Publications by authors named "Alexander Brodsky"

52 Publications

Effects of High Fat Versus Normal Diet on Extracellular Vesicle-Induced Angiogenesis in a Swine Model of Chronic Myocardial Ischemia.

J Am Heart Assoc 2021 Feb 9;10(4):e017437. Epub 2021 Feb 9.

Division of Cardiothoracic Surgery Alpert Medical School of Brown University and Rhode Island Hospital Providence RI.

Background Mesenchymal stem cell-derived extracellular vesicles (EVs) promote angiogenesis in the ischemic myocardium. This study examines the difference in vascular density, myocardial perfusion, molecular signaling, and gene expression between normal diet (ND) and high fat diet (HFD) groups at baseline and following intramyocardial injection of EVs. Methods and Results Intact male Yorkshire swine fed either an ND (n=17) or HFD (n=14) underwent placement of an ameroid constrictor on the left circumflex coronary artery. Subsequently, animals received either intramyocardial injection of vehicle-saline as controls; (ND-controls n=7, HFD-controls, n=6) or EVs; (ND-EVs n=10, HFD-EVs n=8) into the ischemic territory. Five weeks later, myocardial function, perfusion, vascular density, cell signaling, and gene expression were examined. EVs improved indices of myocardial contractile function, myocardial perfusion, and arteriogenesis in both dietary cohorts. Interestingly, quantification of alpha smooth muscle actin demonstrated higher basal arteriolar density in HFD swine compared with their ND counterparts; whereas EVs were associated with increased CD31-labeled endothelial cell density only in the ND tissue, which approached significance. Levels of total endothelial nitric oxide synthase, FOXO1 (forkhead box protein O1) , transforming growth factor-β, phosphorylated VEGFR2 (vascular endothelial growth factor receptor 2), and phosphorylated MAPK ERK1/ERK2 (mitogen-activated protein kinase) were higher in ischemic myocardial lysates from ND-controls compared with HFD-controls. Conversely, HFD-control tissue showed increased expression of phosphorylated endothelial nitric oxide synthase, phosphorylated FOXO1, VEGFR2, and MAPK ERK1/ERK2 with respect to ND-controls. Preliminary gene expression studies indicate differential modulation of transcriptional activity by EVs between the 2 dietary cohorts. Conclusions HFD produces a profound metabolic disorder that dysregulates the molecular mechanisms of collateral vessel formation in the ischemic myocardium, which may hinder the therapeutic angiogenic effects of EVs.
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http://dx.doi.org/10.1161/JAHA.120.017437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7955347PMC
February 2021

Insights from the Menstrual Cycle in Pulmonary Arterial Hypertension.

Ann Am Thorac Soc 2021 02;18(2):218-228

Department of Medicine, Alpert Medical School of Brown University, Providence, Rhode Island.

Sex hormones play a role in pulmonary arterial hypertension (PAH), but the menstrual cycle has never been studied. We conducted a prospective observational study of eight women with stable PAH and 20 healthy controls over one cycle. Participants completed four study visits 1 week apart starting on the first day of menstruation. Relationships between sex hormones, hormone metabolites, and extracellular vesicle microRNA (miRNA) expression and clinical markers were compared with generalized linear mixed modeling. Women with PAH had higher but less variable estradiol (E2) levels ( < 0.001) that tracked with 6-minute walk distance ( < 0.001), N-terminal prohormone of brain natriuretic peptide ( = 0.03) levels, and tricuspid annular plane systolic excursion ( < 0.01); the direction of these associations depended on menstrual phase. Dehydroepiandrosterone sulfate (DHEA-S) levels were lower in women with PAH (all visits,  < 0.001). In PAH, each 100-μg/dl increase in DHEA-S was associated with a 127-m increase in 6-minute walk distance ( < 0.001) and was moderated by the cardioprotective E2 metabolite 2-methoxyestrone ( < 0.001). As DHEA-S increased, N-terminal prohormone of brain natriuretic peptide levels decreased ( = 0.001). Expression of extracellular vesicle miRNAs-21, -29c, and -376a was higher in PAH, moderated by E2 and DHEA-S levels, and tracked with hormone-associated changes in clinical measures. Women with PAH have fluctuations in cardiopulmonary function during menstruation driven by E2 and DHEA-S. These hormones in turn influence transcription of extracellular vesicle miRNAs implicated in the pathobiology of pulmonary vascular disease and cancer.
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http://dx.doi.org/10.1513/AnnalsATS.202006-671OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7869782PMC
February 2021

[FOCUSING AND UPDATING INDICATIONS FOR VENTILATING TUBES INSERTION IN PEDIATRIC COCHLEAR IMPLANT CANDIDATES WHO SUFFER FROM OTITIS MEDIA].

Harefuah 2020 Feb;159(1):93-97

The Ear and Hearing Program, Department of Otolaryngology Head and Neck Surgery, Bnai-Zion Medical Center, Haifa.

Background: After cochlear implantation (CI) there is concern regarding the potential risks of spread of middle ear infection along the electrode array into the cochlea and central nervous system and regarding late sequela of otitis media (OM): eardrum perforation, atelectasis and cholesteatoma. The age for implantation in children overlaps the peak age incidence of acute OM (AOM) and secretory OM (SOM) and delay of implantation reduces the potential benefit from the intervention. Therefore, control of OM by inserting ventilating tubes (VT) is widely performed in pediatric CI candidates who also suffer from otitis media.

Objectives: To refine indications for VT insertion in candidates for cochlear implantation who also suffer from OM.

Methods: Of 200 children referred for CI and implanted one after another, 126 were classified as OM-prone, 98 due to AOM and 28 due to SOM. The rate of development of late sequela of middle ear disease was compared between the two subgroups of OM-proneness.

Results: A total of 15 children (7.5%) developed late sequela of middle ear disease; all belonged to the SOM group; 3.5% developed eardrum perforation; 3.5% atelectasis and 0.5% cholesteatoma.

Conclusions: Pre-CI VT insertion in children with SOM who underwent CI did not prevent development of late sequela of middle ear disease; VT insertion with the object of preventing late sequela of middle ear disease in CI candidates who suffer from SOM only is not required; in otitis-prone children a long term oto-microscopic follow-up is needed in order to identify late sequela of middle ear disease.
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February 2020

Mesenchymal Stem Cell Extracellular Vesicles Reverse Sugen/Hypoxia Pulmonary Hypertension in Rats.

Am J Respir Cell Mol Biol 2020 05;62(5):577-587

Division of Hematology and Oncology, Department of Medicine, and.

Mesenchymal stem cell extracellular vesicles attenuate pulmonary hypertension, but their ability to reverse established disease in larger animal models and the duration and mechanism(s) of their effect are unknown. We sought to determine the efficacy and mechanism of mesenchymal stem cells' extracellular vesicles in attenuating pulmonary hypertension in rats with Sugen/hypoxia-induced pulmonary hypertension. Male rats were treated with mesenchymal stem cell extracellular vesicles or an equal volume of saline vehicle by tail vein injection before or after subcutaneous injection of Sugen 5416 and exposure to 3 weeks of hypoxia. Pulmonary hypertension was assessed by right ventricular systolic pressure, right ventricular weight to left ventricle + septum weight, and muscularization of peripheral pulmonary vessels. Immunohistochemistry was used to measure macrophage activation state and recruitment to lung. Mesenchymal stem cell extracellular vesicles injected before or after induction of pulmonary hypertension normalized right ventricular pressure and reduced right ventricular hypertrophy and muscularization of peripheral pulmonary vessels. The effect was consistent over a range of doses and dosing intervals and was associated with lower numbers of lung macrophages, a higher ratio of alternatively to classically activated macrophages (M2/M1 = 2.00 ± 0.14 vs. 1.09 ± 0.11;  < 0.01), and increased numbers of peripheral blood vessels (11.8 ± 0.66 vs. 6.9 ± 0.57 vessels per field;  < 0.001). Mesenchymal stem cell extracellular vesicles are effective at preventing and reversing pulmonary hypertension in Sugen/hypoxia pulmonary hypertension and may offer a new approach for the treatment of pulmonary arterial hypertension.
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http://dx.doi.org/10.1165/rcmb.2019-0154OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193796PMC
May 2020

Stromal ColXα1 expression correlates with tumor-infiltrating lymphocytes and predicts adjuvant therapy outcome in ER-positive/HER2-positive breast cancer.

BMC Cancer 2019 Nov 1;19(1):1036. Epub 2019 Nov 1.

Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, 593 Eddy St, APC 12, Providence, RI, 02903, USA.

Background: The breast cancer microenvironment contributes to tumor progression and response to chemotherapy. Previously, we reported that increased stromal Type X collagen α1 (ColXα1) and low TILs correlated with poor pathologic response to neoadjuvant therapy in estrogen receptor and HER2-positive (ER+/HER2+) breast cancer. Here, we investigate the relationship of ColXα1 and long-term outcome of ER+/HER2+ breast cancer patients in an adjuvant setting.

Methods: A total of 164 cases with at least 5-year follow-up were included. Immunohistochemistry for ColXα1 was performed on whole tumor sections. Associations between ColXα1expression, clinical pathological features, and outcomes were analyzed.

Results: ColXα1 expression was directly proportional to the amount of tumor associated stroma (p = 0.024) and inversely proportional to TILs. Increased ColXα1 was significantly associated with shorter disease free survival and overall survival by univariate analysis. In multivariate analysis, OS was lower in ColXα1 expressing (HR = 2.1; 95% CI = 1.2-3.9) tumors of older patients (> = 58 years) (HR = 5.3; 95% CI = 1.7-17) with higher stage (HR = 2.6; 95% CI = 1.3-5.2). Similarly, DFS was lower in ColXα1 expressing (HR = 1.8; 95% CI = 1.6-5.7) tumors of older patients (HR = 3.2; 95% CI = 1.3-7.8) with higher stage (HR = 2.7; 95% CI = 1.6-5.7) and low TILs. In low PR+ tumors, higher ColXα1 expression was associated with poorer prognosis.

Conclusion: ColXα1 expression is associated with poor disease free survival and overall survival in ER+/HER2+ breast cancer. This study provides further support for the prognostic utility of ColXα1 as a breast cancer associated stromal factor that predicts response to chemotherapy.
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http://dx.doi.org/10.1186/s12885-019-6134-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6825361PMC
November 2019

Factory optima: a web-based system for composition and analysis of manufacturing service networks based on a reusable model repository.

Int J Comput Integr Manuf 2019 ;32

Department of Computer Science, George Mason University, Fairfax, VA, USA.

This paper reports on the development of Factory Optima, a web-based system that allows manufacturing process engineers to compose, optimise and perform trade-off analysis of manufacturing and contract service networks based on a reusable repository of performance models. Performance models formally describe process feasibility constraints and metrics of interest, such as cost, throughput and emissions, as a function of fixed and control parameters, such as equipment and contract properties and settings. The repository contains performance models representing (1) unit manufacturing processes, (2) base contract services and (3) a composite steady-state service network. The proposed framework allows process engineers to hierarchically compose model instances of service networks, which can represent production cells, lines, factory facilities and supply chains, and perform deterministic optimisation based on mathematical programming and Pareto-optimal trade-off analysis. Factory Optima is demonstrated using a case study of a service network for a heat sink product which involves contract vendors and manufacturing activities, including cutting, shearing, Computer Numerical Control (CNC) machining with milling and drilling operations, quality inspection, finishing, and assembly.
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http://dx.doi.org/10.1080/0951192X.2019.1570805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6605078PMC
January 2019

ColXα1 is a stromal component that colocalizes with elastin in the breast tumor extracellular matrix.

J Pathol Clin Res 2019 01 1;5(1):40-52. Epub 2018 Nov 1.

Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA.

The tumor microenvironment regulates tissue development and homeostasis, and its dysregulation contributes to neoplastic progression. Increased expression of type X collagen α-1 (ColXα1) in tumor-associated stroma correlates with poor pathologic response to neoadjuvant chemotherapy in estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2)-positive breast cancers. Evaluation of ColXα1 expression patterns suggests a potential connection with elastin fibers. To investigate the possible interaction between ColXα1 and elastin, we evaluated the expression of ColXα1 in relation to elastin fibers in normal breast tissue, ductal carcinoma in situ, and invasive breast carcinomas at cellular and subcellular levels. Our findings demonstrate that ColXα1 colocalizes with elastin in invasive breast cancer-associated stroma by immunohistochemistry, immunofluorescence, and electron microscopy. In 212 invasive breast carcinomas, this complex was aberrantly and selectively expressed in tumor extracellular matrix in 79% of ER+/HER2-, 80% of ER+/HER2+, 76% of ER-/HER2+, and 58% of triple negative breast cancers. In contrast, ColXα1 was generally absent, while elastin was present perivascularly in normal breast tissue. ColXα1 and elastin were coexpressed in 58% of ductal carcinoma in situ (DCIS) in periductal areas. In mass-forming DCIS with desmoplastic stroma, the complex was intensely expressed in periductal areas as well as within the tumor-associated stroma in all cases. Our data suggest that the breast carcinoma neoplastic process may involve aberrant expression of ColXα1 and elastin in the tumor microenvironment emerging early at the DCIS stage. Enrichment of these complexes in tumor-associated stroma may represent a stromal signature indicative of intrinsic differences between breast cancers. These findings shed light on investigation into the role of aberrant collagen complex expression in tumorigenesis and tumor progression which may be leveraged in therapeutic and theranostic applications.
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http://dx.doi.org/10.1002/cjp2.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317058PMC
January 2019

Generating flat-top beams with extended depth of focus.

Appl Opt 2018 Jun;57(16):4583-4589

Two approaches for generating flat-top beams (uniform intensity profile) with extended depth of focus are presented. One involves two diffractive optical elements (DOEs) and the other only a single DOE. The results indicate that the depth of focus of such beams strongly depends on the phase distribution at the output of the DOEs. By having uniform phase distribution, it is possible to generate flat-top beams with extended depth of focus.
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http://dx.doi.org/10.1364/AO.57.004583DOI Listing
June 2018

Stromal Clusterin Expression Predicts Therapeutic Response to Neoadjuvant Chemotherapy in Triple Negative Breast Cancer.

Clin Breast Cancer 2018 06 19;18(3):e373-e379. Epub 2017 Aug 19.

Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI.

Background: Expression of clusterin correlates with tumor progression and therapeutic response in several human malignancies, including breast cancer. However, its predictive value in the neoadjuvant setting in breast cancer remains unexplored. The objective of this explorative study was to determine whether clusterin expression in breast cancer correlated with clinical pathologic characteristics and whether its expression was predictive of response to neoadjuvant chemotherapy (NAC).

Materials And Methods: We determined the clusterin expression pattern in 72 triple negative breast cancers (TNBC) treated with NAC before surgery. Clusterin expression was evaluated by immunohistochemistry and was correlated with pathologic characteristics and response to NAC using residual cancer burden score.

Results: Immunohistochemistry analysis revealed a differential pattern of expression between tumor and stroma. Clusterin expression in the tumor associated stroma as opposed to expression by the neoplastic epithelium was significantly associated with neoadjuvant-treated TNBC. Low stromal clusterin, low stromal content, and high tumor-infiltrating lymphocytes were associated with a significantly greater likelihood of achieving a good pathologic response as reflected by lower residual cancer burden scores (P = .002, P = .003, and P = .001, respectively). Tumor and/or stromal clusterin expression were not associated with patient age, tumor histologic grade, stage, and lymph node status.

Conculsion: This study suggests a potential role for the assessment of stromal clusterin as a predictive biomarker for response of TNBC to neoadjuvant therapy. Further validation of this biomarker in a large study is needed.
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http://dx.doi.org/10.1016/j.clbc.2017.08.007DOI Listing
June 2018

Analysis and Optimization based on Reusable Knowledge Base of Process Performance Models.

Int J Adv Manuf Technol 2017 ;88

National Institute of Standards and Technology (NIST), Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.

In this paper, we propose an architectural design and software framework for fast development of descriptive, diagnostic, predictive, and prescriptive analytics solutions for dynamic production processes. The proposed architecture and framework will support the storage of modular, extensible, and reusable Knowledge Base (KB) of process performance models. The approach requires developing automated methods that can translate the high-level models in the reusable KB into low-level specialized models required by a variety of underlying analysis tools, including data manipulation, optimization, statistical learning, estimation, and simulation. We also propose an organization and key structure for the reusable KB, composed of atomic and composite process performance models and domain-specific dashboards. Furthermore, we illustrate the use of the proposed architecture and framework by prototyping a decision-support system for process engineers. The decision support system allows users to hierarchically compose and optimize dynamic production processes via a graphical user interface.
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http://dx.doi.org/10.1007/s00170-016-8761-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604630PMC
January 2017

Collagen type III α1 as a useful diagnostic immunohistochemical marker for fibroepithelial lesions of the breast.

Hum Pathol 2016 11 3;57:176-181. Epub 2016 Aug 3.

Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI 02903.

Phyllodes tumors (PTs) of the breast constitute an uncommon group of fibroepithelial neoplasms that are classified into benign, borderline, and malignant categories based on a constellation of histologic characteristics including cytologic atypia, mitotic count, degree of stromal cellularity, stromal overgrowth, and microscopic margins. Accurately and reproducibly differentiating these tumors is a long-standing diagnostic challenge. In addition, the distinction between benign PT from cellular fibroadenoma (FA) is especially difficult because of overlapping microscopic features. We have previously shown differential expression of various collagens, including collagen type III α1 (Col3A) in breast carcinomas. In this study, we evaluated clinicopathological characteristics of 95 cases of fibroepithelial lesions including 56 PTs and 39 FAs (25 cellular FA, 14 typical FA) and correlated them with the immunohistochemical staining pattern for Col3A. We found that stromal Col3A expression was significantly increased in PTs when compared with FAs (P < .0001). Among the PT groups, there was significantly increased expression from benign tumors through borderline to malignant tumors. High Col3A expression was associated with PT type, irregular margin status, and high mitotic activity. A distinct periductal cuffing pattern of Col3A staining was unique to PTs and absent in FAs. These findings suggest that Col3A can be a potential adjunct marker for both differentiating FA from PT and assessing malignant potential in PTs.
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http://dx.doi.org/10.1016/j.humpath.2016.07.017DOI Listing
November 2016

Does narrow band imaging improve preoperative detection of glottic malignancy? A matched comparison study.

Laryngoscope 2017 04 18;127(4):894-899. Epub 2016 Oct 18.

Department of Otolaryngology-Head and Neck Surgery, Kaplan Medical Center, Rehovot, Israel.

Objectives/hypothesis: The primary suspicion for glottic malignancy during office laryngoendoscopy is based on lesion appearance. Previous studies investigating laryngeal use of narrow band imaging (NBI) are mostly descriptive. The additive value of NBI relative to white light (WL) requires further investigation.

Study Design: Observational matched study.

Methods: NBI was compared with WL images of 45 vocal fold lesions suspected for malignancy (21 carcinoma, 22 dysplasia, two benign). All images were presented randomly and evaluated by six independent otolaryngology specialists. The observers were asked to estimate lesion size, location, and pathology. The results for the two imaging modalities were compared with each other and with the final pathology.

Results: The observers estimated lesion size to be larger in the NBI images by an average of 9% (2.4 mm ; P =.04) compared to WL. In 64.6% of cases, the observers estimated similar pathology for NBI and WL. When there was a discrepancy, the estimated pathology was "malignant" in 24.3% by NBI, compared with 11.1% by WL. Overall, 44.7% of the lesions were estimated to be malignant by NBI, compared with 33.8% by WL (P =.001). The sensitivity and specificity rates for malignancy detection by NBI were 58.6% and 61.2%, respectively, compared to 48.7% and 76.1% by WL.

Conclusions: Observers tend to estimate vocal fold lesions to be larger and more frequently suspect malignancy while assessing NBI images. Compared with WL, NBI demonstrates increased sensitivity and decreased specificity for detection of malignancy. Nevertheless, the specificity and sensitivity of NBI alone are considerably low.

Level Of Evidence: 4 Laryngoscope, 127:894-899, 2017.
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http://dx.doi.org/10.1002/lary.26263DOI Listing
April 2017

Fatty acid-binding protein 1 is preferentially lost in microsatellite instable colorectal carcinomas and is immune modulated via the interferon γ pathway.

Mod Pathol 2017 01 30;30(1):123-133. Epub 2016 Sep 30.

Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, RI, USA.

Fatty acid-binding protein 1 (FABP1) is an intracellular protein responsible for the transportation of long chain fatty acids. Aside from its functions in lipid metabolism and cellular differentiation, FABP1 also plays a role in inflammation through its interaction with peroxisome proliferator-activated receptors (PPARs). Previously, we compared expression of colonic epithelium genes in a subset of microsatellite instable (MSI) colorectal carcinomas (medullary carcinomas) to normal colonic mucosa and found that FABP1 expression was markedly decreased in the tumors. Further analysis of RNA expression in the colorectal subtypes and The Cancer Genome Atlas data set found that FABP1 expression is decreased in the CMS1 subset of colorectal carcinomas, which is characterized by microsatellite instability. As MSI colorectal carcinomas are known for their robust immune response, we then aimed to link FABP1 to the immune microenvironment of MSI carcinomas. To confirm the gene expression results, we performed immunohistochemical analysis of a cohort of colorectal carcinomas. FABP1 was preferentially lost in MSI carcinomas (123/133, 93%) compared with microsatellite stable carcinomas (240/562, 43%, P<0.0001). In addition, higher numbers of tumor-infiltrating lymphocytes were present in tumors with loss of FABP1 (P<0.0001). Decreased expression of the fatty acid storage and glucose regulator, PPARγ, was associated with the loss of FABP1 (P<0.0001). Colorectal cancer cell lines treated with interferon γ exhibited decreased expression of FABP1. FABP1 expression was partially recovered with the treatment of the cell lines with rosiglitazone, a PPARγ agonist. This study demonstrated that the loss of FABP1 expression is associated with MSI carcinomas and that interferon γ stimulation plays a role in this process via its interaction with PPARγ.
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http://dx.doi.org/10.1038/modpathol.2016.170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5218856PMC
January 2017

TAF4b Regulates Oocyte-Specific Genes Essential for Meiosis.

PLoS Genet 2016 06 24;12(6):e1006128. Epub 2016 Jun 24.

MCB Department, Brown University, Providence, Rhode Island, United States of America.

TAF4b is a gonadal-enriched subunit of the general transcription factor TFIID that is implicated in promoting healthy ovarian aging and female fertility in mice and humans. To further explore the potential mechanism of TAF4b in promoting ovarian follicle development, we analyzed global gene expression at multiple time points in the human fetal ovary. This computational analysis revealed coordinate expression of human TAF4B and critical regulators and effectors of meiosis I including SYCP3, YBX2, STAG3, and DAZL. To address the functional relevance of this analysis, we turned to the embryonic Taf4b-deficient mouse ovary where, for the first time, we demonstrate, severe deficits in prophase I progression as well as asynapsis in Taf4b-deficient oocytes. Accordingly, TAF4b occupies the proximal promoters of many essential meiosis and oogenesis regulators, including Stra8, Dazl, Figla, and Nobox, and is required for their proper expression. These data reveal a novel TAF4b function in regulating a meiotic gene expression program in early mouse oogenesis, and support the existence of a highly conserved TAF4b-dependent gene regulatory network promoting early oocyte development in both mice and women.
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http://dx.doi.org/10.1371/journal.pgen.1006128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920394PMC
June 2016

Identification of stromal ColXα1 and tumor-infiltrating lymphocytes as putative predictive markers of neoadjuvant therapy in estrogen receptor-positive/HER2-positive breast cancer.

BMC Cancer 2016 Apr 18;16:274. Epub 2016 Apr 18.

Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, USA.

Background: The influence of the tumor microenvironment and tumor-stromal interactions on the heterogeneity of response within breast cancer subtypes have just begun to be explored. This study focuses on patients with estrogen receptor-positive/human epidermal growth factor receptor 2-positive (ER+/HER2+) breast cancer receiving neoadjuvant chemotherapy and HER2-targeted therapy (NAC+H), and was designed to identify novel predictive biomarkers by combining gene expression analysis and immunohistochemistry with pathologic response.

Methods: We performed gene expression profiling on pre-NAC+H tumor samples from responding (no or minimal residual disease at surgery) and non-responding patients. Gene set enrichment analysis identified potentially relevant pathways, and immunohistochemical staining of pre-treatment biopsies was used to measure protein levels of those pathways, which were correlated with pathologic response in both univariate and multivariate analysis.

Results: Increased expression of genes encoding for stromal collagens, including Col10A1, and reduced expression of immune-associated genes, reflecting lower levels of total tumor-infiltrating lymphocytes (TILs), were strongly associated with poor pathologic response. Lower TILs in tumor biopsies correlated with reduced likelihood of achieving an optimal pathologic response, but increased expression of the Col10A1 gene product, colXα1, had greater predictive value than stromal abundance for poor response (OR = 18.9, p = 0.003), and the combination of increased colXα1 expression and low TILs was significantly associated with poor response in multivariate analysis. ROC analysis suggests strong specificity and sensitivity for this combination in predicting treatment response.

Conclusions: Increased expression of stromal colXα1 and low TILs correlate with poor pathologic response in ER+/HER2+ breast tumors. Further studies are needed to confirm their predictive value and impact on long-term outcomes, and to determine whether this collagen exerts a protective effect on the cancer cells or simply reflects other factors within the tumor microenvironment.
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http://dx.doi.org/10.1186/s12885-016-2302-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835834PMC
April 2016

Cisplatin Resistant Spheroids Model Clinically Relevant Survival Mechanisms in Ovarian Tumors.

PLoS One 2016 17;11(3):e0151089. Epub 2016 Mar 17.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 02139.

The majority of ovarian tumors eventually recur in a drug resistant form. Using cisplatin sensitive and resistant cell lines assembled into 3D spheroids we profiled gene expression and identified candidate mechanisms and biological pathways associated with cisplatin resistance. OVCAR-8 human ovarian carcinoma cells were exposed to sub-lethal concentrations of cisplatin to create a matched cisplatin-resistant cell line, OVCAR-8R. Genome-wide gene expression profiling of sensitive and resistant ovarian cancer spheroids identified 3,331 significantly differentially expressed probesets coding for 3,139 distinct protein-coding genes (Fc >2, FDR < 0.05) (S2 Table). Despite significant expression changes in some transporters including MDR1, cisplatin resistance was not associated with differences in intracellular cisplatin concentration. Cisplatin resistant cells were significantly enriched for a mesenchymal gene expression signature. OVCAR-8R resistance derived gene sets were significantly more biased to patients with shorter survival. From the most differentially expressed genes, we derived a 17-gene expression signature that identifies ovarian cancer patients with shorter overall survival in three independent datasets. We propose that the use of cisplatin resistant cell lines in 3D spheroid models is a viable approach to gain insight into resistance mechanisms relevant to ovarian tumors in patients. Our data support the emerging concept that ovarian cancers can acquire drug resistance through an epithelial-to-mesenchymal transition.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151089PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795743PMC
August 2016

Medullary carcinoma of the colon: a distinct morphology reveals a distinctive immunoregulatory microenvironment.

Mod Pathol 2016 05 11;29(5):528-41. Epub 2016 Mar 11.

Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, RI, USA.

Medullary carcinoma of the colon is a unique histologic subtype of microsatellite unstable colorectal carcinoma but little is known regarding its tumor-immunoregulatory microenvironment. The aims of this study were to characterize the immune environment of medullary carcinoma and compare it with other microsatellite unstable and microsatellite stable colorectal carcinomas. An initial gene expression microarray analysis of six cases of medullary carcinoma was used to detect potentially differentially expressed genes. We extended this analysis utilizing genomic data from the Cancer Genome Atlas to compare eight cases of medullary carcinoma with other microsatellite unstable and stable carcinomas. Finally, we evaluated expression of key immune pathway proteins and lymphocyte subsets via immunohistochemistry of a large group of medullary carcinomas (n=105) and compared these findings with three other groups: poorly differentiated, microsatellite unstable well-differentiated and microsatellite stable well-differentiated carcinomas. Microarray and the Cancer Genome Atlas data analysis identified significant upregulation of several immunoregulatory genes induced by IFNγ including IDO-1, WARS (tRNA(trp)), GBP1, GBP4, GBP5, PDCD1 (PD-1), and CD274 (PD-L1) in medullary carcinoma compared with other microsatellite unstable and microsatellite stable tumors. By immunohistochemistry, IDO-1 was expressed in 64% of medullary carcinomas compared with 19% (9/47) of poorly differentiated carcinomas, 14% (3/22) of microsatellite unstable, and 7% (2/30) of the microsatellite stable well-differentiated carcinomas (P<0.0001). tRNA(trp) was overexpressed in 81% (84/104) of medullary carcinomas, 19% (9/47) of poorly differentiated, 32% (7/22) of microsatellite unstable, and 3% (1/30) of microsatellite stable well-differentiated carcinomas (P<0.0001). Medullary carcinoma had higher mean CD8+ and PD-L1+ tumor-infiltrating lymphocytes compared with all other groups (P<0.0001). This study demonstrates overexpression of several immunoregulatory genes in microsatellite unstable colorectal carcinomas and that expression of these genes and proteins is more prevalent in the medullary carcinoma subtype, which may be of use both diagnostically and therapeutically.
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http://dx.doi.org/10.1038/modpathol.2016.54DOI Listing
May 2016

A Novel SDHA-deficient Renal Cell Carcinoma Revealed by Comprehensive Genomic Profiling.

Am J Surg Pathol 2015 Jun;39(6):858-63

Departments of *Pathology ‡Internal Medicine, Oncology Division, Rhode Island Hospital, and Alpert Medical School at Brown University, Providence, RI †Foundation Medicine Inc., Cambridge, MA §Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY.

Succinate dehydrogenase (SDH)-deficient renal cell carcinoma (RCC) is an emerging provisional entity included in the 2013 International Society of Urological Pathology Vancouver Classification. Most genomic alterations in patients with SDH-deficient RCCs involve the SDHB subunit, and the associated renal tumors have loss of immunohistochemical SDHB expression and distinctive morphologic features. Renal tumors less commonly possess genomic alterations involving the SDHC and SDHD subunits, but no SDHA alterations have as yet been described. Here we identified a novel SDHA homozygous deletion in an aggressive variant of RCC diagnosed initially as unclassified type in a 54-year-old patient. A search for novel actionable mutations by comprehensive genomic profiling based on clinical next-generation sequencing evaluating entire coding regions of 315 cancer-related genes, including all SDH subunits, was performed. Sequencing identified a novel 17 kbp homozygous deletion of 9 SDHA exons on chromosome 5p15. SDHA and SDHB immunohistochemistry further confirmed that the homozygous deletion led to the loss of SDHA and SDHB protein expression. Histologically, the tumor had a mixed pattern of high-grade papillary and collecting duct carcinoma and distinctive pale eosinophilic cytoplasmic inclusions similar to those described in SDHB-deficient RCC. This is the first report that identifies SDHA inactivation in RCC. Additional studies utilizing comprehensive genomic profiling, immunohistochemistry, and careful morphologic evaluation are needed both prospectively and retrospectively to identify the group of RCCs harboring SDHA genomic alterations.
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http://dx.doi.org/10.1097/PAS.0000000000000403DOI Listing
June 2015

Modeling and Optimization of Manufacturing Process Performance using Modelica Graphical Representation and Process Analytics Formalism.

J Intell Manuf 2018 08 17;29(6):1287-1301. Epub 2015 Dec 17.

Department of Computer Science, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080.

This paper concerns the development of a design methodology and its demonstration through a prototype system for performance modeling and optimization of manufacturing processes. The design methodology uses a Modelica simulation tool serving as the graphical user interface for manufacturing domain users such as process engineers to formulate their problems. The Process Analytics Formalism, developed at the National Institute of Standards and Technology, serves as a bridge between the Modelica classes and a commercial optimization solver. The prototype system includes (1) manufacturing model components' libraries created by using Modelica and the Process Analytics Formalism, and (2) a translator of the Modelica classes to Process Analytics Formalism, which are then compiled to mathematical programming models and solved using an optimization solver. This paper provides an experiment toward the goal of enabling manufacturing users to intuitively formulate process performance models, solve problems using optimization-based methods, and automatically get actionable recommendations.
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http://dx.doi.org/10.1007/s10845-015-1178-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391055PMC
August 2018

Notch3 overexpression promotes anoikis resistance in epithelial ovarian cancer via upregulation of COL4A2.

Mol Cancer Res 2015 Jan 28;13(1):78-85. Epub 2014 Aug 28.

Graduate Program in Pathobiology, Brown University, Providence, Rhode Island. Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.

Unlabelled: Ovarian cancer is a lethal disease with the majority of diagnosed women having distant metastases. Interestingly, although Notch3 overexpression has been correlated with poor survival in epithelial ovarian cancer (EOC), little is known about its mechanism of action. Data show that Notch3 specifically promotes anoikis resistance. In addition, data indicate a positive role for focal adhesion kinase (FAK) as well as downstream signaling kinases such as Akt and Erk 1/2 in promoting anchorage-independent growth. Mechanistically, both mRNA transcript and protein levels of type IV collagen (COL4A2) are reduced when Notch3 levels are decreased and exogenous collagen IV supplementation reverses the anoikis sensitivity. Reduction of COL4A2 expression by RNAI-mediated knockdown induces cell death. Finally, elevated Notch3 expression levels correlate with higher COL4A2 expression in human ovarian tumor specimens.

Implications: These data highlight type IV collagen as a novel therapeutic target for metastatic EOC. Visual Overview: http://mcr.aacrjournals.org/content/early/2014/11/25/1541-7786.MCR-14-0334/F1.large.jpg
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http://dx.doi.org/10.1158/1541-7786.MCR-14-0334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312524PMC
January 2015

Oxysterols synergize with statins by inhibiting SREBP-2 in ovarian cancer cells.

Gynecol Oncol 2014 Nov 16;135(2):333-41. Epub 2014 Aug 16.

Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 151 Waterman St., Providence, RI 02912, USA; Center for Genomics and Proteomics, Brown University, 70 Ship St., Providence, RI 02903, USA.

Objective: Determine mechanisms responsible for enhanced statin efficacy in a novel statin combination we name STOX (STatin-OXysterol).

Methods: Ovarian cancer cell lines were treated with combinations of statins and oxysterols. Cell viability was determined by a modified MTT assay. Apoptosis was evaluated by immunoblotting of PARP and DAPI-mediated visualization of apoptotic nuclei. STOX effects on the expression of genes of the mevalonate pathway were assessed by real-time qPCR and immunoblotting. siRNA-mediated gene silencing was used to test the involvement of oxysterol-mediated repression of SREBP-2 in STOX synergy. The impact of statin-mediated inhibition of protein prenylation and on cholesterol homeostasis was evaluated.

Results: Oxysterols dramatically enhance cytotoxicity of statins in ovarian cancer cells through increased apoptosis. Decreased expression of SREBP-2 down-regulates the mevalonate pathway and prevents the active statin-induced sterol feedback, enhancing statin toxicity. Comparison of two ovarian cancer cell lines reveals two distinct mechanisms of statin induced toxicity, namely, dependence on protein geranylgeranylation and/or perturbation of cellular cholesterol levels.

Conclusions: We provide evidence of statins' mechanisms of cytotoxicity in different ovarian cancer cells and discovered a new approach to significantly enhance the anti-tumor activity of statins. These observations provide a potential new path to improve statins as a treatment against ovarian cancer with obtainable dosages.
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http://dx.doi.org/10.1016/j.ygyno.2014.08.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516475PMC
November 2014

Prognostic microRNA expression signature from examination of colorectal primary and metastatic tumors.

Anticancer Res 2014 Aug;34(8):3957-67

Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, U.S.A. Center for Computational Molecular Biology, Brown University, Providence, RI, U.S.A. Center for Genomics and Proteomics, Brown University, Providence, RI, U.S.A.

While previous studies have described associations between specific microRNAs and colorectal cancer (CRC) metastasis, our understanding of microRNA regulation of metastatic spread remains largely unexplored. To identify microRNAs critical for disease progression, we measured microRNA expression in primary CRC tumors and synchronous liver metastases in 19 cases using quantitative polymerase chain reaction (qPCR) arrays. We identified 16 microRNAs significantly differentially expressed between primary tumors and liver metastases that distinguish primary tumors and liver metastases by hierarchical clustering. Combinations of microRNAs expressed in the primary tumor and in the metastatic tumor are associated with survival, but these signatures have no microRNAs in common. We found that increased expression of miR-210 and miR-133b in liver metastases compared to primary tumors is associated with lower survival. We propose that evaluating the change in expression between primary and metastatic tumors in each patient may lead to improved biomarker development.
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August 2014

Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease.

PLoS One 2014 14;9(4):e94476. Epub 2014 Apr 14.

Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America.

The behavior and genetics of serous epithelial ovarian cancer (EOC) metastasis, the form of the disease lethal to patients, is poorly understood. The unique properties of metastases are critical to understand to improve treatments of the disease that remains in patients after debulking surgery. We sought to identify the genetic and phenotypic landscape of metastatic progression of EOC to understand how metastases compare to primary tumors. DNA copy number and mRNA expression differences between matched primary human tumors and omental metastases, collected at the same time during debulking surgery before chemotherapy, were measured using microarrays. qPCR and immunohistochemistry validated findings. Pathway analysis of mRNA expression revealed metastatic cancer cells are more proliferative and less apoptotic than primary tumors, perhaps explaining the aggressive nature of these lesions. Most cases had copy number aberrations (CNAs) that differed between primary and metastatic tumors, but we did not detect CNAs that are recurrent across cases. A six gene expression signature distinguishes primary from metastatic tumors and predicts overall survival in independent datasets. The genetic differences between primary and metastatic tumors, yet common expression changes, suggest that the major clone in metastases is not the same as in primary tumors, but the cancer cells adapt to the omentum similarly. Together, these data highlight how ovarian tumors develop into a distinct, more aggressive metastatic state that should be considered for therapy development.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094476PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986100PMC
January 2015

Identification of ovarian cancer metastatic miRNAs.

PLoS One 2013 12;8(3):e58226. Epub 2013 Mar 12.

Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA.

Serous epithelial ovarian cancer (EOC) patients often succumb to aggressive metastatic disease, yet little is known about the behavior and genetics of ovarian cancer metastasis. Here, we aim to understand how omental metastases differ from primary tumors and how these differences may influence chemotherapy. We analyzed the miRNA expression profiles of primary EOC tumors and their respective omental metastases from 9 patients using miRNA Taqman qPCR arrays. We find 17 miRNAs with differential expression in omental lesions compared to primary tumors. miR-21, miR-150, and miR-146a have low expression in most primary tumors with significantly increased expression in omental lesions, with concomitant decreased expression of predicted mRNA targets based on mRNA expression. We find that miR-150 and miR-146a mediate spheroid size. Both miR-146a and miR-150 increase the number of residual surviving cells by 2-4 fold when challenged with lethal cisplatin concentrations. These observations suggest that at least two of the miRNAs, miR-146a and miR-150, up-regulated in omental lesions, stimulate survival and increase drug tolerance. Our observations suggest that cancer cells in omental tumors express key miRNAs differently than primary tumors, and that at least some of these microRNAs may be critical regulators of the emergence of drug resistant disease.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058226PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595263PMC
September 2013

Acute mastoiditis: the role of imaging for identifying intracranial complications.

Laryngoscope 2012 Dec 7;122(12):2813-7. Epub 2012 Sep 7.

Department of Otolaryngology-Head and Neck Surgery, Bnai Zion Medical Center, Technion-Israel Institute of Technology, Haifa, Israel.

Objectives/hypothesis: Brain CT is performed in patients presenting with acute mastoiditis (AM) to identify intracranial complications (ICC). Recently, however, the need for CT scans in such patients has been questioned owing to concerns regarding long-term effects of brain irradiation, with some clinicians claiming that the decision to scan should be based on a patient's clinical presentation. This study was aimed at characterizing the typical clinical presentation of patients who already have ICCs when diagnosed with AM, and to compare it to that of AM patients presenting without ICCs.

Study Design: Prospective case series.

Methods: All patients hospitalized with AM between July 1997 and December 2009 in an otologic tertiary referral center were divided into those with and those without ICCs on presentation. Prereferral clinical characteristics and the signs, symptoms, and inflammatory indexes at presentation were compared between the two groups.

Results: Of 71 patients presenting with AM, 10 had at least one ICC (sigmoid sinus thrombosis [nine patients], perisinus empyema [five patients], subdural abscess [one patient], and epidural abscess [one patient]). Patients with and without ICCs did not differ regarding most clinical characteristics or presenting signs and symptoms. None presented with neurological signs or cranial nerve deficits.

Conclusions: It is not possible to define an evidence-based index of suspicion for ICCs in patients with AM. Diagnostic imaging at presentation accordingly remains mandatory.
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http://dx.doi.org/10.1002/lary.22193DOI Listing
December 2012

MicroRNA profiling in mucosal biopsies of eosinophilic esophagitis patients pre and post treatment with steroids and relationship with mRNA targets.

PLoS One 2012 16;7(7):e40676. Epub 2012 Jul 16.

Department of Pathology and Laboratory Medicine, Rhode Island Hospital, the Alpert School of Medicine, Brown University, Providence, Rhode Island, United States of America.

Background: The characterization of miRNAs and their target mRNAs involved in regulation of the immune process is an area of intense research and relatively little is known governing these processes in allergic inflammation. Here we present novel findings defining the miRNA and mRNA transcriptome in eosinophilic esophagitis (EoE), an increasing recognized allergic disorder.

Methods: Esophageal epithelial miRNA and mRNA from five paired biopsies pre- and post-treatment with glucocorticosteroids were profiled using Taqman and Affymetrix arrays. Validation was performed on additional paired biopsies, untreated EoE specimens and normal controls. Differentially regulated miRNAs and mRNAs were generated, within which miRNA-mRNA target pairs with high predicted confidence were identified.

Results: Compared to the post-glucocorticoid treated esophageal mucosa, of all the 377 miRNA sequences examined, 32 miRNAs were significantly upregulated and four downregulated in the pre-treated biopsies. MiR-214 was the most upregulated (150 fold) and miR-146b-5b, 146a, 145, 142-3p and 21 were upregulated by at least 10 fold. Out of 12 miRNAs chosen for validation by qRT-PCR, five (miR-214, 146b-5p, 146a, 142-3p and 21) were confirmed and 11 shared the same trend. When the expression of the 12 miRNAs in the EoE mucosa was compared to unrelated normal mucosa, six (miR-214, 146b-5p, 146a, 21, 203, and 489) showed similar significant changes as in the paired samples and 10 of them shared the same trend. In the same five pairs of samples used to profile miRNA, 311 mRNAs were down-regulated and 35 were up-regulated in pre-treated EoE mucosa. Among them, 164 mRNAs were identified as potential targets of differentially regulated miRNAs. Further analysis revealed that immune-related genes, targeted and non-targeted by miRNAs, were among the most important genes involved in the pathogenesis of EoE.

Conclusions: Our findings add to the accumulating body of data defining a regulatory role for miRNA in immune and allergic processes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040676PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398046PMC
March 2013

Efficacy of a non-hypercalcemic vitamin-D2 derived anti-cancer agent (MT19c) and inhibition of fatty acid synthesis in an ovarian cancer xenograft model.

PLoS One 2012 3;7(4):e34443. Epub 2012 Apr 3.

Molecular Therapeutics Laboratory, Program in Women's Oncology, Department of Obstetrics and Gynecology, Women and Infants' Hospital of Rhode Island, Alpert Medical School, Brown University, Providence, Rhode Island, United States of America.

Background: Numerous vitamin-D analogs exhibited poor response rates, high systemic toxicities and hypercalcemia in human trials to treat cancer. We identified the first non-hypercalcemic anti-cancer vitamin D analog MT19c by altering the A-ring of ergocalciferol. This study describes the therapeutic efficacy and mechanism of action of MT19c in both in vitro and in vivo models.

Methodology/principal Finding: Antitumor efficacy of MT19c was evaluated in ovarian cancer cell (SKOV-3) xenografts in nude mice and a syngenic rat ovarian cancer model. Serum calcium levels of MT19c or calcitriol treated animals were measured. In-silico molecular docking simulation and a cell based VDR reporter assay revealed MT19c-VDR interaction. Genomewide mRNA analysis of MT19c treated tumors identified drug targets which were verified by immunoblotting and microscopy. Quantification of cellular malonyl CoA was carried out by HPLC-MS. A binding study with PPAR-Y receptor was performed. MT19c reduced ovarian cancer growth in xenograft and syngeneic animal models without causing hypercalcemia or acute toxicity. MT19c is a weak vitamin-D receptor (VDR) antagonist that disrupted the interaction between VDR and coactivator SRC2-3. Genome-wide mRNA analysis and western blot and microscopy of MT19c treated xenograft tumors showed inhibition of fatty acid synthase (FASN) activity. MT19c reduced cellular levels of malonyl CoA in SKOV-3 cells and inhibited EGFR/phosphoinositol-3kinase (PI-3K) activity independently of PPAR-gamma protein.

Significance: Antitumor effects of non-hypercalcemic agent MT19c provide a new approach to the design of vitamin-D based anticancer molecules and a rationale for developing MT19c as a therapeutic agent for malignant ovarian tumors by targeting oncogenic de novo lipogenesis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034443PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317945PMC
August 2012

T0901317 inhibits cisplatin-induced apoptosis in ovarian cancer cells [corrected].

Int J Gynecol Cancer 2011 Nov;21(8):1350-6

Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.

Objective: To determine the function of T0901317 in combination treatment with cisplatin in ovarian cancer cells.

Methods: We screened the effects of 3 nuclear hormone receptor ligands on cell viability in a panel of ovarian cancer cell lines. T0901317 regulation of apoptosis and cell cycle regulators was determined when applied as a single agent or in combination with cisplatin.

Results: Surprisingly, the liver X receptor agonist T0901317 had no significant effects on a panel of 7 ovarian cancer cell lines as a single agent. T0901317 does, however, significantly decrease cisplatin efficacy in at least 3 ovarian cancer cell lines. T0901317 reduces cisplatin-induced apoptosis and reverses cisplatin-induced expression of cell cycle regulators. T0901317 seems to work in a liver X receptor-, pregnane X receptor-, and farnesoid X receptor-independent manner, as agonists of these nuclear hormone receptors did not show similar effects. Interestingly, in the A2780-cp drug-resistant cell line, the effect of T0901317 is lost, suggesting that the pathways stimulated by T0901317 to reduce cisplatin efficacy could be inherently active features of the selected resistance.

Conclusions: Together, these data suggest that T0901317 inhibits cisplatin in some ovarian cancer cells. These data provide an avenue to investigate when T0901317 may be acting to promote tumor survival and drug resistance through control of apoptosis and when it may be acting as an antitumor agent as has been previously reported.
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http://dx.doi.org/10.1097/IGC.0b013e318228f558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203312PMC
November 2011

Integrated genomics of ovarian xenograft tumor progression and chemotherapy response.

BMC Cancer 2011 Jul 22;11:308. Epub 2011 Jul 22.

Molecular Therapeutics Laboratory, Program in Women’s Oncology, Department of Obstetrics and Gynecology, Women and Infants7 Hospital, Alpert Medical School of Brown University, Providence, RI 02905, USA.

Background: Ovarian cancer is the most deadly gynecological cancer with a very poor prognosis. Xenograft mouse models have proven to be one very useful tool in testing candidate therapeutic agents and gene function in vivo. In this study we identify genes and gene networks important for the efficacy of a pre-clinical anti-tumor therapeutic, MT19c.

Methods: In order to understand how ovarian xenograft tumors may be growing and responding to anti-tumor therapeutics, we used genome-wide mRNA expression and DNA copy number measurements to identify key genes and pathways that may be critical for SKOV-3 xenograft tumor progression. We compared SKOV-3 xenografts treated with the ergocalciferol derived, MT19c, to untreated tumors collected at multiple time points. Cell viability assays were used to test the function of the PPARγ agonist, Rosiglitazone, on SKOV-3 cell growth.

Results: These data indicate that a number of known survival and growth pathways including Notch signaling and general apoptosis factors are differentially expressed in treated vs. untreated xenografts. As tumors grow, cell cycle and DNA replication genes show increased expression, consistent with faster growth. The steroid nuclear receptor, PPARγ, was significantly up-regulated in MT19c treated xenografts. Surprisingly, stimulation of PPARγ with Rosiglitazone reduced the efficacy of MT19c and cisplatin suggesting that PPARγ is regulating a survival pathway in SKOV-3 cells. To identify which genes may be important for tumor growth and treatment response, we observed that MT19c down-regulates some high copy number genes and stimulates expression of some low copy number genes suggesting that these genes are particularly important for SKOV-3 xenograft growth and survival.

Conclusions: We have characterized the time dependent responses of ovarian xenograft tumors to the vitamin D analog, MT19c. Our results suggest that PPARγ promotes survival for some ovarian tumor cells. We propose that a combination of regulated expression and copy number can identify genes that are likely important for chemotherapy response. Our findings suggest a new approach to identify candidate genes that are critical for anti-tumor therapy.
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http://dx.doi.org/10.1186/1471-2407-11-308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155912PMC
July 2011

Chromatin remodeling in the aging genome of Drosophila.

Aging Cell 2010 Dec 21;9(6):971-8. Epub 2010 Oct 21.

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.

Chromatin structure affects the accessibility of DNA to transcription, repair, and replication. Changes in chromatin structure occur during development, but less is known about changes during aging. We examined the state of chromatin structure and its effect on gene expression during aging in Drosophila at the whole genome and cellular level using whole-genome tiling microarrays of activation and repressive chromatin marks, whole-genome transcriptional microarrays and single-cell immunohistochemistry. We found dramatic reorganization of chromosomal regions with age. Mapping of H3K9me3 and HP1 signals to fly chromosomes reveals in young flies the expected high enrichment in the pericentric regions, the 4th chromosome, and islands of facultative heterochromatin dispersed throughout the genome. With age, there is a striking reduction in this enrichment resulting in a nearly equivalent level of H3K9me3 and HP1 in the pericentric regions, the 4th chromosome, facultative heterochromatin, and euchromatin. These extensive changes in repressive chromatin marks are associated with alterations in age-related gene expression. Large-scale changes in repressive marks with age are further substantiated by single-cell immunohistochemistry that shows changes in nuclear distribution of H3K9me3 and HP1 marks with age. Such epigenetic changes are expected to directly or indirectly impinge upon important cellular functions such as gene expression, DNA repair, and DNA replication. The combination of genome-wide approaches such as whole-genome chromatin immunoprecipitation and transcriptional studies in conjunction with single-cell immunohistochemistry as shown here provide a first step toward defining how changes in chromatin may contribute to the process of aging in metazoans.
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http://dx.doi.org/10.1111/j.1474-9726.2010.00624.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2980570PMC
December 2010