Translating genetic findings to epigenetics: identifying the mechanisms associated with aging after high-radiation exposure on earth and in space

Purpose

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.

Methods

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).

Results

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.

Conclusion

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.

A Review: Multi-Omics Approach to Studying the Association between Ionizing Radiation Effects on Biological Aging

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.

Establishing a genomic radiation-age association for space exploration supplements lung disease differentiation

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.

Immune Profile of Exosomes in African American Breast Cancer Patients Is Mediated by Kaiso/THBS1/CD47 Signaling

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.

Arsenite Exposure to Human RPCs (HRTPT) Produces a Reversible Epithelial Mesenchymal Transition (EMT): In-Vitro and In-Silico Study

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.

Schlafen 12 Slows TNBC Tumor Growth, Induces Luminal Markers, and Predicts Favorable Survival

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.

RNA Sequencing of Intestinal Enterocytes Pre- and Post-Roux-en-Y Gastric Bypass Reveals Alteration in Gene Expression Related to Enterocyte Differentiation, Restitution, and Obesity with Regulation by Schlafen 12

Background: The intestinal lining renews itself in a programmed fashion that can be affected by adaptation to surgical procedures such as gastric bypass. Methods: To assess adaptive mechanisms in the human intestine after Roux-en-Y gastric bypass (RYGB), we biopsied proximal jejunum at the anastomotic site during surgery to establish a baseline and endoscopically re-biopsied the same area 6–9 months after bypass for comparison. Laser microdissection was performed on pre- and post-RYGB biopsies to isolate enterocytes for RNA sequencing. Results: RNA sequencing suggested significant decreases in gene expression associated with G2/M DNA damage checkpoint regulation of the cell cycle pathway, and significant increases in gene expression associated with the CDP-diacylglycerol biosynthesis pathway TCA cycle II pathway, and pyrimidine ribonucleotide salvage pathway after RYGB. Since Schlafen 12 (SLFN12) is reported to influence enterocytic differentiation, we stained mucosa for SLFN12 and observed increased SLFN12 immunoreactivity. We investigated SLFN12 overexpression in HIEC-6 and FHs 74 Int intestinal epithelial cells and observed similar increased expression of the following genes that were also increased after RYGB: HES2, CARD9, SLC19A2, FBXW7, STXBP4, SPARCL1, and UTS. Conclusions: Our data suggest that RYGB promotes SLFN12 protein expression, cellular mechanism and replication pathways, and genes associated with differentiation and restitution (HES2, CARD9, SLC19A2), as well as obesity-related genes (FBXW7, STXBP4, SPARCL1, UTS).

Gene modules in association with Kaiso and LC3 regulatory pathways to predict survival and response to therapy

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Background: The protein Kaiso was originally identified as a transcription factor and member of the BTB/POZ, a subfamily of zinc finger proteins that interacts with p120 catenin-binding proteins. Recently, we have shown that the relative abundance of both Kaiso -nuclear and -cytoplasmic as determined by quantitative immune-histochemistry (IHC) are each independent predictors of breast cancer (BC) survival preferentially in women of African ancestry (PMID: 33526872). In this study, we combine quantitative IHC with gene expression data to develop and identify surrogate signatures, and pathways associated with the abundance of kaiso -nuclear, -cytoplasm, and LC3A/B in BC patients. We found 1) Kaiso, and LC3A/B derived signatures predict response to therapy and survival, 2) Reveal novel functional and predictive linkages between Kaiso’s subcellular distribution, LC3A/B, and TIL% in comparison to published and commercially available BC biomarkers. Methods: We used a machine Learning approach to assess a cohort of racially diverse 555 BC patients who underwent surgery for their primary BC in Greenville, NC and develop proteomics-based genomics (PbG) signatures. Statistical models were developed to predict the treatment response (pathological complete response, pCR) and distant recurrence-free survival (DRFS) with the help of those PbG signatures and performance was assessed by Receiver Operating Characteristic. The cross-validated models were developed on a pooled dataset of (N= 845) samples (primarily taxane and anthracycline based) for BC (PMID: 22508827). Again, models were validated on neoadjuvant BC chemotherapy cohort (N=415) including racial disparities. Results: We found that PbG biomarkers are associated with gene regulatory pathways linked to replication, cellular stress, and numerous immunological pathways based on their scoring in GSEA profiling. Our present meta-analysis indicates that gene expression signatures and profiles generated from both Kaiso and LC3A/B subcellular localization provide added prognostic value in predicting pCR or recurrence. Moreover, the utility and accuracy of the model were validated using a second independent data set. We are currently exploring differential modeling outcomes that incorporate patient race and genetic ancestry stratification. Conclusions: The use of surrogate markers of IHC-based protein expression through the generation of gene modules introduces a new class of predictive biomarkers that add predictive value for use in clinical trials to guide treatment decisions with respect to therapeutic response and relapse free survival. Validation of this approach in an independent neoadjuvant BC chemotherapy clinical data set supports further exploration of both these gene expression protein surrogates and the protein biomarkers themselves through further retrospective evaluation and future prospective clinical trials.

Protein expression of the gp78 E3-ligase predicts poor breast cancer outcome based on race

Women of African ancestry suffer higher rates of breast cancer mortality compared to 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 degradation (ERAD) E3 ubiquitin 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-positive and ER-negative 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 new insights into our understanding of racial differences in breast cancer outcomes.

A study to evaluate the role of experience in acquisition of the skill of orotracheal intubation in adults

Background and Aims

To evaluate the role of experience in acquisition of skill of orotracheal intubation in adults.

Material and Methods

A prospective randomized study was conducted on 307 patients of either sex, belonging to ASA grade I and II (aged 18-60 years) posted for surgery under general anaesthesia. The patients were subjected to DL and ETI procedure, which was performed by five different groups of participants. Group 1 consisted of first-year resident of anaesthesiology with experience of less than 10 intubations, group 2 for second-year resident, group 3 for third-year resident, group 4 for senior resident and group 5 for consultant. Ease of mask ventilation, time taken for intubation, number of attempts, success rate, and ease of intubation were assessed for all the groups.

Results

Categorical variables were analysed using Chi-square test. For all statistical tests, a P value less than 0.05 was taken as a significant difference. Maximum difficulty in mask ventilation was encountered by group 1 anaesthesiologist, that is, in 69.2% of the patients. Group 1 took maximum time to intubate, that is, 47.98 ± 31.54 sec and least time was taken by group 5 anaesthesiologist (9.55 ± 6.93) sec. First attempt success rate was least in group (80.0%). Group 1 had success rate of 96.9%, whereas rest all groups had 100% success.

Conclusion

Skill of mask ventilation and intubation and time taken for intubation grossly improves with increasing experience. Minimum of 25 intubation attempts should be required by an anaesthesiologist resident in elective scenario to achieve 100% success rate in our study.

Role of HRTPT in kidney proximal epithelial cell regeneration: Integrative differential expression and pathway analyses using microarray and scRNA-seq

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.

A gp78/AMFR protein-driven gene signature that predicts breast cancer outcome

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Background: gp78, also known as the autocrine motility factor receptor (AMFR) or RNF45, is a polytopic RING-type E3 ubiquitin ligase resident to the endoplasmic reticulum (ER) that plays major role in the cellular response to stress by regulating ER homeostasis and signaling through its participation in the unfolded protein response (UPR) and ER associated degradation. We used machine learning (ML) and statistical modeling (SM) to assess gp78 as a protein biomarker that is an independent predictor of breast cancer (bc) survival exclusively in women of self-reported African descent as opposed to European ancestry. Methods: We examined a cohort of racially diverse 555 BC bc patients who underwent surgery for their primary BC in Greenville, NC using ML and SM approach. We leveraged the availability of RNA-seq gene expression data on a portion of our bc cohort (N=136 of 555) to construct gene expression signatures. Results: Using antibodies developed in the Weissman lab and established methods for quantitative IHC, we have found that gp78 expression is significantly increased in the tumors of bc patients compared to normal breast epithelia. In addition, we found that gp78 is expressed at significantly higher levels in bc of non-Hispanic black women (NHB) compared to non-Hispanic white women (NHW) (p=0.0038), and that bc subtypes known to be more aggressive and associated with higher grades like, Basal (p=1.6e-12), Luminal B (p=2.3e-4) and HER2(8.3e-4), display significantly higher levels of gp78 compare to Luminal A. Moreover, Kaplan-Meier survival curve analyses show that gp78 protein expression is more significantly associated with poor survival in NHB women (HR:1.65, p=0.073) compared to NHW women (HR:2.01, p=0.004). Finally, multivariate analysis reveals that gp78 protein expression, based on quantitative IHC, is an independent predictor of poor bc survival exclusively in women of African (NHB) ancestry (HR:1.99, p=0.017). We leveraged the availability of RNA-seq gene expression data on a portion of our bc cohort to construct gene expression signatures or gene modules. An analysis of pooled publicly available data from 845 patients that underwent neoadjuvant chemotherapy for bc (primarily taxane and anthracycline based), reveals that gp78 gene modules are highly predictive of patient response to therapy. gp78-derived gene modules show both high fold difference and significance in predicting response to therapy (AUC:0.72) which is very similar to other multi-gene panels that are currently in clinical use including Prosigna, MammaPrint, and Oncotype Dx. Conclusions: Our results show that gp78/AMFR is an independent predictor of bc survival and response to therapy, based on race, thus implicating a role for this protein, and potentially the UPR, as underlying biological differences in tumor properties linked to genetic ancestry.

Meta analysis of arsenic exposed genes expression profiles to develop a bladder cancer predictor

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Background: IARC classified arsenic (As) as “carcinogenic to humans”, but despite the health consequences, there is no molecular signature available yet to predict when exposure may lead to the disease development. First aim of this study is to investigate the genetic changes due to the exposure to carcinogenic compounds such as As. Secondly, how accurately we can predict the disease association when exposed to toxic compounds. Methods: The entire analysis was performed in-silico fashion and data was collected from the public resources such as NCBI database. Two Asian population datasets exposed As were used to find significantly differently express genes. In addition, four cancer cell lines with exposure of As compounds were used to identify the association with cancer. The human bladder cancer biopsy datasets were used to develop a risk predictive model. As per the requirements, numerous machine learning (ML) approaches such as random forest, hierarchical clustering, were used to find the classification and association between the samples and outcome. Statistical approaches such as T-Test, and ANOVA, applied to find the differentially expressed genes associated with different conditions and logistic regression models applied to develop risk prediction models. Results: We identified a set of 1183 genes which were common between both the populations and were significantly changed in humans exposed to As. A subset of 157 genes associated with As exposure and involved in cancer progression was selected for risk prediction model development. A set of four genes (NKIRAS2, AKTIP, HLA-DQA1 and TBC1D7) shows the highest prediction ability of primary bladder tumor with AUC 0.96 (95% CI: 0.82- 0.99) and reproducibility of 0.75 (0.34-0.93) when applied on different dataset. Conclusions: This study identified a list of genes and bladder cancer predictive models that would be very helpful to forecast the outcomes of As exposed in humans.

Kaiso (ZBTB33) subcellular partitioning functionally links LC3A/B, the tumor microenvironment, and breast cancer survival

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.

Through automated image analysis, Singhal et al quantify nuclear versus cytoplasmic distribution of the Kaiso transcription factor in breast cancer patient tissue. They find that Kaiso distribution correlates with breast cancer subtype and overall survival, and discover a link between cytoplasmic Kaiso and autophagy marker LC3.

Meta-analysis of gene expression profiling reveals novel basal gene signatures in MCF-10A cells transformed with cadmium

Cadmium (Cd²⁺) is an environmental toxicant and a human carcinogen. Several studies show an association of Cd²⁺ exposure to the development of breast cancer. Previously, we have transformed the immortalized non-tumorigenic cell line MCF-10A with Cd²⁺ 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 (As³⁺) 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 Cd²⁺ 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 Cd²⁺ produces a decreased basal gene expression profile that correlates to patient outcome.

Schlafen 12 Is Prognostically Favorable and Reduces C-Myc and Proliferation in Lung Adenocarcinoma but Not in Lung Squamous Cell Carcinoma

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 C033: Racial differences in the associations between luminal master regulator transcription factor expression and breast cancer survival

Purpose: Women of African ancestry in the United States are more likely to die from breast cancer than their European counterparts. While prior studies suggest differences in the frequency of hormone receptor-negative disease as an underlying cause, recent studies report higher race-based mortality rates in patients with hormone receptor-positive, luminal breast cancer. Here we explore biologic factors that may underly this disparity by comparing racial differences in the level, functional activity, and prognostic significance of 3 master transcriptional regulators of mammary luminal differentiation.

Patients and Methods: Medical records and tissues from 555 patients (293 European and 262 African ancestry) diagnosed with Stage 0 to IV breast cancer, from 2001 to 2010 at a major medical center in East North Carolina, were analyzed for the expression of functional biomarkers of luminal differentiation including estrogen receptor (ESR1), and pioneer transcription factors FOXA1 and GATA3. Differential comparison of protein expression was integrated with network-level gene expression analysis (22% of cohort) to define predictive correlations with race and survival.

Results: Univariate and multivariate odds ratios combined with area under the curve receiver operator characteristics show significant differences in predictive activity of these functional biomarkers based on race and survival—ESR1 (EA OR= 0.47, p = 5e-04; AA OR= 0.77, p = 0.22), FOXA1 (EA OR= 0.38, p= 1.4e-04; AA OR = 0.53, p = 1.3e-02), and GATA3 (EA OR= 0.36, p= 3.7e-06, AA OR= 0.57, p= 0.51)—and uncover genes in the downstream regulons of these biomarkers that strongly correlate either with genetic ancestry or overall survival.

Conclusion: Transcriptional regulatory networks linked to mammary luminal differentiation reveal race-specific differences in master regulatory activity that may underlie tumor characteristics contributing to racial disparities in outcome. These biomarkers and their downstream regulons represent important targets to explore intrinsic mechanisms that drive breast cancer survival disparities.

Citation Format: Jung S. Byun, Sandeep K. Singhal, Sam Park, Dae Ik Yi, Tingfen Yan, Ambar Caban, Alana Jones, Partha Mukhopadhyay, Sara Gil Hernandez, Stephen Hewitt, Lisa A. Newman, Melissa Davis, Jorge Sepulveda, Adrianna De Siervi, Anna Napoles, Nasreen Vohra, Kevin Gardner. Racial differences in the associations between luminal master regulator transcription factor expression and breast cancer survival [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C033.

Subcellular partitioning of Kaiso (ZBTB33) as a biomarker to predict overall breast cancer survival

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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.

Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival

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.

Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data

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 high-level 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.

Tumours of Deep Lobe of Parotid Gland: Our Experience

Parotidectomy surgeries are being routinely performed by ENT surgeons nowadays. Parotid tumours can present with a variety of manifestations ranging from a barely noticeable mass to a large tumour with facial paralysis. Most benign parotid tumours are located in the superficial lobe though rarely deep lobe may also be involved, while malignant tumours are generally seen to involve both the lobes of the gland. We present clinico-radiological-pathological profile of 25 patients who underwent parotid surgeries for tumours involving deep lobe alone or the whole gland, and were operated at our institute during the period from January 2011 to December 2012. This study was a retroprospective observational analysis with the aim of analyzing the epidemiology, radiological, surgical and histopathological profile of these patients. Among 25 patients who underwent parotid surgeries, 17 patients underwent total conservative parotidectomy, while 5 patients underwent radical parotidectomy. In 3 patients, extended radical parotidectomy was performed. We also report the complications and follow-up of these patients. We concluded that fine needle aspiration cytology (FNAC) findings and final histopathological report may not always correlate.

Efficacy of esmolol administration at different time intervals in attenuating hemodynamic response to tracheal intubation

BACKGROUND

Laryngoscopy and endotracheal intubation are known to cause increase in both arterial blood pressure and heart rate. Several strategies have been evolved to blunt the haemodynamic response to tracheal intubation but each method has its own advantages and disadvantages. Esmolol, a cardio selective Beta-1 blocking drug, can alleviate some of these problems. Esmolol, when administered parenterally, exhibits rapid onset and a short duration of action due to its rapid clearance by red blood cell esterases. Hence we conducted the present study to evaluate the efficacy and optimum time of single bolus esmolol administration in attenuating hypertensive- tachycardiac response to laryngoscopy and tracheal intubation.

MATERIALS AND METHODS

The randomized double blind prospective study was conducted in 60 patients, in the age group of 20-40 years, of both sexes, belonging to American Society of Anaesthesiologists (ASA) physical status class I or II and scheduled for elective surgery requiring endotracheal intubation and general anaesthesia. The efficacy and optimum time of single bolus esmolol administration in attenuating hypertensive - tachycardiac response to laryngoscopy and tracheal intubation was evaluated. Patients in group I (n = 20) received bolus administration of injection esmolol 1.5 mg/kg intravenously (iv) 90 seconds before intubation; in group II (n = 20) three minutes before intubation and in group III (n = 20) six minutes before intubation.

RESULTS

There was no clinical and statistically significant variation in heart rate in group I and II at different time intervals of the study period but in group III heart rate increased significantly one minute after tracheal intubation. (P < 0.05) One minute after intubation, the increase in systolic, diastolic and mean blood pressure and rate pressure product was statistically significant in group I (P < 0.01) and group III. (P < 0.05) However, in group II increase in systolic blood pressure and rate pressure product was statistically not significant. (P > 0.05)

CONCLUSION

To conclude, single intravenous bolus dose of esmolol (1.5 mg/kg) is safe and more effective in attenuating haemodynamic response to laryngoscopy and tracheal intubation when administered three minutes prior to intubation.

CD4⁺ follicular helper T cell infiltration predicts breast cancer survival

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.

Genomic grade adds prognostic value in invasive lobular carcinoma

BACKGROUND

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.

METHODS

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).

RESULTS

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].

CONCLUSIONS

GG outperformed HG in ILC and added prognostic value to classic clinicopathologic variables, including nodal status.

Urokinase-type plasminogen activator gene (PLAU) to predict clinical outcome in invasive lobular carcinoma

e21010

Background: At the molecular level invasive lobular carcinoma (ILC) is mostly composed of luminal A (LA) (≈80%) followed by luminal B (≈15%) and a small fraction of HER2-positive (≈5%) tumors (Metzger et al SABCS2011). In ILC, Genomic Grade (GG) adds prognostic information to clinico-pathological (CP) characteristics (Metzger et al ASCO 2011). In this study we sought to evaluate the prognostic value of different gene signatures/modules in patients diagnosed with LA classic ILC. Methods: Gene expression data were generated from 184 consecutive frozen tumor samples using Affymetrix U133 Plus 2.0 arrays. ILC tumors were classified into molecular subtypes using the PAM50 classifier. ILC tumors characterized as classic ILC by pahtologists and as LA by PAM50 were selected for this analysis. Invasive disease free survival (IDFS) was defined as the interval between date of surgery and date of any invasive recurrence or death. Multivariate analyses for IDFS and overall survival (OS) adjusted for age, tumor size, nodal status and chemotherapy was performed for gene signatures/modules related to proliferation, invasion, immune response and signaling pathways (IGF1, PI3K, MAPK, Src, Wnt). Results: 125 LA classic ILC tumors were identified with a median follow-up of 6.6 years (95% CI 5.6-7.6). The addition of PLAU gene expression as continous variable to CP variables yielded a significant hazard ratio (HR) for IDFS (HR= 2.1 [1.1 – 4.1], Δx2= 4.5, likelihood ratio p = 0.03) and for OS (HR = 3.6 [1.4 – 9.6], Δx2= 6.9, likelihood ratio p = 0.009). GG as a continous variable yielded a significant HR for IDFS (HR= 2.6 [1.2 – 5.7], Δx2= 6.2, likelihood ratio p = 0.01), but not for OS (HR= 2.1 [0.8 – 5.5], Δx2= 2.5, likelihood ratio p = 0.11). In contrast, IGF1, PI3K, MAPK, Src, Wnt, immune response, gene-70 and gene-76 failed failed to add signficant independent prognostic value. Conclusions: In addition to GG, PLAU adds prognostic information to CP factors in LA classic ILC and may guide future drug development in this difficult to treat BC subset. Of interest, PLAU is involved in degradation of extracellular matrix contributing to cell migration and metastasis and is a major component of a validated breast cancer biomarker (UPA/PAI1).

Gene modules and response to neoadjuvant chemotherapy in breast cancer subtypes: a pooled analysis

PURPOSE

To investigate the association between chemotherapy response and gene expression modules describing important biologic processes and druggable oncogenic pathways in breast cancer (BC) subtypes.

PATIENTS AND METHODS

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.

RESULTS

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).

CONCLUSION

Different processes and pathways are associated with pCR in different BC subtypes.

Elucidating prognosis and biology of breast cancer arising in young women using gene expression profiling

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.

Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment

PURPOSE

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.

EXPERIMENTAL DESIGN

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.

RESULTS

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.

CONCLUSIONS

Our results highlight the importance of CD10(+) cells in breast cancer prognosis and efficacy of chemotherapy, particularly within the HER2(+) breast cancer disease.

P1-02-05: Invasive Lobular Carcinoma – A Luminal Breast Cancer Histotype Enriched for Epithelial-to-Mesenchymal Transition Features

Background: Invasive lobular carcinoma (ILC) represent the second most common breast cancer (BC) histotype, but little information is available about its molecular features. We sought to perform a comprehensive molecular classification of ILC and to investigate the molecular features that can differentiate ILC from invasive ductal carcinoma (IDC).

Methods: A consecutive series of 174 ILC tumors from three different centers with mininum 5-year follow-up was selected. Gene expression data were generated using Affymetrix U133 Plus 2.0 arrays. Data were analyzed by using frozen robust multiarray analysis (Matthew et al. 2009). ILC tumors were classified into BC molecular subtypes using the PAM50 classifier. Invasive Disease Free Survival (IDFS) was defined as the interval between the date of surgery and the date of any invasive recurrence or death. Multivariate analyses for 10-y IDFS containing classical clinico-pathologic characteristics were performed for different gene signatures, which were scaled so that 2.5 and 97.5% percentiles equal −1 and 1. A cohort of 90 IDC tumor samples, normalised with the same method, was used to compare expression data between ILC and IDC.

Results: ILCs were mainly characterized as luminal A (LA: 76%, n=133) and luminal B (LB:; 20%, n=34) followed by a minority of HER2−positive (2%, n=3), basal (1%, n=2) and normal-like (1%, n=2) based on Perou's classification. LB had inferior 10-y IDFS than LA in univariate cox regression analysis (HR = 1.99, 95% CI, 1.08−3.67, p=0.026). The EMT gene module was significantly higher expressed in ILC as compared to IDC (p &lt; 0.001). Adjusted hazard ratios (HR) for different gene modules investigated are detailed in the table below.

PD03-10: Gene Modules and Response to Neoadjuvant Chemotherapy in Breast Cancer: A Meta-Analysis

Background: We and others have shown that high expression of proliferation and immune related genes are associated with pathological complete response (pCR) after neoadjuvant chemotherapy in breast cancer (BC). Here, we performed a meta-analysis to validate these findings and to interrogate the association between pCR and several other gene expression modules beyond standard clinico-pathological characteristics in BC subtypes.

Methods: We searched for publicly available gene expression studies evaluating anthracycline ± taxane-based neoadjuvant chemotherapy. We identified 7 studies with complete genomic and clinico-pathological data including pCR totaling 788 patients. Relapse-free survival (RFS) data were available for 427 patients. We used gene expression data generated from pretreatment biopsies and computed 17 gene modules corresponding to proliferation-driven signatures, immune response, stroma activation, phosphatase and tensin homolog (PTEN) loss, chromosomal instability, and several other oncogenic pathways. We calculated odds ratios (OR) for pCR for one-unit increases in scaled modules, all adjusting for pretreatment clinico-pathological characteristics. Moreover, we tested for interactions between gene modules and ER or HER2 status for their association with pCR after adjusting for clinicopathological characteristics. We used the false discovery rate (FDR) to adjust for multiple testing.

Results: We observed pCR in 178(22.6%) of 788 patients: 112(30.1%) of 372 with ER−/HER2− BC, 41(36%) of 113 with HER2+ BC, and 25(8.2%) of 303 with ER+/HER2− BC. High values of the proliferation-driven modules were associated with increased pCR rates in ER−/HER2− (e.g. Gene70 OR=2.34, 95%CI 1.22−4.59, p=0.01, FDR=0.10) and ER+/HER2− (e.g. Gene70 OR=3.26, CI 1.13−9.60, p=0.03, FDR=0.16), but not in the HER2+ subtype (e.g. Gene70 OR=0.82, CI 0.23−2.67, p=0.74, FDR=0.86). There was a trend for interaction between proliferation-driven modules (e.g. Gene70) and HER2 status (p=0.08, FDR=0.23). Interestingly, we demonstrated a strong association between high values of immune module and increased pCR rates in the HER2+ (OR=6.58, CI 2.20−23.40, p&lt;0.01, FDR=0.03) and ER−/HER2− (OR=1.75, CI 1.12−2.76, p=0.02, FDR=0.10) but not in the ER+/HER2− subtype (OR=1.50, CI 0.63−3.42, p=0.35, FDR=0.49). Moreover, high values of AKT activation module were associated with decreased pCR rates in HER2+ (OR=0.38, CI 0.14−0.98, p=0.05, FDR=0.29) but not in the ER−/HER2− (OR=0.87, CI 0.56−1.37, p=0.56, FDR=0.68) or ER+/HER2− (OR=1.81, CI 0.65−5.30, p=0.27, FDR=0.47) subtype. Interactions between immune module and HER2 status and between AKT module and HER2 status were nominally significant (p=0.04 and p=0.05, respectively), but came with an FDR of 0.23. Of interest after a median follow-up of 3.47 years, (95% CI 3.18−3.70 years) patients with pCR had significantly longer RFS irrespective of BC subtypes (HR=0.20, 95% CI 0.08 to 0.50, p&lt;0.001).

Conclusion: Different biological processes namely proliferation, immune response and AKT activation are associated with pCR in different BC subtypes. Our results suggest that new drugs that modulate immune responses in ER−/HER2− and HER2+ BC and target AKT activation in HER2+ BC might be evaluated in these subtypes.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr PD03-10.

Low residual proliferation after short-term letrozole therapy is an early predictive marker of response in high proliferative ER-positive breast cancer

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.

DNA methylation profiling reveals a predominant immune component in breast cancers

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.

Abstract LB-180: Epigenetic portraits of human breast cancers

Background:

Understanding the diversity of breast cancer is essential to improving diagnosis and optimising treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but information is scant on the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease. Our goal was to explore the DNA methylation landscapes of phenotypically heterogeneous tumours, to relate this diversity to landscape features, and extract biological and clinical meaningful information.

Methods:

We performed comprehensive DNA methylation profiling to assess the methylomes of two independent sets of frozen breast tissue samples: a “main set” of 123 samples (4 normal and 119 infiltrating ductal carcinomas, IDCs), and a “validation set” of 125 samples (8 normal and 117 IDCs). We used the recently developed Illumina's Infinium Methylation Assay, that allows to assess the methylation status of more than 27,000 CpGs corresponding to over 14,000 genes.

Results:

Firstly, it emerged that the two major phenotypes of breast cancers determined by ER status are widely epigenetically controlled. Secondly, we have distinguished, and validated in an independent set of tumours, 6 methylation-profile-based tumour groups, some coinciding with known “expression subtypes” but also new entities that may provide a meaningful basis for refining breast tumour taxonomy. Thirdly, we showed that DNA methylation profiling can reflect the cell type composition of the tumour microenvironment. Lastly, we highlighted an unexpectedly strong epigenetic component in the regulation of key immune pathways, revealing a set of immune genes having high prognostic value in specific tumour categories.

Conclusions:

In this study, we have generated the largest and most comprehensive DNA methylation data set for human breast tumor tissues. Several novel findings and original concepts for breast cancer emerge, that previous RNA expression profiling has not highlighted. By laying the ground for better understanding of breast cancer heterogeneity and improved tumor taxonomy, the precise epigenetic portraits drawn in our work should contribute to better management of breast cancer patients.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-180. doi:10.1158/1538-7445.AM2011-LB-180

Abstract 839: HER2 expression occurs early in breast cancer dissemination

Background: Systemic spread of disseminated tumor cells from the primary site may occur early in breast tumorigenesis. The role of HER2 in breast cancer (BC) dissemination is not well understood. We evaluated the expression of HER2 on peripheral blood Circulating Tumor Cells (CTCs) from women with various stages of breast cancer (BC).

Methods: 81 women with preinvasive breast lesions (Atypical Ductal Hyperplasia, Lobular Carcinoma In Situ and Ductal Carcinoma In Situ), 101 women with early invasive BC and 35 women with metastatic BC were included. CTCs were defined as Cytokeratin 8,18,19+/CD45-/DAPI+ cells detected using the CellSearch® technology. Any staining for HER2 on CTCs using the CellSearch® HER2 profiling kit was considered positive. HER2 detection was calibrated through peripheral blood spiking experiments with MCF7 and SKBR3 cells.

Results: &gt; 1 CTCs/22.5mL of blood were detected in 6 of 81 (7%) women with preinvasive breast lesions (range 0-3 CTCs) and 15 of 101 (15%) women with early invasive BC (range 0-8 CTCs), whereas &gt; 1 CTCs/7.5mL of blood were detected in 17 of 35 (49%) women with metastatic BC (range 0-1160 CTCs) (p&lt;0.001). HER2 expression on CTCs was not associated with estrogen receptor (ER) and progesterone receptor (PR) expression or the histological grade of the primary tumor. In women with detectable CTCs, the ratio of HER2-positive CTCs/total CTCs was higher in HER2-positive than HER2-negative primary tumors (p=0.023). Despite a higher detection rate of CTCs, the ratio of HER2-positive CTCs/total CTCs was lower in metastatic BC (median 0.15, range 0-1.0) than in preinvasive (median 1.0, range 0-1.0) or early invasive BC (median 1.0, range 0.3-1.0) (p&lt;0.001). Similar results were observed when only HER2-negative primary tumors were considered (p=0.004).

Conclusion: This is the first report showing that HER2-positive CTCs can be detected in women with preinvasive breast lesions, further supporting the hypothesis that dissemination occurs early in breast tumorigenesis. HER2 expression on CTCs is more commonly observed in earlier stages of breast cancer, suggesting that HER2 plays an important role in early dissemination. The EORTC 90091-10093 trial will test the hypothesis that trastuzumab can eliminate HER2-positive CTCs in patients with HER2-negative early breast cancer.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 839.

Morphological observation of Y and T junctions in nanostructured boron nitride thin films

Formations of Y and T nano junctions have been observed in boron nitride films deposited on silicon substrates by plasma chemical reaction of diborane (B2H6 diluted in hydrogen) and ammonia (NH3) gases using dual frequency (microwave/radio) plasma enhanced chemical vapor deposition technique without any intentional heating of the substrates. It has been observed that these nano junctions form at a critical feed gas ratio of ammonia and diborane. We have investigated the effect of gas feed ratio R (=NH3/B2H6) in the plasma reaction chamber, keeping all other deposition parameters constant, on the morphology of boron nitride films. The deposited films are characterized by SEM, AFM, TEM and Laser Raman. For gas feed ratio, R < 100, octahedron and cubic morphologies have been observed in BN films and on increasing R to >100, size of the crystallites reduces to nanometer level. In some of our BN samples deposited at a critical value of gas ratio (R = 400), uniform Y and T junctions having bamboo like morphologies, in nanometer level, have been observed, which we wish to emphasis here as an interesting and newer observation in boron nitride films deposited by the dual frequency PECVD technique. This change in morphology exhibited by varying gas feed ratio is mainly due to excess nitrogen ions in the plasma.

Development and validation of a stability indicating HPLC assay method for cyclosporine in cyclosporine oral solution USP

The suitability of the United States Pharmacopeia (USP) assay method for analysing stressed samples of cyclosporine oral solution USP was evaluated for stability samples by analyzing cyclosporine oral solution after acid, alkali, hydrogen peroxide, heat and light treatment. Some of the degradants generated during stress testing, as well as dihydrocyclosporine A, which is a known degradant of cyclosporine A, were not adequately resolved from the cyclosporine peak and mobile phase adjustments did not improve the resolution. In addition, isocyclosporine A, another known degradant of cyclosporine, could not be quantitated as it was eluting too early with the system peaks. Therefore, a binary gradient, reverse phase, stability indicating, HPLC method for the assay of cyclosporine in cyclosporine oral solution USP has been developed and validated. Analysis of degraded samples showed that the cyclosporine A eluted as a spectrally pure peak resolved from its degradation products.

Prevention of bladder tumor formation in mice by a novel bone marrow-derived factor, reptimed

BACKGROUND

Reptimed is a novel, species-conserved, bone marrow-derived molecule which possesses anti-neoplastic activity. Previously, we established an orthotopic murine bladder tumor (MBT-2) model and reported accurate documentation of the presence and the extent of intravesical involvement of bladder tumor implants using magnetic resonance imaging (MRI) (1). Herein, we investigated the activity of exogenously administered Reptimed in the MBT-2 model.

MATERIALS AND METHODS

Intravesicular and intraperitoneal administration of Reptimed concurrently with and following transurethral tumor cell implantation was performed and MBT-2 tumor response was assessed at several time points post tumor implant.

RESULTS

Serial MRI scans of Reptimed-treated mice at days 14 to 33 post tumor transplant revealed significant inhibition of bladder tumor growth with no significant tumor growth observed by MRI on day 33 post-implant. The corresponding histological examination of the whole mount bladder sections revealed similar inhibitory effects of Reptimed with respect to the topography and depth of intravesical tumor involvement. In contrast, control, untreated bladders revealed extensive exophytic tumors with deeply invasive transitional cell carcinoma.

CONCLUSIONS

These studies demonstrate the anti-tumor effect of Reptimed and highlight its importance as a potential therapy for cancer.

Genetic correlation in otosclerosis

PURPOSE

The aim of this study was to determine the relationship of HLA typing in patients with otosclerosis.

MATERIALS AND METHODS

We used a prospective study in which HLA typing of 100 surgically confirmed otosclerosis patients were compared with age and sex matched normal individuals.

RESULTS

HLA-A3, HLA-A9, HLA-A11, and HLA-B13 were found to be significantly higher (P < .05, .01, and .01, respectively). HLA-A9 and HLA-A11 were found to be higher (P < .01) in patients with a positive family history, indicating genetic heterogenicity.

CONCLUSIONS

Higher values of HLA-A9, HLA-11, and HLA-B13 in patients with otosclerosis compared with normal individuals strongly suggests a genetic, HLA-related component.

CXCR1 and CXCR2 are rapidly down-modulated by bacterial endotoxin through a unique agonist-independent, tyrosine kinase-dependent mechanism

The expression of the seven-transmembrane domain chemokine receptors CXCR1 and CXCR2 modulates neutrophil responsiveness to the chemoattractant IL-8 and a number of closely related CXC chemokines. In the present study, we investigated the mechanism by which bacterial LPS induces the down-modulation of IL-8 responsiveness and CXCR1 and CXCR2 expression on human neutrophils. Treating neutrophils with LPS reduced IL-8R expression to 55 +/- 5% of the control within 30 min and to 23 +/- 2% within 1 h of stimulation. Furthermore, this down-modulation could not be attributed to increased concentrations of IL-8, TNF-alpha, or IL-1beta, since ELISA studies indicated that LPS-stimulated neutrophils did not release detectable amounts of these proteins before 2 h poststimulation. The tyrosine kinase (TK) inhibitors genistein and herbimycin A attenuated the LPS-mediated down-modulation of CXCR1 and CXCR2, indicating that the activation of a TK is required for LPS to mediate its effect. The effect of LPS on receptor expression paralleled the hyperphosphorylation of the protein TK p72syk. Although IL-8 induced a comparable down-modulation of CXCR1 and CXCR2, TK inhibitors did not attenuate this effect. These studies provide the first evidence of an agonist-independent, TK-dependent pathway of chemokine receptor regulation by endotoxin.

Uterus didelphys, a rare cause for tubal sterilization failure

Uterus didelphys is a rare congenital anomaly. It can result in a variety of misadventures even in the hands of an expert. The present case reports uterus didelphys as the cause for tubal sterilization failure. This is the first case of this type seen in our institution in 35 years.