Biology subjects

Houghton, P. J.

Publications and source records attributed to Houghton, P. J..

6 recordsLinked to original sources

bioRxiv2022

DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer

Large-scale genetic and pharmacologic dependency maps are generated to reveal genetic vulnerabilities and drug sensitivities of cancer. However, user-friendly software is needed to systematically link such maps. Here we present DepLink, an R Shiny server to identify genetic and pharmacologic perturbations that induce similar effects on cell viability or molecular changes. DepLink integrates heterogeneous datasets of genome-wide CRISPR loss-of-function screens, high-throughput pharmacologic screens, and perturbation expression signatures. The datasets are systematically connected by four complementary modules tailored for different query scenarios. In summary, DepLink enables easy navigation, visualization, and linkage of rapidly evolving cancer dependency maps.

bioinformatics↗

bioRxiv2022

Sensitization to Ionizing Radiation by MEK inhibition is Dependent on SNAI2 in Fusion-negative Rhabdomyosarcoma

In fusion-negative rhabdomyosarcoma (FN-RMS), a pediatric malignancy with skeletal muscle characteristics, > 90% of high-risk patients have mutations that activate the RAS/MEK signaling pathway. We recently discovered that SNAI2, in addition to blocking myogenic differentiation downstream of MEK signaling in FN-RMS, represses pro-apoptotic BIM expression to protect RMS tumors from ionizing radiation (IR). As clinically relevant concentrations of the MEK inhibitor trametinib elicit poor responses in preclinical xenograft models, we investigated the utility of low-dose trametinib in combination with IR for the treatment of RAS-mutant FN-RMS. We hypothesized that trametinib would sensitize FN-RMS to IR through its downregulation of SNAI2 expression. While we observed little to no difference in myogenic differentiation or cell survival with trametinib treatment alone, robust differentiation and reduced survival were observed after IR. Additionally, IR-induced apoptosis was significantly increased in FN-RMS cells treated concurrently with trametinib, as was increased BIM expression. SNAI2s role in these processes was established using overexpression rescue experiments, where overexpression of SNAI2 prevented IR-induced myogenic differentiation and apoptosis. Moreover, combining MEK inhibitor with IR resulted in complete tumor regression and a 2-4-week delay in event free survival (EFS) in preclinical xenograft and PDX models. Our findings demonstrate that the combination of MEK inhibition and IR results in robust differentiation and apoptosis, due to the reduction of SNAI2, which leads to extended EFS in FN-RMS. SNAI2 thus is a biomarker of IR insensitivity and target for future therapies to sensitize aggressive sarcomas to IR.

cancer biology↗

bioRxiv2021

SNAI2-mediated direct repression of BIM protects rhabdomyosarcoma from ionizing radiation

Ionizing radiation (IR) and chemotherapy are the mainstays of treatment for patients with rhabdomyosarcoma (RMS). Yet, the molecular mechanisms that underlie the success or failure of radiotherapy remain unclear. The transcriptional repressor SNAI2 was previously identified as a key regulator of IR sensitivity in normal and malignant stem cells through its repression of the proapoptotic BH3-only gene PUMA. Here, we demonstrate a clear correlation between SNAI2 expression levels and radiosensitivity across multiple RMS cell lines. Moreover, modulating SNAI2 levels in RMS cells through its overexpression or knockdown can alter radiosensitivity in vitro and in vivo. SNAI2 expression reliably promotes overall cell growth and inhibits mitochondrial apoptosis following exposure to IR, with either variable or minimal effects on differentiation and senescence, respectively. Importantly, SNAI2 knockdown results in a striking increase in expression of the proapoptotic BH3-only gene BIM, and ChIP-seq experiments establish that SNAI2 is a direct repressor of BIM. Since the P53 pathway is nonfunctional in the RMS cells used in this study, we have identified a new, P53-independent SNAI2/BIM axis that could potentially predict clinical responses to IR treatment and be exploited to improve RMS therapy. HighlightsO_LISNAI2 expression levels are directly correlated with protection from radiation in rhabdomyosarcoma. C_LIO_LILoss of SNAI2 primes rhabdomyosarcomas for IR-induced apoptosis. C_LIO_LISNAI2 directly represses the expression of the proapoptotic BH3-only gene BIM. C_LI

cancer biology↗

bioRxiv2020

PCAT: An integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models

Although cancer is the leading cause of disease-related mortality in children, the relative rarity of pediatric cancers poses a significant challenge for developing novel therapeutics to further improve prognosis. Patient-derived xenograft (PDX) models, which are usually developed from high-risk tumors, are a useful platform to study molecular driver events, identify biomarkers, and prioritize therapeutic agents. Here we develop PDX for Childhood Cancer Therapeutics (PCAT), a new integrated portal for pediatric cancer PDX models. Distinct from previously reported PDX portals, PCAT is focused on pediatric cancer models and provides intuitive interfaces for querying and data mining. The current release comprises 324 models and their associated clinical and genomic data, including gene expression, mutation, and copy number alteration. Importantly, PCAT curates preclinical testing results for 68 models and 79 therapeutic agents manually collected from individual agent testing studies published since 2008. To facilitate comparisons of patterns between patient tumors and PDX models, PCAT curates clinical and molecular data of patient tumors from the TARGET project. In addition, PCAT provides access to gene fusions identified in nearly 1,000 TARGET samples. PCAT was built using R-shiny and MySQL. The portal can be accessed at http://pcat.zhenglab.info or http://www.pedtranscriptome.org.

genomics↗

bioRxiv2019

Single-cell RNA Profiling Identifies Diverse Cellular Responses to EWSR1-FLI1 Down-regulation in Ewing Sarcoma

Single-cell analyses provide insight into time dependent behaviors in response to dynamic changes of oncogene expression. We developed an unbiased approach to study gene expression variation using a model of cellular dormancy induced via EWSR1-FLI1 down-regulation in Ewing sarcoma (EWS) cells. We propose that variation in the expression of EWSR1-FLI1 over time determines cellular responses. Cell state and functions were assigned using random forest feature selection in combination with machine learning. Notably, three distinct expression profiles were uncovered contributing to Ewing sarcoma cell heterogeneity. Our predictive model identified [~]1% cells in a dormant-like state and [~]2-4% with higher stem-like and neural stem-like features in an exponentially proliferating EWS cell line and EWS xenografts. Following oncogene knockdown, cells re-entering the proliferative cycle have greater stem-like properties, whereas for those remaining quiescent, FAM134B-dependent dormancy provides a survival mechanism. We also show cell cycle heterogeneity related to EWSR1-FLI1 expression as an independent feature driving cancer heterogeneity, and drug resistance.\n\nSIGNIFICANCEWe show that time-dependent changes induced by suppression of oncogenic EWSR1-FLI1 induces dormancy, with different subpopulation dynamics, including stem-like characteristics and prolonged dormancy. Cells with these characteristics are identified in exponentially growing cell populations and confer drug resistance, and could potentially contribute to metastasis or late recurrence in patients.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC=\"FIGDIR/small/750539v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (24K):\norg.highwire.dtl.DTLVardef@6a5449org.highwire.dtl.DTLVardef@c39124org.highwire.dtl.DTLVardef@16e0a45org.highwire.dtl.DTLVardef@1644614_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2017

EWS-FLI-1 creates a cell surface microenvironment conducive to IGF signaling by inducing pappalysin-1.

Ewing sarcoma is an aggressive cancer of bone and soft tissue in children with poor prognosis. It is characterized by the chromosomal translocation between EWS and an Ets family transcription factor, most commonly FLI-1. EWS-FLI-1 fusion accounts for 85% of Ewing sarcoma cases. EWS-FLI-1 regulates the expression of a number of genes important for sarcomagenesis, can transform NIH3T3 and C3H10T1/2 cells, and is necessary for proliferation and tumorigenicity of Ewing sarcoma cells, suggesting that EWS-FLI-1 is the causative oncoprotein.\n\nHere we report that EWS-FLI-1 induces the expression of pappalysin-1 (PAPPA), a cell surface protease that degrades IGF binding proteins (IGFBPs) and increases the bioavailability of IGF. EWS-FLI-1 binds to the pappalysin-1 gene promoter and stimulates the expression of pappalysin-1, leading to degradation of IGFBPs and enhanced IGF signaling. Silencing of pappalysin-1 strongly inhibited anchorage-dependent and anchorage-independent growth as well as xenograft tumorigenicity of Ewing sarcoma cells. These results suggest that EWS-FLI-1 creates a cell surface microenvironment conducive to IGF signaling by inducing pappalysin-1, which emerged as a novel target to inhibit IGF signaling in Ewing sarcoma.

cancer biology↗