Search tips
Search criteria

Results 1-25 (1045)

Clipboard (0)

Select a Filter Below

more »
Year of Publication
more »
1.  Interferon Lambda Alleles Predict Innate Antiviral Immune Responses and Hepatitis C Virus Permissiveness 
Cell host & microbe  2014;15(2):190-202.
Hepatitis C virus (HCV) infection can result in viral chronicity or clearance. Although host genetics and particularly genetic variation in the interferon lambda (IFNL) locus are associated with spontaneous HCV clearance and treatment success, the mechanisms guiding these clinical outcomes remain unknown. Using a laser capture microdissection-driven unbiased systems virology approach, we isolated and transcriptionally profiled HCV-infected and adjacent primary human hepatocytes (PHH) approaching single cell resolution. An innate antiviral immune signature dominated the transcriptional response, but differed in magnitude and diversity between HCV-infected and adjacent cells. Molecular signatures associated with more effective antiviral control were determined by comparing donors with high and low infection frequencies. Cells from donors with clinically unfavorable IFNL genotypes were infected at a greater frequency and exhibited dampened antiviral and cell death responses. These data suggest that early virus-host interactions, particularly host genetics and induction of innate immunity, critically determine the outcome of HCV infection.
PMCID: PMC4104123  PMID: 24528865
2.  Systemic Therapy, Clinical Outcomes, and Overall Survival in Locally Advanced or Metastatic Pulmonary Carcinoid 
Data to guide the management of advanced pulmonary carcinoid (APC) come from retrospective reports and subgroup analyses of trials that included mainly extrapulmonary carcinoid tumors. We report the largest series to date of 49 patients with locally advanced or metastatic pulmonary carcinoid.
The Johns Hopkins Pathology Database was reviewed for APC patients treated between January 1992 and December 2012. Data on time to recurrence, progression-free survival, and overall survival were estimated by using the Kaplan–Meier method.
Forty-nine patients were treated for APC in the specified time period. Median time to recurrence after surgical resection was 2.5 years (atypical carcinoid [AC] versus typical carcinoid [TC], 2.5 versus 6.3 years; p = 0.063). Median survival with advanced disease was 7.1 years and significantly longer for TC compared with AC (10.2 versus 4 years; p = 0.009). Among the diverse systemic therapies used, responses occurred in four of 17 patients (23.5%) who received platinum/ etoposide with a median progression-free survival of 7 months.
Although systemic chemotherapy has moderate activity for APC, novel approaches are required. TC and AC, although both classified as pulmonary carcinoid, are clearly different clinical and molecular entities and require separate treatment paradigms in the advanced/metastatic setting.
PMCID: PMC4322909  PMID: 24518093
Pulmonary carcinoid; Metastatic carcinoid; Chemotherapy pulmonary carcinoid; Chemotherapy bronchial carcinoid; Therapy carcinoid; Atypical carcinoid; Typical carcinoid
3.  Interferon-Stimulated Genes: A Complex Web of Host Defenses 
Annual review of immunology  2014;32:513-545.
Interferon-stimulated gene (ISG) products take on a number of diverse roles. Collectively, they are highly effective at resisting and controlling pathogens. In this review, we begin by introducing interferon (IFN) and the JAK-STAT signaling pathway to highlight features that impact ISG production. Next, we describe ways in which ISGs both enhance innate pathogen-sensing capabilities and negatively regulate signaling through the JAK-STAT pathway. Several ISGs that directly inhibit virus infection are described with an emphasis on those that impact early and late stages of the virus life cycle. Finally, we describe ongoing efforts to identify and characterize antiviral ISGs, and we provide a forward-looking perspective on the ISG landscape.
PMCID: PMC4313732  PMID: 24555472
innate immunity; pathogen recognition; desensitization; antiviral effectors
4.  Tumor-Associated Macrophages Are a Useful Biomarker to Predict Recurrence After Surgical Resection of Non-Functional Pancreatic Neuroendocrine Tumors 
Annals of surgery  2014;260(6):1088-1094.
PMCID: PMC4312612  PMID: 25389924
pancreatic neoplasm; neuroendocrine tumors; tumor-associated macrophages; Ki-67 index
5.  Multifaceted Activities of Type I Interferon Are Revealed by a Receptor Antagonist 
Science signaling  2014;7(327):ra50.
Type I interferons (IFNs), including various IFN-α isoforms and IFN-β, are a family of homologous, multifunctional cytokines. IFNs activate different cellular responses by binding to a common receptor that consists of two subunits, IFNAR1 and IFNAR2. In addition to stimulating antiviral responses, they also inhibit cell proliferation and modulate other immune responses. We characterized various IFNs, including a mutant IFN-α2 (IFN-1ant) that bound tightly to IFNAR2 but had markedly reduced binding to IFNAR1. Whereas IFN-1ant stimulated antiviral activity in a range of cell lines, it failed to elicit immunomodulatory and antiproliferative activities. The antiviral activities of the various IFNs tested depended on a set of IFN-sensitive genes (the “robust” genes) that were controlled by canonical IFN response elements and responded at low concentrations of IFNs. Conversely, these elements were not found in the promoters of genes required for the antiproliferative responses of IFNs (the “tunable” genes). The extent of expression of tunable genes was cell type–specific and correlated with the magnitude of the antiproliferative effects of the various IFNs. Although IFN-1ant induced the expression of robust genes similarly in five different cell lines, its antiviral activity was virus- and cell type–specific. Our findings suggest that IFN-1ant may be a therapeutic candidate for the treatment of specific viral infections without inducing the immunomodulatory and antiproliferative functions of wild-type IFN.
PMCID: PMC4311876  PMID: 24866020
6.  Evaluation of Commercially Available RNA Amplification Kits for RNA Sequencing Using Very Low Input Amounts of Total RNA 
This article includes supplemental data. Please visit to obtain this information.Multiple recent publications on RNA sequencing (RNA-seq) have demonstrated the power of next-generation sequencing technologies in whole-transcriptome analysis. Vendor-specific protocols used for RNA library construction often require at least 100 ng total RNA. However, under certain conditions, much less RNA is available for library construction. In these cases, effective transcriptome profiling requires amplification of subnanogram amounts of RNA. Several commercial RNA amplification kits are available for amplification prior to library construction for next-generation sequencing, but these kits have not been comprehensively field evaluated for accuracy and performance of RNA-seq for picogram amounts of RNA. To address this, 4 types of amplification kits were tested with 3 different concentrations, from 5 ng to 50 pg, of a commercially available RNA. Kits were tested at multiple sites to assess reproducibility and ease of use. The human total reference RNA used was spiked with a control pool of RNA molecules in order to further evaluate quantitative recovery of input material. Additional control data sets were generated from libraries constructed following polyA selection or ribosomal depletion using established kits and protocols. cDNA was collected from the different sites, and libraries were synthesized at a single site using established protocols. Sequencing runs were carried out on the Illumina platform. Numerous metrics were compared among the kits and dilutions used. Overall, no single kit appeared to meet all the challenges of small input material. However, it is encouraging that excellent data can be recovered with even the 50 pg input total RNA.
PMCID: PMC4310221  PMID: 25649271
cDNA synthesis kits; polyA; ribodepletion
7.  Factors associated with adherence to oral antihyperglycemic monotherapy in patients with type 2 diabetes 
To estimate the rate of adherence to oral antihyperglycemic monotherapy for patients with type 2 diabetes in the US and describe factors associated with adherence in these patients.
Materials and methods
In this retrospective cohort analysis, patients aged 18 years or older with a type 2 diabetes diagnosis received between 1 January 2007 and 31 March 2010 were identified using a large US-based health care claims database. The index date was defined as the date of the first prescription for oral antihyperglycemic monotherapy during this period. Patients had to have continuous enrollment in the claims database for 12 months before and after the index date. Adherence was assessed using proportion of days covered (PDC) and an adjusted logistic regression analysis was performed to evaluate factors associated with adherence (PDC ≥80%).
Of the 133,449 eligible patients, the mean age was 61 years and 51% were men. Mean PDC was 75% and the proportion of patients adherent to oral antihyperglycemic monotherapy was 59%. Both mean PDC and PDC ≥80% increased with increasing age and the number of concomitant medications, and were slightly higher in men compared to women. Results from the logistic regression demonstrate an increased likelihood of non-adherence for patients who were younger, new to therapy, on a twice-daily dose, female, or on fewer than three concomitant medications compared to their reference groups. Higher average daily out-of-pocket pharmacy expense was also associated with an increased likelihood of non-adherence. All results were statistically significant (P<0.05).
Patient characteristics, treatment regimens, and out-of-pocket expenses were associated with adherence to oral antihyperglycemic monotherapy in our study.
PMCID: PMC4315552
compliance; proportion of days covered; PDC; MPR; T2DM; treatment; medication
8.  Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots 
BMC Genomics  2015;16(1):8.
Members of the fungal genus Trichoderma directly antagonize soil-borne fungal pathogens, and an increasing number of species are studied for their potential in biocontrol of plant pathogens in agriculture. Some species also colonize plant roots, promoting systemic resistance. The Trichoderma-root interaction is hosted by a wide range of plant species, including monocots and dicots.
To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on microarrays of 11645 unique oligonucleotides designed from the predicted protein-coding gene models. Transcript levels of 210 genes were modulated by interaction with roots. Almost all were up-regulated. Glycoside hydrolases and transporters were highly represented among transcripts induced by co-culture with roots. Of the genes up-regulated on either or both host plants, 35 differed significantly in their expression levels between maize and tomato. Ten of these were expressed higher in the fungus in co-culture with tomato roots than with maize. Average transcript levels for these genes ranged from 1.9 fold higher on tomato than on maize to 60.9 fold for the most tomato-specific gene. The other 25 host-specific transcripts were expressed more strongly in co-culture with maize than with tomato. Average transcript levels for these genes were 2.5 to 196 fold higher on maize than on tomato.
Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner. The differentially expressed genes encode proteins belonging to several functional classes including enzymes, transporters and small secreted proteins. Among them, glycoside hydrolases and transporters are highlighted by their abundance and suggest an important factor in the metabolism of host cell walls during colonization of the outer root layers. Host-specific gene expression may contribute to the ability of T. virens to colonize the roots of a wide range of plant species.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-014-1208-3) contains supplementary material, which is available to authorized users.
PMCID: PMC4326404  PMID: 25608961
9.  Luminal progenitor and fetal mammary stem cell expression features predict breast tumor response to neoadjuvant chemotherapy 
Mammary gland morphology and physiology are supported by an underlying cellular differentiation hierarchy. Molecular features associated with particular cell types along this hierarchy may contribute to the biological and clinical heterogeneity observed in human breast carcinomas. Investigating the normal cellular developmental phenotypes in breast tumors may provide new prognostic paradigms, identify new targetable pathways, and explain breast cancer subtype etiology. We used transcriptomic profiles coming from fluorescence-activated cell sorted (FACS) normal mammary epithelial cell types from several independent human and murine studies. Using a meta-analysis approach, we derived consensus gene signatures for both species and used these to relate tumors to normal mammary epithelial cell phenotypes. We then compiled a dataset of breast cancer patients treated with neoadjuvant anthracycline and taxane chemotherapy regimens to determine if normal cellular traits predict the likelihood of a pathological complete response (pCR) in a multivariate logistic regression analysis with clinical markers and genomic features such as cell proliferation. Most human and murine tumor subtypes shared some, but not all, features with a specific FACS-purified normal cell type; thus for most tumors a potential distinct cell type of ‘origin’ could be assigned. We found that both human luminal progenitor and mouse fetal mammary stem cell features predicted pCR sensitivity across all breast cancer patients even after controlling for intrinsic subtype, proliferation, and clinical variables. This work identifies new clinically relevant gene signatures and highlights the value of a developmental biology perspective for uncovering relationships between tumor subtypes and their potential normal cellular counterparts.
Electronic supplementary material
The online version of this article (doi:10.1007/s10549-014-3262-6) contains supplementary material, which is available to authorized users.
PMCID: PMC4308649  PMID: 25575446
Breast cancer; Comparative genomics; Genetically engineered mouse models; Genomic signatures; Neoadjuvant chemotherapy; Normal mammary tissue
10.  Age-Related Variation in Foraging Behaviour in the Wandering Albatross at South Georgia: No Evidence for Senescence 
PLoS ONE  2015;10(1):e0116415.
Age-related variation in demographic rates is now widely documented in wild vertebrate systems, and has significant consequences for population and evolutionary dynamics. However, the mechanisms underpinning such variation, particularly in later life, are less well understood. Foraging efficiency is a key determinant of fitness, with implications for individual life history trade-offs. A variety of faculties known to decline in old age, such as muscular function and visual acuity, are likely to influence foraging performance. We examine age-related variation in the foraging behaviour of a long-lived, wide-ranging oceanic seabird, the wandering albatross Diomedea exulans. Using miniaturised tracking technologies, we compared foraging trip characteristics of birds breeding at Bird Island, South Georgia. Based on movement and immersion data collected during the incubation phase of a single breeding season, and from extensive tracking data collected in previous years from different stages of the breeding cycle, we found limited evidence for age-related variation in commonly reported trip parameters, and failed to detect signs of senescent decline. Our results contrast with the limited number of past studies that have examined foraging behaviour in later life, since these have documented changes in performance consistent with senescence. This highlights the importance of studies across different wild animal populations to gain a broader perspective on the processes driving variation in ageing rates.
PMCID: PMC4289070  PMID: 25574995
11.  Antagonism of EGFR and HER3 Enhances the Response to Inhibitors of the PI3K-Akt Pathway in Triple-Negative Breast Cancer 
Science signaling  2014;7(318):ra29.
Both abundant epidermal growth factor receptor (EGFR or ErbB1) and high activity of the phosphatidyl-inositol 3-kinase (PI3K)–Akt pathway are common and therapeutically targeted in triple-negative breast cancer (TNBC). However, activation of another EGFR family member [human epidermal growth factor receptor 3 (HER3) (or ErbB3)] may limit the antitumor effects of these drugs. We found that TNBC cell lines cultured with the EGFR or HER3 ligand EGF or heregulin, respectively, and treated with either an Akt inhibitor (GDC-0068) or a PI3K inhibitor (GDC-0941) had increased abundance and phosphorylation of HER3. The phosphorylation of HER3 and EGFR in response to these treatments was reduced by the addition of a dual EGFR and HER3 inhibitor (MEHD7945A). MEHD7945A also decreased the phosphorylation (and activation) of EGFR and HER3 and the phosphorylation of downstream targets that occurred in response to the combination of EGFR ligands and PI3K-Akt pathway inhibitors. In culture, inhibition of the PI3K-Akt pathway combined with either MEHD7945A or knockdown of HER3 decreased cell proliferation compared with inhibition of the PI3K-Akt pathway alone. Combining either GDC-0068 or GDC-0941 with MEHD7945A inhibited the growth of xenografts derived from TNBC cell lines or from TNBC patient tumors, and this combination treatment was also more effective than combining either GDC-0068 or GDC-0941 with cetuximab, an EGFR-targeted antibody. After therapy with EGFR-targeted antibodies, some patients had residual tumors with increased HER3 abundance and EGFR/HER3 dimerization (an activating interaction). Thus, we propose that concomitant blockade of EGFR, HER3, and the PI3K-Akt pathway in TNBC should be investigated in the clinical setting.
PMCID: PMC4283215  PMID: 24667376
12.  Molecular Pathways: SWI/SNF (BAF) complexes are frequently mutated in cancer—mechanisms and potential therapeutic insights 
SWI/SNF chromatin remodeling complexes are pleomorphic multi-subunit cellular machines that utilize the energy of ATP hydrolysis to modulate chromatin structure. The complexes interact with transcription factors at promoters and enhancers to modulate gene expression and contribute to lineage specification, differentiation and development. Initial clues to a role in tumor suppression for SWI/SNF complexes came over a decade ago when the gene encoding the SMARCB1/SNF5 core subunit was found specifically inactivated in nearly all pediatric rhabdoid tumors. In the last 3 years, cancer genome sequencing efforts have revealed an unexpectedly high mutation rate of SWI/SNF subunit genes, which are collectively mutated in 20% of all human cancers and approach the frequency of p53 mutations. Here we provide a background on these newly recognized tumor suppressor complexes, discuss mechanisms implicated in the tumor suppressor activity, and highlight findings that may lead to potential therapeutic targets for SWI/SNF mutant cancers.
PMCID: PMC3947303  PMID: 24122795
13.  Prostate laser vaporization is safe and effective in elderly men 
Urology Annals  2015;7(1):36-40.
There are few data on the safety and efficacy of laser photoselective vaporization (LVP) in elderly men. We compared the safety and efficacy of LVP for the treatment of symptomatic benign prostatic hyperplasia (BPH) in men ≥75 years, who we defined as elderly, to those <75 years.
Materials and Methods:
Safety and efficacy outcomes in elderly men undergoing LVP for lower urinary tract symptoms secondary to BPH from 2005 to 2012 were compared with men <75 years. Differences between-groups in demographics, perioperative outcomes, complications, and postoperative changes in International Prostate Symptom Score (I-PSS) were calculated.
Of 202 patients, 49 (24%) were elderly (range: 75-95 years) and 153 (76%) were <75 years. Preoperatively, elderly men were more likely to have heart disease (35% vs. 20%, P = 0.03), gross hematuria (6.1% vs. 0.7%, P = 0.05), urinary retention (57% vs. 41%, P = 0.07), and take anti-coagulants (61% vs. 35%, P = 0.002). Elderly men had a longer median length of stay (1 day vs. 0 day, P = 0.001). There were no significant between-group differences in transfusion frequency (4.4% vs. 0.7%, P = 0.14) or Clavien III complications (2% vs. 2.6%, P = 1.0). One month postsurgery, elderly patients reported smaller median decreases in I-PSS (5.5 vs. 9, P = 0.02) and urinary bother (1 point vs. 2, P = 0.03) compared with preoperative values. At till 9 months follow-up, there were no significant between-group differences in median I-PSS or urinary bother scores.
Despite a higher prevalence of preoperative comorbidity and urinary retention, elderly LVP patients experienced perioperative safety and shorter term efficacy outcomes comparable to younger men.
PMCID: PMC4310114  PMID: 25657541
Benign prostatic hyperplasia; complications; elderly; lower urinary tract symptoms; outcomes
14.  PET/CT Artifacts 
Clinical imaging  2011;35(1):49-63.
There are several artifacts encountered in PET/CT imaging, including attenuation correction (AC) artifacts associated with using CT for attenuation correction. Several artifacts can mimic a 2-deoxy-2-[18F] fluoro-D-glucose (FDG) avid malignant lesions and therefore recognition of these artifacts is clinically relevant. Our goal was to identify and characterize these artifacts and also discuss some protocol variables that may affect image quality in PET/CT.
PMCID: PMC4277262  PMID: 21237418
PET/CT; artifact; attenuation correction; image quality; protocol variable
15.  Conditional deletion of p53 and Rb in the renin-expressing compartment of the pancreas leads to a highly penetrant metastatic pancreatic neuroendocrine carcinoma 
Oncogene  2013;33(50):5706-5715.
Efforts to model human pancreatic neuroendocrine tumors (PanNET) in animals have been moderately successful, with minimal evidence for glucagonomas or metastatic spread. The renin gene while classically associated with expression in the kidney is also expressed in many other extra-renal tissues including the pancreas. To induce tumorigenesis within renin specific tissues, floxed alleles of p53 and Rb were selectively abrogated using Cre-recombinase driven by the renin promoter. The primary neoplasm generated is a highly metastatic islet cell carcinoma of the pancreas. Lineage tracing identifies descendants of renin-expressing cells as pancreatic alpha cells despite a lack of active renin expression in the mature pancreas. Both primary and metastatic tumors express high levels of glucagon, furthermore an increased level of glucagon is found in the serum identifying the pancreatic cancer as a functional glucagonoma. This new model is highly penetrant and exhibits robust frequency of metastases to lymph nodes and liver, mimicking human disease and provides a useful platform for better understanding pancreatic endocrine differentiation and development, as well as islet cell carcinogenesis. The use of fluorescent reporters for lineage tracing of the cells contributing to disease initiation and progression provides a unique opportunity to dissect the timeline of disease, examining mechanisms of the metastatic process, as well as recovering primary and metastatic cells for identifying co-operating mutations that are necessary for progression of disease.
PMCID: PMC4041964  PMID: 24292676
Glucagonoma; Renin; Pancreas; PanNET
16.  The Prognostic Contribution of Clinical Breast Cancer Subtype, Age and Race among Patients with Breast Cancer Brain Metastases 
Cancer  2010;117(8):1602-1611.
Brain metastases (BM) arising from Triple-negative breast cancer (TNBC) portend poor prognosis. TNBC is more common in premenopausal and African-American (AA) patients; both also confer poor prognosis. In a single institution cohort study, we sought to determine if inferior outcome of TN BCBM is more reflective of a higher-risk population or subtype itself.
The UNC Breast Cancer Database identified pts with BCBM diagnosed 1988 – 2008. BC subtype was assigned by IHC: HR+ (hormone receptor, ER+ and/or PR+)/HER2−, HR+/HER2+, HR−/HER2+ and TN (ER−/PR−/HER2−). Survival and recurrence patterns were evaluated by subtype, age (< vs ≥ 40 years) and race (AA vs non-AA) using the Kaplan-Meier method and Cox regression.
Among 119 patients with BCBM, 33% were AA and 31% aged < 40 yrs. BC subtype was confirmed in 98 patients: 30% HR+/HER2−, 21% HR+/HER2+, 18% HR−/HER2+, 31% TN. Survival after BM was impacted by subtype (p=0.002), shortest for TNBC (0.24 yrs, CI 0.17 – 0.48). There were no age- (p=0.84) or race-specific (p=0.09) differences in survival after BM; stratification of subtypes by age and race revealed no difference (all, p > 0.1). Receipt of systemic therapy after BCBM was an important predictor of survival following BCBM (HR = 0.29, p=0.002) when adjusted for race, age, number of CNS lesions and BC subtype.
TNBC confers a high risk of death following BM regardless of race and age supporting the need for novel agents capable of controlling both intra- and extracranial TNBC across all races and ages.
PMCID: PMC4265570  PMID: 21472708
17.  Utility of Alpha-methylacyl-CoA racemase (p504s) Immunohistochemistry In Distinguishing Endometrial Clear Cell Carcinomas from Serous and Endometrioid Carcinomas 
Human pathology  2013;44(12):10.1016/j.humpath.2013.07.033.
The expression of alpha-methylacyl-coenzyme-A-racemase (AMACR) has previously been reported in 75 to 100% of urethral/bladder clear cell carcinomas, tumors that are known to display broad phenotypic overlap with their identically-named müllerian counterparts. Herein, we assess the utility of AMACR in distinguishing endometrial clear cell carcinomas (CCC) from endometrial serous carcinomas (ESC) and endometrial endometrioid carcinomas (EEC). 111 endometrial carcinomas in a tissue microarray, including 49 CCC, 13 ESC and 49 EEC, were assessed for AMACR immunoreactivity, with results scored semi-quantitatively (scores 0, 1+, 2+, 3+ for 0%, 1-5%, 6-50%, >50% immunoreactive cells respectively). 50 (45%) of the 111 carcinomas were AMACR-positive, with the following score distribution: CCC: 0 (n=12), 1+ (n=12), 2+ (n=3), 3+ (n=22); EEC: 0 (n=38), 1+ (n=4), 2+ (n=4), 3+ (n=3); ESC: 0 (n=11), 1+ (n=1), 2+ (n=0), 3+ (n=1). AMACR expression was significantly more frequent in CCC (75%) than in ESC (15%) or EEC (22%), p<0.0001. The sensitivity and specificity of AMACR expression in classifying a carcinoma as CCC were 0.75 (95% CI: 0.61-0.86) and 0.79 (95% CI: 0.66-0.88) respectively, with an odds ratio of 11.62 (95% CI: 5-28, p < 0.001), and an area under the curve of 0.79 (95% CI: 0.68 to 0.88). These findings indicate that AMACR expression is strongly associated with CCC and displays a relatively robust diagnostic test performance. However, its practical utility may be limited by the focal nature of its expression in 32% of the AMACR-positive CCC cases, as well as its expression in 15-22% of the non-CCC histotypes.
PMCID: PMC3865867  PMID: 24119561
Alpha-methylacyl-CoA-racemase; p504s; AMACR; immunohistochemistry; endometrial clear cell carcinoma
18.  Role of HGF in obesity-associated tumorigenesis: C3(1)-TAg mice as a model for human basal-like breast cancer 
Obesity is associated with basal-like breast cancer (BBC), an aggressive breast cancer subtype. The objective of this study was to determine whether obesity promotes BBC onset in adulthood and to evaluate the role of stromal-epithelial interactions in obesity-associated tumorigenesis. We hypothesized that hepatocyte growth factor (HGF) plays a promoting role in BBC, which express the HGF receptor, c-Met. In C3(1)-Tag mice, a murine model of BBC, we demonstrated that obesity leads to a significant increase in HGF secretion and an associated decrease in tumor latency. By immunohistochemical analysis, normal mammary gland exhibited obesity-induced HGF, c-Met and phospho-c-Met, indicating that activation of the cascade was obesity-driven. HGF secretion was also increased from primary mammary fibroblasts isolated from normal mammary glands and tumors of obese mice compared to lean. These results demonstrate that obesity-induced elevation of HGF expression is a stable phenotype, maintained after several passages, and after removal of dietary stimulation. Conditioned media from primary tumor fibroblasts from obese mice drove tumor cell proliferation. In co-culture, neutralization of secreted HGF blunted tumor cell migration, further linking obesity-mediated HGF-dependent effects to in vitro measures of tumor aggressiveness. In sum, these results demonstrate that HGF/c-Met plays an important role in obesity-associated carcinogenesis. Understanding the effects of obesity on risk and progression is important given that epidemiologic studies imply a portion of BBC could be eliminated by reducing obesity.
PMCID: PMC3904507  PMID: 24218051
Basal-like breast cancer; tumor latency; microenvironment; normal mammary gland; high fat diet-induced obesity; fibroblast
19.  Long-term Effects of Nutrient Addition and Phytoremediation on Diesel and Crude Oil Contaminated Soils in subarctic Alaska 
Phytoremediation is a potentially inexpensive method of detoxifying contaminated soils using plants and associated soil microorganisms. The remote locations and cold climate of Alaska provide unique challenges associated with phytoremediation such as finding effective plant species that can achieve successful site clean-up despite the extreme environmental conditions and with minimal site management. A long-term assessment of phytoremediation was performed which capitalized on a study established in Fairbanks in 1995. The original study sought to determine how the introduction of plants (Festuca rubra, Lolium multiflorum), nutrients (fertilizer), or their combination would affect degradation of petroleum hydrocarbon (TPH) contaminated soils (crude oil or diesel) over time. Within the year following initial treatments, the plots subjected to both planting and/or fertilization showed greater overall decreases in TPH concentrations in both the diesel and crude oil contaminated soils relative to untreated plots. We re-examined this field site after 15 years with no active site management to assess the long-term effects of phytoremediation on colonization by native and non-native plants, their rhizosphere microbial communities and on petroleum removal from soil. Native and non-native vegetation had extensively colonized the site, with more abundant vegetation found on the diesel contaminated soils than the more nutrient-poor, more coarse, and acidic crude oil contaminated soils. TPH concentrations achieved regulatory clean up levels in all treatment groups, with lower TPH concentrations correlating with higher amounts of woody vegetation (trees & shrubs). In addition, original treatment type has affected vegetation recruitment to each plot with woody vegetation and more native plants in unfertilized plots. Bacterial community structure also varies according to the originally applied treatments. This study suggests that initial treatment with native tree species in combination with grasses could be an effective means for phytoremediating petroleum contaminated soils and promoting ecological recovery in cold regions.
PMCID: PMC3909700  PMID: 24501438
Remediation; Re-vegetation; Soil petroleum hydrocarbon; Microbial Degradation
20.  Multi-Tiered Analysis of Brain Injury in Neonates with Congenital Heart Disease 
Pediatric cardiology  2013;34(8):1772-1784.
Early brain injury occurs in newborns with congenital heart disease (CHD) placing them at risk for impaired neurodevelopmental outcomes. Predictors for preoperative brain injury have not been well described in CHD newborns. This study aimed to analyze, retrospectively, brain magnetic resonance imaging (MRI) in a heterogeneous group of newborns who had CHD surgery during the first month of life using a detailed qualitative CHD MRI Injury Score, quantitative imaging assessments (regional apparent diffusion coefficient [ADC] values and brain volumes), and clinical characteristics. Seventy-three newborns that had CHD surgery at 8 ± 5 (mean ± standard deviation) days of life and preoperative brain MRI were included; 38 also had postoperative MRI. Thirty-four (34/73, 47%) had at least 1 type of preoperative brain injury, and 28/38 (74%) had postoperative brain injury. The 5-minute APGAR score was negatively associated with preoperative injury, but there was no difference between CHD types. Infants with intraparenchymal hemorrhage, deep gray matter injury, and/or watershed infarcts had the highest CHD MRI Injury Scores. ADC values and brain volumes were not different in infants with different CHD types, or in those with and without brain injury. In a mixed group of CHD newborns, brain injury was found preoperatively on MRI in almost 50%, and there were no significant baseline characteristic differences to predict this early brain injury, except 5-minute APGAR score. We conclude that all infants, regardless of CHD type, who require early surgery, should be evaluated with MRI as they are all at high risk for brain injury.
PMCID: PMC3973037  PMID: 23652966
brain injury; brain magnetic resonance imaging; congenital heart disease; congenital heart surgery; neonate; infant
21.  Identification of AP80978, a Novel Small-Molecule Inhibitor of Hepatitis C Virus Replication That Targets NS4B 
A small-molecule inhibitor of hepatitis C virus (HCV) designated AP89652 was identified by screening a compound library with an HCV genotype 1b subgenomic replicon assay. AP89652 contains two chiral centers, and testing of two syn enantiomers revealed that activity in the replicon assay resided with only one, AP80978, whose 50% effective concentration (EC50) (the concentration at which a 50% reduction in Renilla luciferase levels was observed relative to an untreated control) was 630 nM. AP80978 was inhibitory against HCV genotypes 1a and 1b but not genotype 2a. In a replicon clearance assay, the potency and clearance rate of AP80978 were similar to those of telaprevir (VX950) and cyclosporine (CsA). AP80978 was nontoxic when tested against a panel of human cell lines, and inhibitory activity was HCV specific in that there was limited activity against negative-strand viruses, an alphavirus, and flaviviruses. By selection of resistant replicons and assessment of activity in genotype 1b/2a intergenotypic replicons, the viral protein target of this compound was identified as NS4B. NS4B F98V/L substitutions were confirmed by site-directed mutagenesis as AP80978 resistance-associated mutations. When tested against HCV produced in cell culture, the compound was significantly more potent than other HCV inhibitors, including VX950, CsA, and 2′-C-methyladenosine (2′C-meA). In addition, AP80977, the enantiomer that was inactive in the replicon assay, had activity against the virus, although it was lower than the activity of AP80978. These results suggest that AP80978 has the potential to be optimized into an effective antiviral drug and is a useful tool to further study the role of NS4B in HCV replication.
PMCID: PMC4068439  PMID: 24709254
22.  Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq in the ABRF Next-Generation Sequencing Study 
Nature biotechnology  2014;32(9):915-925.
High-throughput RNA sequencing (RNA-seq) dramatically expands the potential for novel genomics discoveries, but the wide variety of platforms, protocols and performance has created the need for comprehensive reference data. Here we describe the Association of Biomolecular Resource Facilities next-generation sequencing (ABRF-NGS) study on RNA-seq. We tested replicate experiments across 15 laboratory sites using reference RNA standards to test four protocols (polyA-selected, ribo-depleted, size-selected and degraded) on five sequencing platforms (Illumina HiSeq, Life Technologies’ PGM and Proton, Pacific Biosciences RS and Roche’s 454). The results show high intra-platform and inter-platform concordance for expression measures across the deep-count platforms, but highly variable efficiency and cost for splice junction and variant detection between all platforms. These data also demonstrate that ribosomal RNA depletion can both enable effective analysis of degraded RNA samples and be readily compared to polyA-enriched fractions. This study provides a broad foundation for cross-platform standardization, evaluation and improvement of RNA-seq.
PMCID: PMC4167418  PMID: 25150835
23.  Dietary Glutamate Supplementation Ameliorates Mycotoxin-Induced Abnormalities in the Intestinal Structure and Expression of Amino Acid Transporters in Young Pigs 
PLoS ONE  2014;9(11):e112357.
The purpose of this study was to investigate the hypothesis that dietary supplementation with glutamic acid has beneficial effects on growth performance, antioxidant system, intestinal morphology, serum amino acid profile and the gene expression of intestinal amino acid transporters in growing swine fed mold-contaminated feed. Fifteen pigs (Landrace×Large White) with a mean body weight (BW) of 55 kg were randomly divided into control group (basal feed), mycotoxin group (contaminated feed) and glutamate group (2% glutamate+contaminated feed). Compared with control group, mold-contaminated feed decreased average daily gain (ADG) and increased feed conversion rate (FCR). Meanwhile, fed mold-contaminated feed impaired anti-oxidative system and intestinal morphology, as well as modified the serum amino acid profile in growing pigs. However, supplementation with glutamate exhibited potential positive effects on growth performance of pigs fed mold-contaminated feed, ameliorated the imbalance antioxidant system and abnormalities of intestinal structure caused by mycotoxins. In addition, dietary glutamate supplementation to some extent restored changed serum amino acid profile caused by mold-contaminated feed. In conclusion, glutamic acid may be act as a nutritional regulating factor to ameliorate the adverse effects induced by mycotoxins.
PMCID: PMC4236086  PMID: 25405987
24.  A prospective, randomised comparative study of weekly versus biweekly application of dehydrated human amnion/chorion membrane allograft in the management of diabetic foot ulcers 
International Wound Journal  2014;11(2):122-128.
The aim of this study is to determine if weekly application of dehydrated human amnion/chorion membrane allograft reduce time to heal more effectively than biweekly application for treatment of diabetic foot ulcers.
This was an institutional review board-approved, registered, prospective, randomised, comparative, non-blinded, single-centre clinical trial. Patients with non-infected ulcers of ≥ 4 weeks duration were included for the study. They were randomised to receive weekly or biweekly application of allograft in addition to a non-adherent, moist dressing with compressive wrapping. All wounds were offloaded. The primary study outcome was mean time to healing.
Overall, during the 12-week study period, 92·5% (37/40) ulcers completely healed. Mean time to complete healing was 4·1 ± 2·9 versus 2·4 ± 1·8 weeks (P = 0·039) in the biweekly versus weekly groups, respectively. Complete healing occurred in 50% versus 90% by 4 weeks in the biweekly and weekly groups, respectively (P = 0·014). Number of grafts applied to healed wounds was similar at 2·4 ± 1·5 and 2·3 ± 1·8 for biweekly versus weekly groups, respectively (P = 0·841).
These results validate previous studies showing that the allograft is an effective treatment for diabetic ulcers and show that wounds treated with weekly application heal more rapidly than with biweekly application. More rapid healing may decrease clinical operational costs and prevent long-term medical complications.
PMCID: PMC4235421  PMID: 24618401
Amniotic membrane allograft; Diabetic ulcer; Dehydrated amnion/chorion
25.  Enhanced Gastrointestinal Expression of Cytosolic Malic Enzyme (ME1) Induces Intestinal and Liver Lipogenic Gene Expression and Intestinal Cell Proliferation in Mice 
PLoS ONE  2014;9(11):e113058.
The small intestine participates in lipid digestion, metabolism and transport. Cytosolic malic enzyme 1 (ME1) is an enzyme that generates NADPH used in fatty acid and cholesterol biosynthesis. Previous work has correlated liver and adipose ME1 expression with susceptibility to obesity and diabetes; however, the contributions of intestine-expressed ME1 to these conditions are unknown. We generated transgenic (Tg) mice expressing rat ME1 in the gastrointestinal epithelium under the control of the murine villin1 promoter/enhancer. Levels of intestinal ME1 protein (endogenous plus transgene) were greater in Tg than wildtype (WT) littermates. Effects of elevated intestinal ME1 on body weight, circulating insulin, select adipocytokines, blood glucose, and metabolism-related genes were examined. Male Tg mice fed a high-fat (HF) diet gained significantly more body weight than WT male littermates and had heavier livers. ME1-Tg mice had deeper intestinal and colon crypts, a greater intestinal 5-bromodeoxyuridine labeling index, and increased expression of intestinal lipogenic (Fasn, Srebf1) and cholesterol biosynthetic (Hmgcsr, Hmgcs1), genes. The livers from HF diet-fed Tg mice also exhibited an induction of cholesterol and lipogenic pathway genes and altered measures (Irs1, Irs2, Prkce) of insulin sensitivity. Results indicate that gastrointestinal ME1 via its influence on intestinal epithelial proliferation, and lipogenic and cholesterologenic genes may concomitantly impact signaling in liver to modify this tissue’s metabolic state. Our work highlights a new mouse model to address the role of intestine-expressed ME1 in whole body metabolism, hepatomegaly, and crypt cell proliferation. Intestinal ME1 may thus constitute a therapeutic target to reduce obesity-associated pathologies.
PMCID: PMC4234650  PMID: 25402228

Results 1-25 (1045)