is a major pathway that leads to cell survival with the ability to “cross-talk” with other survival pathways, including PI3K/AKT, in various cancers.

“Since activation of PI3K/AKT pathway is known to promote cell proliferation, cell survival, growth and angiogenesis in cancers [40], it is important to know if Notch2 propels cancer progression through activation of this pathway. “

However, the researchers mention that the exact mechanism that Notch2 regulates NF-kB activity through the activation of PI3K/AKT and inhibits apoptosis in B-cell lymphoma still need to be determined. 

“Nevertheless, establishing the role of PI3K/AKT pathway in Notch2 activated cancers could be very important to consider it as an alternative treatment target in mitigating the effects of Notch2 transactivity in these cancers.” 

Click here to read the full study, published in Oncotarget.

Oncotarget is a unique platform designed to house scientific studies in a journal format that is available for anyone to read—without a paywall making access more difficult. This means information that has the potential to benefit our societies from the inside out can be shared with friends, neighbors, colleagues and other researchers, far and wide.

For media inquiries, please contact media@impactjournals.com.