Analysis of CD74 Occurrence in Oncogenic Fusion Proteins

Vargas, Jasmine; Pantouris, Georgios

doi:10.3390/ijms242115981

Cited by 3 publications

(1 citation statement)

References 157 publications

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“…In addition, reports indicate that CD74 is expressed mainly by the malignant cells of NSCLC and other cancers. Five in-frame fusion proteins have been reported [49]. In the current study, RT-qPCR analyses confirmed CD74 expression in osimertinib-DTP cells from the cell lines and lung adenocarcinoma biopsies.…”

Section: Discussionsupporting

confidence: 78%

Transcriptomic Analysis Reveals Early Alterations Associated with Intrinsic Resistance to Target Therapy in Lung Adenocarcinoma Cell Lines

Perez-Medina,

Lopez-Gonzalez,

Benito-Lopez

et al. 2024

Preprint

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Lung adenocarcinoma is the most prevalent form of lung cancer, and drug resistance is a significant obstacle in its treatment. This study aimed to investigate the overexpression of long non-coding RNAs (lncRNAs) as a mechanism that promotes intrinsic resistance in tumor cells from the onset of treatment. Drug-tolerant persister cells (DTP) are a subset of cancer cells that survive and proliferate after exposure to therapeutic drugs, making them an essential object of study for cancer treatment. The molecular mechanisms underlying DTP cell survival are not fully understood; however, long non-coding RNAs (lncRNAs) have been proposed to play a crucial role. DTP cells from lung adenocarcinoma cell lines were obtained after a single exposure to tyrosine kinase inhibitor TKIs (erlotinib or osimertinib). After establishing DTPs, RNA sequencing was performed to investigate the differential expression of the lncRNAs. Some lncRNAs and one mRNA were found to be overexpressed in DTP cells. The clinical relevance of lncRNAs was evaluated in a cohort of patients with lung adenocarcinoma from The Cancer Genome Atlas (TCGA). RT-qPCR validated the overexpression of lncRNAs and mRNA in residual DTP cells and LUAD biopsies. Knockdown of these lncRNAs increases the sensitivity of DTP cells to therapeutic drugs. This study provides an opportunity to investigate the involvement of lncRNAs in the genetic and epigenetic mechanisms underlying intrinsic resistance. The identified lncRNAs and CD74 mRNA may serve as potential prognostic markers or therapeutic targets to improve the overall survival of patients with lung cancer.

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Section: Discussionsupporting

confidence: 78%

Transcriptomic Analysis Reveals Early Alterations Associated with Intrinsic Resistance to Target Therapy in Lung Adenocarcinoma Cell Lines

Perez-Medina,

Lopez-Gonzalez,

Benito-Lopez

et al. 2024

Preprint

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Comprehensive genomic characterization of hematologic malignancies at a pediatric tertiary care center

Kebede,

Garfinkle,

Mathew

et al. 2024

Front. Oncol.

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Despite the increasing availability of comprehensive next generation sequencing (NGS), its role in characterizing pediatric hematologic malignancies remains undefined. We describe findings from comprehensive genomic profiling of hematologic malignancies at a pediatric tertiary care center. Patients enrolled on a translational research protocol to aid in cancer diagnosis, prognostication, treatment, and detection of cancer predisposition. Disease-involved samples underwent exome and RNA sequencing and analysis for single nucleotide variation, insertion/deletions, copy number alteration, structural variation, fusions, and gene expression. Twenty-eight patients with hematologic malignancies were nominated between 2018-2021. Eighteen individuals received both germline and somatic sequencing; two received germline sequencing only. Germline testing identified patients with cancer predisposition syndromes and non-cancer carrier states. Fifteen patients (15/18, 83%) had cancer-relevant somatic findings. Potential therapeutic targets were identified in seven patients (7/18, 38.9%); three (3/7, 42.9%) received targeted therapies and remain in remission an average of 47 months later.

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Insight into NSCLC through novel analysis of gene interactions and characteristics

Pan

2024

Am J Clin Exp Immunol

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Around 80 to 85% of all lung cancers are non-small cell lung cancer (NSCLC). Previous research has aimed at exploring the genetic basis of NSCLC through individual approaches, but studies have yet to investigate the results of combining them. Here we show that analyzing NSCLC genetics through three approaches simultaneously creates unique insights into our understanding of the disease. Through a combination of previous research and bioinformatics tools, we determined 35 NSCLC candidate genes. We analyzed these genes in 3 different approaches. First, we found the gene fusions between these candidate genes. Second, we found the common superfamilies between genes. Finally, we identified mutational signatures that are possibly associated with NSCLC. Each approach has its individual, unique results. Fusion relationships identify specific gene fusion targets, common superfamilies identify possible avenues to determine novel target genes, and identifying NSCLC associated mutational signatures has diagnostic and prognostic benefits. Combining the approaches, we found that gene CD74 has significant fusion relationships, but it has no association with the other two approaches, suggesting that CD74 is associated with NSCLC mainly because of its fusion relationships. Targeting the gene fusions of CD74 may be an alternative NSCLC treatment. This genetic analysis has indeed created unique insight into NSCLC genes. Both the results from each of the approaches separately and combined allow pursuit of more effective treatment strategies for this cancer. The methodology presented can also apply to other cancers, creating insights that current analytical methods could not find.

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Analysis of CD74 Occurrence in Oncogenic Fusion Proteins

Cited by 3 publications

References 157 publications

Transcriptomic Analysis Reveals Early Alterations Associated with Intrinsic Resistance to Target Therapy in Lung Adenocarcinoma Cell Lines

Transcriptomic Analysis Reveals Early Alterations Associated with Intrinsic Resistance to Target Therapy in Lung Adenocarcinoma Cell Lines

Comprehensive genomic characterization of hematologic malignancies at a pediatric tertiary care center

Insight into NSCLC through novel analysis of gene interactions and characteristics

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