Biology subjects

Newberg, J. Y.

Publications and source records attributed to Newberg, J. Y..

5 recordsLinked to original sources

bioRxiv2022

RBFOX2 deregulation promotes pancreatic cancer metastasis through alternative splicing

RNA splicing is an important biological process associated with cancer initiation and progression, yet in pancreatic cancer the role and regulation of splicing is not well understood. From a forward genetic screen in a mouse model of pancreatic cancer, we identified an enrichment of RNA binding proteins (RBPs) associated with the spliceosome. Here, we link deregulation of RBFOX2, an RBP of the FOX family, to pancreatic cancer progression and liver metastasis. We show that RBFOX2 regulation in pancreatic cancer occurs at both the RNA and protein level, and that nuclear localization of RBFOX2 is significantly reduced in poorly differentiated PDAC. Deregulation of RBFOX2 in PDAC is associated with an enrichment of exon exclusion events in transcripts encoding proteins involved in cytoskeletal remodeling and invadopodia programs that potentiate metastatic potential in vivo. Using splice-switching antisense oligonucleotides (AONs) and inducible cDNA isoforms, we demonstrate that RBFOX2 mediated exon exclusion in ABI1 controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells, and that ABI1 splice-switching enhances cellular phenotypes associated with cancer cell stemness. Together, our data identify a novel role for RBFOX2 deregulation in promoting PDAC progression through alternative splicing regulation.

cancer biology↗

bioRxiv2022

"Transposon Mutagenesis Reveals RBMS3 as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis."

Mutationally-activated BRAFV600E is detected in ~2% of all human non-small cell lung cancers (NSCLC), and serves as a predictive biomarker for treatment of patients with FDA-approved pathway-targeted therapies that inhibit signaling by the BRAFV600E oncoprotein kinase. In genetically engineered mouse (GEM) models, expression of BRAFV600E in alveolar type 2 (AT2) pneumocytes initiates the development of benign lung tumors that, without additional genetic alterations, rarely progress to malignant lung adenocarcinomas. To identify genes that might cooperate with BRAFV600E for malignant lung cancer progression we employed Sleeping Beauty (SB)-mediated transposon mutagenesis, which dramatically accelerated the onset of lethal lung adenocarcinomas. Amongst the diverse group of genes identified by this in vivo screen was Rbms3 (RNA binding motif single-stranded interacting protein 3), an RNA-binding protein implicated as a possible tumor suppressor. Using CRISPR/CAS9 gene editing we confirmed that RBMS3 silencing cooperated with BRAFV600E to promote progression of malignant lung cancer with a distinct micropapillary architecture. Moreover, RBMS3 silencing also cooperated with BRAFV600E to promote the growth of lung organoids in vitro. BRAFV600E/RBMS3Null lung tumors displayed elevated expression of b-catenin (CTNNB1), suggesting that RBMS3 silencing may result in elevated signaling through the WNT>CTNNB1>c-MYC pathway. Finally, analyses of patient samples in The Cancer Genome Atlas (TCGA) revealed that the region of chromosome 3 encompassing RBMS3 is frequently lost in NSCLC and correlates with poor patient prognosis. Collectively, SB-mediated transposon mutagenesis has revealed the ability of a novel tumor suppressor, RBMS3, to cooperate with BRAFV600E to promote lung carcinogenesis, and suggests that RBMS3 silencing may contribute to malignant progression of numerous human lung cancers. SIGNIFICANCEThe BRAFV600E oncoprotein kinase is a potent initiator of benign lung tumorigenesis, but is insufficient to elicit malignant lung adenocarcinoma without additional cooperating alterations. Sleeping Beauty-mediated transposon mutagenesis has revealed a number of genes that cooperate with BRAFV600E to promote lung cancer progression, in particular Rbms3, which encodes an RNA binding protein. Hence, this genetic screen provides a deeper understanding of the molecular mechanisms underlying BRAFV600E-driven lung carcinogenesis, and is an important step improving our ability to successfully target this disease.

cancer biology↗

bioRxiv2020

Insertional mutagenesis defines drivers and evolutionary relationships in pancreatic cancer metastasis

Metastasis is a defining feature of pancreatic cancer, impacting patient quality of life and therapeutic outcomes. While recurrent mutations in KRAS and TP53 play important roles in primary tumor development and persist in metastases, the contributions of other genes to the metastatic process is understudied. Here, we define a network of metastasis-promoting genes and uncover positively selected genes in metastatic lesions from our Sleeping Beauty mouse model of pancreatic cancer using our recently described SB Driver Analysis statistical pipeline. We show that loss of single genes DLG1, PARD3, PKP4 and PTPRK promote pancreas cancer progression in a context-specific manner. Finally, we define clonal and sub-clonal insertion events that distinguish primary and individual metastatic tumors and use single cell sequencing to gain insight into the evolutionary relationships between sub-regions of primary pancreatic tumors and related metastases, which has important implications for pancreatic disease progression and therapeutic opportunities for patients.

cancer biology↗

bioRxiv2020

Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation

A central challenge in cancer genomics is the systematic identification of single and cooperating tumor suppressor genes driving cellular transformation and tumor progression in the absence of oncogenic driver mutation(s). Multiple in vitro and in vivo gene inactivation screens have enhanced our understanding of the tumor suppressor gene landscape in various cancers. However, these studies are limited to single or combination gene effects, specific organs, or require sensitizing mutations. In this study, we developed and utilized a Sleeping Beauty transposon mutagenesis system that functions only as a gene trap to exclusively inactivate tumor suppressor genes. Using whole body transposon mobilization in wild type mice, we observed that cumulative gene inactivation can drive tumorigenesis of solid cancers. We provide a quantitative landscape of the tumor suppressor genes inactivated in these cancers, and show that despite the absence of oncogenic drivers, these genes converge on key biological pathways and processes associated with cancer hallmarks.

cancer biology↗

bioRxiv2019

Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression

The systematic identification of genetic events driving cellular transformation and tumor progression in the absence of a highly recurrent oncogenic driver mutation is a challenge in cutaneous oncology. In cutaneous squamous cell carcinoma (cuSCC), the high UV-induced mutational burden poses a hurdle to achieve a complete molecular landscape of this disease. Here, we utilized the Sleeping Beauty transposon mutagenesis system to statistically define drivers of keratinocyte transformation and cuSCC progression in vivo in the absence of UV-IR, and identified both known tumor suppressor genes and novel oncogenic drivers of cuSCC. Functional analysis confirms an oncogenic role for the ZMIZ genes, and tumor suppressive roles for KMT2C, CREBBP and NCOA2, in the initiation or progression of human cuSCC. Taken together, our in vivo screen demonstrates an extremely heterogeneous genetic landscape of cuSCC initiation and progression, which can be harnessed to better understand skin oncogenic etiology and prioritize therapeutic candidates.

cancer biology↗