Publications by authors named "Jeanne Kowalski"

99 Publications

Acetylation of KLF5 maintains EMT and tumorigenicity to cause chemoresistant bone metastasis in prostate cancer.

Nat Commun 2021 03 17;12(1):1714. Epub 2021 Mar 17.

Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA.

Advanced prostate cancer (PCa) often develops bone metastasis, for which therapies are very limited and the underlying mechanisms are poorly understood. We report that bone-borne TGF-β induces the acetylation of transcription factor KLF5 in PCa bone metastases, and acetylated KLF5 (Ac-KLF5) causes osteoclastogenesis and bone metastatic lesions by activating CXCR4, which leads to IL-11 secretion, and stimulating SHH/IL-6 paracrine signaling. While essential for maintaining the mesenchymal phenotype and tumorigenicity, Ac-KLF5 also causes resistance to docetaxel in tumors and bone metastases, which is overcome by targeting CXCR4 with FDA-approved plerixafor. Establishing a mechanism for bone metastasis and chemoresistance in PCa, these findings provide a rationale for treating chemoresistant bone metastasis of PCa with inhibitors of Ac-KLF5/CXCR4 signaling.
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http://dx.doi.org/10.1038/s41467-021-21976-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7969754PMC
March 2021

Melanoma Cell Intrinsic GABA Receptor Enhancement Potentiates Radiation and Immune Checkpoint Inhibitor Response by Promoting Direct and T Cell-Mediated Antitumor Activity.

Int J Radiat Oncol Biol Phys 2021 Mar 24;109(4):1040-1053. Epub 2020 Oct 24.

Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio. Electronic address:

Purpose: Most patients with metastatic melanoma show variable responses to radiation therapy and do not benefit from immune checkpoint inhibitors. Improved strategies for combination therapy that leverage potential benefits from radiation therapy and immune checkpoint inhibitors are critical.

Methods And Materials: We analyzed metastatic melanoma tumors in the TCGA cohort for expression of genes coding for subunits of type A γ-aminobutyric acid (GABA) receptor (GABAR), a chloride ion channel and major inhibitory neurotransmitter receptor. Electrophysiology was used to determine whether melanoma cells possess intrinsic GABAR activity. Melanoma cell viability studies were conducted to test whether enhancing GABAR mediated chloride transport using benzodiazepine-impaired viability. A syngeneic melanoma mouse model was used to assay the effect of benzodiazepine on tumor volume and its ability to potentiate radiation therapy or immunotherapy. Treated tumors were analyzed for changes in gene expression by RNA sequencing and presence of tumor-infiltrating lymphocytes by flow cytometry.

Results: Genes coding for subunits of GABARs express functional GABARs in melanoma cells. By enhancing GABAR-mediated anion transport, benzodiazepines depolarize melanoma cells and impair their viability. In vivo, benzodiazepine alone reduces tumor growth and potentiates radiation therapy and α-PD-L1 antitumor activity. The combination of benzodiazepine, radiation therapy, and α-PD-L1 results in near complete regression of treated tumors and a potent abscopal effect, mediated by increased infiltration of polyfunctional CD8 T cells. Treated tumors show expression of cytokine-cytokine receptor interactions and overrepresentation of p53 signaling.

Conclusions: This study identifies an antitumor strategy combining radiation and/or an immune checkpoint inhibitor with modulation of GABARs in melanoma using benzodiazepine.
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http://dx.doi.org/10.1016/j.ijrobp.2020.10.025DOI Listing
March 2021

Evaluating patient-specific neoadjuvant regimens for breast cancer via a mathematical model constrained by quantitative magnetic resonance imaging data.

Neoplasia 2020 12 14;22(12):820-830. Epub 2020 Nov 14.

Oden Institute for Computational Engineering and Sciences, Austin, TX, USA; Livestrong Cancer Institutes, Austin, TX, USA; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA; Department of Diagnostic Medicine, The University of Texas at Austin, Austin, TX, USA; Department of Oncology, The University of Texas at Austin, Austin, TX, USA; Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA. Electronic address:

The ability to accurately predict response and then rigorously optimize a therapeutic regimen on a patient-specific basis, would transform oncology. Toward this end, we have developed an experimental-mathematical framework that integrates quantitative magnetic resonance imaging (MRI) data into a biophysical model to predict patient-specific treatment response of locally advanced breast cancer to neoadjuvant therapy. Diffusion-weighted and dynamic contrast-enhanced MRI data is collected prior to therapy, after 1 cycle of therapy, and at the completion of the first therapeutic regimen. The model is initialized and calibrated with the first 2 patient-specific MRI data sets to predict response at the third, which is then compared to patient outcomes (N = 18). The model's predictions for total cellularity, total volume, and the longest axis at the completion of the regimen are significant within expected measurement precision (P< 0.05) and strongly correlated with measured response (P < 0.01). Further, we use the model to investigate, in silico, a range of (practical) alternative treatment plans to achieve the greatest possible tumor control for each individual in a subgroup of patients (N = 13). The model identifies alternative dosing strategies predicted to achieve greater tumor control compared to the standard of care for 12 of 13 patients (P < 0.01). In summary, a predictive, mechanism-based mathematical model has demonstrated the ability to identify alternative treatment regimens that are forecasted to outperform the therapeutic regimens the patients clinically. This has important implications for clinical trial design with the opportunity to alter oncology care in the future.
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http://dx.doi.org/10.1016/j.neo.2020.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7677708PMC
December 2020

Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC).

PLoS One 2020 28;15(9):e0238497. Epub 2020 Sep 28.

Winship Cancer Institute, Emory University, Atlanta, GA, United States of America.

Human papilloma virus (HPV) causes a subset of head and neck squamous cell carcinomas (HNSCC) of the oropharynx. We combined targeted DNA- and genome-wide RNA-sequencing to identify genetic variants and gene expression signatures respectively from patients with HNSCC including oropharyngeal squamous cell carcinomas (OPSCC). DNA and RNA were purified from 35- formalin fixed and paraffin embedded (FFPE) HNSCC tumor samples. Immuno-histochemical evaluation of tumors was performed to determine the expression levels of p16INK4A and classified tumor samples either p16+ or p16-. Using ClearSeq Comprehensive Cancer panel, we examined the distribution of somatic mutations. Somatic single-nucleotide variants (SNV) were called using GATK-Mutect2 ("tumor-only" mode) approach. Using RNA-seq, we identified a catalog of 1,044 and 8 genes as significantly expressed between p16+ and p16-, respectively at FDR 0.05 (5%) and 0.1 (10%). The clinicopathological characteristics of the patients including anatomical site, smoking and survival were analyzed when comparing p16+ and p16- tumors. The majority of tumors (65%) were p16+. Population sequence variant databases, including gnomAD, ExAC, COSMIC and dbSNP, were used to identify the mutational landscape of somatic sequence variants within sequenced genes. Hierarchical clustering of The Cancer Genome Atlas (TCGA) samples based on HPV-status was observed using differentially expressed genes. Using RNA-seq in parallel with targeted DNA-seq, we identified mutational and gene expression signatures characteristic of p16+ and p16- HNSCC. Our gene signatures are consistent with previously published data including TCGA and support the need to further explore the biologic relevance of these alterations in HNSCC.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238497PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7521680PMC
October 2020

Epigenetically heterogeneous tumor cells direct collective invasion through filopodia-driven fibronectin micropatterning.

Sci Adv 2020 Jul 24;6(30):eaaz6197. Epub 2020 Jul 24.

Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA.

Tumor heterogeneity drives disease progression, treatment resistance, and patient relapse, yet remains largely underexplored in invasion and metastasis. Here, we investigated heterogeneity within collective cancer invasion by integrating DNA methylation and gene expression analysis in rare purified lung cancer leader and follower cells. Our results showed global DNA methylation rewiring in leader cells and revealed the filopodial motor as a critical gene at the intersection of epigenetic heterogeneity and three-dimensional (3D) collective invasion. We further identified JAG1 signaling as a previously unknown upstream activator of expression in leader cells. Using live-cell imaging, we found that MYO10 drives filopodial persistence necessary for micropatterning extracellular fibronectin into linear tracks at the edge of 3D collective invasion exclusively in leaders. Our data fit a model where epigenetic heterogeneity and JAG1 signaling jointly drive collective cancer invasion through MYO10 up-regulation in epigenetically permissive leader cells, which induces filopodia dynamics necessary for linearized fibronectin micropatterning.
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http://dx.doi.org/10.1126/sciadv.aaz6197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7439406PMC
July 2020

Prognostic significance of an invasive leader cell-derived mutation cluster on chromosome 16q.

Cancer 2020 07 21;126(13):3140-3150. Epub 2020 Apr 21.

Winship Cancer Institute, Emory University, Atlanta, Georgia.

Background: Intratumoral heterogeneity is defined by subpopulations with varying genotypes and phenotypes. Specialized, highly invasive leader cells and less invasive follower cells are phenotypically distinct subpopulations that cooperate during collective cancer invasion. Because leader cells are a rare subpopulation that would be missed by bulk sequencing, a novel image-guided genomics platform was used to precisely select this subpopulation. This study identified a novel leader cell mutation signature and tested its ability to predict prognosis in non-small cell lung cancer (NSCLC) patient cohorts.

Methods: Spatiotemporal genomic and cellular analysis was used to isolate and perform RNA sequencing on leader and follower populations from the H1299 NSCLC cell line, and it revealed a leader-specific mutation cluster on chromosome 16q. Genomic data from patients with lung squamous cell carcinoma (LUSC; n = 475) and lung adenocarcinoma (LUAD; n = 501) from The Cancer Genome Atlas were stratified by 16q mutation cluster (16qMC) status (16qMC+ vs 16qMC-) and compared for overall survival (OS), progression-free survival (PFS), and gene set enrichment analysis (GSEA).

Results: Poorer OS, poorer PFS, or both were found across all stages and among early-stage patients with 16qMC+ tumors within the LUSC and LUAD cohorts. GSEA revealed 16qMC+ tumors to be enriched for the expression of metastasis- and survival-associated gene sets.

Conclusions: This represents the first leader cell mutation signature identified in patients and has the potential to better stratify high-risk NSCLC and ultimately improve patient outcomes.
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http://dx.doi.org/10.1002/cncr.32903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275903PMC
July 2020

Impact of Sequencing Radiation Therapy and Immune Checkpoint Inhibitors in the Treatment of Melanoma Brain Metastases.

Int J Radiat Oncol Biol Phys 2020 09 11;108(1):157-163. Epub 2020 Feb 11.

Department of Neurology, University of Cincinnati College of Medicine, Cincinnati, Ohio; University of Cincinnati Gardner Neuroscience Institute, Cincinnati, Ohio. Electronic address:

Purpose: Melanoma brain metastases (MBM) occur in ∼50% of melanoma patients. Although both radiation therapy (RT) and immune checkpoint inhibitor (ICI) are used alone or in combination for MBM treatment, the role of this combination and how these treatments could best be sequenced remains unclear.

Methods And Materials: We conducted a retrospective analysis of patients with resected MBM who underwent treatment with RT, ICI, or a combination of RT and ICI. Among the latter, we specifically investigated the differential gene expression via RNA-sequencing between patients who received RT first then ICI (RT → ICI) versus ICI first then RT (ICI → RT). We used a glycoprotein-transduced syngeneic melanoma mouse model for validation experiments.

Results: We found that for patients with resected MBM, a combination of RT and ICI confers superior survival compared with RT alone. Specifically, we found that RT → ICI was superior compared with ICI → RT. Transcriptome analysis of resected MBM revealed that the RT → ICI cohort demonstrated deregulation of genes involved in apoptotic signaling and key modulators of inflammation that are most implicated in nuclear factor kappa-light-chain-enhancer of activated B cells signaling. In a preclinical model, we showed that RT followed by anti-programmed death-ligand 1 therapy was superior to the reverse sequence of therapy, supporting the observations we made in patients with MBM.

Conclusions: Our study provides initial insights into the optimal sequence of RT and ICI in the treatment of MBM after surgical resection. Prospective studies examining the best sequence of RT and ICI are necessary, and our study contributes to the rationale to pursue these.
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http://dx.doi.org/10.1016/j.ijrobp.2020.01.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7839060PMC
September 2020

ETV2/ER71 regulates the generation of FLK1 cells from mouse embryonic stem cells through miR-126-MAPK signaling.

Stem Cell Res Ther 2019 11 19;10(1):328. Epub 2019 Nov 19.

Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Dr. Atlanta, Atlanta, GA, 30322, USA.

Previous studies including ours have demonstrated a critical function of the transcription factor ETV2 (ets variant 2; also known as ER71) in determining the fate of cardiovascular lineage development. However, the underlying mechanisms of ETV2 function remain largely unknown. In this study, we demonstrated the novel function of the miR (micro RNA)-126-MAPK (mitogen-activated protein kinase) pathway in ETV2-mediated FLK1 (fetal liver kinase 1; also known as VEGFR2) cell generation from the mouse embryonic stem cells (mESCs). By performing a series of experiments including miRNA sequencing and ChIP (chromatin immunoprecipitation)-PCR, we found that miR-126 is directly induced by ETV2. Further, we identified that miR-126 can positively regulate the generation of FLK1 cells by activating the MAPK pathway through targeting SPRED1 (sprouty-related EVH1 domain containing 1). Further, we showed evidence that JUN/FOS activate the enhancer region of FLK1 through AP1 (activator protein 1) binding sequences. Our findings provide insight into the novel molecular mechanisms of ETV2 function in regulating cardiovascular lineage development from mESCs.
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http://dx.doi.org/10.1186/s13287-019-1466-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862833PMC
November 2019

Genetic heterogeneity within collective invasion packs drives leader and follower cell phenotypes.

J Cell Sci 2019 10 9;132(19). Epub 2019 Oct 9.

Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA

Collective invasion, the coordinated movement of cohesive packs of cells, has become recognized as a major mode of metastasis for solid tumors. These packs are phenotypically heterogeneous and include specialized cells that lead the invasive pack and others that follow behind. To better understand how these unique cell types cooperate to facilitate collective invasion, we analyzed transcriptomic sequence variation between leader and follower populations isolated from the H1299 non-small cell lung cancer cell line using an image-guided selection technique. We now identify 14 expressed mutations that are selectively enriched in leader or follower cells, suggesting a novel link between genomic and phenotypic heterogeneity within a collectively invading tumor cell population. Functional characterization of two phenotype-specific candidate mutations showed that ARP3 enhances collective invasion by promoting the leader cell phenotype and that wild-type KDM5B suppresses chain-like cooperative behavior. These results demonstrate an important role for distinct genetic variants in establishing leader and follower phenotypes and highlight the necessity of maintaining a capacity for phenotypic plasticity during collective cancer invasion.
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http://dx.doi.org/10.1242/jcs.231514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803364PMC
October 2019

Carrying out streamlined routine data analyses with reports for observational studies: introduction to a series of generic SAS macros.

F1000Res 2018 19;7:1955. Epub 2018 Dec 19.

Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30322, USA.

For a typical medical research project based on observational data, sequential routine analyses are often essential to comprehend the data on hand and to draw valid conclusions.  However, generating reports in SAS for routine analyses can be a time-consuming and tedious process, especially when dealing with large databases with a massive number of variables in an iterative and collaborative research environment. In this work, we present a general workflow of research based on an observational database and a series of SAS macros that fits this framework, which covers a streamlined data analyses and produces journal-quality summary tables. The system is generic enough to fit a variety of research projects and enables researchers to build a highly organized and concise coding for quick updates as research evolves. The result reports promote communication in collaborations and will escort the research with ease and efficiency.
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http://dx.doi.org/10.12688/f1000research.16866.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567291PMC
October 2019

Host Genome Variation is Associated with Neurocognitive Outcome in Survivors of Pediatric Medulloblastoma.

Transl Oncol 2019 Jul 9;12(7):908-916. Epub 2019 May 9.

Department of Pediatrics, Emory University School of Medicine, Atlanta, GA; Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA.

Host genome analysis is a promising source of predictive information for long-term morbidity in cancer survivors. However, studies on genetic predictors of long-term outcome, particularly neurocognitive function following chemoradiation in pediatric oncology, are limited. Here, we evaluated variation in host genome of long-term survivors of medulloblastoma and its association with neurocognitive outcome. Whole-genome sequencing was conducted on peripheral blood of long-term survivors of pediatric medulloblastoma who also completed neuropsychological testing. Cognitively impaired and less impaired survivors did not differ in exposure to chemoradiation therapy or age at treatment. Unsupervised consensus clustering yielded two distinct variant clusters that were significantly associated with neurocognitive outcome. Interestingly, 34 of the 36 significant variants were found in noncoding DNA regions with unknown regulatory function. A separate unsupervised cluster analysis of variants within DNA repair genes identified discrete variant groups that were not associated with neurocognitive outcome, suggesting that variations in genes corresponding to a single functional group may be insufficient to predict long-term outcome alone. These findings are supportive of the presence of a genetic diathesis for treatment-related neurocognitive morbidity in medulloblastoma that may be driven by variation in noncoding regulatory elements.
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http://dx.doi.org/10.1016/j.tranon.2019.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6515414PMC
July 2019

Gliosarcoma: distinct molecular pathways and genomic alterations identified by DNA copy number/SNP microarray analysis.

J Neurooncol 2019 Jul 9;143(3):381-392. Epub 2019 May 9.

Departments Neurology, Hematology & Medical Oncology, Winship Cancer Institute, Emory University, 1365 Clifton Rd. NE, Atlanta, GA, 30322, USA.

Purpose: Gliosarcoma is a histologic variant of glioblastoma (GBM), and like GBM carries a poor prognosis. Median survival is less than one (1) year with less than 5% of patients alive after 5 years. Although there is no cure, standard treatment includes surgery, radiation and chemotherapy. While very similar to GBM, gliosarcoma exhibits several distinct differences, morphologically and molecularly. Therefore, we report a comprehensive analysis of DNA copy number changes in gliosarcoma using a cytogenomic DNA copy number (CN) microarray (OncoScan).

Methods: Cytogenomic DNA copy number microarray (OncoScan) was performed on 18 cases of gliosarcoma. MetaCore™ enrichment was applied to the array results to detect associated molecular pathways.

Results: The most frequent alteration was copy number loss, comprising 57% of total copy number changes. The number of losses far exceeded the number of amplifications (***, < 0.001) and loss of heterozygosity events (***, < 0.001). Amplifications were infrequent (4.6%), particularly for EGFR. Chromosomes 9 and 10 had the highest number of losses; a large portion of which correlated to CDKN2A/B loss. Copy number gains were the second most common alteration (26.2%), with the majority occurring on chromosome 7. MetaCore™ enrichment detected notable pathways for copy number gains including: HOXA, Rho family of GTPases, and EGFR; copy number loss including: WNT, NF-kß, and CDKN2A; and copy number loss of heterozygosity including: WNT and p53.

Conclusions: The pathways and copy number alterations detected in this study may represent key drivers in gliosarcoma oncogenesis and may provide a starting point toward targeted oncologic analysis with therapeutic potential.
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http://dx.doi.org/10.1007/s11060-019-03184-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591191PMC
July 2019

NOJAH: NOt Just Another Heatmap for genome-wide cluster analysis.

PLoS One 2019 28;14(3):e0204542. Epub 2019 Mar 28.

Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America.

Since their inception, several tools have been developed for cluster analysis and heatmap construction. The application of such tools to the number and types of genome-wide data available from next generation sequencing (NGS) technologies requires the adaptation of statistical concepts, such as in defining a most variable gene set, and more intricate cluster analyses method to address multiple omic data types. Additionally, the growing number of publicly available datasets has created the desire to estimate the statistical significance of a gene signature derived from one dataset to similarly group samples based on another dataset. The currently available number of tools and their combined use for generating heatmaps, along with the several adaptations of statistical concepts for addressing the higher dimensionality of genome-wide NGS-derived data, has created a further challenge in the ability to replicate heatmap results. We introduce NOJAH (NOt Just Another Heatmap), an interactive tool that defines and implements a workflow for genome-wide cluster analysis and heatmap construction by creating and combining several tools into a single user interface. NOJAH includes several newly developed scripts for techniques that though frequently applied are not sufficiently documented to allow for replicability of results. These techniques include: defining a most variable gene set (a.k.a., 'core genes'), estimating the statistical significance of a gene signature to separate samples into clusters, and performing a result merging integrated cluster analysis. With only a user uploaded dataset, NOJAH provides as output, among other things, the minimum documentation required for replicating heatmap results. Additionally, NOJAH contains five different existing R packages that are connected in the interface by their functionality as part of a defined workflow for genome-wide cluster analysis. The NOJAH application tool is available at http://bbisr.shinyapps.winship.emory.edu/NOJAH/ http://shinygispa.winship.emory.edu/shinyGISPA/ with corresponding source code available at https://github.com/bbisr-shinyapps/NOJAH/.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204542PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438523PMC
November 2019

Modulating native GABA receptors in medulloblastoma with positive allosteric benzodiazepine-derivatives induces cell death.

J Neurooncol 2019 May 6;142(3):411-422. Epub 2019 Feb 6.

Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.

Purpose: Pediatric brain cancer medulloblastoma (MB) standard-of-care results in numerous comorbidities. MB is comprised of distinct molecular subgroups. Group 3 molecular subgroup patients have the highest relapse rates and after standard-of-care have a 20% survival. Group 3 tumors have high expression of GABRA5, which codes for the α5 subunit of the γ-aminobutyric acid type A receptor (GABAR). We are advancing a therapeutic approach for group 3 based on GABAR modulation using benzodiazepine-derivatives.

Methods: We performed analysis of GABR and MYC expression in MB tumors and used molecular, cell biological, and whole-cell electrophysiology approaches to establish presence of a functional 'druggable' GABAR in group 3 cells.

Results: Analysis of expression of 763 MB tumors reveals that group 3 tumors share high subgroup-specific and correlative expression of GABR genes, which code for GABAR subunits α5, β3 and γ2 and 3. There are ~ 1000 functional α5-GABARs per group 3 patient-derived cell that mediate a basal chloride-anion efflux of 2 × 10 ions/s. Benzodiazepines, designed to prefer α5-GABAR, impair group 3 cell viability by enhancing chloride-anion efflux with subtle changes in their structure having significant impact on potency. A potent, non-toxic benzodiazepine ('KRM-II-08') binds to the α5-GABAR (0.8 µM EC) enhancing a chloride-anion efflux that induces mitochondrial membrane depolarization and in response, TP53 upregulation and p53, constitutively phosphorylated at S392, cytoplasmic localization. This correlates with pro-apoptotic Bcl-2-associated death promoter protein localization.

Conclusion: GABRA5 expression can serve as a diagnostic biomarker for group 3 tumors, while α5-GABAR is a therapeutic target for benzodiazepine binding, enhancing an ion imbalance that induces apoptosis.
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http://dx.doi.org/10.1007/s11060-019-03115-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478651PMC
May 2019

Interactive calculator for operating characteristics of phase I cancer clinical trials using standard 3+3 designs.

Contemp Clin Trials Commun 2018 Dec 7;12:145-153. Epub 2018 Nov 7.

Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, United States.

Among various Phase I clinical trial designs, rule-based standard 3 + 3 designs are the most widely utilized for their simplicity and robustness. It is necessary to define crucial operating characteristics of a Phase I clinical trial before it starts. Based on the assumed probability of dose limiting toxicity (DLT) at each tested dose level, Lin and Shih elaborated formulas to calculate the five key operating characteristics of Phase I clinical trials using the two subtypes of standard 3 + 3 designs (with vs without dose de-escalation): probability of each dose level being chosen as the maximum tolerated dose (MTD); expected number of patients treated at each dose level; expected number of patients experiencing DLT at each dose level; target toxicity level (TTL) (expected probability of DLT at MTD); expected total number of patients experiencing DLT. Understanding these formulas requires advanced statistical knowledge and the formulas are too complicated to be used directly. To facilitate their application, we have developed stand-alone interactive software for convenient calculation of these key operating characteristics. The calculated results are presented in tables and plots that can be saved and easily edited for further use. Some examples of calculation using the software are presented and discussed.
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http://dx.doi.org/10.1016/j.conctc.2018.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6261803PMC
December 2018

Flt3L Treatment of Bone Marrow Donors Increases Graft Plasmacytoid Dendritic Cell Content and Improves Allogeneic Transplantation Outcomes.

Biol Blood Marrow Transplant 2019 06 29;25(6):1075-1084. Epub 2018 Nov 29.

Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia. Electronic address:

A higher number of donor plasmacytoid dendritic cells (pDCs) is associated with increased survival and reduced graft-versus-host disease (GVHD) in human recipients of unrelated donor bone marrow (BM) grafts, but not granulocyte colony-stimulating factor (G-CSF)-mobilized peripheral blood grafts. We show that in murine models, donor BM pDCs are associated with increased survival and decreased GVHD compared with G-CSF-mobilized pDCs. To increase the content of pDCs in BM grafts, we studied the effect of FMS-like tyrosine kinase 3 ligand (Flt3L) treatment of murine BM donors on transplantation outcomes. Flt3L treatment (300 μg/kg/day) resulted in a schedule-dependent increase in the content of pDCs in the BM. Mice treated on days -4 and -1 had a >5-fold increase in pDC content without significant changes in numbers of HSCs, T cells, B cells, and natural killer cells in the BM graft. In an MHC-mismatched murine transplant model, recipients of Flt3L-treated T cell-depleted (TCD) BM (TCD F-BM) and cytokine-untreated T cells had increased survival and decreased GVHD scores with fewer Th1 and Th17 polarized T cells post-transplantation compared with recipients of equivalent numbers of untreated donor TCD BM and T cells. Gene array analyses of pDCs from Flt3L-treated human and murine donors showed up-regulation of adaptive immune pathways and immunoregulatory checkpoints compared with pDCs from untreated BM donors. Transplantation of TCD F-BM plus T cells resulted in no loss of the graft-versus-leukemia (GVL) effect compared with grafts from untreated donors in 2 murine GVL models. Thus, Flt3L treatment of BM donors is a novel method for increasing the pDC content in allografts, improving survival, and decreasing GVHD without diminishing the GVL effect.
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http://dx.doi.org/10.1016/j.bbmt.2018.11.029DOI Listing
June 2019

shinySISPA: A web tool for defining sample groups using gene sets from multiple-omics data.

F1000Res 2018 22;7:213. Epub 2018 Feb 22.

Winship Cancer Institute , Emory University, Atlanta, GA, 30322, USA.

As opposed to genome-wide testing of several hundreds of thousands of genes on very few samples, gene panels target as few as tens of genes and enable the simultaneous testing of many samples.  For example, some cancer gene panels test for 50 genes that can affect tumor growth and potentially identify treatment options directed against the genetic mutation.  The increasing popularity of gene panel testing has spurred the technological development of panels that test for diverse data types such as expression and mutation.   Once samples are tested, there is the desire to examine clinical associations based on the panel and for this purpose, one would like to identify, among the samples tested, which show support for a molecular profile (e.g., presence of mutation with increased expression) versus those samples that do not among the genes tested.  With user-specified molecular profile of interest, and gene panel data matrices (e.g., gene expression, variants, etc.) that define the profile, shinySISPA (Sample Integrated Set Profile Analysis) is a web-based shiny tool to define two sample groups with and without profile support based on our previously published method from which clinical associations may be readily examined. The shinySISPA can be accessed from http://shinygispa.winship.emory.edu/shinySISPA/.
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http://dx.doi.org/10.12688/f1000research.13934.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097349PMC
August 2019

Distinct Gene Expression Profiles Define Anaplastic Grade in Retinoblastoma.

Am J Pathol 2018 10 21;188(10):2328-2338. Epub 2018 Jul 21.

Department of Ophthalmology, Rollins School of Public Health, Emory University, Atlanta, Georgia; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia. Electronic address:

Morbidity and mortality associated with retinoblastoma have decreased drastically in recent decades, in large part owing to better prediction of high-risk disease and appropriate treatment stratification. High-risk histopathologic features and severe anaplasia both predict the need for more aggressive treatment; however, not all centers are able to assess tumor samples easily for the degree of anaplasia. Instead, identification of genetic signatures that are able to distinguish among anaplastic grades and thus predict high- versus low-risk retinoblastoma would facilitate appropriate risk stratification in a wider patient population. A better understanding of genes dysregulated in anaplasia also would yield valuable insights into pathways underlying the development of more severe retinoblastoma. Here, we present the histopathologic and gene expression analysis of 28 retinoblastoma cases using microarray analysis. Tumors of differing anaplastic grade show clear differential gene expression, with significant dysregulation of unique genes and pathways in severe anaplasia. Photoreceptor and nucleoporin expression in particular are identified as highly dysregulated in severe anaplasia and suggest particular cellular processes contributing to the development of increased retinoblastoma severity. A limited set of highly differentially expressed genes also are able to predict severe anaplasia accurately in our data set. Together, these data contribute to the understanding of the development of anaplasia and facilitate the identification of genetic markers of high-risk retinoblastoma.
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http://dx.doi.org/10.1016/j.ajpath.2018.06.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168968PMC
October 2018

MAST1 Drives Cisplatin Resistance in Human Cancers by Rewiring cRaf-Independent MEK Activation.

Cancer Cell 2018 08 19;34(2):315-330.e7. Epub 2018 Jul 19.

Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory, Emory University School of Medicine, Atlanta, GA 30322, USA. Electronic address:

Platinum-based chemotherapeutics represent a mainstay of cancer therapy, but resistance limits their curative potential. Through a kinome RNAi screen, we identified microtubule-associated serine/threonine kinase 1 (MAST1) as a main driver of cisplatin resistance in human cancers. Mechanistically, cisplatin but no other DNA-damaging agents inhibit the MAPK pathway by dissociating cRaf from MEK1, while MAST1 replaces cRaf to reactivate the MAPK pathway in a cRaf-independent manner. We show clinical evidence that expression of MAST1, both initial and cisplatin-induced, contributes to platinum resistance and worse clinical outcome. Targeting MAST1 with lestaurtinib, a recently identified MAST1 inhibitor, restores cisplatin sensitivity, leading to the synergistic attenuation of cancer cell proliferation and tumor growth in human cancer cells and patient-derived xenograft models.
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http://dx.doi.org/10.1016/j.ccell.2018.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092215PMC
August 2018

CDK5 Inhibition Resolves PKA/cAMP-Independent Activation of CREB1 Signaling in Glioma Stem Cells.

Cell Rep 2018 05;23(6):1651-1664

Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA. Electronic address:

Cancer stem cells promote neoplastic growth, in part by deregulating asymmetric cell division and enhancing self-renewal. To uncover mechanisms and potential therapeutic targets in glioma stem cell (GSC) self-renewal, we performed a genetic suppressor screen for kinases to reverse the tumor phenotype of our Drosophila brain tumor model and identified dCdk5 as a critical regulator. CDK5, the human ortholog of dCdk5 (79% identity), is aberrantly activated in GBMs and tightly aligned with both chromosome 7 gains and stem cell markers affecting tumor-propagation. Our investigation revealed that pharmaceutical inhibition of CDK5 prevents GSC self-renewal in vitro and in xenografted tumors, at least partially by suppressing CREB1 activation independently of PKA/cAMP. Finally, our TCGA GBM data analysis revealed that CDK5, stem cell, and asymmetric cell division markers segregate within non-mesenchymal patient clusters, which may indicate preferential dependence on CDK5 signaling and sensitivity to its inhibition in this group.
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http://dx.doi.org/10.1016/j.celrep.2018.04.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987254PMC
May 2018

GAC: Gene Associations with Clinical, a web based application.

F1000Res 2017 3;6:1039. Epub 2017 Jul 3.

Winship Cancer Institute of Emory University, Atlanta, GA, 30322, USA.

We present GAC, a shiny R based tool for interactive visualization of clinical associations based on high-dimensional data. The tool provides a web-based suite to perform supervised principal component analysis (SuperPC), an approach that uses both high-dimensional data, such as gene expression, combined with clinical data to infer clinical associations. We extended the approach to address binary outcomes, in addition to continuous and time-to-event data in our package, thereby increasing the use and flexibility of SuperPC.  Additionally, the tool provides an interactive visualization for summarizing results based on a forest plot for both binary and time-to-event data.  In summary, the GAC suite of tools provide a one stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types, such as genomic data. Our GAC package has been implemented in R and is available via http://shinygispa.winship.emory.edu/GAC/. The developmental repository is available at https://github.com/manalirupji/GAC.
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http://dx.doi.org/10.12688/f1000research.11840.4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658710PMC
July 2017

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations.

PLoS One 2018 7;13(2):e0192563. Epub 2018 Feb 7.

Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America.

While many methods exist for integrating multi-omics data or defining gene sets, there is no one single tool that defines gene sets based on merging of multiple omics data sets. We present shinyGISPA, an open-source application with a user-friendly web-based interface to define genes according to their similarity in several molecular changes that are driving a disease phenotype. This tool was developed to help facilitate the usability of a previously published method, Gene Integrated Set Profile Analysis (GISPA), among researchers with limited computer-programming skills. The GISPA method allows the identification of multiple gene sets that may play a role in the characterization, clinical application, or functional relevance of a disease phenotype. The tool provides an automated workflow that is highly scalable and adaptable to applications that go beyond genomic data merging analysis. It is available at http://shinygispa.winship.emory.edu/shinyGISPA/.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192563PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802933PMC
April 2018

CASAS: Cancer Survival Analysis Suite, a web based application.

F1000Res 2017 15;6:919. Epub 2017 Jun 15.

Winship Cancer Institute of Emory University, Atlanta, GA, 30322, USA.

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis:  quantile, landmark and competing risks, in addition to standard survival analysis.  The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots.  Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/. The developmental repository is available at https://github.com/manalirupji/CASAS/.
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http://dx.doi.org/10.12688/f1000research.11830.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580407PMC
June 2017

Targeting adhesion signaling in mutant lung adenocarcinoma.

JCI Insight 2017 03 9;2(5):e90487. Epub 2017 Mar 9.

Department of Hematology and Medical Oncology, Emory University School of Medicine.

Loss of LKB1 activity is prevalent in mutant lung adenocarcinoma and promotes aggressive and treatment-resistant tumors. Previous studies have shown that LKB1 is a negative regulator of the focal adhesion kinase (FAK), but in vivo studies testing the efficacy of FAK inhibition in mutant cancers are lacking. Here, we took a pharmacologic approach to show that FAK inhibition is an effective early-treatment strategy for this high-risk molecular subtype. We established a lenti-Cre-induced and mutant genetically engineered mouse model () that develops 100% lung adenocarcinoma and showed that high spatiotemporal FAK activation occurs in collective invasive cells that are surrounded by high levels of collagen. Modeling invasion in 3D, loss of , but not , was sufficient to drive collective invasion and collagen alignment that was highly sensitive to FAK inhibition. Treatment of early, stage-matched tumors with FAK inhibitor monotherapy resulted in a striking effect on tumor progression, invasion, and tumor-associated collagen. Chronic treatment extended survival and impeded local lymph node spread. Lastly, we identified focally upregulated FAK and collagen-associated collective invasion in and comutated human lung adenocarcinoma patients. Our results suggest that patients with mutant tumors should be stratified for early treatment with FAK inhibitors.
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http://dx.doi.org/10.1172/jci.insight.90487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333956PMC
March 2017

Adaptive Estimation of Personalized Maximum Tolerated Dose in Cancer Phase I Clinical Trials Based on All Toxicities and Individual Genomic Profile.

PLoS One 2017 26;12(1):e0170187. Epub 2017 Jan 26.

Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, United States of America.

Background: Many biomarkers have been shown to be associated with the efficacy of cancer therapy. Estimation of personalized maximum tolerated doses (pMTDs) is a critical step toward personalized medicine, which aims to maximize the therapeutic effect of a treatment for individual patients. In this study, we have established a Bayesian adaptive Phase I design which can estimate pMTDs by utilizing patient biomarkers that can predict susceptibility to specific adverse events and response as covariates.

Methods: Based on a cutting-edge cancer Phase I clinical trial design called escalation with overdose control using normalized equivalent toxicity score (EWOC-NETS), which fully utilizes all toxicities, we propose new models to incorporate patient biomarker information in the estimation of pMTDs for novel cancer therapeutic agents. The methodology is fully elaborated and the design operating characteristics are evaluated with extensive simulations.

Results: Simulation studies demonstrate that the utilization of biomarkers in EWOC-NETS can estimate pMTDs while maintaining the original merits of this Phase I trial design, such as ethical constraint of overdose control and full utilization of all toxicity information, to improve the accuracy and efficiency of the pMTD estimation.

Conclusions: Our novel cancer Phase I designs with inclusion of covariate(s) in the EWOC-NETS model are useful to estimate a personalized MTD and have substantial potential to improve the therapeutic effect of drug treatment.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170187PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5268707PMC
August 2017

MERTK Inhibition Induces Polyploidy and Promotes Cell Death and Cellular Senescence in Glioblastoma Multiforme.

PLoS One 2016 26;11(10):e0165107. Epub 2016 Oct 26.

Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University Department of Pediatrics, Atlanta, GA, 30322, United States of America.

Background: MER receptor tyrosine kinase (MERTK) is expressed in a variety of malignancies, including glioblastoma multiforme (GBM). Our previous work demonstrated that inhibition of MERTK using RNA interference induced cell death and chemosensitivity in GBM cells, implicating MERTK as a potential therapeutic target. Here we investigate whether a novel MERTK-selective small molecule tyrosine kinase inhibitor, UNC2025, has similar anti-tumor effects in GBM cell lines.

Methods: Correlations between expression of GAS6, a MERTK ligand, and prognosis were determined using data from the TCGA database. GBM cell lines (A172, SF188, U251) were treated in vitro with increasing doses of UNC2025 (50-400nM). Cell count and viability were determined by trypan blue exclusion. Cell cycle profiles and induction of apoptosis were assessed by flow cytometric analysis after BrdU or Po-Pro-1/propidium iodide staining, respectively. Polyploidy was detected by propidium iodide staining and metaphase spread. Cellular senescence was determined by β-galactosidase staining and senescence-associated secretory cytokine analysis.

Results: Decreased overall survival significantly correlated with high levels of GAS6 expression in GBM, highlighting the importance of TAM kinase signaling in GBM tumorigenesis and/or therapy resistance and providing strong rationale for targeting these pathways in the clinic. All three GBM cell lines exhibited dose dependent reductions in cell number and colony formation (>90% at 200nM) after treatment with UNC2025. Cell cycle analysis demonstrated accumulation of cells in the G2/M phase and development of polyploidy. After extended exposure, 60-80% of cells underwent apoptosis. The majority of surviving cells (65-95%) were senescent and did not recover after drug removal. Thus, UNC2025 mediates anti-tumor activity in GBM by multiple mechanisms.

Conclusions: The findings described here provide further evidence of oncogenic roles for MERTK in GBM, demonstrate the importance of kinase activity for MERTK tumorigenicity and validate UNC2025, a novel MERTK inhibitor, as a potential therapeutic agent for treatment of GBM.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165107PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5081168PMC
June 2017

Differentiation therapy in poor risk myeloid malignancies: Results of companion phase II studies.

Leuk Res 2016 10 3;49:90-7. Epub 2016 Sep 3.

Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, United States. Electronic address:

Pre-clinical data in non-M3 AML supports the use of differentiation therapy, but clinical activity has been limited. Myeloid growth factors can enhance anti-leukemic activity of differentiating agents in vitro. We conducted companion phase II trials investigating sargramostim (GM-CSF) 125μg/m(2)/day plus 1) bexarotene (BEX) 300mg/m(2)/day or 2) entinostat (ENT) 4-8mg/m(2)/week in patients with MDS or relapsed/refractory AML. Primary endpoints were response after at least two treatment cycles and toxicity. 26 patients enrolled on the BEX trial had a median of 2 prior treatments and 24 enrolled on the ENT trial had a median of 1. Of 13 response-evaluable patients treated with BEX, the best response noted was hematologic improvement in neutrophils (HI-N) seen in 4 (31%) patients; none achieved complete (CR) or partial remission (PR). Of 10 treated with ENT, there was 1 (10%) partial remission (PR) and 2 (20%) with HI-N. The secondary endpoint responses of HI-N with each combination were accompanied by a numerical increase in ANC (BEX: 524 to 931 cells/mm(3), p=0.096; ENT: 578 to 1 137 cells/mm(3), p=0.15) without increasing marrow blasts. Shared grade 3-4 non-hematologic toxicities included febrile neutropenia, bone pain, fatigue, and dyspnea. GM-CSF plus either BEX or ENT are well tolerated in resistant and refractory MDS and AML and showed modest clinical and biologic activity, most commonly HI-N.
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http://dx.doi.org/10.1016/j.leukres.2016.09.003DOI Listing
October 2016

TNFRSF10C copy number variation is associated with metastatic colorectal cancer.

J Gastrointest Oncol 2016 Jun;7(3):306-14

1 Department of Radiation Oncology, 2 Winship Cancer Institute, Emory University, GA, USA ; 3 Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA ; 4 Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA ; 5 Department of Pathology and Laboratory Medicine, 6 Department of Biomedical Informatics, 7 Department of Biostatistics and Bioinformatics, 8 Biostatistics and Bioinformatics Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Background: Genetic markers for distant metastatic disease in patients with colorectal cancer (CRC) are not well defined. Identification of genetic alterations associated with metastatic CRC could help to guide systemic and local treatment strategies. We evaluated the association of tumor necrosis factor receptor superfamily member 10C (TNFRSF10C) copy number variation (CNV) with distant metastatic disease in patients with CRC using The Cancer Genome Atlas (TCGA).

Methods: Genetic sequencing data and clinical characteristics were obtained from TCGA for all available patients with CRC. There were 515 CRC patient samples with CNV and clinical outcome data, including a subset of 144 rectal adenocarcinoma patient samples. Using the TCGA CRC dataset, CNV of TNFRSF10C was evaluated for association with distant metastatic disease (M1 vs. M0). Multivariate logistic regression analysis with odds ratio (OR) using a 95% confidence interval (CI) was performed adjusting for age, T stage, N stage, adjuvant chemotherapy, gender, microsatellite instability (MSI), location, and surgical margin status.

Results: TNFRSF10C CNV in patients with CRC was associated with distant metastatic disease [OR 4.81 (95% CI, 2.13-10.85) P<0.001] and positive lymph nodes [OR 18.83 (95% CI, 8.42-42.09)]; P<0.001) but not MSI (OR P=0.799). On multivariate analysis, after adjusting for pathologic T stage, N stage, adjuvant chemotherapy, gender, and MSI, TNFRSF10C CNV remained significantly associated with distant metastatic disease (OR P=0.018). Subset analysis revealed that TNFRSF10C CNV was also significantly associated with distant metastatic disease in patients with rectal adenocarcinoma (OR P=0.016).

Conclusions: TNFRSF10C CNV in patients with CRC is associated with distant metastatic disease. With further validation, such genetic profiles could be used clinically to support optimal systemic treatment strategies versus more aggressive local therapies in patients with CRC, including radiation therapy for rectal adenocarcinoma.
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http://dx.doi.org/10.21037/jgo.2015.11.04DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880759PMC
June 2016

Factors affecting the persistence of drug-induced reprogramming of the cancer methylome.

Epigenetics 2016 04 15;11(4):273-87. Epub 2016 Apr 15.

b Winship Cancer Institute , Emory University , Atlanta , GA , USA.

Aberrant DNA methylation is a critical feature of cancer. Epigenetic therapy seeks to reverse these changes to restore normal gene expression. DNA demethylating agents, including 5-aza-2'-deoxycytidine (DAC), are currently used to treat certain leukemias, and can sensitize solid tumors to chemotherapy and immunotherapy. However, it has been difficult to pin the clinical efficacy of these agents to specific demethylation events, and the factors that contribute to the durability of response remain largely unknown. Here we examined the genome-wide kinetics of DAC-induced DNA demethylation and subsequent remethylation after drug withdrawal in breast cancer cells. We find that CpGs differ in both their susceptibility to demethylation and propensity for remethylation after drug removal. DAC-induced demethylation was most apparent at CpGs with higher initial methylation levels and further from CpG islands. Once demethylated, such sites exhibited varied remethylation potentials. The most rapidly remethylating CpGs regained >75% of their starting methylation within a month of drug withdrawal. These sites had higher pretreatment methylation levels, were enriched in gene bodies, marked by H3K36me3, and tended to be methylated in normal breast cells. In contrast, a more resistant class of CpG sites failed to regain even 20% of their initial methylation after 3 months. These sites had lower pretreatment methylation levels, were within or near CpG islands, marked by H3K79me2 or H3K4me2/3, and were overrepresented in sites that become aberrantly hypermethylated in breast cancers. Thus, whereas DAC-induced demethylation affects both endogenous and aberrantly methylated sites, tumor-specific hypermethylation is more slowly regained, even as normal methylation promptly recovers. Taken together, these data suggest that the durability of DAC response is linked to its selective ability to stably reset at least a portion of the cancer methylome.
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http://dx.doi.org/10.1080/15592294.2016.1158364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889262PMC
April 2016

Rank-preserving regression: a more robust rank regression model against outliers.

Stat Med 2016 08 2;35(19):3333-46. Epub 2016 Mar 2.

Department of Biostatistics and Computational Biology, University of Rochester, Rochester, 14642, NY, U.S.A.

Mean-based semi-parametric regression models such as the popular generalized estimating equations are widely used to improve robustness of inference over parametric models. Unfortunately, such models are quite sensitive to outlying observations. The Wilcoxon-score-based rank regression (RR) provides more robust estimates over generalized estimating equations against outliers. However, the RR and its extensions do not sufficiently address missing data arising in longitudinal studies. In this paper, we propose a new approach to address outliers under a different framework based on the functional response models. This functional-response-model-based alternative not only addresses limitations of the RR and its extensions for longitudinal data, but, with its rank-preserving property, even provides more robust estimates than these alternatives. The proposed approach is illustrated with both real and simulated data. Copyright © 2016 John Wiley & Sons, Ltd.
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http://dx.doi.org/10.1002/sim.6930DOI Listing
August 2016