Publications by authors named "Amy L Olex"

24 Publications

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Associations between HIV infection and clinical spectrum of COVID-19: a population level analysis based on US National COVID Cohort Collaborative (N3C) data.

Lancet HIV 2021 Oct 13. Epub 2021 Oct 13.

South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA; Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA; Big Data Health Science Center, University of South Carolina, Columbia, SC, USA.

Background: Evidence of whether people living with HIV are at elevated risk of adverse COVID-19 outcomes is inconclusive. We aimed to investigate this association using the population-based National COVID Cohort Collaborative (N3C) data in the USA.

Methods: We included all adult (aged ≥18 years) COVID-19 cases with any health-care encounter from 54 clinical sites in the USA, with data being deposited into the N3C. The outcomes were COVID-19 disease severity, hospitalisation, and mortality. Encounters in the same health-care system beginning on or after January 1, 2018, were also included to provide information about pre-existing health conditions (eg, comorbidities). Logistic regression models were employed to estimate the association of HIV infection and HIV markers (CD4 cell count, viral load) with hospitalisation, mortality, and clinical severity of COVID-19 (multinomial). The models were initially adjusted for demographic characteristics, then subsequently adjusted for smoking, obesity, and a broad range of comorbidities. Interaction terms were added to assess moderation effects by demographic characteristics.

Findings: In the harmonised N3C data release set from Jan 1, 2020, to May 8, 2021, there were 1 436 622 adult COVID-19 cases, of these, 13 170 individuals had HIV infection. A total of 26 130 COVID-19 related deaths occurred, with 445 among people with HIV. After adjusting for all the covariates, people with HIV had higher odds of COVID-19 death (adjusted odds ratio 1·29, 95% CI 1·16-1·44) and hospitalisation (1·20, 1·15-1·26), but lower odds of mild or moderate COVID-19 (0·61, 0·59-0·64) than people without HIV. Interaction terms revealed that the elevated odds were higher among older age groups, male, Black, African American, Hispanic, or Latinx adults. A lower CD4 cell count (<200 cells per μL) was associated with all the adverse COVID-19 outcomes, while viral suppression was only associated with reduced hospitalisation.

Interpretation: Given the COVID-19 pandemic's exacerbating effects on health inequities, public health and clinical communities must strengthen services and support to prevent aggravated COVID-19 outcomes among people with HIV, particularly for those with pronounced immunodeficiency.

Funding: National Center for Advancing Translational Sciences, National Institute of Allergy and Infectious Diseases, National Institutes of Health, USA.
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http://dx.doi.org/10.1016/S2352-3018(21)00239-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8514200PMC
October 2021

Sex and Organ-Specific Risk of Major Adverse Renal or Cardiac Events in Solid Organ Transplant Recipients with COVID-19.

Am J Transplant 2021 Oct 12. Epub 2021 Oct 12.

Division of Nephology, Department of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA.

While older males are at highest risk for poor COVID-19 outcomes, it is not known if this applies to the immunosuppressed recipient of a solid organ transplant (SOT), nor how the type of allograft transplanted may impact outcomes. In a cohort study of adult (>18 years) patients testing positive for COVID-19 (Jan 01, 2020-June 21, 2021) from 56 sites across the United States identified using the National COVID Cohort Collaborative (N3C) Enclave, we used multivariable Cox proportional hazards models to assess time to MARCE after COVID-19 diagnosis in those with and without SOT. We examined the exposure of age-stratified recipient sex overall and separately in kidney, liver, lung, and heart transplant recipients. 3,996 (36.4%) SOT and 91,646 (4.8%) non-SOT patients developed MARCE. Risk of post-COVID outcomes differed by transplant allograft type with heart and kidney recipients at highest risk. Males with SOT were at increased risk of MARCE, but to a lesser degree than the non-SOT cohort (HR 0.89, 95% CI 0.81-0.98 for SOT and HR 0.61, 95% CI 0.60-0.62 for non-SOT (females versus males)). This represents the largest COVID-19 SOT cohort to date and the first-time sex-age stratified and allograft-specific COVID-19 outcomes have been explored in those with SOT.
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http://dx.doi.org/10.1111/ajt.16865DOI Listing
October 2021

Identification of nuclear export inhibitor-based combination therapies in preclinical models of triple-negative breast cancer.

Transl Oncol 2021 Dec 7;14(12):101235. Epub 2021 Oct 7.

Department of Pathology, School of Medicine, Virginia Commonwealth University, 1101 East Marshall St, Office 4-007, P.O. Box 980662, Richmond, VA 23298-0662, USA; C. Kenneth and Diane Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA USA. Electronic address:

An estimated 284,000 Americans will be diagnosed with breast cancer in 2021. Of these individuals, 15-20% have basal-like triple-negative breast cancer (TNBC), which is known to be highly metastatic. Chemotherapy is standard of care for TNBC patients, but chemoresistance is a common clinical problem. There is currently a lack of alternative, targeted treatment strategies for TNBC; this study sought to identify novel therapeutic combinations to treat basal-like TNBCs. For these studies, four human basal-like TNBC cell lines were utilized to determine the cytotoxicity profile of 1363 clinically-used drugs. Ten promising therapeutic candidates were identified, and synergism studies were performed in vitro. Two drug combinations that included KPT-330, an XPO1 inhibitor, were synergistic in all four cell lines. In vivo testing of four basal-like patient-derived xenografts (PDX) identified one combination, KPT-330 and GSK2126458 (a PI3K/mTOR inhibitor), that decreased tumor burden in mice significantly more than monotherapy with either single agent. Bulk and single-cell RNA-sequencing, immunohistochemistry, and analysis of published genomic datasets found that XPO1 was abundantly expressed in human basal-like TNBC cell lines, PDXs, and patient tumor samples. Within basal-like PDXs, XPO1 overexpression was associated with increased proliferation at the cellular level. Within patient datasets, XPO1 overexpression was correlated with greater rates of metastasis in patients with basal-like tumors. These studies identify a promising potential new combination therapy for patients with basal-like breast cancer.
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http://dx.doi.org/10.1016/j.tranon.2021.101235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8512760PMC
December 2021

COVID-19 Disease Severity among People with HIV Infection or Solid Organ Transplant in the United States: A Nationally-representative, Multicenter, Observational Cohort Study.

medRxiv 2021 Jul 28. Epub 2021 Jul 28.

Background: Individuals with immune dysfunction, including people with HIV (PWH) or solid organ transplant recipients (SOT), might have worse outcomes from COVID-19. We compared odds of COVID-19 outcomes between patients with and without immune dysfunction.

Methods: We evaluated data from the National COVID-19 Cohort Collaborative (N3C), a multicenter retrospective cohort of electronic medical record (EMR) data from across the United States, on. 1,446,913 adult patients with laboratory-confirmed SARS-CoV-2 infection. HIV, SOT, comorbidity, and HIV markers were identified from EMR data prior to SARS-CoV-2 infection. COVID-19 disease severity within 45 days of SARS-CoV-2 infection was classified into 5 categories: asymptomatic/mild disease with outpatient care; mild disease with emergency department (ED) visit; moderate disease requiring hospitalization; severe disease requiring ventilation or extracorporeal membrane oxygenation (ECMO); and death. We used multivariable, multinomial logistic regression models to compare odds of COVID-19 outcomes between patients with and without immune dysfunction.

Findings: Compared to patients without immune dysfunction, PWH and SOT had a greater likelihood of having ED visits (adjusted odds ratio [aOR]: 1.28, 95% confidence interval [CI] 1.27-1.29; aOR: 2.61, CI: 2.58-2.65, respectively), requiring ventilation or ECMO (aOR: 1.43, CI: 1.43-1.43; aOR: 4.82, CI: 4.78-4.86, respectively), and death (aOR: 1.20, CI: 1.19-1.20; aOR: 3.38, CI: 3.35-3.41, respectively). Associations were independent of sociodemographic and comorbidity burden. Compared to PWH with CD4>500 cells/mm , PWH with CD4<350 cells/mm were independently at 4.4-, 5.4-, and 7.6-times higher odds for hospitalization, requiring ventilation, and death, respectively. Increased COVID-19 severity was associated with higher levels of HIV viremia.

Interpretation: Individuals with immune dysfunction have greater risk for severe COVID-19 outcomes. More advanced HIV disease (greater immunosuppression and HIV viremia) was associated with higher odds of severe COVID-19 outcomes. Appropriate prevention and treatment strategies should be investigated to reduce the higher morbidity and mortality associated with COVID-19 among PWH and SOT.
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http://dx.doi.org/10.1101/2021.07.26.21261028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8328066PMC
July 2021

Serine residues 726 and 780 have nonredundant roles regulating STAT5a activity in luminal breast cancer.

Sci Rep 2021 06 29;11(1):13506. Epub 2021 Jun 29.

Department of Pathology, Virginia Commonwealth University, 1101 E. Marshall St, Sanger 4-006A, Richmond, VA, 23298-06629, USA.

In breast cancer, prolactin-induced activation of the transcription factor STAT5a results from the phosphorylation of STAT5a tyrosine residue 694. However, its role in mammary oncogenesis remains an unsettled debate as STAT5a exhibits functional dichotomy with both pro-differentiative and pro-proliferative target genes. Phosphorylation of STAT5a serine residues, S726 and S780, may regulate STAT5a in such a way to underlie this duality. Given hematopoiesis studies showing phospho-serine STAT5a as necessary for transformation, we hypothesized that serine phosphorylation regulates STAT5a activity to contribute to its role in mammary oncogenesis, specifically in luminal breast cancer. Here, phosphorylation of S726-, S780-, and Y694-STAT5a in response to prolactin in MCF7 luminal breast cancer cells was investigated with STAT5a knockdown and rescue with Y694F-, S726A-, or S780A-STAT5a, where the phospho-sites were mutated. RNA-sequencing and subsequent Ingenuity Pathway Analysis predicted that loss of each phospho-site differentially affected both prolactin-induced gene expression as well as functional pathways of breast cancer (e.g. cell survival, proliferation, and colony formation). In vitro studies of anchorage-independent growth and proliferation confirmed distinct phenotypes: whereas S780A-STAT5a decreased clonogenicity, S726A-STAT5a decreased proliferation in response to prolactin compared to wild type STAT5a. Collectively, these studies provide novel insights into STAT5a activation in breast cancer pathogenesis.
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http://dx.doi.org/10.1038/s41598-021-92830-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8242097PMC
June 2021

Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines.

Gigascience 2021 Apr;10(4)

Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA.

Background: Sequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined.

Results: We evaluated the effect of mouse read removal on the quality of Hi-C data using in silico created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated 2 experimental PDX Hi-C datasets using different library preparation strategies. We evaluated 3 alignment strategies (Direct, Xenome, Combined) and 3 pipelines (Juicer, HiC-Pro, HiCExplorer) on Hi-C data quality.

Conclusions: Removal of mouse reads had little-to-no effect on data quality as compared with the results obtained with the Direct alignment strategy. Juicer extracted more valid chromatin interactions for Hi-C matrices, regardless of the mouse read removal strategy. However, the pipeline effect was minimal, while the library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.
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http://dx.doi.org/10.1093/gigascience/giab022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8058593PMC
April 2021

Review of Temporal Reasoning in the Clinical Domain for Timeline Extraction: Where we are and where we need to be.

J Biomed Inform 2021 06 14;118:103784. Epub 2021 Apr 14.

Virginia Commonwealth University, 401 S. Main St., Richmond, VA 23284, USA.

Understanding a patient's medical history, such as how long symptoms last or when a procedure was performed, is vital to diagnosing problems and providing good care. Frequently, important information regarding a patient's medical timeline is buried in their Electronic Health Record (EHR) in the form of unstructured clinical notes. This results in care providers spending time reading notes in a patient's record in order to become familiar with their condition prior to developing a diagnosis or treatment plan. Valuable time could be saved if this information was readily accessible for searching and visualization for fast comprehension by the medical team. Clinical Natural Language Processing (NLP) is an area of research that aims to build computational methods to automatically extract medically relevant information from unstructured clinical texts. A key component of Clinical NLP is Temporal Reasoning, as understanding a patient's medical history relies heavily on the ability to identify, assimilate, and reason over temporal information. In this work, we review the current state of Temporal Reasoning in the clinical domain with respect to Clinical Timeline Extraction. While much progress has been made, the current state-of-the-art still has a ways to go before practical application in the clinical setting will be possible. Areas such as handling relative and implicit temporal expressions, both in normalization and in identifying temporal relationships, improving co-reference resolution, and building inter-operable timeline extraction tools that can integrate multiple types of data are in need of new and innovative solutions to improve performance on clinical data.
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http://dx.doi.org/10.1016/j.jbi.2021.103784DOI Listing
June 2021

The human intermediate prolactin receptor is a mammary proto-oncogene.

NPJ Breast Cancer 2021 Mar 26;7(1):37. Epub 2021 Mar 26.

Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.

The hormone prolactin (PRL) and its receptor (hPRLr) are significantly involved in breast cancer pathogenesis. The intermediate hPRLr (hPRLrI) is an alternatively-spliced isoform, capable of stimulating cellular viability and proliferation. An analogous truncated mouse PRLr (mPRLr) was recently found to be oncogenic when co-expressed with wild-type mPRLr. The goal of this study was to determine if a similar transforming event occurs with the hPRLr in human breast epithelial cells and to better understand the mechanism behind such transformation. hPRLrL+I co-expression in MCF10AT cells resulted in robust in vivo and in vitro transformation, while hPRLrI knock-down in MCF7 cells significantly decreased in vitro malignant potential. hPRLrL+I heterodimers displayed greater stability than hPRLrL homodimers, and while being capable of activating Jak2, Ras, and MAPK, they were unable to induce Stat5a tyrosine phosphorylation. Both immunohistochemical breast cancer tissue microarray data and RNA sequencing analyses using The Cancer Genome Atlas (TCGA) identified that higher hPRLrI expression associates with triple-negative breast cancer. These studies indicate the hPRLrI, when expressed alongside hPRLrL, participates in mammary transformation, and represents a novel oncogenic mechanism.
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http://dx.doi.org/10.1038/s41523-021-00243-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7997966PMC
March 2021

Regulatory T Cells Support Breast Cancer Progression by Opposing IFN-γ-Dependent Functional Reprogramming of Myeloid Cells.

Cell Rep 2020 12;33(10):108482

Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA. Electronic address:

Regulatory T (Treg) cell infiltration of solid tumors often correlates with poor prognosis, but their tumor-suppressive function lacks mechanistic understanding. Through a combination of transgenic mice, cell fate mapping, adoptive transfer, and co-injection strategies, we demonstrate that Treg cell ablation-dependent anti-tumor effects in murine breast cancer require intratumoral recruitment of CCR2 inflammatory monocytes, which primarily differentiate into tumor-associated macrophages (TAMs), and lead to reprogramming of their function in an IFN-γ-dependent manner. Furthermore, transcriptomic signatures from murine TAMs in Treg cell-ablated conditions correlate with increased overall survival in human breast cancer. Our studies highlight the strong myeloid dependency of breast cancer and provide the basis for the development of therapeutic strategies based on manipulation of the IFN-γ signaling pathway in monocytes.
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http://dx.doi.org/10.1016/j.celrep.2020.108482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7811278PMC
December 2020

Local Topic Mining for Reflective Medical Writing.

AMIA Jt Summits Transl Sci Proc 2020 30;2020:459-468. Epub 2020 May 30.

Virginia Commonwealth University Health System, Richmond, VA, USA.

Reflective writing is used by medical educators to identify challenges and promote inter-professional skills. These non-medical skills are central to leadership and career development, and are clinically relevant and vital to a trainees success as a practicing physician. However, identification of actionable feedback from reflective writings can be chal- lenging. In this work, we utilize a Natural Language Processing pipeline that incorporates a seeded Term Frequency- Inverse Document Frequency matrix along with sentence-level summarization, sentiment analysis, and clustering to organize sentences into groups, which can aid educators in assessing common challenges experienced by Acting In- terns. Automated analysis of reflective writing is difficult due to its subjective nature; however, our method is able to identify known and new challenges such as issues accessing the electronic health system and adjusting to specialty differences. Medical educators can utilize these topics to identify areas needing attention in the medical curriculum and help students through this transitional time.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233034PMC
May 2020

Analysis of Inter-Domain and Cross-Domain Drug Review Polarity Classification.

AMIA Jt Summits Transl Sci Proc 2020 30;2020:201-210. Epub 2020 May 30.

Virginia Commonwealth University, Richmond, VA.

Individuals increasingly rely on social media to discuss health-related issues. One way to provide easier access to relevant in- formation is through sentiment analysis - classifying text into polarity classes such as positive and negative. In this paper, we generated freely available datasets of WebMD.com drug reviews and star ratings for , , , , and drugs. We explored four supervised learning models: Naive Bayes, Random Forests, Support Vector Machines, and Convolutional Neural Networks for the purpose of determining the polarity of drug reviews. We conducted inter-domain and cross-domain evaluations. We found that SVM obtained the highest f-measure on average and that cross-domain training produced similar or higher results to models trained directly on their respective datasets.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233089PMC
May 2020

Separation of breast cancer and organ microenvironment transcriptomes in metastases.

Breast Cancer Res 2019 03 6;21(1):36. Epub 2019 Mar 6.

Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA.

Background: The seed and soil hypothesis was proposed over a century ago to describe why cancer cells (seeds) grow in certain organs (soil). Since then, the genetic properties that define the cancer cells have been heavily investigated; however, genomic mediators within the organ microenvironment that mediate successful metastatic growth are less understood. These studies sought to identify cancer- and organ-specific genomic programs that mediate metastasis.

Methods: In these studies, a set of 14 human breast cancer patient-derived xenograft (PDX) metastasis models was developed and then tested for metastatic tropism with two approaches: spontaneous metastases from mammary tumors and intravenous injection of PDX cells. The transcriptomes of the cancer cells when growing as tumors or metastases were separated from the transcriptomes of the microenvironment via species-specific separation of the genomes. Drug treatment of PDX spheroids was performed to determine if genes activated in metastases may identify targetable mediators of viability.

Results: The experimental approaches that generated metastases in PDX models were identified. RNA sequencing of 134 tumors, metastases, and normal non-metastatic organs identified cancer- and organ-specific genomic properties that mediated metastasis. A common genomic response of the liver microenvironment was found to occur in reaction to the invading PDX cells. Genes within the cancer cells were found to be either transiently regulated by the microenvironment or permanently altered due to clonal selection of metastatic sublines. Gene Set Enrichment Analyses identified more than 400 gene signatures that were commonly activated in metastases across basal-like PDXs. A Src signaling signature was found to be extensively upregulated in metastases, and Src inhibitors were found to be cytotoxic to PDX spheroids.

Conclusions: These studies identified that during the growth of breast cancer metastases, there were genomic changes that occurred within both the cancer cells and the organ microenvironment. We hypothesize that pathways upregulated in metastases are mediators of viability and that simultaneously targeting changes within different cancer cell pathways and/or different tissue compartments may be needed for inhibition of disease progression.
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http://dx.doi.org/10.1186/s13058-019-1123-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404325PMC
March 2019

Characterizing the efficacy of cancer therapeutics in patient-derived xenograft models of metastatic breast cancer.

Breast Cancer Res Treat 2018 Jul 12;170(2):221-234. Epub 2018 Mar 12.

Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23298, USA.

Purpose: Basal-like breast cancers are aggressive and often metastasize to vital organs. Treatment is largely limited to chemotherapy. This study aims to characterize the efficacy of cancer therapeutics in vitro and in vivo within the primary tumor and metastatic setting, using patient-derived xenograft (PDX) models.

Methods: We employed two basal-like, triple-negative PDX models, WHIM2 and WHIM30. PDX cells, obtained from mammary tumors grown in mice, were treated with twelve cancer therapeutics to evaluate their cytotoxicity in vitro. Four of the effective drugs-carboplatin, cyclophosphamide, bortezomib, and dacarbazine-were tested in vivo for their efficacy in treating mammary tumors, and metastases generated by intracardiac injection of tumor cells.

Results: RNA sequencing showed that global gene expression of PDX cells grown in the mammary gland was similar to those tested in culture. In vitro, carboplatin was cytotoxic to WHIM30 but not WHIM2, whereas bortezomib, dacarbazine, and cyclophosphamide were cytotoxic to both lines. Yet, these drugs were ineffective in treating both primary and metastatic WHIM2 tumors in vivo. Carboplatin and cyclophosphamide were effective in treating WHIM30 mammary tumors and reducing metastatic burden in the brain, liver, and lungs. WHIM2 and WHIM30 metastases showed distinct patterns of cytokeratin and vimentin expression, regardless of treatment, suggesting that different tumor cell subpopulations may preferentially seed in different organs.

Conclusions: This study highlights the utility of PDX models for studying the efficacy of therapeutics in reducing metastatic burden in specific organs. The differential treatment responses between two PDX models of the same intrinsic subtype, in both the primary and metastatic setting, recapitulates the challenges faced in treating cancer patients and highlights the need for combination therapies and predictive biomarkers.
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http://dx.doi.org/10.1007/s10549-018-4748-4DOI Listing
July 2018

Identification of Transcriptional and Receptor Networks That Control Root Responses to Ethylene.

Plant Physiol 2018 03 19;176(3):2095-2118. Epub 2017 Dec 19.

Department of Biology and Center for Molecular Signaling, Wake Forest University, Winston-Salem, North Carolina 27109

Transcriptomic analyses with high temporal resolution provide substantial new insight into hormonal response networks. This study identified the kinetics of genome-wide transcript abundance changes in response to elevated levels of the plant hormone ethylene in roots from light-grown Arabidopsis () seedlings, which were overlaid on time-matched developmental changes. Functional annotation of clusters of transcripts with similar temporal patterns revealed rapidly induced clusters with known ethylene function and more slowly regulated clusters with novel predicted functions linked to root development. In contrast to studies with dark-grown seedlings, where the canonical ethylene response transcription factor, EIN3, is central to ethylene-mediated development, the roots of and single and double mutants still respond to ethylene in light-grown seedlings. Additionally, a subset of these clusters of ethylene-responsive transcripts were enriched in targets of EIN3 and ERFs. These results are consistent with EIN3-independent developmental and transcriptional changes in light-grown roots. Examination of single and multiple gain-of-function and loss-of-function receptor mutants revealed that, of the five ethylene receptors, ETR1 controls lateral root and root hair initiation and elongation and the synthesis of other receptors. These results provide new insight into the transcriptional and developmental responses to ethylene in light-grown seedlings.
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http://dx.doi.org/10.1104/pp.17.00907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841720PMC
March 2018

Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma.

Oncotarget 2017 03;8(11):17684-17699

Department of Oral and Craniofacial Molecular Biology, VCU Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, VA, USA.

Human papillomavirus (HPV) DNA is detected in up to 80% of oropharyngeal carcinomas (OPC) and this HPV positive disease has reached epidemic proportions. To increase our understanding of the disease, we investigated the status of the HPV16 genome in HPV-positive head and neck cancers (HNC). Raw RNA-Seq and Whole Genome Sequence data from The Cancer Genome Atlas HNC samples were analyzed to gain a full understanding of the HPV genome status for these tumors. Several remarkable and novel observations were made following this analysis. Firstly, there are three main HPV genome states in these tumors that are split relatively evenly: An episomal only state, an integrated state, and a state in which the viral genome exists as a hybrid episome with human DNA. Secondly, none of the tumors expressed high levels of E6; E6*I is the dominant variant expressed in all tumors. The most striking conclusion from this study is that around three quarters of HPV16 positive HNC contain episomal versions of the viral genome that are likely replicating in an E1-E2 dependent manner. The clinical and therapeutic implications of these observations are discussed.
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http://dx.doi.org/10.18632/oncotarget.15179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5392278PMC
March 2017

Angiopoietin pathway gene expression associated with poor breast cancer survival.

Breast Cancer Res Treat 2017 02 6;162(1):191-198. Epub 2017 Jan 6.

Breast Surgery Service, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo NY 14263.

Purpose: Angiogenesis is one of the hallmarks of cancer and is essential for cancer progression and metastasis. However, clinical trials with vascular endothelial growth factor (VEGF) pathway inhibitors have failed to show overall survival benefit in breast cancer. Targeted therapy against the angiopoietin pathway, a downstream angiogenesis cascade, could be effective in breast cancer. This study investigates the association of angiopoietin pathway gene expression with breast cancer survival using a "big data" approach employing RNA sequencing data from The Cancer Genome Atlas (TCGA).

Methods: A total of 888 patients with adequate gene expression, disease-free survival (DFS), and overall survival (OS) data were selected for analysis. DFS and OS were calculated for patients with high and low expression of angiopoietin and VEGF pathway genes using TCGA data. Gene-specific thresholds to dichotomize patients into high and low expression were determined and survival plots were generated.

Results: The TCGA cohort was representative of national breast cancer patients with respect to stage, pathology, and survival. High Ang2 gene expression was associated with not only decreased DFS (p = 0.05), but also decreased OS (p < 0.05). High co-expression of Ang2 and its receptor Tie2 was associated with both decreased DFS and OS (p < 0.05). There was strong correlation between angiopoietin and VEGF pathway genes. While high expression of VEGFA alone was not associated with survival, high co-expression with Ang2 was associated with decreased OS.

Conclusions: This study validates TCGA as a representative database providing genomic data and survival outcomes in breast cancer. Our TCGA data support the angiopoietin pathway as a key mediator in the pathologic angiogenic switch in breast cancer.
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http://dx.doi.org/10.1007/s10549-017-4102-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5290093PMC
February 2017

Impact of the Type I Interferon Receptor on the Global Gene Expression Program During the Course of Dendritic Cell Maturation Induced by Polyinosinic Polycytidylic Acid.

J Interferon Cytokine Res 2016 06 1;36(6):382-400. Epub 2016 Apr 1.

4 Department of Biological Sciences, Auburn University , Auburn, Alabama.

Dendritic cell (DC) maturation involves widespread changes in cellular function and gene expression. The regulatory role of IFNAR in the program of DC maturation remains incompletely defined. Thus, the time evolution impact of IFNAR on this process was evaluated. Changes in DC phenotype, function, and gene expression induced by poly I:C were measured in wild-type and IFNAR(-/-) DC at 9 time points over 24 h. Temporal gene expression profiles were filtered on consistency and response magnitude across replicates. The number of genes whose expression was altered by poly I:C treatment was greatly reduced in IFNAR(-/-) DC, including the majority of the downregulated gene expression program previously observed in wild-type (WT) DC. Furthermore, the number of genes upregulated was almost equal between WT and IFNAR(-/-) DC, yet the identities of those genes were distinct. Integrating these data with protein-protein interaction data revealed several novel subnetworks active during maturation, including nucleotide synthesis, metabolism, and repair. A subnetwork associated with redox activity was uniquely identified in IFNAR(-/-) DC. Overall, temporal gene expression and network analyses identified many genes regulated by the type I interferon response and revealed previously unidentified aspects of the DC maturation process.
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http://dx.doi.org/10.1089/jir.2014.0150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892211PMC
June 2016

Integration of gene expression data with network-based analysis to identify signaling and metabolic pathways regulated during the development of osteoarthritis.

Gene 2014 May 12;542(1):38-45. Epub 2014 Mar 12.

Department of Internal Medicine, Section of Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA. Electronic address:

Osteoarthritis (OA) is characterized by remodeling and degradation of joint tissues. Microarray studies have led to a better understanding of the molecular changes that occur in tissues affected by conditions such as OA; however, such analyses are limited to the identification of a list of genes with altered transcript expression, usually at a single time point during disease progression. While these lists have identified many novel genes that are altered during the disease process, they are unable to identify perturbed relationships between genes and gene products. In this work, we have integrated a time course gene expression dataset with network analysis to gain a better systems level understanding of the early events that occur during the development of OA in a mouse model. The subnetworks that were enriched at one or more of the time points examined (2, 4, 8, and 16 weeks after induction of OA) contained genes from several pathways proposed to be important to the OA process, including the extracellular matrix-receptor interaction and the focal adhesion pathways and the Wnt, Hedgehog and TGF-β signaling pathways. The genes within the subnetworks were most active at the 2 and 4 week time points and included genes not previously studied in the OA process. A unique pathway, riboflavin metabolism, was active at the 4 week time point. These results suggest that the incorporation of network-type analyses along with time series microarray data will lead to advancements in our understanding of complex diseases such as OA at a systems level, and may provide novel insights into the pathways and processes involved in disease pathogenesis.
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http://dx.doi.org/10.1016/j.gene.2014.03.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031746PMC
May 2014

Broad phenotypic changes associated with gain of radiation resistance in head and neck squamous cell cancer.

Antioxid Redox Signal 2014 Jul 10;21(2):221-36. Epub 2014 Apr 10.

1 Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina.

Aims: The central issue of resistance to radiation remains a significant challenge in the treatment of cancer despite improvements in treatment modality and emergence of new therapies. To facilitate the identification of molecular factors that elicit protection against ionizing radiation, we developed a matched model of radiation resistance for head and neck squamous cell cancer (HNSCC) and characterized its properties using quantitative mass spectrometry and complementary assays.

Results: Functional network analysis of proteomics data identified DNA replication and base excision repair, extracellular matrix-receptor interaction, cell cycle, focal adhesion, and regulation of actin cytoskeleton as significantly up- or downregulated networks in resistant (rSCC-61) HNSCC cells. Upregulated proteins in rSCC-61 included a number of cytokeratins, fatty acid synthase, and antioxidant proteins. In addition, the rSCC-61 cells displayed two unexpected features compared with parental radiation-sensitive SCC-61 cells: (i) rSCC-61 had increased sensitivity to Erlotinib, a small-molecule inhibitor of epidermal growth factor receptor; and (ii) there was evidence of mesenchymal-to-epithelial transition in rSCC-61, confirmed by the expression of protein markers and functional assays (e.g., Vimentin, migration).

Innovation: The matched model of radiation resistance presented here shows that multiple signaling and metabolic pathways converge to produce the rSCC-61 phenotype, and this points to the function of the antioxidant system as a major regulator of resistance to ionizing radiation in rSCC-61, a phenomenon further confirmed by analysis of HNSCC tumor samples.

Conclusion: The rSCC-61/SCC-61 model provides the opportunity for future investigations of the redox-regulated mechanisms of response to combined radiation and Erlotinib in a preclinical setting.
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http://dx.doi.org/10.1089/ars.2013.5690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060837PMC
July 2014

A kinetic analysis of the auxin transcriptome reveals cell wall remodeling proteins that modulate lateral root development in Arabidopsis.

Plant Cell 2013 Sep 17;25(9):3329-46. Epub 2013 Sep 17.

Department of Biology, Wake Forest University, Winston Salem, North Carolina 27109.

To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction. Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA-regulated root growth and development. This reverse-genetic screen yielded eight mutants with root phenotypes. Detailed characterization of seedlings with mutations in cellulase3/glycosylhydrolase9b3 and leucine rich extensin2, genes not normally linked to auxin response, revealed defects in the early and late stages of lateral root development, respectively. The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development.
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http://dx.doi.org/10.1105/tpc.113.114868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809535PMC
September 2013

Disease progression and phasic changes in gene expression in a mouse model of osteoarthritis.

PLoS One 2013 28;8(1):e54633. Epub 2013 Jan 28.

Department of Internal Medicine, Section of Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA.

Osteoarthritis (OA) is the most common form of arthritis and has multiple risk factors including joint injury. The purpose of this study was to characterize the histologic development of OA in a mouse model where OA is induced by destabilization of the medial meniscus (DMM model) and to identify genes regulated during different stages of the disease, using RNA isolated from the joint "organ" and analyzed using microarrays. Histologic changes seen in OA, including articular cartilage lesions and osteophytes, were present in the medial tibial plateaus of the DMM knees beginning at the earliest (2 week) time point and became progressively more severe by 16 weeks. 427 probe sets (371 genes) from the microarrays passed consistency and significance filters. There was an initial up-regulation at 2 and 4 weeks of genes involved in morphogenesis, differentiation, and development, including growth factor and matrix genes, as well as transcription factors including Atf2, Creb3l1, and Erg. Most genes were off or down-regulated at 8 weeks with the most highly down-regulated genes involved in cell division and the cytoskeleton. Gene expression increased at 16 weeks, in particular extracellular matrix genes including Prelp, Col3a1 and fibromodulin. Immunostaining revealed the presence of these three proteins in cartilage and soft tissues including ligaments as well as in the fibrocartilage covering osteophytes. The results support a phasic development of OA with early matrix remodeling and transcriptional activity followed by a more quiescent period that is not maintained. This implies that the response to an OA intervention will depend on the timing of the intervention. The quiescent period at 8 weeks may be due to the maturation of the osteophytes which are thought to temporarily stabilize the joint.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054633PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557277PMC
August 2013

Microarray analysis reveals age-related differences in gene expression during the development of osteoarthritis in mice.

Arthritis Rheum 2012 Mar;64(3):705-17

Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA.

Objective: To better understand the contribution of age to the development of osteoarthritis (OA).

Methods: Surgical destabilization of the medial meniscus (DMM) was used to model OA in 12-week-old and 12-month-old male C57BL/6 mice. OA severity was evaluated histologically. RNA used for microarray and real-time polymerase chain reaction analysis was isolated from joint tissue collected from the medial side of the joint, including cartilage, meniscus, subchondral bone, and the joint capsule with synovium. Computational analysis was used to identify patterns of gene expression, and immunohistochemistry was used to evaluate tissue distribution of selected proteins.

Results: OA was more severe in older mice than in young mice. Only 55 genes showed a similar expression with DMM-induced OA in the 2 age groups, while 493 genes showed differential expression, the majority having increased expression in older mice. Functional categories for similarly expressed genes included extracellular matrix- and cell adhesion-related genes; differentially expressed genes included those related to muscle structure and development and immune response genes. Comparison of expression in sham-operated control joints revealed an age-related decrease in matrix gene expression and an increase in immune and defense response gene expression. Interleukin-33 was present in multiple joint tissue cells, while CCL21 was more localized to chondrocytes and meniscal cells. Periostin was found in the extracellular matrix of cartilage and meniscus.

Conclusion: Age affects both the basal pattern of gene expression in joint tissues and the response to surgically induced OA. Examining tissue from the joint beyond only cartilage revealed novel genes and proteins that would be important to consider in OA.
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http://dx.doi.org/10.1002/art.33388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269534PMC
March 2012

SC²ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data.

Bioinformatics 2011 May 3;27(9):1330-1. Epub 2011 Mar 3.

Department of Computer Science and Department of Physics, Wake Forest University, Winston-Salem, NC 27109, USA.

Unlabelled: Standard and Consensus Clustering Analysis Tool for Microarray Data (SC²ATmd) is a MATLAB-implemented application specifically designed for the exploration of microarray gene expression data via clustering. Implementation of two versions of the clustering validation method figure of merit allows for performance comparisons between different clustering algorithms, and tailors the cluster analysis process to the varying characteristics of each dataset. Along with standard clustering algorithms this application also offers a consensus clustering method that can generate reproducible clusters across replicate experiments or different clustering algorithms. This application was designed specifically for the analysis of gene expression data, but may be used with any numerical data as long as it is in the right format.

Availability: SC²ATmd may be freely downloaded from http://www.compbiosci.wfu.edu/tools.htm.
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http://dx.doi.org/10.1093/bioinformatics/btr115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109516PMC
May 2011

Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates.

BMC Immunol 2010 Aug 3;11:41. Epub 2010 Aug 3.

Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109, USA.

Background: Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment.

Results: The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism.

Conclusions: The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates.
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http://dx.doi.org/10.1186/1471-2172-11-41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928180PMC
August 2010
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