Cancer Cell: Amplification of Distant Estrogen Response Elements Deregulates Target Genes Associated with Tamoxifen Resistance in Breast Cancer

August 12, 2013

Pei-YinHsu1  Hang-KaiHsu1  XunLan6  LiranJuan9  Pearlly S.Yan7  JadwigaLabanowska8  NylaHeerema8  Tzu-HungHsiao4  Yu-ChiaoChiu5  YidongChen34  YunlongLiu9  LangLi9RongLi1I  an M.Thompson2  Kenneth P.Nephew10  Zelton D.Sharp  1 Nameer B.Kirma1  Victor X.Jin6  Tim H.-M.Huang1 Summary A causal role of gene amplification in tumorigenesis is well known, whereas amplification of DNA regulatory elements as an oncogenic driver remains unclear. In this study, we integrated next-generation sequencing approaches to map distant estrogen response elements (DEREs) that […]

Experimental Hematology: Myelodysplastic syndrome: An inability to appropriately respond to damaged DNA?

August 1, 2013

Author links open overlay panelTingZhouab PaulHastycde Christi A.Walterbdef Alexander J.R.Bishopabde Linda M.Scottg Vivienne I.Rebelabde Myelodysplastic syndrome (MDS) is considered a hematopoietic stem cell disease that is characterized by abnormal hematopoietic differentiation and a high propensity to develop acute myeloid leukemia. It is mostly associated with advanced age, but also with prior cancer therapy and inherited […]

Pediatric Blood & Cancer: Outcomes for patients with congenital hepatoblastoma

June 24, 2013

Angela D Trobaugh-Lotrario 1, Barbara H Chaiyachati, Rebecka L Meyers, Beate Häberle, Gail E Tomlinson, Howard M Katzenstein, Marcio H Malogolowkin, Dietrich von Schweinitz, Mark Krailo, James H Feusner Abstract Background: Congenital hepatoblastoma, diagnosed in the first month of life, has been reported to have a poor prognosis; however, a comprehensive evaluation of this entity is lacking. Procedure: We retrospectively reviewed two patients from the senior authors’ […]

Bioinformatics: Exome-based analysis for RNA epigenome sequencing data

June 15, 2013

Jia Meng, Xiaodong Cui, Manjeet K. Rao, Yidong Chen, Yufei Huang Abstract Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques. Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data […]

Echocardiography: Cardiac Assessment in Pediatric Mice: Strain Analysis as a Diagnostic Measurement

June 7, 2013

Thomas G. Andrews, M.Sc.,* Merry L. Lindsey, PhD,† Richard A. Lange, MD, M.B.A,‡ and Gregory J. Aune, MD, PhD§ Echocardiography is a robust tool for assessing cardiac function in both humans and laboratory animals. Conventional echocardiographic measurements, including chamber dimensions, wall thickness, and ejection fraction are routinely obtained to assess cardiac function in mice. Recently, […]

IEEE: Estimating Conditional Probabilities for the Detection of Unfavorable Copy Number Alterations in a Targeted Therapy

June 5, 2013

Fang-Han Hsu; Edward R. Dougherty; Yidong Chen; Erchin Serpedin Abstract: Emerging targeted therapies have shown benefits such as less toxicity and higher effectiveness in specific types of cancer treatment; however, the accessibility of these advantages may rely on the correct identification of suitable patients, which remains highly immature. We assume that copy number profiles, being accessible genomic data […]

Diabetes Journal: Enhanced NF-κB Activity Impairs Vascular Function Through PARP-1–, SP-1–, and COX-2–Dependent Mechanisms in Type 2 Diabetes

June 1, 2013

Modar Kassan1,2, Soo-Kyoung Choi1,  Maria Galán1,2, Alexander Bishop3, Kazuo Umezawa4, Mohamed Trebak5, Souad Belmadani2⇑ , and Khalid Matrougui1,2⇑ Abstract Type 2 diabetes (T2D) is associated with vascular dysfunction. We hypothesized that increased nuclear factor-κB (NF-κB) signaling contributes to vascular dysfunction in T2D. We treated type 2 diabetic (db−/db−) and control (db−/db+) mice with two NF-κB inhibitors (6 mg/kg dehydroxymethylepoxyquinomicin twice a week […]

Cancer Epidemiology: Maternal pregnancy events and exposures and risk of hepatoblastoma: a Children’s Oncology Group (COG) study

June 1, 2013

Jessica R B Musselman 1, Michael K Georgieff, Julie A Ross, Gail E Tomlinson, James Feusner, Mark Krailo, Logan G Spector Abstract Background: Hepatoblastoma is a rare childhood liver cancer with an obscure etiology, however, it is potentially associated with selected pregnancy events and hepatoblastoma risk in offspring. Methods: Adjusted unconditional logistic regression estimated odds ratios (OR) and corresponding 95% confidence intervals (CI) for […]

PLOS One: CMS: A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers

April 22, 2013

Fei Gu ,Mark S. Doderer ,Yi-Wen Huang,Juan C. Roa,Paul J. Goodfellow,E. Lynette Kizer,Tim H. M. Huang ,Yidong Chen  Abstract Background DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. […]

Proteomics Clinical Applications: Using proteomics to uncover extracellular matrix interactions during cardiac remodeling

March 23, 2013

Nicolle L. Patterson, Rugmani Padmanabhan Iyer,  Lisandra E. de Castro Brás, Yaojun Li, Thomas G. Andrews, Gregory J. Aune, Richard A. Lange, Merry L. Lindsey Abstract The left ventricle (LV) responds to myocardial infarction with an orchestrated sequence of events that result in fundamental changes to both the structure and function of the myocardium. This collection of responses is termed LV […]