Publications by authors named "Kenneth L Scott"

49 Publications

POT1 Regulates Proliferation and Confers Sexual Dimorphism in Glioma.

Cancer Res 2021 05 29;81(10):2703-2713. Epub 2021 Mar 29.

Department of Neurosurgery, Baylor College of Medicine, Houston, Texas.

Germline POT1 mutations are found in a spectrum of cancers and confer increased risk. Recently, we identified a series of novel germline POT1 mutations that predispose carrier families to the development of glioma. Despite these strong associations, how these glioma-associated POT1 mutations contribute to glioma tumorigenesis remains undefined. Here we show that POT1-G95C increases proliferation in glioma-initiating cells and in progenitor populations in the developing brain. In a native mouse model of glioma, loss of Pot1a/b resulted in decreased survival in females compared with males. These findings were corroborated in human glioma, where low POT1 expression correlated with decreased survival in females. Transcriptomic and IHC profiling of Pot1a/b-deficient glioma revealed that tumors in females exhibited decreased expression of immune markers and increased expression of cell-cycle signatures. Similar sex-dependent trends were observed in human gliomas that had low expression of POT1. Together, our studies demonstrate context-dependent functions for POT1 mutation or loss in driving progenitor proliferation in the developing brain and sexual dimorphism in glioma. SIGNIFICANCE: This study shows that manipulation of POT1 expression in glioma has sex-specific effects on tumorigenesis and associated immune signatures.
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http://dx.doi.org/10.1158/0008-5472.CAN-20-3755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8243722PMC
May 2021

IMPAD1 and KDELR2 drive invasion and metastasis by enhancing Golgi-mediated secretion.

Oncogene 2020 09 4;39(37):5979-5994. Epub 2020 Aug 4.

Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.

Non-small cell lung cancer (NSCLC) is the deadliest form of cancer worldwide, due in part to its proclivity to metastasize. Identifying novel drivers of invasion and metastasis holds therapeutic potential for the disease. We conducted a gain-of-function invasion screen, which identified two separate hits, IMPAD1 and KDELR2, as robust, independent drivers of lung cancer invasion and metastasis. Given that IMPAD1 and KDELR2 are known to be localized to the ER-Golgi pathway, we studied their common mechanism of driving in vitro invasion and in vivo metastasis and demonstrated that they enhance Golgi-mediated function and secretion. Therapeutically inhibiting matrix metalloproteases (MMPs) suppressed both IMPAD1- and KDELR2-mediated invasion. The hits from this unbiased screen and the mechanistic validation highlight Golgi function as one of the key cellular features altered during invasion and metastasis.
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http://dx.doi.org/10.1038/s41388-020-01410-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7539228PMC
September 2020

Differential expression of MAGEA6 toggles autophagy to promote pancreatic cancer progression.

Elife 2020 04 9;9. Epub 2020 Apr 9.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.

The melanoma-associated antigen family A (MAGEA) antigens are expressed in a wide variety of malignant tumors but not in adult somatic cells, rendering them attractive targets for cancer immunotherapy. Here we show that a number of cancer-associated MAGEA mutants that undergo proteasome-dependent degradation in vitro could negatively impact their utility as immunotherapeutic targets. Importantly, in pancreatic ductal adenocarcinoma cell models, MAGEA6 suppresses macroautophagy (autophagy). The inhibition of autophagy is released upon MAGEA6 degradation, which can be induced by nutrient deficiency or by acquisition of cancer-associated mutations. Using xenograft mouse models, we demonstrated that inhibition of autophagy is critical for tumor initiation whereas reinstitution of autophagy as a consequence of MAGEA6 degradation contributes to tumor progression. These findings could inform cancer immunotherapeutic strategies for targeting MAGEA antigens and provide mechanistic insight into the divergent roles of during pancreatic cancer initiation and progression.
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http://dx.doi.org/10.7554/eLife.48963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164953PMC
April 2020

PIK3CA variants selectively initiate brain hyperactivity during gliomagenesis.

Nature 2020 02 29;578(7793):166-171. Epub 2020 Jan 29.

Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.

Glioblastoma is a universally lethal form of brain cancer that exhibits an array of pathophysiological phenotypes, many of which are mediated by interactions with the neuronal microenvironment. Recent studies have shown that increases in neuronal activity have an important role in the proliferation and progression of glioblastoma. Whether there is reciprocal crosstalk between glioblastoma and neurons remains poorly defined, as the mechanisms that underlie how these tumours remodel the neuronal milieu towards increased activity are unknown. Here, using a native mouse model of glioblastoma, we develop a high-throughput in vivo screening platform and discover several driver variants of PIK3CA. We show that tumours driven by these variants have divergent molecular properties that manifest in selective initiation of brain hyperexcitability and remodelling of the synaptic constituency. Furthermore, secreted members of the glypican (GPC) family are selectively expressed in these tumours, and GPC3 drives gliomagenesis and hyperexcitability. Together, our studies illustrate the importance of functionally interrogating diverse tumour phenotypes driven by individual, yet related, variants and reveal how glioblastoma alters the neuronal microenvironment.
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http://dx.doi.org/10.1038/s41586-020-1952-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7577741PMC
February 2020

The RNA-binding protein AKAP8 suppresses tumor metastasis by antagonizing EMT-associated alternative splicing.

Nat Commun 2020 01 24;11(1):486. Epub 2020 Jan 24.

Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.

Alternative splicing has been shown to causally contribute to the epithelial-mesenchymal transition (EMT) and tumor metastasis. However, the scope of splicing factors that govern alternative splicing in these processes remains largely unexplored. Here we report the identification of A-Kinase Anchor Protein (AKAP8) as a splicing regulatory factor that impedes EMT and breast cancer metastasis. AKAP8 not only is capable of inhibiting splicing activity of the EMT-promoting splicing regulator hnRNPM through protein-protein interaction, it also directly binds to RNA and alters splicing outcomes. Genome-wide analysis shows that AKAP8 promotes an epithelial cell state splicing program. Experimental manipulation of an AKAP8 splicing target CLSTN1 revealed that splice isoform switching of CLSTN1 is crucial for EMT. Moreover, AKAP8 expression and the alternative splicing of CLSTN1 predict breast cancer patient survival. Together, our work demonstrates the essentiality of RNA metabolism that impinges on metastatic breast cancer.
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http://dx.doi.org/10.1038/s41467-020-14304-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981122PMC
January 2020

PI4KIIIβ is a therapeutic target in chromosome 1q-amplified lung adenocarcinoma.

Sci Transl Med 2020 01;12(527)

Department of Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Heightened secretion of protumorigenic effector proteins is a feature of malignant cells. Yet, the molecular underpinnings and therapeutic implications of this feature remain unclear. Here, we identify a chromosome 1q region that is frequently amplified in diverse cancer types and encodes multiple regulators of secretory vesicle biogenesis and trafficking, including the Golgi-dedicated enzyme phosphatidylinositol (PI)-4-kinase IIIβ (PI4KIIIβ). Molecular, biochemical, and cell biological studies show that PI4KIIIβ-derived PI-4-phosphate (PI4P) synthesis enhances secretion and accelerates lung adenocarcinoma progression by activating Golgi phosphoprotein 3 (GOLPH3)-dependent vesicular release from the Golgi. PI4KIIIβ-dependent secreted factors maintain 1q-amplified cancer cell survival and influence prometastatic processes in the tumor microenvironment. Disruption of this functional circuitry in 1q-amplified cancer cells with selective PI4KIIIβ antagonists induces apoptosis and suppresses tumor growth and metastasis. These results support a model in which chromosome 1q amplifications create a dependency on PI4KIIIβ-dependent secretion for cancer cell survival and tumor progression.
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http://dx.doi.org/10.1126/scitranslmed.aax3772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7702266PMC
January 2020

Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage.

Cell 2019 01;176(1-2):127-143.e24

Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis. Half of the tested human homologs promote DNA damage and mutation when overproduced in human cells, with DNA damage-elevating mechanisms like those in E. coli. Our work identifies networks of DDPs that provoke endogenous DNA damage and may reveal DNA damage-associated functions of many human known and newly implicated cancer-promoting proteins.
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http://dx.doi.org/10.1016/j.cell.2018.12.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344048PMC
January 2019

Neomorphic PDGFRA extracellular domain driver mutations are resistant to PDGFRA targeted therapies.

Nat Commun 2018 11 2;9(1):4583. Epub 2018 Nov 2.

Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.

Activation of platelet-derived growth factor receptor alpha (PDGFRA) by genomic aberrations contributes to tumor progression in several tumor types. In this study, we characterize 16 novel PDGFRA mutations identified from different tumor types and identify three previously uncharacterized activating mutations that promote cell survival and proliferation. PDGFRA Y288C, an extracellular domain mutation, is primarily high mannose glycosylated consistent with trapping in the endoplasmic reticulum (ER). Strikingly, PDGFRA Y288C is constitutively dimerized and phosphorylated in the absence of ligand suggesting that trapping in the ER or aberrant glycosylation is sufficient for receptor activation. Importantly, PDGFRA Y288C induces constitutive phosphorylation of Akt, ERK1/2, and STAT3. PDGFRA Y288C is resistant to PDGFR inhibitors but sensitive to PI3K/mTOR and MEK inhibitors consistent with pathway activation results. Our findings further highlight the importance of characterizing functional consequences of individual mutations for precision medicine.
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http://dx.doi.org/10.1038/s41467-018-06949-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214970PMC
November 2018

Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2.

Proc Natl Acad Sci U S A 2018 10 28;115(42):10666-10671. Epub 2018 Sep 28.

Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030;

Scientific progress depends on formulating testable hypotheses informed by the literature. In many domains, however, this model is strained because the number of research papers exceeds human readability. Here, we developed computational assistance to analyze the biomedical literature by reading PubMed abstracts to suggest new hypotheses. The approach was tested experimentally on the tumor suppressor p53 by ranking its most likely kinases, based on all available abstracts. Many of the best-ranked kinases were found to bind and phosphorylate p53 ( value = 0.005), suggesting six likely p53 kinases so far. One of these, NEK2, was studied in detail. A known mitosis promoter, NEK2 was shown to phosphorylate p53 at Ser315 in vitro and in vivo and to functionally inhibit p53. These bona fide validations of text-based predictions of p53 phosphorylation, and the discovery of an inhibitory p53 kinase of pharmaceutical interest, suggest that automated reasoning using a large body of literature can generate valuable molecular hypotheses and has the potential to accelerate scientific discovery.
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http://dx.doi.org/10.1073/pnas.1806643115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6196525PMC
October 2018

RNA editing derived epitopes function as cancer antigens to elicit immune responses.

Nat Commun 2018 09 25;9(1):3919. Epub 2018 Sep 25.

Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 7455 Fannin Street, Unit 904, Houston, TX, 77054, USA.

In addition to genomic mutations, RNA editing is another major mechanism creating sequence variations in proteins by introducing nucleotide changes in mRNA sequences. Deregulated RNA editing contributes to different types of human diseases, including cancers. Here we report that peptides generated as a consequence of RNA editing are indeed naturally presented by human leukocyte antigen (HLA) molecules. We provide evidence that effector CD8 T cells specific for edited peptides derived from cyclin I are present in human tumours and attack tumour cells that are presenting these epitopes. We show that subpopulations of cancer patients have increased peptide levels and that levels of edited RNA correlate with peptide copy numbers. These findings demonstrate that RNA editing extends the classes of HLA presented self-antigens and that these antigens can be recognised by the immune system.
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http://dx.doi.org/10.1038/s41467-018-06405-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156571PMC
September 2018

TMEM106B drives lung cancer metastasis by inducing TFEB-dependent lysosome synthesis and secretion of cathepsins.

Nat Commun 2018 07 16;9(1):2731. Epub 2018 Jul 16.

Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.

Metastatic lung cancer is the leading cause of cancer-associated mortality worldwide, therefore necessitating novel approaches to identify specific genetic drivers for lung cancer progression and metastasis. We recently performed an in vivo gain-of-function genetic screen to identify driver genes of lung cancer metastasis. In the study reported here, we identify TMEM106B as a primary robust driver of lung cancer metastasis. Ectopic expression of TMEM106B could significantly promote the synthesis of enlarged vesicular lysosomes that are laden with elevated levels of active cathepsins. In a TFEB-dependent manner, TMEM106B could modulate the expression of lysosomal genes of the coordinated lysosomal expression and regulation (CLEAR) pathway in lung cancer cells and patient samples. We also demonstrate that TMEM106B-induced lysosomes undergo calcium-dependent exocytosis, thereby releasing active lysosomal cathepsins necessary for TMEM106B-mediated cancer cell invasion and metastasis in vivo, which could be therapeutically prevented by pharmacological inhibition of cathepsins. Further, in TCGA LUAD data sets, 19% of patients show elevated expression of TMEM106B, which predicts for poor disease-free and overall-survival.
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http://dx.doi.org/10.1038/s41467-018-05013-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048095PMC
July 2018

In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer.

Nat Commun 2018 07 16;9(1):2732. Epub 2018 Jul 16.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

Genetic aberrations driving pro-oncogenic and pro-metastatic activity remain an elusive target in the quest of precision oncology. To identify such drivers, we use an animal model of KRAS-mutant lung adenocarcinoma to perform an in vivo functional screen of 217 genetic aberrations selected from lung cancer genomics datasets. We identify 28 genes whose expression promoted tumor metastasis to the lung in mice. We employ two tools for examining the KRAS-dependence of genes identified from our screen: 1) a human lung cell model containing a regulatable mutant KRAS allele and 2) a lentiviral system permitting co-expression of DNA-barcoded cDNAs with Cre recombinase to activate a mutant KRAS allele in the lungs of mice. Mechanistic evaluation of one gene, GATAD2B, illuminates its role as a dual activity gene, promoting both pro-tumorigenic and pro-metastatic activities in KRAS-mutant lung cancer through interaction with c-MYC and hyperactivation of the c-MYC pathway.
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http://dx.doi.org/10.1038/s41467-018-04572-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048166PMC
July 2018

Cancer driver mutation prediction through Bayesian integration of multi-omic data.

PLoS One 2018 8;13(5):e0196939. Epub 2018 May 8.

Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America.

Identification of cancer driver mutations is critical for advancing cancer research and personalized medicine. Due to inter-tumor genetic heterogeneity, many driver mutations occur at low frequencies, which make it challenging to distinguish them from passenger mutations. Here, we show that a novel Bayesian hierarchical modeling approach, named rDriver can achieve enhanced prediction accuracy by identifying mutations that not only have high functional impact scores but also are associated with systemic variation in gene expression levels. In examining 3,080 tumor samples from 8 cancer types in The Cancer Genome Atlas, rDriver predicted 1,389 driver mutations. Compared with existing tools, rDriver identified more low frequency mutations associated with lineage specific functional properties, timing of occurrence and patient survival. Evaluation of rDriver predictions using engineered cell-line models resulted in a positive predictive value of 0.94 in PIK3CA genes. Our study highlights the importance of integrating multi-omic data in predicting cancer driver mutations and provides a statistically rigorous solution for cancer target discovery and development.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196939PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940219PMC
August 2018

A functional genomic screen in vivo identifies CEACAM5 as a clinically relevant driver of breast cancer metastasis.

NPJ Breast Cancer 2018 30;4. Epub 2018 Apr 30.

1Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.

Tumor cells disseminate early in tumor development making metastasis-prevention strategies difficult. Identifying proteins that promote the outgrowth of disseminated tumor cells may provide opportunities for novel therapeutic strategies. Despite multiple studies demonstrating that the mesenchymal-to-epithelial transition (MET) is critical for metastatic colonization, key regulators that initiate this transition remain unknown. We serially passaged lung metastases from a primary triple negative breast cancer xenograft to the mammary fat pads of recipient mice to enrich for gene expression changes that drive metastasis. An unbiased transcriptomic signature of potential metastatic drivers was generated, and a high throughput gain-of-function screen was performed in vivo to validate candidates. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) was identified as a metastatic driver. CEACAM5 overproduction enriched for an epithelial gene expression pattern and facilitated tumor outgrowth at metastatic sites. Tissues from patients with metastatic breast cancer confirmed elevated levels of CEACAM5 in lung metastases relative to breast tumors, and an inverse correlation between CEACAM5 and the mesenchymal marker vimentin was demonstrated. Thus, CEACAM5 facilitates tumor outgrowth at metastatic sites by promoting MET, warranting its investigation as a therapeutic target and biomarker of aggressiveness in breast cancer.
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http://dx.doi.org/10.1038/s41523-018-0062-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928229PMC
April 2018

A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer.

Cancer Cell 2018 05 26;33(5):817-828.e7. Epub 2018 Apr 26.

Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Adenosine (A) to inosine (I) RNA editing introduces many nucleotide changes in cancer transcriptomes. However, due to the complexity of post-transcriptional regulation, the contribution of RNA editing to proteomic diversity in human cancers remains unclear. Here, we performed an integrated analysis of TCGA genomic data and CPTAC proteomic data. Despite limited site diversity, we demonstrate that A-to-I RNA editing contributes to proteomic diversity in breast cancer through changes in amino acid sequences. We validate the presence of editing events at both RNA and protein levels. The edited COPA protein increases proliferation, migration, and invasion of cancer cells in vitro. Our study suggests an important contribution of A-to-I RNA editing to protein diversity in cancer and highlights its translational potential.
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http://dx.doi.org/10.1016/j.ccell.2018.03.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5953833PMC
May 2018

Combinatorial inhibition of PTPN12-regulated receptors leads to a broadly effective therapeutic strategy in triple-negative breast cancer.

Nat Med 2018 05 26;24(4):505-511. Epub 2018 Mar 26.

Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA.

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer diagnosed in more than 200,000 women each year and is recalcitrant to targeted therapies. Although TNBCs harbor multiple hyperactive receptor tyrosine kinases (RTKs), RTK inhibitors have been largely ineffective in TNBC patients thus far. We developed a broadly effective therapeutic strategy for TNBC that is based on combined inhibition of receptors that share the negative regulator PTPN12. Previously, we and others identified the tyrosine phosphatase PTPN12 as a tumor suppressor that is frequently inactivated in TNBC. PTPN12 restrains several RTKs, suggesting that PTPN12 deficiency leads to aberrant activation of multiple RTKs and a co-dependency on these receptors. This in turn leads to the therapeutic hypothesis that PTPN12-deficient TNBCs may be responsive to combined RTK inhibition. However, the repertoire of RTKs that are restrained by PTPN12 in human cells has not been systematically explored. By methodically identifying the suite of RTK substrates (MET, PDGFRβ, EGFR, and others) inhibited by PTPN12, we rationalized a combination RTK-inhibitor therapy that induced potent tumor regression across heterogeneous models of TNBC. Orthogonal approaches revealed that PTPN12 was recruited to and inhibited these receptors after ligand stimulation, thereby serving as a feedback mechanism to limit receptor signaling. Cancer-associated mutation of PTPN12 or reduced PTPN12 protein levels diminished this feedback mechanism, leading to aberrant activity of these receptors. Restoring PTPN12 protein levels restrained signaling from RTKs, including PDGFRβ and MET, and impaired TNBC survival. In contrast with single agents, combined inhibitors targeting the PDGFRβ and MET receptors induced the apoptosis in TNBC cells in vitro and in vivo. This therapeutic strategy resulted in tumor regressions in chemo-refractory patient-derived TNBC models. Notably, response correlated with PTPN12 deficiency, suggesting that impaired receptor feedback may establish a combined addiction to these proto-oncogenic receptors. Taken together, our data provide a rationale for combining RTK inhibitors in TNBC and other malignancies that lack receptor-activating mutations.
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http://dx.doi.org/10.1038/nm.4507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6675908PMC
May 2018

Systematic Functional Annotation of Somatic Mutations in Cancer.

Cancer Cell 2018 03;33(3):450-462.e10

Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63108, USA.

The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate >1,000 genomic aberrations, including gene amplifications, point mutations, indels, and gene fusions, potentially doubling the number of driver mutations characterized in clinically actionable genes. Further, the platform is sufficiently sensitive to identify weak drivers. Our data are accessible through a user-friendly, public data portal. Our study will facilitate biomarker discovery, prediction algorithm improvement, and drug development.
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http://dx.doi.org/10.1016/j.ccell.2018.01.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5926201PMC
March 2018

The epithelial-to-mesenchymal transition activator ZEB1 initiates a prometastatic competing endogenous RNA network.

J Clin Invest 2018 04 26;128(4):1267-1282. Epub 2018 Feb 26.

Department of Thoracic/Head and Neck Medical Oncology and.

Epithelial tumor cells undergo epithelial-to-mesenchymal transition (EMT) to gain metastatic activity. Competing endogenous RNAs (ceRNAs) have binding sites for a common set of microRNAs (miRs) and regulate each other's expression by sponging miRs. Here, we address whether ceRNAs govern metastasis driven by the EMT-activating transcription factor ZEB1. High miR-181b levels were correlated with an improved prognosis in human lung adenocarcinomas, and metastatic tumor cell lines derived from a murine lung adenocarcinoma model in which metastasis is ZEB1-driven were enriched in miR-181b targets. ZEB1 relieved a strong basal repression of α1 integrin (ITGA1) mRNA, which in turn upregulated adenylyl cyclase 9 mRNA (ADCY9) by sponging miR181b. Ectopic expression of the ITGA1 3'-untranslated region reversed miR-181b-mediated metastasis suppression and increased the levels of adenylyl cyclase 9 protein (AC9), which promoted tumor cell migration and metastasis. In human lung adenocarcinomas, ITGA1 and ADCY9 levels were positively correlated, and an AC9-activated transcriptomic signature had poor-prognostic value. Thus, ZEB1 initiates a miR-181b-regulated ceRNA network to drive metastasis.
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http://dx.doi.org/10.1172/JCI97225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5873879PMC
April 2018

Daam2 driven degradation of VHL promotes gliomagenesis.

Elife 2017 10 20;6. Epub 2017 Oct 20.

Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, United States.

Von Hippel-Landau (VHL) protein is a potent tumor suppressor regulating numerous pathways that drive cancer, but mutations in VHL are restricted to limited subsets of malignancies. Here we identified a novel mechanism for VHL suppression in tumors that do not have inactivating mutations. Using developmental processes to uncover new pathways contributing to tumorigenesis, we found that Daam2 promotes glioma formation. Protein expression screening identified an inverse correlation between Daam2 and VHL expression across a host of cancers, including glioma. These in silico insights guided corroborating functional studies, which revealed that Daam2 promotes tumorigenesis by suppressing VHL expression. Furthermore, biochemical analyses demonstrate that Daam2 associates with VHL and facilitates its ubiquitination and degradation. Together, these studies are the first to define an upstream mechanism regulating VHL suppression in cancer and describe the role of Daam2 in tumorigenesis.
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http://dx.doi.org/10.7554/eLife.31926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5650470PMC
October 2017

Differential UBE2C and HOXA1 expression in melanocytic nevi and melanoma.

J Cutan Pathol 2017 Oct 21;44(10):843-850. Epub 2017 Jul 21.

Pathology Service and Dermatopathology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.

Background: Recent molecular advances suggest that Spitz nevi and other spitzoid neoplasms are biologically distinct from melanoma and conventional nevi. The ubiquitin ligase UBE2C and the homeobox transcription factor HOXA1 are candidate oncogenes in melanoma.

Methods: Using RNA expression analysis and immunohistochemistry, we evaluated these biomarkers in Spitz nevi (n = 20), melanoma (n = 20), and by immunohistochemistry in conventional nevi (n = 20).

Results: RNA analysis with branched DNA multiplex assay identified upregulation of UBE2C in melanomas vs Spitz nevi (P = .003), whereas HOXA1 was downregulated in melanoma (P < .0001). Immunohistochemical analysis confirmed increased nuclear expression of UBE2C in melanoma (mean = 18% of cells; range 3%-44%) when compared with Spitz nevi (mean = 9%; range 2%-28%; P = .001) and conventional nevi (mean = 1.5%; range 0-9%; P < .0001). Strong UBE2C staining was identified in cells undergoing mitosis. UBE2C RNA and protein detection correlated with mitotic rate (P < .0001). On the other hand, HOXA1 nuclear staining was low in melanoma (mean = 69%; range 5%-100%) when compared with Spitz nevi (mean = 94%; range 66%-100%; P = .0024) and conventional nevi (mean = 94%; range 83%-99%; P = .009).

Conclusions: UBE2C and HOXA1 RNA and protein are differentially expressed in conventional and Spitz nevi and melanoma.
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http://dx.doi.org/10.1111/cup.12997DOI Listing
October 2017

Rational combination therapy with PARP and MEK inhibitors capitalizes on therapeutic liabilities in mutant cancers.

Sci Transl Med 2017 05;9(392)

Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Mutant has remained recalcitrant to targeted therapy efforts. We demonstrate that combined treatment with poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors and mitogen-activated protein kinase (MAPK) kinase (MEK) inhibitors evokes unanticipated, synergistic cytotoxic effects in vitro and in vivo in multiple mutant tumor models across tumor lineages where mutations are prevalent. The effects of PARP and MEK inhibitor combinations are independent of and mutation status, suggesting that the synergistic activity is likely to be generalizable. Synergistic activity of PARP and MEK inhibitor combinations in mutant tumors is associated with (i) induction of BIM-mediated apoptosis, (ii) decrease in expression of components of the homologous recombination DNA repair pathway, (iii) decrease in homologous recombination DNA damage repair capacity, (iv) decrease in DNA damage checkpoint activity, (v) increase in PARP inhibitor-induced DNA damage, (vi) decrease in vascularity that could increase PARP inhibitor efficacy by inducing hypoxia, and (vii) elevated PARP1 protein, which increases trapping activity of PARP inhibitors. Mechanistically, enforced expression of FOXO3a, which is a target of the RAS/MAPK pathway, was sufficient to recapitulate the functional consequences of MEK inhibitors including synergy with PARP inhibitors. Thus, the ability of mutant to suppress FOXO3a and its reversal by MEK inhibitors accounts, at least in part, for the synergy of PARP and MEK inhibitors in mutant tumors. The rational combination of PARP and MEK inhibitors warrants clinical investigation in patients with mutant tumors where there are few effective therapeutic options.
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http://dx.doi.org/10.1126/scitranslmed.aal5148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5919217PMC
May 2017

A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations.

Cancer Cell 2017 06 18;31(6):820-832.e3. Epub 2017 May 18.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

Molecular alterations involving the PI3K/AKT/mTOR pathway (including mutation, copy number, protein, or RNA) were examined across 11,219 human cancers representing 32 major types. Within specific mutated genes, frequency, mutation hotspot residues, in silico predictions, and functional assays were all informative in distinguishing the subset of genetic variants more likely to have functional relevance. Multiple oncogenic pathways including PI3K/AKT/mTOR converged on similar sets of downstream transcriptional targets. In addition to mutation, structural variations and partial copy losses involving PTEN and STK11 showed evidence for having functional relevance. A substantial fraction of cancers showed high mTOR pathway activity without an associated canonical genetic or genomic alteration, including cancers harboring IDH1 or VHL mutations, suggesting multiple mechanisms for pathway activation.
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http://dx.doi.org/10.1016/j.ccell.2017.04.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502825PMC
June 2017

Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer.

Cancer Res 2017 07 16;77(13):3502-3512. Epub 2017 May 16.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

Oncogenic gene fusions drive many human cancers, but tools to more quickly unravel their functional contributions are needed. Here we describe methodology permitting fusion gene construction for functional evaluation. Using this strategy, we engineered the known fusion oncogenes, , and as well as 20 previously uncharacterized fusion genes identified in The Cancer Genome Atlas datasets. In addition to confirming oncogenic activity of the known fusion oncogenes engineered by our construction strategy, we validated five novel fusion genes involving , and kinases that exhibited potent transforming activity and conferred sensitivity to FDA-approved kinase inhibitors. Our fusion construction strategy also enabled domain-function studies of fusion genes. Our results confirmed other reports that the transforming activity of fusions results from truncation-mediated loss of inhibitory domains within the N-terminus of the BRAF protein. mutations residing within this inhibitory region may provide a means for BRAF activation in cancer, therefore we leveraged the modular design of our fusion gene construction methodology to screen N-terminal domain mutations discovered in tumors that are wild-type at the mutation hotspot, V600. We identified an oncogenic mutation, F247L, whose expression robustly activated the MAPK pathway and sensitized cells to BRAF and MEK inhibitors. When applied broadly, these tools will facilitate rapid fusion gene construction for subsequent functional characterization and translation into personalized treatment strategies. .
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http://dx.doi.org/10.1158/0008-5472.CAN-16-2745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568774PMC
July 2017

Ba/F3 transformation assays.

Oncotarget 2017 May;8(22):35488-35489

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.18632/oncotarget.17828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482591PMC
May 2017

HER2 Reactivation through Acquisition of the HER2 L755S Mutation as a Mechanism of Acquired Resistance to HER2-targeted Therapy in HER2 Breast Cancer.

Clin Cancer Res 2017 Sep 9;23(17):5123-5134. Epub 2017 May 9.

Department of Biomedical Engineering and Oregon Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon.

Resistance to anti-HER2 therapies in HER2 breast cancer can occur through activation of alternative survival pathways or reactivation of the HER signaling network. Here we employed BT474 parental and treatment-resistant cell line models to investigate a mechanism by which HER2 breast cancer can reactivate the HER network under potent HER2-targeted therapies. Resistant derivatives to lapatinib (L), trastuzumab (T), or the combination (LR/TR/LTR) were developed independently from two independent estrogen receptor ER/HER2 BT474 cell lines (AZ/ATCC). Two derivatives resistant to the lapatinib-containing regimens (BT474/AZ-LR and BT474/ATCC-LTR lines) that showed HER2 reactivation at the time of resistance were subjected to massive parallel sequencing and compared with parental lines. Ectopic expression and mutant-specific siRNA interference were applied to analyze the mutation functionally. and experiments were performed to test alternative therapies for mutant HER2 inhibition. Genomic analyses revealed that the L755S mutation was the only common somatic mutation gained in the BT474/AZ-LR and BT474/ATCC-LTR lines. Ectopic expression of L755S induced acquired lapatinib resistance in the BT474/AZ, SK-BR-3, and AU565 parental cell lines. L755S-specific siRNA knockdown reversed the resistance in BT474/AZ-LR and BT474/ATCC-LTR lines. The HER1/2-irreversible inhibitors afatinib and neratinib substantially inhibited both resistant cell growth and the HER2 and downstream AKT/MAPK signaling driven by L755S and HER2 reactivation through acquisition of the L755S mutation was identified as a mechanism of acquired resistance to lapatinib-containing HER2-targeted therapy in preclinical HER2-amplified breast cancer models, which can be overcome by irreversible HER1/2 inhibitors. .
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http://dx.doi.org/10.1158/1078-0432.CCR-16-2191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5762201PMC
September 2017

Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers.

Genome Res 2017 07 14;27(7):1112-1125. Epub 2017 Apr 14.

Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.

RNA editing, a widespread post-transcriptional mechanism, has emerged as a new player in cancer biology. Recent studies have reported key roles for individual miRNA editing events, but a comprehensive picture of miRNA editing in human cancers remains largely unexplored. Here, we systematically characterized the miRNA editing profiles of 8595 samples across 20 cancer types from miRNA sequencing data of The Cancer Genome Atlas and identified 19 adenosine-to-inosine (A-to-I) RNA editing hotspots. We independently validated 15 of them by perturbation experiments in several cancer cell lines. These miRNA editing events show extensive correlations with key clinical variables (e.g., tumor subtype, disease stage, and patient survival time) and other molecular drivers. Focusing on the RNA editing hotspot in miR-200b, a key tumor metastasis suppressor, we found that the miR-200b editing level correlates with patient prognosis opposite to the pattern observed for the wild-type miR-200b expression. We further experimentally showed that, in contrast to wild-type miRNA, the edited miR-200b can promote cell invasion and migration through its impaired ability to inhibit and acquired concomitant ability to repress new targets, including , a well-characterized metastasis suppressor. Our study highlights the importance of miRNA editing in gene regulation and suggests its potential as a biomarker for cancer prognosis and therapy.
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http://dx.doi.org/10.1101/gr.219741.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495064PMC
July 2017

Functionally Assessing Candidate Drivers Advances Precision Cancer Medicine.

Cancer Cell 2016 08;30(2):187-189

Department of Pathology, Stony Brook University, One Nichols Drive, Stony Brook, NY 11794, USA. Electronic address:

The complexity of genomic alterations in cancer has made it difficult to identify oncogenic drivers for the development of targeted therapies. The study by Berger et al. in this issue of Cancer Cell demonstrates that high-throughput functional profiling can uncover impactful mutations and oncogenic driver alleles.
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http://dx.doi.org/10.1016/j.ccell.2016.07.011DOI Listing
August 2016

Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing.

Am J Hum Genet 2016 05;98(5):843-856

Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Ludwig Center, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

Although exome sequencing data are generated primarily to detect single-nucleotide variants and indels, they can also be used to identify a subset of genomic rearrangements whose breakpoints are located in or near exons. Using >4,600 tumor and normal pairs across 15 cancer types, we identified over 9,000 high confidence somatic rearrangements, including a large number of gene fusions. We find that the 5' fusion partners of functional fusions are often housekeeping genes, whereas the 3' fusion partners are enriched in tyrosine kinases. We establish the oncogenic potential of ROR1-DNAJC6 and CEP85L-ROS1 fusions by showing that they can promote cell proliferation in vitro and tumor formation in vivo. Furthermore, we found that ∼4% of the samples have massively rearranged chromosomes, many of which are associated with upregulation of oncogenes such as ERBB2 and TERT. Although the sensitivity of detecting structural alterations from exomes is considerably lower than that from whole genomes, this approach will be fruitful for the multitude of exomes that have been and will be generated, both in cancer and in other diseases.
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http://dx.doi.org/10.1016/j.ajhg.2016.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863662PMC
May 2016

Functional annotation of rare gene aberration drivers of pancreatic cancer.

Nat Commun 2016 Jan 25;7:10500. Epub 2016 Jan 25.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

As we enter the era of precision medicine, characterization of cancer genomes will directly influence therapeutic decisions in the clinic. Here we describe a platform enabling functionalization of rare gene mutations through their high-throughput construction, molecular barcoding and delivery to cancer models for in vivo tumour driver screens. We apply these technologies to identify oncogenic drivers of pancreatic ductal adenocarcinoma (PDAC). This approach reveals oncogenic activity for rare gene aberrations in genes including NAD Kinase (NADK), which regulates NADP(H) homeostasis and cellular redox state. We further validate mutant NADK, whose expression provides gain-of-function enzymatic activity leading to a reduction in cellular reactive oxygen species and tumorigenesis, and show that depletion of wild-type NADK in PDAC cell lines attenuates cancer cell growth in vitro and in vivo. These data indicate that annotating rare aberrations can reveal important cancer signalling pathways representing additional therapeutic targets.
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http://dx.doi.org/10.1038/ncomms10500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737758PMC
January 2016
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