Sandeep K. Singhal

The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB’s chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC–MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.

CD4⁺ T cells are critical regulators of immune responses, but their functional role in human breast cancer is relatively unknown. The goal of this study was to produce an image of CD4⁺ T cells infiltrating breast tumors using limited ex vivo manipulation to better understand the in vivo differences associated with patient prognosis. We performed comprehensive molecular profiling of infiltrating CD4⁺ T cells isolated from untreated invasive primary tumors and found that the infiltrating T cell subpopulations included follicular helper T (Tfh) cells, which have not previously been found in solid tumors, as well as Th1, Th2, and Th17 effector memory cells and Tregs. T cell signaling pathway alterations included a mixture of activation and suppression characterized by restricted cytokine/chemokine production, which inversely paralleled lymphoid infiltration levels and could be reproduced in activated donor CD4⁺ T cells treated with primary tumor supernatant. A comparison of extensively versus minimally infiltrated tumors showed that CXCL13-producing CD4⁺ Tfh cells distinguish extensive immune infiltrates, principally located in tertiary lymphoid structure germinal centers. An 8-gene Tfh signature, signifying organized antitumor immunity, robustly predicted survival or preoperative response to chemotherapy. Our identification of CD4⁺ Tfh cells in breast cancer suggests that they are an important immune element whose presence in the tumor is a prognostic factor.

Abstract Purpose: Breast cancer in young women is associated with poor prognosis. We aimed to define the role of gene expression signatures in predicting prognosis in young women and to understand biological differences according to age. Experimental Design: Patients were assigned to molecular subtypes [estrogen receptor (ER)+/HER2−; HER2+, ER−/HER2−)] using a three-gene classifier. We evaluated whether previously published proliferation, stroma, and immune-related gene signatures added prognostic information to Adjuvant! online and tested their interaction with age in a Cox model for relapse-free survival (RFS). Furthermore, we evaluated the association between candidate age-related genes or gene sets with age in an adjusted linear regression model. Results: A total of 3,522 patients (20 data sets) were eligible. Patients aged 40 years or less had a higher proportion of ER−/HER2− tumors (P < 0.0001) and were associated with poorer RFS after adjustment for breast cancer subtype, tumor size, nodal status, and histologic grade and stratification for data set and treatment modality (HR = 1.34, 95% CI = 1.10–1.63, P = 0.004). The proliferation gene signatures showed no significant interaction with age in ER+/HER2− tumors after adjustment for Adjuvant! online. Further analyses suggested that breast cancer in the young is enriched with processes related to immature mammary epithelial cells (luminal progenitors, mammary stem, c-kit, RANKL) and growth factor signaling in two independent cohorts (n = 1,188 and 2,334). Conclusions: Proliferation-related prognostic gene signatures can aid treatment decision-making for young women. However, breast cancer arising at a young age seems to be biologically distinct beyond subtype distribution. Separate therapeutic approaches such as targeting RANKL or mammary stem cells could therefore be needed. Clin Cancer Res; 18(5); 1341–51. ©2012 AACR.

To investigate the association between chemotherapy response and gene expression modules describing important biologic processes and druggable oncogenic pathways in breast cancer (BC) subtypes.We searched for publicly available gene expression studies evaluating anthracycline with or without taxane-based neoadjuvant chemotherapy and identified eight studies with 996 patients. We computed 17 gene modules and calculated odds ratios (ORs) for pathologic complete response (pCR) for one-unit increases in scaled modules with and without adjustment for clinicopathologic characteristics. Added predictive accuracy was evaluated using the area under the receiver operating characteristic curve (AUC) and integrated discrimination index (IDI). We used the false discovery rate (FDR) to adjust for multiple testing.High immune module scores were associated with increased pCR probability in all BC subtypes. High module scores of chromosomal instability, phosphatase and tensin homolog (PTEN) loss, and E2F3 transcription factor were associated with increased pCR probability in estrogen receptor (ER) -negative/human epidermal growth factor receptor 2 (HER2) -negative and ER-positive/HER2-negative but not in HER2-positive tumors (interactions between HER2 and each of these modules for their association with pCR: P < .05; FDR, 0.17; trend for interaction between HER2 and PTEN). High values of insulin-like growth factor 1 activation module were associated with increased pCR probability only in ER-positive/HER2-negative tumors (interaction between insulin-like growth factor 1 and ER: P = .002; FDR, 0.03). When adding the immune module to clinicopathologic characteristics, we observed substantial increases in predictive accuracy for pCR in the HER2-positive subtype (IDI, 0.093; P = .004; increase in AUC from 0.760 to 0.836).Different processes and pathways are associated with pCR in different BC subtypes.

Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimizing treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease are still poorly understood. By means of DNA methylation profiling of 248 breast tissues, we have highlighted the existence of previously unrecognized breast cancer groups that go beyond the currently known 'expression subtypes'. Interestingly, we showed that DNA methylation profiling can reflect the cell type composition of the tumour microenvironment, and in particular a T lymphocyte infiltration of the tumours. Further, we highlighted a set of immune genes having high prognostic value in specific tumour categories. The immune component uncovered here by DNA methylation profiles provides a new perspective for the importance of the microenvironment in breast cancer, holding implications for better management of breast cancer patients.

Circulating Tumor Cells (CTCs) detection and phenotyping are currently evaluated in Breast Cancer (BC). Tumor cell dissemination has been suggested to occur early in BC progression. To interrogate dissemination in BC, we studied CTCs and HER2 expression on CTCs across the spectrum of BC staging.Spiking experiments with 6 BC cell lines were performed and blood samples from healthy women and women with BC were analyzed for HER2-positive CTCs using the CellSearch®.Based on BC cell lines experiments, HER2-positive CTCs were defined as CTCs with HER2 immunofluorescence intensity that was at least 2.5 times higher than the background. No HER2-positive CTC was detected in 42 women without BC (95% confidence interval (CI) 0-8.4%) whereas 4.1% (95%CI 1.4-11.4%) of 73 patients with ductal/lobular carcinoma in situ (DCIS/LCIS) had 1 HER2-positive CTC/22.5 mL, 7.9%, (95%CI 4.1-14.9%) of 101 women with non metastatic (M0) BC had ≥1 HER2-positive CTC/22.5 mL (median 1 cell, range 1-3 cells) and 35.9% (95%CI 22.7-51.9%) of 39 patients with metastatic BC had ≥1 HER2-positive CTC/7.5 mL (median 1.5 cells, range 1-42 cells). In CTC-positive women with DCIS/LCIS or M0 BC, HER2-positive CTCs were more commonly detected in HER2-positive (5 of 5 women) than HER2-negative BC (5 of 12 women) (p = 0.03).HER2-positive CTCs were detected in DCIS/LCIS or M0 BC irrespective of the primary tumor HER2 status. Nevertheless, their presence was more common in women with HER2-positive disease. Monitoring of HER2 expression on CTCs might be useful in trials with anti-HER2 therapies.

A total of 10%-20% of patients develop long-term toxicity following radiotherapy for prostate cancer. Identification of common genetic variants associated with susceptibility to radiotoxicity might improve risk prediction and inform functional mechanistic studies.We conducted an individual patient data meta-analysis of six genome-wide association studies (n = 3871) in men of European ancestry who underwent radiotherapy for prostate cancer. Radiotoxicities (increased urinary frequency, decreased urinary stream, hematuria, rectal bleeding) were graded prospectively. We used grouped relative risk models to test associations with approximately 6 million genotyped or imputed variants (time to first grade 2 or higher toxicity event). Variants with two-sided Pmeta less than 5 × 10-8 were considered statistically significant. Bayesian false discovery probability provided an additional measure of confidence. Statistically significant variants were evaluated in three Japanese cohorts (n = 962). All statistical tests were two-sided.Meta-analysis of the European ancestry cohorts identified three genomic signals: single nucleotide polymorphism rs17055178 with rectal bleeding (Pmeta = 6.2 × 10-10), rs10969913 with decreased urinary stream (Pmeta = 2.9 × 10-10), and rs11122573 with hematuria (Pmeta = 1.8 × 10-8). Fine-scale mapping of these three regions was used to identify another independent signal (rs147121532) associated with hematuria (Pconditional = 4.7 × 10-6). Credible causal variants at these four signals lie in gene-regulatory regions, some modulating expression of nearby genes. Previously identified variants showed consistent associations (rs17599026 with increased urinary frequency, rs7720298 with decreased urinary stream, rs1801516 with overall toxicity) in new cohorts. rs10969913 and rs17599026 had similar effects in the photon-treated Japanese cohorts.This study increases the understanding of the architecture of common genetic variants affecting radiotoxicity, points to novel radio-pathogenic mechanisms, and develops risk models for testing in clinical studies. Further multinational radiogenomics studies in larger cohorts are worthwhile.

Multi-omics studies have emerged as powerful tools for tailoring individualized responses to various conditions, capitalizing on genome sequencing technologies’ increasing affordability and efficiency. This paper delves into the potential of multi-omics in deepening our understanding of biological age, examining the techniques available in light of evolving technology and computational models. The primary objective is to review the relationship between ionizing radiation and biological age, exploring a wide array of functional, physiological, and psychological parameters. This comprehensive review draws upon an extensive range of sources, including peer-reviewed journal articles, government documents, and reputable websites. The literature review spans from fundamental insights into radiation effects to the latest developments in aging research. Ionizing radiation exerts its influence through direct mechanisms, notably single- and double-strand DNA breaks and cross links, along with other critical cellular events. The cumulative impact of DNA damage forms the foundation for the intricate process of natural aging, intersecting with numerous diseases and pivotal biomarkers. Furthermore, there is a resurgence of interest in ionizing radiation research from various organizations and countries, reinvigorating its importance as a key contributor to the study of biological age. Biological age serves as a vital reference point for the monitoring and mitigation of the effects of various stressors, including ionizing radiation. Ionizing radiation emerges as a potent candidate for modeling the separation of biological age from chronological age, offering a promising avenue for tailoring protocols across diverse fields, including the rigorous demands of space exploration.

The phosphatidylinositol 3′ kinase (PI3K) pathway is commonly activated in breast cancer and aberrations such as PI3K mutations are common. Recent exciting clinical trial results in advanced estrogen receptor-positive (ER) breast cancer support mTOR activation is a major means of estrogen-independent tumor growth. Hence the means to identify a responsive breast cancer population that would most benefit from these compounds in the adjuvant or earlier stage setting is of high interest. Here we study PIK3CA genotype as well as a previously reported PI3K/mTOR-pathway gene signature (PIK3CA-GS) and their ability to estimate the level of PI3K pathway activation in two clinical trials of newly diagnosed ER-positive breast cancer patients- a total of 81 patients- one of which was randomized between letrozole and placebo vs letrozole and everolimus. The main objectives were to correlate the baseline PIK3CA genotype and GS with the relative change from baseline to day 15 in Ki67 (which has been shown to be prognostic in breast cancer) and phosphorylated S6 (S240) immunohistochemistry (a substrate of mTOR). In the randomized dataset, the PIK3CA-GS could identify those patients with the largest relative decreases in Ki67 to letrozole/everolimus (R = −0.43, p = 0.008) compared with letrozole/placebo (R = 0.07, p = 0.58; interaction test p = 0.02). In a second dataset of pre-surgical everolimus alone, the PIK3CA-GS was not significantly correlated with relative change in Ki67 (R = −0.11, p = 0.37) but with relative change in phosphorlyated S6 (S240) (R = −0.46, p = 0.028). PIK3CA genotype was not significantly associated with any endpoint in either datasets. Our results suggest that the PIK3CA-GS has potential to identify those ER-positive BCs who may benefit from the addition of everolimus to letrozole. Further evaluation of the PIK3CA-GS as a predictive biomarker is warranted as it may facilitate better selection of responsive patient populations for mTOR inhibition in combination with letrozole.

The prognostic value of histologic grade (HG) in invasive lobular carcinoma (ILC) remains uncertain, and most ILC tumors are graded as HG2. Genomic grade (GG) is a 97-gene signature that improves the prognostic value of HG. This study evaluates whether GG may overcome the limitations of HG in ILC.Gene expression data were generated from frozen tumor samples, and GG calculated according to the expression of 97 genes. The prognostic value of GG was assessed in a stratified Cox regression model for invasive disease-free survival (IDFS) and overall survival (OS).A total of 166 patients were classified by GG. HG classified 33 (20%) tumors as HG1, 120 (73%) as HG2 and 12 (7%) as HG3. GG classified 106 (64%) tumors as GG low (GG1), 29 (17%) as GG high (GG3) and 31 (19%) as equivocal (cases not classified as GG1 or GG3). The median follow-up time was 6.5 years. In multivariate analyses, GG was associated with IDFS [HR(GG3 vs GG1) 5.6 (2.1-15.3); P < 0.001] and OS [HR(GG3 vs GG1) 7.2, 95% CI (1.6-32.2); P = 0.01].GG outperformed HG in ILC and added prognostic value to classic clinicopathologic variables, including nodal status.

Radiotherapy is a mainstay of cancer treatment, used in either a curative or palliative manner to treat approximately 50% of patients with cancer. Normal tissue toxicity limits the doses used in standard radiation therapy protocols and impedes improvements in radiotherapy efficacy. Damage to surrounding normal tissues can produce reactions ranging from bothersome symptoms that negatively affect quality of life to severe life-threatening complications. Improved ways of predicting, before treatment, the risk for development of normal tissue toxicity may allow for more personalized treatment and reduce the incidence and severity of late effects. There is increasing recognition that the cause of normal tissue toxicity is multifactorial and includes genetic factors in addition to radiation dose and volume of exposure, underlying comorbidities, age, concomitant chemotherapy or hormonal therapy, and use of other medications. An understanding of the specific genetic risk factors for normal tissue response to radiation has the potential to enhance our ability to predict adverse outcomes at the treatment-planning stage. Therefore, the field of radiogenomics has focused upon the identification of genetic variants associated with normal tissue toxicity resulting from radiotherapy. Innovative analytic methods are being applied to the discovery of risk variants and development of integrative predictive models that build on traditional normal tissue complication probability models by incorporating genetic information. Results from initial studies provide promising evidence that genetic-based risk models could play an important role in the implementation of precision medicine for radiation oncology through enhancing the ability to predict normal tissue reactions and thereby improve cancer treatment.

Phase change materials (PCMs) are popular because they can store and release latent heat for energy saving and thermal management. Despite PCMs' latent heat and melting temperatures variety, their low thermal conductivity (TC) limits their usage. This problem and attempts to overcome the poor heat conductivity of PCMs are discussed in length in this publication. High TC nanoparticles, encapsulation and porous metal foams are solutions for the problem. PCMs may be used to store and release energy in electrical gadgets, photovoltaic panels, desalination solar stills, thermoelectric generators, textiles, air conditioning, battery thermal management, water heating, food packaging and heat exchangers. In this review we discuss the different methods which are being used to increase the thermal conductivity.

There is growing evidence that interaction between stromal and tumor cells is pivotal in breast cancer progression and response to therapy. Based on earlier research suggesting that during breast cancer progression, striking changes occur in CD10(+) stromal cells, we aimed to better characterize this cell population and its clinical relevance.We developed a CD10(+) stroma gene expression signature (using HG U133 Plus 2.0) on the basis of the comparison of CD10 cells isolated from tumoral (n = 28) and normal (n = 3) breast tissue. We further characterized the CD10(+) cells by coculture experiments of representative breast cancer cell lines with the different CD10(+) stromal cell types (fibroblasts, myoepithelial, and mesenchymal stem cells). We then evaluated its clinical relevance in terms of in situ to invasive progression, invasive breast cancer prognosis, and prediction of efficacy of chemotherapy using publicly available data sets.This 12-gene CD10(+) stroma signature includes, among others, genes involved in matrix remodeling (MMP11, MMP13, and COL10A1) and genes related to osteoblast differentiation (periostin). The coculture experiments showed that all 3 CD10(+) cell types contribute to the CD10(+) stroma signature, although mesenchymal stem cells have the highest CD10(+) stroma signature score. Of interest, this signature showed an important role in differentiating in situ from invasive breast cancer, in prognosis of the HER2(+) subpopulation of breast cancer only, and potentially in nonresponse to chemotherapy for those patients.Our results highlight the importance of CD10(+) cells in breast cancer prognosis and efficacy of chemotherapy, particularly within the HER2(+) breast cancer disease.

Background: Statins (3‐hydroxy‐3‐methylglutaryl coenzyme A reductase inhibitors) are an important group of hypolipidemic drugs that are able to modulate inflammation and alveolar bone loss. Rosuvastatin (RSV) and atorvastatin (ATV) are known to inhibit osteoclastic bone resorption and have been proposed to have osteostimulative properties. The aim of this study is to evaluate and compare the efficacy of 1.2% RSV and 1.2% ATV gel local drug delivery (LDD) and redelivery systems, in addition to scaling and root planing (SRP), for the treatment of intrabony defects (IBDs) in patients with chronic periodontitis (CP). Methods: A total of 90 individuals with 90 IBDs was randomly allocated to treatment with SRP followed by LDD of 1.2% RSV, 1.2% ATV, or placebo gel. Clinical and radiographic parameters, including plaque index (PI), modified sulcus bleeding index (mSBI), probing depth (PD), clinical attachment level (CAL), and IBD depth, were recorded at baseline and 6 and 9 months. Results: All three groups showed significant reduction in PI and mSBI at all intervals. Mean mSBI and PD reductions, CAL gain, and IBD depth reduction with statin drugs were significantly greater than with placebo gel LDD. Improvements in these parameters were significantly greater with RSV LDD than ATV or placebo gels at 6 and 9 months. Conclusion: LDD of 1.2% RSV results in significantly greater clinico‐radiographic improvement than 1.2% ATV or placebo gels as adjunct to mechanical periodontal therapy.

Background: Different materials have been investigated for renewal of lost supporting periodontal structures and tested for furcation defect treatment. Platelet‐rich fibrin (PRF) is a pool of growth‐promoting factors and cytokines that promote bone regeneration and maturation of soft tissue. Alendronate (ALN), an influential member of the bisphosphonate group, is known to enhance osteoblastogenesis and inhibit osteoclastic bone resorption, thus promoting tissue regeneration. This randomized trial was done to assess effectiveness of PRF and 1% ALN gel combination in mandibular degree II furcation defect treatment in comparison with PRF and access therapy alone. Methods: Seventy‐two mandibular molar furcation defects were treated with either access therapy alone (group 1), access therapy with PRF (group 2), or access therapy with PRF and 1% ALN (group 3). Plaque index, modified sulcus bleeding index, probing depth (PD), relative vertical attachment level (RVAL) and relative horizontal attachment level (RHAL), and intrabony defect depth were recorded at baseline and 9 months postoperatively. Radiographically, defect fill, assessed in percentage, was evaluated at baseline, before surgery, and 9 months post‐therapy. Results: Group 3 showed greater PD reduction and RVAL and RHAL gain when compared with groups 1 and 2 postoperatively. Moreover, group 3 sites showed a significantly greater percentage of radiographic defect fill (56.01% ± 2.64%) when compared with group 2 (49.43% ± 3.70%) and group 1 (10.25% ± 3.66%) at 9 months. Conclusions: Furcation defect treatment with autologous PRF combined with 1% ALN gel results in significant therapeutic outcomes when compared with PRF and access therapy alone. Combining ALN with PRF has potential for regeneration of furcation defects without any adverse effect on healing process.

Platelet-rich fibrin (PRF) is a reservoir of concentrated platelets that provides a pool of biologic growth-promoting factors and cytokines, which help in mediating regeneration of lost bone and soft tissue maturation. Alendronate (ALN), a member of the amino-bisphosphonate group, is known to enhance periodontal tissue regeneration by inhibiting osteoclast-mediated bone resorption and promoting osteoblast-mediated osteogenesis. The current intervention aims to assess combined effectiveness of PRF and 1% ALN with access therapy in intrabony defect (IBD) treatment in patients with chronic periodontitis (CP).Single IBDs in 90 patients were categorized into three groups: 1) group 1 had access therapy alone; 2) group 2 had access therapy with PRF; and 3) group 3 had access therapy with PRF + 1% ALN. Site-specific plaque index, modified sulcus bleeding index, probing depth (PD), clinical attachment level (CAL), and gingival marginal level, included as parameters for clinical assessment, were evaluated before surgery at baseline and 9 months postoperatively. Percentage IBD depth reduction, assessed using radiographs, was evaluated at baseline and postoperatively.Compared with groups 1 and 2, group 3 exhibited significantly greater reduction in PD and gain in CAL postoperatively. Significantly greater IBD depth reduction was shown in group 3 (54.05% ± 2.88%) compared with group 2 (46% ± 1.89%) and group 1 (7.33% ± 4.86%) postoperatively.Combined approach therapy of PRF + 1% ALN for IBD treatment in patients with CP showed better clinical parameter outcomes with greater IBD depth reduction compared with PRF and access therapy alone.

Regenerative periodontal therapy encompasses use of various bioactive agents that are not only inflammomodulatory but also osteoclast-inhibitory or, rather, osteostimulative. Hypolipidemic statin drugs, particularly rosuvastatin (RSV), are known to be associated with alveolar bone formation and periodontal improvements. Platelet analogs such as platelet-rich fibrin (PRF), being rich sources of growth factors, have also come into widespread periodontal regenerative use. The aim of this study is to evaluate and compare efficacy of open flap debridement (OFD) with or without PRF or PRF + 1.2% RSV gel in treatment of intrabony defects (IBDs) in patients with chronic periodontitis (CP).Ninety individuals with a total of 90 IBDs were randomly assigned to one of three treatment groups: 1) OFD alone; 2) OFD + PRF; and 3) OFD + PRF + 1.2% RSV gel placement. Measurements recorded at baseline and 9 months after surgery were: 1) plaque index (PI); 2) modified sulcus bleeding index (mSBI); 3) probing depth (PD); 4) clinical attachment level (CAL); and 5) IBD depth.Significant PI and mSBI reductions were observed in all three groups. PRF placement significantly enhanced improvements in periodontal parameters compared with OFD alone. Addition of 1.2% RSV gel to PRF resulted in significantly greater CAL gain and PD and IBD depth reductions over 9 months compared with other groups.OFD with RSV (1.2%) and PRF results in significantly greater periodontal benefits compared with OFD alone or with PRF.

Abstract Aim Alendronate ( ALN ) and atorvastatin ( ATV ) are known to inhibit osteoclastic bone resorption and were proposed to have osteostimulative properties. The aim of the study was to evaluate and compare the efficacy of 1% ALN and 1.2% ATV gel as a local drug‐delivery system in adjunct to scaling and root planning ( SRP ) for the treatment of intrabony defects in chronic periodontitis patients. Methods A total of 90 intrabony defects were treated with either 1% ALN , 1.2% ATV , or placebo gel. Clinical parameters (plaque index, modified sulcus bleeding index, probing depth ( PD ), and clinical attachment level ( CAL )) were recorded at baseline, 3, 6, and 9 months. Intrabony defect depth ( IBD ) and defect depth reduction ( DDR %) was calculated on standardized radiographs at 6 and 9 months. Results The mean PD reduction, CAL gain, and DDR % were greater in the ALN and ATV group than in the placebo group at 3, 6, and 9 months. Furthermore, a significantly greater DDR % was found in the ALN group at 6 and 9 months than in the ATV and placebo groups. Conclusion Local delivery of 1% ALN results in significantly greater improvement in PD , CAL , IBD depth, and DDR % as compared to 1.2% ATV gel.

Abstract Purpose: Compared with their European American (EA) counterparts, African American (AA) women are more likely to die from breast cancer in the United States. This disparity is greatest in hormone receptor–positive subtypes. Here we uncover biological factors underlying this disparity by comparing functional expression and prognostic significance of master transcriptional regulators of luminal differentiation. Experimental Design: Data and biospecimens from 262 AA and 293 EA patients diagnosed with breast cancer from 2001 to 2010 at a major medical center were analyzed by IHC for functional biomarkers of luminal differentiation, including estrogen receptor (ESR1) and its pioneer factors, FOXA1 and GATA3. Integrated comparison of protein levels with network-level gene expression analysis uncovered predictive correlations with race and survival. Results: Univariate or multivariate HRs for overall survival, estimated from digital IHC scoring of nuclear antigen, show distinct differences in the magnitude and significance of these biomarkers to predict survival based on race: ESR1 [EA HR = 0.47; 95% confidence interval (CI), 0.31–0.72 and AA HR = 0.77; 95% CI, 0.48–1.18]; FOXA1 (EA HR = 0.38; 95% CI, 0.23–0.63 and AA HR = 0.53; 95% CI, 0.31–0.88), and GATA3 (EA HR = 0.36; 95% CI, 0.23–0.56; AA HR = 0.57; CI, 0.56–1.4). In addition, we identify genes in the downstream regulons of these biomarkers highly correlated with race and survival. Conclusions: Even within clinically homogeneous tumor groups, regulatory networks that drive mammary luminal differentiation reveal race-specific differences in their association with clinical outcome. Understanding these biomarkers and their downstream regulons will elucidate the intrinsic mechanisms that drive racial disparities in breast cancer survival.

SPARC is an important regulator of the extracellular matrix and has been suggested to improve delivery of albumin-bound cytotoxics. However, little is known regarding its role in breast cancer (BC).We conducted a pooled analysis of publically available datasets, in which BC patients who received no systemic therapy or received neoadjuvant chemotherapy were eligible. Patients were assigned to molecular subtypes using PAM-50. We computed a SPARC module (SPARC7), composed of genes with an absolute correlation with SPARC >0.7. In the systemically untreated cohort, we evaluated 1) expression of SPARC/SPARC7 according to breast cancer subtype, 2) association between SPARC/SPARC7 and biological processes related to proliferation, immune and stroma, and 3) association between SPARC/SPARC7 and relapse-free survival in a Cox model in all patients and in the different molecular subtypes adjusted for tumor size, nodal status, histological grade, and age. In the neoadjuvant cohort, we evaluated the association between SPARC and pCR in a logistic regression model, adjusted for the same clinicopathologic factors.948 (10 datasets), and 791 (8 datasets) patients were included in the systemically untreated and neoadjuvant cohorts, respectively. High SPARC expression was associated with small tumor size, low histological grade and luminal-A tumors (all p<0.0001). There was a positive correlation between SPARC and stroma-related modules but negative correlation with proliferation modules. High SPARC expression was associated with poor prognosis in patients with basal and HER2+ breast cancer even after adjusting for clinicopathologic parameters. In the neoadjuvant cohort, a subgroup analysis suggested that high SPARC is associated with low rates of pCR in the HER2 subtype. Same results were observed on replacing SPARC by SPARC7.This analysis suggests a potential role of SPARC in determining prognosis and response to primary chemotherapy in early BC. This information could guide further development of albumin-bound cytotoxics in BC.

The present study aimed to evaluate the levels of soluble receptor for advanced glycation end products (sRAGE) and tumor necrosis factor-α (TNF-α) in serum and gingival crevicular fluid (GCF) in chronic periodontitis (CP) patients with and without type 2 diabetes mellitus (T2DM). A total of 70 subjects were divided into four groups: group 1 (n = 15; subjects with healthy periodontium); group 2 (n = 20; CP patients); group 3 (n = 20; CP patients with T2DM); and group 4 (n = 15; CP patients without T2DM). The serum and GCF levels of human sRAGE and TNF-α were assessed using enzyme-linked immunosorbent assay and correlated with clinical parameters, including probing depth, gingival index and clinical attachment level. Both sRAGE and TNF-α levels varied with the inflammatory state of the patient; the highest levels of sRAGE were seen in group 1, whereas the lowest levels in group 3 (P < 0.05). Conversely, TNF-α levels were found to be the highest in group 3 and lowest in group 1 (P < 0.05). Thus, human sRAGE and TNF-α can be considered as possible GCF and serum markers of inflammatory activity in CP and T2DM.(J Oral Sci 58, 547-553, 2016).

Background: Lung cancer is the most common cause of cancer-related deaths worldwide. Early diagnosis is crucial to increase the curability chance of the patients. Low dose CT screening can reduce lung cancer mortality, but it is associated with several limitations. Metabolomics is a promising technique for cancer diagnosis due to its ability to provide chemical phenotyping data. The intent of our study was to explore metabolomic effects and profiles of lung cancer patients to determine if metabolic perturbations in the SSAT-1/polyamine pathway can distinguish between healthy participants and lung cancer patients as a diagnostic and treatment monitoring tool. Patients and Methods: Plasma samples were collected as part of the SSAT1 Amantadine Cancer Study. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify and quantify metabolite concentrations in lung cancer patient and control samples. Standard statistical analyses were performed to determine whether metabolite concentrations could differentiate between healthy subjects and lung cancer patients, as well as risk prediction modeling applied to determine whether metabolic profiles could provide an indication of cancer progression in later stage patients. Results: A panel consisting of 14 metabolites, which included 6 metabolites in the polyamine pathway, was identified that correctly discriminated lung cancer patients from controls with an area under the curve of 0.97 (95% CI: 0.875-1.0). Conclusion: When used in conjunction with the SSAT-1/polyamine pathway, these metabolites may provide the specificity required for diagnosing lung cancer from other cancer types and could be used as a diagnostic and treatment monitoring tool.

Induced pluripotent stem cells (iPSCs) can be derived from differentiated cells, enabling the generation of personalized disease models by differentiating patient-derived iPSCs into disease-relevant cell lines. While genetic variability between different iPSC lines affects differentiation potential, how this variability in somatic cells affects pluripotent potential is less understood. We generated and compared transcriptomic data from 72 dermal fibroblast-iPSC pairs with consistent variation in reprogramming efficiency. By considering equal numbers of samples from self-reported African Americans and White Americans, we identified both ancestry-dependent and ancestry-independent transcripts associated with reprogramming efficiency, suggesting that transcriptomic heterogeneity can substantially affect reprogramming. Moreover, reprogramming efficiency-associated genes are involved in diverse dynamic biological processes, including cancer and wound healing, and are predictive of 5-year breast cancer survival in an independent cohort. Candidate genes may provide insight into mechanisms of ancestry-dependent regulation of cell fate transitions and motivate additional studies for improvement of reprogramming.

Until recently, an elevated disease risk has been ascribed to a genetic predisposition, however, exciting progress over the past years has discovered alternate elements of inheritance that involve epigenetic regulation.Epigenetic changes are heritably stable alterations that include DNA methylation, histone modifications and RNA-mediated silencing.Aberrant DNA methylation is a common molecular basis for a number of important human diseases, including breast cancer.Changes in DNA methylation profoundly affect global gene expression patterns.What is emerging is a more dynamic and complex association between DNA methylation and gene expression than previously believed.Although many tools have already been developed for analyzing genome-wide gene expression data, tools for analyzing genome-wide DNA methylation have not yet reached the same level of refinement.Here we provide an in-depth analysis of DNA methylation in parallel with gene expression data characteristics and describe the particularities of low-level and highlevel analyses of DNA methylation data.Low-level analysis refers to pre-processing of methylation data (i.e.normalization, transformation and filtering), whereas high-level analysis is focused on illustrating the application of the widely used class comparison, class prediction and class discovery methods to DNA methylation data.Furthermore, we investigate the influence of DNA methylation on gene expression by measuring the correlation between the degree of CpG methylation and the level of expression and to explore the pattern of methylation as a function of the promoter region.

Abstract Aim Borinic acid quinoline esters are a recently‐identified class of new antibacterial and anti‐inflammatory compounds known to inhibit osteoclastic bone resorption. They have proposed to have osteostimulative properties by causing osteoblast differentiation in vivo and in vitro. The purpose of this double‐masked, randomized, controlled clinical trial was to evaluate the effects of the subgingival delivery of boric acid gel as an adjunct to scaling and root planing ( SRP ) on clinical and radiographic parameters, and compare this method with SRP plus placebo gel alone in chronic periodontitis ( CP ) patients. Methods Thirty‐nine systemically‐healthy patients with CP were included in the present study. They were divided into two groups: (a) SRP + 0.75% boric acid gel (BA group); and (b) SRP + placebo gel (placebo group). At baseline, 3 and 6 months after treatment, clinical measurements, including plaque index, modified sulcus bleeding index, probing depth ( PD ), clinical attachment level ( CAL ), intrabony defect depth, and percentage change in radiographic defect depth reduction ( DDR %) as radiographic parameters were assessed. Results The mean PD reduction and mean CAL gain were greater in the BA group than the placebo group at 3 and 6 months. A significantly greater mean percentage of radiographic DDR % was found in the BA group (36.97±3.47%) compared to the placebo group (2.88±0.89%) after 6 months. Conclusion BA as an adjunct to SRP can provide a new insight into therapeutic strategies for the management of CP, but further clinical evaluations are needed.

The Schlafen 12 (SLFN12) protein regulates triple-negative breast cancer (TNBC) growth, differentiation, and proliferation. SLFN12 mRNA expression strongly correlates with TNBC patient survival. We sought to explore SLFN12 overexpression effects on in vivo human TNBC tumor xenograft growth and performed RNA-seq on xenografts to investigate related SLFN12 pathways. Stable SLFN12 overexpression reduced tumorigenesis, increased tumor latency, and reduced tumor volume. RNA-seq showed that SLFN12 overexpressing xenografts had higher luminal markers levels, suggesting that TNBC cells switched from an undifferentiated basal phenotype to a more differentiated, less aggressive luminal phenotype. SLFN12-overexpressing xenografts increased less aggressive BC markers, HER2 receptors ERBB2 and EGFR expression, which are not detectable by immunostaining in TNBC. Two cancer progression pathways, the NAD signaling pathway and the superpathway of cholesterol biosynthesis, were downregulated with SLFN12 overexpression. RNA-seq identified gene signatures associated with SLFN12 overexpression. Higher gene signature levels indicated good survival when tested on four independent BC datasets. These signatures behaved differently in African Americans than in Caucasian Americans, indicating a possible biological difference between these races that could contribute to the worse survival observed in African Americans with BC. These results suggest an increased SLFN12 expression modulates TNBC aggressiveness through a gene signature that could offer new treatment targets.

Purpose One possible way to quantify each individual's response or damage from ionizing radiation is to estimate their accelerated biological age following exposure. Since there is currently no definitive way to know if biological age estimations are accurate, we aim to establish a rad-age association using genomics as its foundation. Methods Two datasets were combined and used to empirically find the age cutoff between young and old patients. With age as both a categorical and continuous variable, two other datasets that included radiation exposure are used to test the interaction between radiation and age. The gene lists are oriented in preranked lists for both pathway and diseases analysis. Finally, these genes are used to evaluate another dataset on the clinical relevance in differentiating lung disease given ethnicity and sex using both pairwise t -tests and linear models. Results Using 12 well-known genes associated with aging, a threshold of 29-years-old was found to be the difference between young and old patients. The two interaction tests yielded 234 unique genes such that pathway analysis flagged IL-1 signaling and PRPP biosynthesis as significant with high cell proliferation diseases and carcinomas being a common trend. LAPTM4B was the only gene with significant interaction among lung disease, ethnicity, and sex, with fold change greater than two. Conclusion The results corroborate an initial association between radiation and age, given inflammation and metabolic pathways and multiple genes emphasizing mitochondrial function, oxidation, and histone modification. Being able to tie rad-age genes to lung disease supplements future work for risk assessment following radiation exposure.

Exposure to radiation is a health concern within and beyond the Earth's atmosphere for aircrew and astronauts in their respective austere environments. The biological effects of radiation exposure from a multiomics standpoint are relatively unexplored and stand to shed light on tailored monitoring and treatment for those in these career fields. To establish a reference variable for genetic damage, biological age seems to be closely associated with the effect of radiation. Following a genetic-based study, this study explores the epigenetic landscape of radiation exposure along with its associative effects on aging processes.We imported the results of the genetics-based study that was a secondary analysis of five publicly available datasets (noted as Data1). The overlap of these genes with new data involving methylation data from two datasets (noted as Data2) following similar secondary analysis procedures is the basis of this study. We performed the standard statistical analysis on these datasets along with supervised and unsupervised learning to create preranked gene lists used for functional analysis in Ingenuity Pathway Analysis (IPA).There were 664 genes of interest from Data1 and 577 genes from Data2. There were 40 statistically significant methylation probes within 500 base pairs of the gene's transcription start site and 10 probes within 100 base pairs, which are discussed in depth. IPA yielded 21 significant pathways involving metabolism, cellular development, cell death, and diseases. Compared to gold standards for gestational age, we observed relatively low error and standard deviation using newly identified biomarkers.We have identified 17 methylated genes that exhibited particular interest and potential in future studies. This study suggests that there are common trends in oxidative stress, cell development, and metabolism that indicate an association between aging processes and the effects of ionizing radiation exposure.

Abstract The use of digital pathology for the histomorphologic profiling of pathological specimens is expanding the precision and specificity of quantitative tissue analysis at an unprecedented scale; thus, enabling the discovery of new and functionally relevant histological features of both predictive and prognostic significance. In this study, we apply quantitative automated image processing and computational methods to profile the subcellular distribution of the multi-functional transcriptional regulator, Kaiso ( ZBTB33 ), in the tumors of a large racially diverse breast cancer cohort from a designated health disparities region in the United States. Multiplex multivariate analysis of the association of Kaiso’s subcellular distribution with other breast cancer biomarkers reveals novel functional and predictive linkages between Kaiso and the autophagy-related proteins, LC3A/B, that are associated with features of the tumor immune microenvironment, survival, and race. These findings identify effective modalities of Kaiso biomarker assessment and uncover unanticipated insights into Kaiso’s role in breast cancer progression.

Women of African ancestry suffer higher rates of breast cancer mortality compared with all other groups in the United States. Though the precise reasons for these disparities remain unclear, many recent studies have implicated a role for differences in tumor biology. Using an epitope-validated antibody against the endoplasmic reticulum-associated E3 ligase, gp78, we show that elevated levels of gp78 in patient breast cancer cells predict poor survival. Moreover, high levels of gp78 are associated with poor outcomes in both ER+ and ER- tumors, and breast cancers expressing elevated amounts of gp78 protein are enriched in gene expression pathways that influence cell cycle, metabolism, receptor-mediated signaling, and cell stress response pathways. In multivariate analysis adjusted for subtype and grade, gp78 protein is an independent predictor of poor outcomes in women of African ancestry. Furthermore, gene expression signatures, derived from patients stratified by gp78 protein expression, are strong predictors of recurrence and pathological complete response in retrospective clinical trial data and share many common features with gene sets previously identified to be overrepresented in breast cancers based on race. These findings implicate a prominent role for gp78 in tumor progression and offer insights into our understanding of racial differences in breast cancer outcomes.

Schlafen 12 (SLFN12) is an intermediate human Schlafen that induces differentiation in enterocytes, prostate, and breast cancer. We hypothesized that SLFN12 influences lung cancer biology. We investigated survival differences in high versus low SLFN12-expressing tumors in two databases. We then adenovirally overexpressed SLFN12 (AdSLFN12) in HCC827, H23, and H1975 cells to model lung adenocarcinoma (LUAD), and in H2170 and HTB-182 cells representing lung squamous cell carcinoma (LUSC). We analyzed proliferation using a colorimetric assay, mRNA expression by RT-qPCR, and protein by Western blot. To further explore the functional relevance of SLFN12, we correlated SLFN12 with seventeen functional oncogenic gene signatures in human tumors. Low tumoral SLFN12 expression predicted worse survival in LUAD patients, but not in LUSC. AdSLFN12 modulated expression of SCGB1A1, SFTPC, HOPX, CK-5, CDH1, and P63 in a complex fashion in these cells. AdSLFN12 reduced proliferation in all LUAD cell lines, but not in LUSC cells. SLFN12 expression inversely correlated with expression of a myc-associated gene signature in LUAD, but not LUSC tumors. SLFN12 overexpression reduced c-myc protein in LUAD cell lines but not in LUSC, by inhibiting c-myc translation. Our results suggest SLFN12 improves prognosis in LUAD in part via a c-myc-dependent slowing of proliferation.

Abstract Aim Boric acid ( BA ) exhibits antibacterial, anti‐inflammatory, as well as osteoblastic, activity. The aim of the present study was to explore the efficacy of 0.75% BA gel as a local drug‐delivery system in adjunct to scaling and root planing ( SRP ) for the treatment of class II furcation defects in comparison with placebo gel. Methods A total of 48 mandibular class II furcation defects were randomized and treated with either 0.75% BA gel or placebo gel. Clinical parameters were recorded at baseline, 3 months, and 6 months, while radiographic parameters were recorded at baseline and 6 months. Results Greater mean probing depth reduction and mean relative vertical and horizontal clinical attachment level gain were shown to be greater in group 1 than in group 2 at 3 and 6 months. Furthermore, a significantly greater mean percentage of bone fill was found in group 1 (16.98%±1.03%) than in the placebo (2.86%±0.92%) at 6 months. Conclusion The .75% BA group showed significant improvement in clinical parameters compared to placebo gel as an adjunct to SRP . This implies an alternative for treatment of class II furcation.

Vitex negundo (Nirgundi) is one of the widely studied and used medicinal plants amongst those mentioned in ancient books. The name “Chinese Chaste tree” is derived from one of its therapeutic activity, which depresses the sexual desire. The long list of thesaurus is result of its wide distribution throughout the world. It’s important constituents are Vitexin, Nishindaside and Negundoside. A number of experts have worked on this plant for its different therapeutic uses such as: antiandrogenic, anti-inflammatory, analgesic, hepatoprotective, anxiolytic and mosquito repellant potential etc. Key Words-Chaste tree, Negundoside, Nishindaside, Nirgundi, Vitexin

Abstract The C-terminal binding protein (CtBP) is an NADH-dependent dimeric family of nuclear proteins that scaffold interactions between transcriptional regulators and chromatin-modifying complexes. Its association with poor survival in several cancers implicates CtBP as a promising target for pharmacological intervention. We employed computer-assisted drug design to search for CtBP inhibitors, using quantitative structure-activity relationship (QSAR) modeling and docking. Functional screening of these drugs identified 4 compounds with low toxicity and high water solubility. Micro molar concentrations of these CtBP inhibitors produces significant de-repression of epigenetically silenced pro-epithelial genes, preferentially in the triple-negative breast cancer cell line MDA-MB-231. This epigenetic reprogramming occurs through eviction of CtBP from gene promoters; disrupted recruitment of chromatin-modifying protein complexes containing LSD1, and HDAC1; and re-wiring of activating histone marks at targeted genes. In functional assays, CtBP inhibition disrupts CtBP dimerization, decreases cell migration, abolishes cellular invasion, and improves DNA repair. Combinatorial use of CtBP inhibitors with the LSD1 inhibitor pargyline has synergistic influence. Finally, integrated correlation of gene expression in breast cancer patients with nuclear levels of CtBP1 and LSD1, reveals new potential therapeutic vulnerabilities. These findings implicate a broad role for this class of compounds in strategies for epigenetically targeted therapeutic intervention.

The gene expression grade index (GGI) is a 97-gene algorithm that measures proliferation and divides intermediate histological grade tumors into two distinct groups. We investigated the association between early changes in GGI and clinical response to neoadjuvant letrozole and compared this to Ki67 values. The paired gene expression data at the beginning and after 10-14 days of neoadjuvant letrozole treatment were available for 52 post-menopausal patients with estrogen receptor (ER)-positive breast cancer. Baseline values and changes in GGI, Ki67, and RNA expression modules representing oncogenic signaling pathways were compared to sonographic tumor volume changes after 3 months of treatment in the subsets of patients defined by high and low baseline GGI. The clinical response was observed in 80% genomic low-grade (24/30) and 59% genomic high-grade (13/22) tumors (P=0.10). Low residual proliferation after 10-14 days of neoadjuvant letrozole therapy, measured by either GGI or Ki67, was associated with sonographic response in genomic high-grade (GGI, P=0.003; Ki67, P=0.017) but not genomic low-grade (GGI, P=0.25; Ki67, P=1.0) tumors. The analysis of expression modules suggested that sonographic response to letrozole in genomic high-grade tumors was associated with an early reduction in IGF1 signaling (unadjusted P=0.018). The major conclusion of this study is that the early assessment of proliferation after short-term endocrine therapy may be useful to evaluate endocrine responsiveness, particularly in genomic high-grade ER-positive breast cancer.

In the present study, Sugar Remedy, a polyherbal formulation (manufactured by Umalaxmi Organics Pvt Ltd, Jodhpur, Rajasthan, India) was evaluated for its antihyperglycemic, antihyperlipidemic, and antioxidant effects against normal and streptozotocin (STZ)-induced diabetic rats. Type II diabetes was induced in male Wistar rats by administration of a single intraperitoneal (IP) injection of STZ at a dose of 60 mg/kg. Effects of three different doses of Sugar Remedy suspension (185, 370, and 740 mg/kg/day, orally) and Metformin (500 mg/kg/day, orally) administered for 21 days were studied on parameters such as blood glucose, lipid profile, and antioxidant levels. Results were analyzed using one-way analysis of variance (ANOVA) followed by Dunnett's test. No significant changes were noticed in blood glucose, serum lipid levels, and kidney parameters in normal rats treated with Sugar Remedy suspension alone. The efficacy of Sugar Remedy as an antihyperglycemic, antihyperlipidemic, and antioxidant agent in STZ-induced diabetes was comparable to that of the standard, 500 mg/kg of Metformin. Present findings provide experimental evidence that Sugar Remedy has significant antihyperglycemic, antihyperlipidemic, and antioxidative effects in diabetic experimental rats. Hence, Sugar Remedy may be regarded as a promising natural and safe remedy for the prevention or delay of diabetic complications.

Abstract Background: Basal-like breast cancer is characterized by an increased risk of early distant relapse.Adjuvant cytotoxic chemotherapy is the only treatment option available. Understanding the biological heterogeneity of basal-like breast cancer may lead to improved targeted therapies.Methods: 957 systemically untreated patients with early breast cancer were identified from 4 large publicly available datasets. Among these patients, 192 were basal-like according to the “intrinsic gene set” (Sorlie PNAS 2003) and 212 were ER-/HER2- according to “subtype clustering model” (Desmedt CCR 2008). We calculated the hazard ratio (HR) for distant metastasis-free survival for several published gene signatures and biologically relevant single genes.Results: There was a significant overlap between the two classifications, with 190 (99%) cases of basal-like breast cancers identified also as ER-/HER2- (p&amp;lt;0.001). Among the 192 patients with basal-like breast cancer, 62% were T1, 93% were node-negative, 87% were grade 3 tumors. At a median follow-up of 7.3-years, 31% experienced a distant relapse. First generation gene signatures were not prognostic in basal-like tumors.Summary of Univariate HRs for Distant Metastasis-Free Survival in basal-like breast cancer (N=192) HR (95% CI)P-valueFirst Generation Prognostic SignaturesONCOTYPE (Paik NEJM 2004)1.31 (0.43-3.95)0.6270-gene signature (Van't Veer Nature2002)1.81 (0.72-4.55)0.20GGI (Sotiriou JNCI 2006)0.89 (0.40-1.97)0.77Pathway Specific SignaturesSRC (Bild Nature 2006)0.60 (0.37-1.00)0.05RAS (Bild Nature 2006)0.88 (0.53-1.45)0.63MYC (Bild Nature 2006)1.07 (0.68-1.70)0.75E2F3 (Bild Nature 2006)1.46 (0.91-2.37)0.12Stroma (Farmer Nat Med 2009 )1.85 (1.08-3.21)0.03Immune Response (Teschendorff Genome Biol 2007)0.46 (0.28-0.75)&amp;lt;0.01IGF1 Pathway (Creighton JCO 2008)0.55 (0.29-1.03)0.06PI3K mutant-like (Loi AACR 2009)0.54 (0.28-1.02)0.06Androgen Pathway (Doane Oncogene 2006)1.11 (0.47-2.64)0.79BRCA1 mutant-like (Van't Veer Nature 2002)0.41 (0.21-0.82)0.01Single Gene ExpressionPARP1 mRNA0.87 (0.55-1.37)0.55c-KIT mRNA1.42 (0.91-2.25)0.12EGFR mRNA0.80 (0.41-1.58)0.53GRB7 mRNA (Sparano ASCO 2009)1.11 (0.52-2.39)0.78 An activated stroma signature was associated with a poorer prognosis, whereas signatures reflecting BRCA1 loss, enhanced immune response, down-regulation of mTOR signaling and an activated SRC pathway were all associated with better prognosis in basal-like tumors. Intriguingly, an activated IGF1 signaling, known to be associated with poorer prognosis in ER-positive tumors (Creighton JCO 2008), was associated with better prognosis in basal-like cancers particularly those with an activated androgen pathway signaling (HR 0.26, p&amp;lt;0.01).Conclusion: Nearly all genomically ER- /HER2- tumors are basal-like. Basal-like breast cancer is heterogeneous with distinct oncogenic pathways associated with long term outcome. Trials with novel agents in basal-like breast cancer should account for this biological heterogeneity. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 106.

Purpose Urethral strictures are a rare complication of prostate brachytherapy (BXT), with prior studies showing radiation dose to the bulbomembranous urethra as being associated with stricture formation. This retrospective case–control study explored clinical and dosimetric parameters associated with the development of BXT-related urethral strictures. Methods and Materials A cohort of 34 patients developed urethral strictures after BXT at our institution for the period of 2008–2014. Each case was matched with two controls (68 controls) that had not developed a urethral stricture according to similar baseline clinical and dosimetric parameters. Stricture development was compared with clinical (i.e., age, smoking status, diabetes, hypertension, vascular disease, International Prostate Symptom Score, hormones) and dosimetric (i.e., prostate, urethra, urethral segments [base, midgland, apex, extraprostatic, and 5 mm margin]) variables. Statistical modeling approaches such as univariate, multivariate, and subset selection methods for risk prediction were applied to identify parameter(s) with best predictive ability of toxicity. The performances of models were ranked according to Akaike information criterion score. Results The results show that the R2 statistic increases from 6%, when only one parameter is included in the model, to almost 33%, when all the parameters are included. The best-fit subset of parameters included pretreatment International Prostate Symptom Score sum, urethra D30 Gy, urethra D5 Gy, and intraprostatic urethra with 5-mm margin V200 at the apex having the highest ability to predict the development of urinary strictures. Conclusions This study used statistical modeling, a novel approach in prostate BXT dosimetric studies, to identify a subset of parameters with predictive ability in identifying patients who develop urethral strictures.

Hyperglycemia is one of the major health concern in many parts of the world. One of the serious complications of high glucose levels is diabetic nephropathy. The preliminary microarray study performed on primary human renal tubular epithelial (hRTE) cells exposed to high glucose levels showed a significant downregulation of mTOR as well as its associated genes as well as lysosomal genes. Based on this preliminary data, the expression of various lysosomal genes as well as mTOR and its associated genes were analyzed in hRTE cells exposed to 5.5, 7.5, 11 and 16 mM glucose. The results validated the microarray analysis, which showed a significant decrease in the mRNA as well as protein expression of the selected genes as the concentration of glucose increased. Co-localization of lysosomal marker, LAMP1 with mTOR showed lower expression of mTOR as the glucose concentration increased, suggesting decrease in mTOR activity. Although the mechanism by which glucose affects the regulation of lysosomal genes is not well known, our results suggest that high levels of glucose may lead to decrease in mTOR expression causing the cells to enter an anabolic state with subsequent downregulation of lysosomal genes.

Cadmium (Cd 2+) is an environmental toxicant and a human carcinogen.Several studies show an association of Cd 2+ exposure to the development of breast cancer.Previously, we have transformed the immortalized non-tumorigenic cell line MCF-10A with Cd 2+ and have demonstrated that the transformed cells have anchorage independent growth.In a separate study, we showed that transformation of the immortalized urothelial cells with the environmental carcinogen arsenite (As 3+) results in an increase in expression of genes associated with the basal subtype of bladder cancer.In this study, we determined if transformation of the MCF-10A cells with Cd 2+ would have a similar effect on the expression of basal genes.The results of our study indicate that there is a decrease in expression of genes associated with keratinization and cornification and this gene signature includes the genes associated with the basal subtype of breast cancer.An analysis of human breast cancer databases indicates an increased expression of this gene signature is associated with a positive correlation to patient survival whereas a reduced expression/absence of this gene signature is associated with poor patient survival.Thus, our study suggests that transformation of the MCF-10A cells with Cd 2+ produces a decreased basal gene expression profile that correlates to patient outcome.

Abstract Damage to proximal tubules due to exposure to toxicants can lead to conditions such as acute kidney injury (AKI), chronic kidney disease (CKD) and ultimately end‐stage renal failure (ESRF). Studies have shown that kidney proximal epithelial cells can regenerate particularly after acute injury. In the previous study, we utilized an immortalized in vitro model of human renal proximal tubule epithelial cells, RPTEC/TERT1, to isolate HRTPT cell line that co‐expresses stem cell markers CD133 and CD24, and HREC24T cell line that expresses only CD24. HRTPT cells showed most of the key characteristics of stem/progenitor cells; however, HREC24T cells did not show any of these characteristics. The goal of this study was to further characterize and understand the global gene expression differences, upregulated pathways and gene interaction using scRNA‐seq in HRTPT cells. Affymetrix microarray analysis identified common gene sets and pathways specific to HRTPT and HREC24T cells analysed using DAVID, Reactome and Ingenuity software. Gene sets of HRTPT cells, in comparison with publicly available data set for CD133+ infant kidney, urine‐derived renal progenitor cells and human kidney‐derived epithelial proximal tubule cells showed substantial similarity in organization and interactions of the apical membrane. Single‐cell analysis of HRTPT cells identified unique gene clusters associated with CD133 and the 92 common gene sets from three data sets. In conclusion, the gene expression analysis identified a unique gene set for HRTPT cells and narrowed the co‐expressed gene set compared with other human renal–derived cell lines expressing CD133, which may provide deeper understanding in their role as progenitor/stem cells that participate in renal repair.

To report on the importance of cancer location from diagnostic prostate biopsies in predicting biochemical relapse for patients treated with (125)I seed implant brachytherapy as monotherapy for favorable risk disease; specifically, to assess the clinical significance of potentially underdosing the base region of the prostate gland.Of 1145 consecutive patients, 846 had pretreatment biopsies allowing for sextant analysis and consequent evaluation of biochemical failure tendencies. Biochemical failure was defined as a posttreatment rise in the nadir prostate-specific antigen (PSA) by at least 2 ng/mL. Patient and tumor characteristics, dosimetry, the use of hormone therapy, source strength, and postimplant PSA kinetics were analyzed between sextant subgroups.Sixty-two patients (7.3%) with sextant pathology had biochemical failure. There was no significant difference between the failure locations. There were 528 patients (62.4%) with some element of base involvement (BI), and 318 patients (37.6%) with no evidence of BI. Of the 62 patients with biochemical failure, 42 (67.7%) showed BI on biopsy and 20 (32.3%) had no BI. The 10-year relapse-free survival rate is 88.2% (95% confidence interval: 84.3%, 92.2%) and 92.0% (95% confidence interval: 88.4%, 95.8%) for the BI and no BI groups, respectively (p = 0.17). The mean D90 delivered to the base, midgland, and apex was 140.8 (±21.8) Gy, 170.8 (±22.5) Gy, and 177.9 (±29.5) Gy, respectively, for all patients.There are no significantly worse outcomes for patients treated with an (125)I seed implant for favorable risk prostate cancer with some element of BI, despite lower doses of radiation delivered to the base region.

Arrangement of the facilities on shop floor in industries termed as facility layout planning.It is a vital issue at the premature stage while designing a manufacturing structure because it affects the total manufacturing cost considerably.The dynamic environment is such an industrial condition in which flexibility exists in the demand of the product.The purpose of this research paper is to present a review on the implementation of meta-heuristics approaches for handling the problem of facility layout in a dynamic environment.Various meta-heuristic approaches which have been implemented in facility layout planning (FLP) are discussed briefly and the percent utilisation of different approaches is analysed in various time spans.Tabu search (TS), genetic algorithm (GA), particle swarm optimisation (PSO), and ant colony optimisation (ACO) are several typically used methods by researchers for layout optimisation.In the present study, % utilisation of these algorithms has been analysed for different time span, ACO utilised by maximum researchers in the time span '2010-2015'.The present study also revealed GA has been executed by most of the researchers (25%), whereas PSO (8%) utilised by very least designers.

ABSTRACT Background Breast cancer (BC) in young women is associated with poor prognosis. Whether age impacts the biology of BC or is just a surrogate for aggressive BC subtypes is unclear. Patients and methods We searched gene expression publically available datasets for patients (pts) with known age. Pts were assigned to BC molecular subtypes using a 3-gene classifier (ESR1, ERRB2, AURKA). First, we evaluated the difference in relapse-free survival (RFS) using a Cox regression model stratified by dataset & adjuvant treatment, and adjusted for age, BC subtypes, pT, pN & grade. We then performed a MEDLINE search on molecular aberrations related to the biology of BC in young women. We evaluated if the expression of these genes is associated with age after adjustment for multiple confounding factors (dataset, pT, pN, BC subtype & grade) in a linear regression model. For the biological analysis, two cohorts were used: systemically untreated pts (n = 1188) and treated ones (n = 2334). FDR was used to control for multiple testing. Results 3522 pts (20 datasets) were eligible. Pts ≤ 40 had a higher proportion of ER-/HER2- tumors but less luminal-A (p Conclusions BC arising at a young age appears to be biologically unique beyond subtype distribution. Separate therapeutic approaches such as targeting RANKL or mammary stem cells could be worth investigating in this pt subset. We are now launching a pre-operative window study evaluating the role of a RANKL inhibitor in young BC pts (EudraCT number 2011-006224-21) Disclosure All authors have declared no conflicts of interest.

Introduction: SPARC is an important regulator of the extracellular matrix and has been suggested to improve delivery of albumin-bound cytotoxics.However, little is known regarding its role in breast cancer (BC). Methods:We conducted a pooled analysis of publically available datasets, in which BC patients who received no systemic therapy or received neoadjuvant chemotherapy were eligible.Patients were assigned to molecular subtypes using PAM-50.We computed a SPARC module (SPARC7), composed of genes with an absolute correlation with SPARC .0.7.In the systemically untreated cohort, we evaluated 1) expression of SPARC/SPARC7 according to breast cancer subtype, 2) association between SPARC/SPARC7 and biological processes related to proliferation, immune and stroma, and 3) association between SPARC/SPARC7 and relapse-free survival in a Cox model in all patients and in the different molecular subtypes adjusted for tumor size, nodal status, histological grade, and age.In the neoadjuvant cohort, we evaluated the association between SPARC and pCR in a logistic regression model, adjusted for the same clinicopathologic factors.Results: 948 (10 datasets), and 791 (8 datasets) patients were included in the systemically untreated and neoadjuvant cohorts, respectively.High SPARC expression was associated with small tumor size, low histological grade and luminal-A tumors (all p,0.0001).There was a positive correlation between SPARC and stroma-related modules but negative correlation with proliferation modules.High SPARC expression was associated with poor prognosis in patients with basal and HER2+ breast cancer even after adjusting for clinicopathologic parameters.In the neoadjuvant cohort, a subgroup analysis suggested that high SPARC is associated with low rates of pCR in the HER2 subtype.Same results were observed on replacing SPARC by SPARC7. Conclusion:This analysis suggests a potential role of SPARC in determining prognosis and response to primary chemotherapy in early BC.This information could guide further development of albumin-bound cytotoxics in BC.

Old people are a growing minority. They comprise approximately 12% of the UK population, but consume an increasing proportion of health care resources. Gastrointestinal (GI) disorders are the third most common reason why patients over 65 years seek primary care advice, and 40% of these consultations relate to the upper GI tract.

3534 Background: The epigenetic transcriptional regulator, Kaiso (ZBTB33) has been identified as a member of the C2H2 zinc finger proteins containing a BTB/POZ -zinc finger family of transcription factors that are implicated in development of cancer. Although, our understanding of clinical relevance of subcellular distribution (cytoplasmic/nuclear) Kaiso in the growth and survival of human Breast cancer (BC) is limited. Methods: We examined a cohort of 555 BC patients who underwent surgery for their primary BC in Greenville, NC using AI and SM approach. Results: The sub-classification BC shows, cytoplasmic Kaiso is differentially enriched in ER- BC (p=0.001) compared nuclear Kaiso (p=0.8) and is significantly enriched in the more aggressive classes LumB (p=0.0017), HER2+ (p=0.05) and TNBC (p=6.1e-07) with respect to LumA BC patients. Additionally, the survival analysis of different compartments of Kaiso demonstrates that high cytoplasmic Kaiso (HR = 16.29 (7.6 – 34.8), p = 5.5e−13) is much more predictive of poor survival compared to nuclear Kaiso (HR = 2.83 (2.02 – 3.8), p = 6.1e−11). At gene expression level, ZBTB33 mRNA levels do not correlate with either nuclear (Spearman correlation: -0.03157, p= 0.7267) or cytoplasmic levels (Spearman correlation: -0.03526, p= 0.6962) of Kaiso. Surprisingly, ZBTB33 mRNA abundance is predictive of poor overall BC survival as demonstrated in two independent publicly available BC cohorts Metabric (HR = 2.14 (1.49 − 3.08), p = 2.7e−05) and Gyorffy B et al. (HR = 1.81 (1.55 − 2.12), p = 2.5e−14). Nuclear and cytoplasmic levels of Kaiso do not show significant differences based on race p=0.27 and p=0.1 respectively. Conclusions: Our data suggest subcellular distribution of high Kaiso is associated with poor prognosis of BC survival and subcellular localizations of Kaiso may play differential biological roles in BC prognosis.

Abstract Introduction: Racial/ethnic disparities in cancer survival in the United States are well documented, but the underlying biology is not well understood. Compared with European American (EA) counterparts, African American (AA) women are more likely to die from breast cancer in the United States. Our recent studies were aimed to evaluate trends in survival, by race-ethnicity, for women diagnosed with breast cancer. We uncovered some biological factors underlying this disparity by comparing functional expression and prognostic significance of several biomarkers including master transcriptional regulators of luminal differentiation. Materials &amp; Methods: We used a ML approach to assess a cohort of racially diverse 555 primary BC patients who underwent surgery in Greenville, NC and develop proteomics-based genomics (PbG) signatures. We apply quantitative automated image processing and computational methods to profile the subcellular distribution of the multi-functional transcriptional regulator, Kaiso (ZBTB33), and GP78. The cross-validated models were developed on a BC pooled dataset of (N= 845) samples (primarily taxane and anthracycline based) and chemotherapy cohort (N=415) including racial disparities. Results: Multiplex multivariate analysis of the association of Kaiso’s subcellular distribution with other breast cancer biomarkers reveals novel functional and predictive linkages between Kaiso and the autophagy-related proteins, LC3A/B, that are associated with features of the tumor immune microenvironment, survival, and race. Univariate or multivariate HRs for overall survival, estimated from digital IHC scoring of nuclear antigen, show distinct differences in the magnitude and significance of these biomarkers to predict survival based on race: ESR1 [EA HR 0.47; 95% confidence interval (CI), 0.31–0.72 and AA HR 0.77; 95% CI, 0.48–1.18]; FOXA1 (EA HR 0.38; 95% CI, 0.23–0.63 and AA HR 0.53; 95% CI, 0.31–0.88), and GATA3 (EA HR 0.36; 95% CI, 0.23–0.56; AA HR 0.57; CI, 0.56–1.4). In addition, elevated levels of gp78 in patient breast cancer cells predict poor survival. Moreover, high levels of gp78 are associated with poor outcomes in both ER+ and ER– tumors, and breast cancers expressing elevated amounts of gp78 protein are enriched in gene expression pathways that influence cell cycle, metabolism, receptor-mediated signaling, and cell stress response pathways. Conclusion: Understanding these biomarkers and their downstream regulons will elucidate the intrinsic mechanisms that drive racial disparities in breast cancer survival. These findings identify effective modalities of Kaiso biomarker assessment and uncover unanticipated insights into Kaiso’s role in breast cancer progression. Even within clinically homogeneous tumor groups, regulatory networks that drive mammary luminal differentiation reveal race-specific differences in their association with clinical out- come. Our findings implicate a prominent role for gp78 in tumor progression and offer insights into our understanding of racial differences in breast cancer outcomes. Citation Format: Sandeep K. Singhal, Kevin L. Gardner. The breast cancer biomarkers as predictors of survival: Do they vary by race and ethnicity? [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr IA039.

The integrated approach to testing and assessment, also referred to as IATA, is an approach which integrates multiple sources of data to be assessed at the same time for chemical hazard characterization. IATA is important to assess the chemical toxicity of heavy metals such as arsenic. Recent studies have shown that arsenic is a natural environmental adulterant to which humans are exposed daily through drinking water, food, air, and soil. Arsenic exposure has been associated with different diseases such as bladder cancer, skin diseases, diabetes, and kidney and lung cancer. The IATA offers a platform to integrate and analyze the data generated by toxicity testing methods and serves as an accurate and flexible tool to support regulatory decision making. This chapter discusses the importance of IATA in toxicology and different types of approaches for testing and assessment in detail. It highlights the case studies which have discussed the importance of an integrated approach to testing, assessment, and development in toxicology and how current research is adapting IATA to minimize animal testing. This chapter aims to offer an understanding of how IATA can play a major role in assessing arsenic heavy metal toxicity.

Arsenic exposure can cause toxicity in humans and is widespread throughout the world, leading to many areas of research with arsenic toxicology. Adverse outcome pathways (AOPs) are often studied in arsenic toxicology because they can deliver insight into the interactions and outcomes between toxic substances and organisms. In this chapter, we discuss high content of risk predictive models and new alternative methods (NAMs) to streamline the study of AOPs in arsenic toxicology using transcriptomic analysis techniques. Previous studies have shown how artificial intelligence and machine learning with pathway enrichment analysis can be used to create prediction models for examining high arsenic exposure and disease risk using genomic data. NAMs including in vitro and in silico are environmentally friendly and reduce the time it takes to perform studies. Use of pathway analysis tools alongside NAMs can be applied to further our understanding of arsenic heavy metal toxicology.

The human kidney is known to possess renal progenitor cells (RPCs) that can assist in the repair of acute tubular injury. The RPCs are sparsely located as single cells throughout the kidney. We recently generated an immortalized human renal progenitor cell line (HRTPT) that co-expresses PROM1/CD24 and expresses features expected on RPCs. This included the ability to form nephrospheres, differentiate on the surface of Matrigel, and undergo adipogenic, neurogenic, and osteogenic differentiation. These cells were used in the present study to determine how the cells would respond when exposed to nephrotoxin. Inorganic arsenite (iAs) was chosen as the nephrotoxin since the kidney is susceptible to this toxin and there is evidence of its involvement in renal disease. Gene expression profiles when the cells were exposed to iAs for 3, 8, and 10 passages (subcultured at 1:3 ratio) identified a shift from the control unexposed cells. The cells exposed to iAs for eight passages were then referred with growth media containing no iAs and within two passages the cells returned to an epithelial morphology with strong agreement in differential gene expression between control and cells recovered from iAs exposure. Results show within three serial passages of the cells exposed to iAs there was a shift in morphology from an epithelial to a mesenchymal phenotype. EMT was suggested based on an increase in known mesenchymal markers. We found RPCs can undergo EMT when exposed to a nephrotoxin and undergo MET when the agent is removed from the growth media.

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&lt;p&gt;Supplemental Table 3 Race and Survival Predictor Regulon Gene Enrichment Ontology Processes&lt;/p&gt;

&lt;p&gt;Supplemental Table 1 Survival and Race Predictor Regulon Gene Descriptions &amp; Regulons&lt;/p&gt;

&lt;p&gt;Supplemental data&lt;/p&gt;

&lt;p&gt;Supplemental Figure 5 Overall breast cancer survival based on median income of county of diagnosis in European American (EA) (A) compared to African American (AA) patients (B). CI, confidence interval.&lt;/p&gt;

&lt;p&gt;Supplemental Figure 4 Quantitative correlation of biomarker expression stratified by race.&lt;/p&gt;

&lt;p&gt;Supplemental Table 2 Race and 3-year Survival Regulon RFS&lt;/p&gt;

&lt;p&gt;Supplemental Figure 1 Comparison of subtype distribution by ancestry in the current cohort study&lt;/p&gt;

&lt;p&gt;Supplemental Figure 2 Subtype specific breast cancer survival comparisons.&lt;/p&gt;

&lt;p&gt;Supplemental Figure 3 Racial difference in survival in (A) Luminal A compared to (B) TNBC breast cancer. CI, confidence interval.&lt;/p&gt;

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&lt;p&gt;Supplemental Figure 5 Overall breast cancer survival based on median income of county of diagnosis in European American (EA) (A) compared to African American (AA) patients (B). CI, confidence interval.&lt;/p&gt;

&lt;p&gt;Supplemental Figure 2 Subtype specific breast cancer survival comparisons.&lt;/p&gt;

&lt;p&gt;Supplemental Figure 3 Racial difference in survival in (A) Luminal A compared to (B) TNBC breast cancer. CI, confidence interval.&lt;/p&gt;

&lt;p&gt;Supplemental data&lt;/p&gt;

&lt;p&gt;Supplemental Table 1 Survival and Race Predictor Regulon Gene Descriptions &amp; Regulons&lt;/p&gt;

&lt;p&gt;Supplemental Table 2 Race and 3-year Survival Regulon RFS&lt;/p&gt;

&lt;p&gt;Supplemental Figure 4 Quantitative correlation of biomarker expression stratified by race.&lt;/p&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; There is growing evidence that interaction between stromal and tumor cells is pivotal in breast cancer progression and response to therapy. Based on earlier research suggesting that during breast cancer progression, striking changes occur in CD10&lt;sup&gt;+&lt;/sup&gt; stromal cells, we aimed to better characterize this cell population and its clinical relevance.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We developed a CD10&lt;sup&gt;+&lt;/sup&gt; stroma gene expression signature (using HG U133 Plus 2.0) on the basis of the comparison of CD10 cells isolated from tumoral (&lt;i&gt;n&lt;/i&gt; = 28) and normal (&lt;i&gt;n&lt;/i&gt; = 3) breast tissue. We further characterized the CD10&lt;sup&gt;+&lt;/sup&gt; cells by coculture experiments of representative breast cancer cell lines with the different CD10&lt;sup&gt;+&lt;/sup&gt; stromal cell types (fibroblasts, myoepithelial, and mesenchymal stem cells). We then evaluated its clinical relevance in terms of &lt;i&gt;in situ&lt;/i&gt; to invasive progression, invasive breast cancer prognosis, and prediction of efficacy of chemotherapy using publicly available data sets.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; This 12-gene CD10&lt;sup&gt;+&lt;/sup&gt; stroma signature includes, among others, genes involved in matrix remodeling (&lt;i&gt;MMP11&lt;/i&gt;, &lt;i&gt;MMP13&lt;/i&gt;, and &lt;i&gt;COL10A1&lt;/i&gt;) and genes related to osteoblast differentiation (periostin). The coculture experiments showed that all 3 CD10&lt;sup&gt;+&lt;/sup&gt; cell types contribute to the CD10&lt;sup&gt;+&lt;/sup&gt; stroma signature, although mesenchymal stem cells have the highest CD10&lt;sup&gt;+&lt;/sup&gt; stroma signature score. Of interest, this signature showed an important role in differentiating &lt;i&gt;in situ&lt;/i&gt; from invasive breast cancer, in prognosis of the HER2&lt;sup&gt;+&lt;/sup&gt; subpopulation of breast cancer only, and potentially in nonresponse to chemotherapy for those patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our results highlight the importance of CD10&lt;sup&gt;+&lt;/sup&gt; cells in breast cancer prognosis and efficacy of chemotherapy, particularly within the HER2&lt;sup&gt;+&lt;/sup&gt; breast cancer disease. &lt;i&gt;Clin Cancer Res; 18(4); 1004–14. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Breast cancer in young women is associated with poor prognosis. We aimed to define the role of gene expression signatures in predicting prognosis in young women and to understand biological differences according to age.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Patients were assigned to molecular subtypes [estrogen receptor (ER)&lt;sup&gt;+&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt;; HER2&lt;sup&gt;+&lt;/sup&gt;, ER&lt;sup&gt;−&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt;)] using a three-gene classifier. We evaluated whether previously published proliferation, stroma, and immune-related gene signatures added prognostic information to Adjuvant! online and tested their interaction with age in a Cox model for relapse-free survival (RFS). Furthermore, we evaluated the association between candidate age-related genes or gene sets with age in an adjusted linear regression model.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; A total of 3,522 patients (20 data sets) were eligible. Patients aged 40 years or less had a higher proportion of ER&lt;sup&gt;−&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt; tumors (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001) and were associated with poorer RFS after adjustment for breast cancer subtype, tumor size, nodal status, and histologic grade and stratification for data set and treatment modality (HR = 1.34, 95% CI = 1.10–1.63, &lt;i&gt;P&lt;/i&gt; = 0.004). The proliferation gene signatures showed no significant interaction with age in ER&lt;sup&gt;+&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt; tumors after adjustment for Adjuvant! online. Further analyses suggested that breast cancer in the young is enriched with processes related to immature mammary epithelial cells (luminal progenitors, mammary stem, &lt;i&gt;c-kit&lt;/i&gt;, &lt;i&gt;RANKL&lt;/i&gt;) and growth factor signaling in two independent cohorts (&lt;i&gt;n&lt;/i&gt; = 1,188 and 2,334).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Proliferation-related prognostic gene signatures can aid treatment decision-making for young women. However, breast cancer arising at a young age seems to be biologically distinct beyond subtype distribution. Separate therapeutic approaches such as targeting RANKL or mammary stem cells could therefore be needed. &lt;i&gt;Clin Cancer Res; 18(5); 1341–51. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; There is growing evidence that interaction between stromal and tumor cells is pivotal in breast cancer progression and response to therapy. Based on earlier research suggesting that during breast cancer progression, striking changes occur in CD10&lt;sup&gt;+&lt;/sup&gt; stromal cells, we aimed to better characterize this cell population and its clinical relevance.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We developed a CD10&lt;sup&gt;+&lt;/sup&gt; stroma gene expression signature (using HG U133 Plus 2.0) on the basis of the comparison of CD10 cells isolated from tumoral (&lt;i&gt;n&lt;/i&gt; = 28) and normal (&lt;i&gt;n&lt;/i&gt; = 3) breast tissue. We further characterized the CD10&lt;sup&gt;+&lt;/sup&gt; cells by coculture experiments of representative breast cancer cell lines with the different CD10&lt;sup&gt;+&lt;/sup&gt; stromal cell types (fibroblasts, myoepithelial, and mesenchymal stem cells). We then evaluated its clinical relevance in terms of &lt;i&gt;in situ&lt;/i&gt; to invasive progression, invasive breast cancer prognosis, and prediction of efficacy of chemotherapy using publicly available data sets.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; This 12-gene CD10&lt;sup&gt;+&lt;/sup&gt; stroma signature includes, among others, genes involved in matrix remodeling (&lt;i&gt;MMP11&lt;/i&gt;, &lt;i&gt;MMP13&lt;/i&gt;, and &lt;i&gt;COL10A1&lt;/i&gt;) and genes related to osteoblast differentiation (periostin). The coculture experiments showed that all 3 CD10&lt;sup&gt;+&lt;/sup&gt; cell types contribute to the CD10&lt;sup&gt;+&lt;/sup&gt; stroma signature, although mesenchymal stem cells have the highest CD10&lt;sup&gt;+&lt;/sup&gt; stroma signature score. Of interest, this signature showed an important role in differentiating &lt;i&gt;in situ&lt;/i&gt; from invasive breast cancer, in prognosis of the HER2&lt;sup&gt;+&lt;/sup&gt; subpopulation of breast cancer only, and potentially in nonresponse to chemotherapy for those patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our results highlight the importance of CD10&lt;sup&gt;+&lt;/sup&gt; cells in breast cancer prognosis and efficacy of chemotherapy, particularly within the HER2&lt;sup&gt;+&lt;/sup&gt; breast cancer disease. &lt;i&gt;Clin Cancer Res; 18(4); 1004–14. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;AbstractPurpose:&lt;p&gt;Compared with their European American (EA) counterparts, African American (AA) women are more likely to die from breast cancer in the United States. This disparity is greatest in hormone receptor–positive subtypes. Here we uncover biological factors underlying this disparity by comparing functional expression and prognostic significance of master transcriptional regulators of luminal differentiation.&lt;/p&gt;Experimental Design:&lt;p&gt;Data and biospecimens from 262 AA and 293 EA patients diagnosed with breast cancer from 2001 to 2010 at a major medical center were analyzed by IHC for functional biomarkers of luminal differentiation, including estrogen receptor (&lt;i&gt;ESR1&lt;/i&gt;) and its pioneer factors, &lt;i&gt;FOXA1&lt;/i&gt; and &lt;i&gt;GATA3&lt;/i&gt;. Integrated comparison of protein levels with network-level gene expression analysis uncovered predictive correlations with race and survival.&lt;/p&gt;Results:&lt;p&gt;Univariate or multivariate HRs for overall survival, estimated from digital IHC scoring of nuclear antigen, show distinct differences in the magnitude and significance of these biomarkers to predict survival based on race: &lt;i&gt;ESR1&lt;/i&gt; [EA HR = 0.47; 95% confidence interval (CI), 0.31–0.72 and AA HR = 0.77; 95% CI, 0.48–1.18]; &lt;i&gt;FOXA1&lt;/i&gt; (EA HR = 0.38; 95% CI, 0.23–0.63 and AA HR = 0.53; 95% CI, 0.31–0.88), and &lt;i&gt;GATA3&lt;/i&gt; (EA HR = 0.36; 95% CI, 0.23–0.56; AA HR = 0.57; CI, 0.56–1.4). In addition, we identify genes in the downstream regulons of these biomarkers highly correlated with race and survival.&lt;/p&gt;Conclusions:&lt;p&gt;Even within clinically homogeneous tumor groups, regulatory networks that drive mammary luminal differentiation reveal race-specific differences in their association with clinical outcome. Understanding these biomarkers and their downstream regulons will elucidate the intrinsic mechanisms that drive racial disparities in breast cancer survival.&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;AbstractPurpose:&lt;p&gt;Compared with their European American (EA) counterparts, African American (AA) women are more likely to die from breast cancer in the United States. This disparity is greatest in hormone receptor–positive subtypes. Here we uncover biological factors underlying this disparity by comparing functional expression and prognostic significance of master transcriptional regulators of luminal differentiation.&lt;/p&gt;Experimental Design:&lt;p&gt;Data and biospecimens from 262 AA and 293 EA patients diagnosed with breast cancer from 2001 to 2010 at a major medical center were analyzed by IHC for functional biomarkers of luminal differentiation, including estrogen receptor (&lt;i&gt;ESR1&lt;/i&gt;) and its pioneer factors, &lt;i&gt;FOXA1&lt;/i&gt; and &lt;i&gt;GATA3&lt;/i&gt;. Integrated comparison of protein levels with network-level gene expression analysis uncovered predictive correlations with race and survival.&lt;/p&gt;Results:&lt;p&gt;Univariate or multivariate HRs for overall survival, estimated from digital IHC scoring of nuclear antigen, show distinct differences in the magnitude and significance of these biomarkers to predict survival based on race: &lt;i&gt;ESR1&lt;/i&gt; [EA HR = 0.47; 95% confidence interval (CI), 0.31–0.72 and AA HR = 0.77; 95% CI, 0.48–1.18]; &lt;i&gt;FOXA1&lt;/i&gt; (EA HR = 0.38; 95% CI, 0.23–0.63 and AA HR = 0.53; 95% CI, 0.31–0.88), and &lt;i&gt;GATA3&lt;/i&gt; (EA HR = 0.36; 95% CI, 0.23–0.56; AA HR = 0.57; CI, 0.56–1.4). In addition, we identify genes in the downstream regulons of these biomarkers highly correlated with race and survival.&lt;/p&gt;Conclusions:&lt;p&gt;Even within clinically homogeneous tumor groups, regulatory networks that drive mammary luminal differentiation reveal race-specific differences in their association with clinical outcome. Understanding these biomarkers and their downstream regulons will elucidate the intrinsic mechanisms that drive racial disparities in breast cancer survival.&lt;/p&gt;&lt;/div&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Breast cancer in young women is associated with poor prognosis. We aimed to define the role of gene expression signatures in predicting prognosis in young women and to understand biological differences according to age.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Patients were assigned to molecular subtypes [estrogen receptor (ER)&lt;sup&gt;+&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt;; HER2&lt;sup&gt;+&lt;/sup&gt;, ER&lt;sup&gt;−&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt;)] using a three-gene classifier. We evaluated whether previously published proliferation, stroma, and immune-related gene signatures added prognostic information to Adjuvant! online and tested their interaction with age in a Cox model for relapse-free survival (RFS). Furthermore, we evaluated the association between candidate age-related genes or gene sets with age in an adjusted linear regression model.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; A total of 3,522 patients (20 data sets) were eligible. Patients aged 40 years or less had a higher proportion of ER&lt;sup&gt;−&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt; tumors (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001) and were associated with poorer RFS after adjustment for breast cancer subtype, tumor size, nodal status, and histologic grade and stratification for data set and treatment modality (HR = 1.34, 95% CI = 1.10–1.63, &lt;i&gt;P&lt;/i&gt; = 0.004). The proliferation gene signatures showed no significant interaction with age in ER&lt;sup&gt;+&lt;/sup&gt;/HER2&lt;sup&gt;−&lt;/sup&gt; tumors after adjustment for Adjuvant! online. Further analyses suggested that breast cancer in the young is enriched with processes related to immature mammary epithelial cells (luminal progenitors, mammary stem, &lt;i&gt;c-kit&lt;/i&gt;, &lt;i&gt;RANKL&lt;/i&gt;) and growth factor signaling in two independent cohorts (&lt;i&gt;n&lt;/i&gt; = 1,188 and 2,334).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Proliferation-related prognostic gene signatures can aid treatment decision-making for young women. However, breast cancer arising at a young age seems to be biologically distinct beyond subtype distribution. Separate therapeutic approaches such as targeting RANKL or mammary stem cells could therefore be needed. &lt;i&gt;Clin Cancer Res; 18(5); 1341–51. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

&lt;p&gt;Supplemental Figure 1 Comparison of subtype distribution by ancestry in the current cohort study&lt;/p&gt;

&lt;p&gt;Supplemental Table 3 Race and Survival Predictor Regulon Gene Enrichment Ontology Processes&lt;/p&gt;

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African American (AA) women with breast cancer are more likely to have higher inflammation and a stronger overall immune response, which correlate with poorer outcomes. In this report, we applied the nanostring immune panel to identify differences in inflammatory and immune gene expression by race. We observed a higher expression of multiple cytokines in AA patients compared to EA patients, with high expression of CD47, TGFB1, and NFKB1 associated with the transcriptional repressor Kaiso. To investigate the mechanism associated with this expression pattern, we observed that Kaiso depletion results in decreased expression of CD47, and its ligand SIRPA. Furthermore, Kaiso appears to directly bind to the methylated sequences of the THBS1 promotor and repress gene expression. Similarly, Kaiso depletion attenuated tumor formation in athymic nude mice, and these Kaiso-depleted xenograft tissues showed significantly higher phagocytosis and increased infiltration of M1 macrophages. In vitro validation using MCF7 and THP1 macrophages treated with Kaiso-depleted exosomes showed a reduced expression of immune-related markers (CD47 and SIRPA) and macrophage polarization towards the M1 phenotype compared to MCF7 cells treated with exosomes isolated from high-Kaiso cells. Lastly, analysis of TCGA breast cancer patient data demonstrates that this gene signature is most prominent in the basal-like subtype, which is more frequently observed in AA breast cancer patients.