Category: Oncotarget

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

January 14, 2021

“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.

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.

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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.

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Trending with Impact: Nimotuzumab Improves Non-HPV Oropharynx Cancers

January 7, 2021

Researchers perform a subgroup analysis study demonstrating positive results in patients with HPV-negative oropharyngeal cancers due to the addition of nimotuzumab while receiving cisplatin and radiation treatment.

An image depicting the nasopharynx, pharynx, and the oropharynx.

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.

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Oral cancer in any part of the oropharynx (the back-third of the tongue, tonsils, soft palate, and back and sides of the throat) is called oropharyngeal cancer. Each year, oral cancer accounts for around 53,000 new patient diagnoses in the United States. However, the highest number of cases of oral cancer in the world are found in India, and this number is increasing.

“As opposed to HPV related oropharyngeal cancer, HPV negative oropharyngeal cancers have worse prognosis.”

Researchers from Tata Memorial Hospital and Tata Memorial Centre in Mumbai, India, previously reported that in a phase three randomized study of an epidermal growth factor receptor inhibitor medication and, called cetuximab, showed a trend towards improvement when used in patients with locally advanced head and neck cancers. Compared with results in other similar studies, they believe their results were likely due to a younger cohort of patients with predominantly HPV negative diseases.

“Taking this into consideration, we decided to perform a subgroup analysis of the HPV negative oropharyngeal cancer cohort, to study the absolute improvement in 2-year outcomes with the addition of nimotuzumab. We compared 2 year progression free survival (PFS), disease free survival (DFS), locoregional control (LRC) and overall survival (OS) between both arms.”

The Study

“HPV negative oropharyngeal cancer has unsatisfactory treatment outcomes and is a candidate for escalation of treatment. We wanted to determine whether the addition of nimotuzumab to cisplatin-radiation could improve outcomes in these poor-risk tumors.”

In this study, the researchers gathered 536 patients undergoing definitive chemoradiation for locally advanced head and neck cancers, with 269 having a primary tumor located in the oropharynx. Of these patients, 187 were p16 protein negative and were divided into two treatment arms: 91 in the cisplatin-radiotherapy (CRT) treatment arm and 97 in the nimotuzumab-cisplatin-radiotherapy (NCRT) treatment arm. Nimotuzumab is an antibody that binds to epidermal growth factor receptor IgG1 and a radiosensitizer.

The cohort consisted of only 21 females, therefore the participants were primarily male, with a median age of 54.5, 90% reported tobacco use, and 80% were in disease stage IV. Patients in the CRT treatment arm were given 30mg/m2 of cisplatin weekly, in addition to radiation therapy. In the NCRT treatment arm, in addition to radiation therapy, patients received 200 mg of nimotuzumab and 30 mg/m2 cisplatin weekly.

Results

Researchers found that the HPV positive/negative interaction test using immunohistochemistry staining taken by each participant was a significant determinant in progression free survival, locoregional control, and overall survival, but not in disease free survival. They suggest this data shows that the addition of nimotuzumab has a differential patient impact on disease free survival with respect to HPV status.

In patients taking nimotuzumab, improvement in locoregional control was largely responsible for their improvement in progression free survival. On average, time to locoregional failure in the CRT treatment arm was 17.3 months, and in the NCRT treatment arm, it was 60.3 months. The team also found that the addition of nimotuzumab led to an 18.6% improvement in 2-year overall survival, jumping from 39.0% to 57.6%.

Figure 4: Restricted mean overall survival plots of both arms. arm = 0 represents the plot of the cisplatin radiotherapy arm while arm = 1 represents the plot of the Nimotuzumab-cisplatin radiotherapy arm. — **Figure 4:** Restricted mean overall survival plots of both arms. arm = 0 represents the plot of the cisplatin radiotherapy arm while arm = 1 represents the plot of the Nimotuzumab-cisplatin radiotherapy arm.

“Locoregional control, progression-free survival and overall survival were improved with the addition of nimotuzumab to cisplatin and radiation.”

Conclusion

“The addition of nimotuzumab to weekly cisplatin-radiation improves outcomes inclusive of OS in HPV negative oropharyngeal cancers.”

“The results of the current study clarify the importance of treatment intensification in HPV negative oropharyngeal cancers.”

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

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Trending with Impact: Review of HER2 Variants in Breast Cancer Tumors

December 31, 2020

This review compiles splice variations in HER2 breast cancer, specifically in the context of the tumor environment, and co-expression of variants. The study also provides an up-to-date (as of Nov. 2020) account of HER2 and HER2 variant patterns of resistance to anti-HER2 therapies and other interventions.

Photomicrograph of immunohistochemistry for HER2, showing positive cell membrane staining in this infiltrating ductal carcinoma

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According to Cancer Research UK, breast cancer occurs in one in every eight women within their lifetime and is the second highest cause of cancer related deaths in the UK. Breast cancer is a blanketed term for a wide variety of tumors that occur in the mammary glands. In over 20% of breast cancers, the human epidermal growth factor receptor two gene, officially named ErbB2 but otherwise known as HER2, is overexpressed. HER2 is a member of the epidermal growth factor receptor family of EGFR, HER2, HER3, and HER4. Overexpression of the HER2 protein was discovered in 1987 as a biomarker associated with poor prognosis and aggressive tumor types in breast cancer. This finding has accelerated research studies and progress in HER2 diagnostic testing and targeted therapeutics. However, the issue of HER2 resistance in these targeted therapies remains problematic.

“At the present time, we have an incomplete understanding of why patients with HER2+ breast cancer exhibit variable responses or resistance to targeted therapies [73, 74].”

Researchers from the Translational and Clinical Research Institute at Newcastle University in the United Kingdom have compiled a review of variations in HER2 breast cancer, specifically in the context of the tumor environment and when multiple variants are co-expressed at altered ratios. Their study also provides an up-to-date (as of Nov. 2020) account of the current landscape of HER2 variants and links this to patterns of resistance against HER2 therapies and other interventions.

“It is clear HER2 expression is not as simple as a single oncogenic overexpressed protein. It is likely many variants, arising from splicing and other mechanisms, are present in tandem. The relative ratios of these are likely to fluctuate depending on cellular conditions, during tumorigenesis and breast cancer progression.”

HER2 Variants & Co-expression

This paper provides an exquisitely detailed description and explanation of the HER2 protein structure, signaling pathways, sub-typing, and in-depth treatment functionality of a number of different HER2 targeted therapeutics.

“Different forms of the HER2 protein exist within tumours in tandem and can display altered biological activities.”

The unique interest in researching variations in HER2 breast cancer has increased since the identification of Δ16-HER2: a particular splice variant and link to resistance of anti-HER2 therapies. The “Δ16” in Δ16-HER2 refers to the lack of exon-16, which encodes a small extracellular portion of the DNA. Δ16-HER2 represents approximately 9% of the normal HER2 transcripts and its expression is considered common in breast cancer. Previous studies have identified Δ16-HER2 and HER2 normal transcripts can be co-expressed at varying levels in breast carcinomas.

In the variant P100, less is known about this truncated HER2 protein. It has been hypothesized that P100 reduces the efficacy of monoclonal antibody HER2 treatments.

The splice variant Herstatin is produced by the retention of intron-8 in the HER2 protein. Herstatin acts as a tumor suppressor by blocking HER2 activity and cell proliferation, while promoting apoptosis. The researchers mention that it is important to note that cells expressing high levels of Herstatin are more sensitive to Tamoxifen.

“It’s noteworthy that one study proposed that the presence of Herstatin transcript does not segregate by tumour grade or size, patient age, lymph node involvement or ER status and that mRNA transcripts were present in matched non-cancerous breast tissue and breast carcinomas [96].”

Researchers in this review note that identifying and assessing the expression ratios of these different variants and classifying them as prognostic and predictive biomarkers may aid in further personalized treatment of breast cancer in HER2 positive patients.

Testing and Research Landscape

“Studying splicing regulation and how this is altered in breast cancer could explain patterns of expression and how these link to treatment resistance [111].”

The researchers write that tests assessing for both HER2 status and HER2 variant expression could potentially refine their predictions of a patients’ response to treatment. One common way that researchers gauge levels of HER2 proteins, and only some HER2 variants, is through immunohistochemistry tests. mRNA assessments are also used to identify gene expression patterns. Another biomarker test the researchers noted that may be best used for prognostic predictions is the Enzyme-Immunoassay—to assess levels of plasma or serum HER2 (sHER2) in the blood produced by cleavage or splicing.

“Cohort studies have identified sHER2 testing as a useful complementary test to IHC owing to the correlations between high sHER2 and aggressive tumour phenotypes such as invasion and metastases.”

Targeted HER2 Treatments

The review elaborates in detail about targeted treatments for HER2 breast cancer, which include: trastuzumab, pertuzumab, lapatinib, and T-DM1. They note that endocrine therapy is utilized for ER positive patients and chemotherapy, radiotherapy, and surgery are all still utilized.

Conclusion

“Work in vitro and in vivo as well as analysis from clinical trials has identified patterns of resistance to the standard of care treatment options in HER2+ patients which are correlated to variant expression.”

This goal of their review was to summarise the current landscape of HER2 variant research and to explain why researchers should consider HER2 variant levels and ratios when offering the best treatment plan for breast cancer patients.

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

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Special Collection by Oncotarget: Lung Cancer

December 11, 2020

Oncotarget Special Collection: Lung Cancer

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Lung cancer is still the leading cause of cancer-related mortality worldwide. According to the CDC, smoking cigarettes is linked to 80-90% of lung cancer deaths in the United States. In non-smokers, lung cancer can be caused by exposure to radon, secondhand smoke, air pollution, asbestos, diesel exhaust, and other chemicals and factors.

Some symptoms of lung cancer include pain in chest or ribs, frequent respiratory infections, shortness of breath, wheezing, fatigue or loss of appetite. As numerous research studies about lung cancer are currently underway, we hope this Special Collection will set future research in motion to discover more causes and treatments for this disease.

Special Collections: Lung Cancer

Oncotarget publishes open access peer-reviewed literature about research studies, clinical studies, reviews, case reports, and meta-analyses on a variety of different topics pertaining to cancer. Lung cancer continues to be an area of interest for researchers, therefore, the Special Collection on Lung Cancer was created by Oncotarget for scientists and researchers to discover new biomarkers, mechanisms, and therapies to treat this cancer.

All content submitted for publication has been reviewed by a diligent board of academic editors and world-renowned scientists and researchers. In this Special Collection, the content focussing on lung cancer is organized together in one place, including papers such as “Molecular pathways and therapeutic targets in lung cancer” by Emma Shtivelman, Thomas Hensing, George R. Simon, Phillip A. Dennis, Gregory A. Otterson, Raphael Bueno, and Ravi Salgia. This review is a summary of the pathways and mechanisms involved in current treatment methods for lung cancer of various types.

This meta-analysis examines the relationship between exposure to PM2.5 (particulate matter or fine particles) and lung cancer incidence and mortality: “Relationship between exposure to PM2.5 and lung cancer incidence and mortality: A meta-analysis” by Feifei Huang, Bing Pan, Jun Wu, Engeng Chen, and Liying Chen.

This review focuses on improved anticancer agents and therapy options for lung cancer patients with acquired EGFR TKI (chemotherapy) resistance: “Clinical strategies for acquired epidermal growth factor receptor tyrosine kinase inhibitor resistance in non-small-cell lung cancer patients” by Lijun Dong, Dan Lei, and Haijun Zhang.

Read more about lung cancer on Oncotarget.com.

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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.