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COVID-19 infection caused by the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has resulted in a global pandemic with the number of deaths growing exponentially. Early evidence points to significant endothelial dysfunction, micro-thromboses, pro-inflammation as well as a dysregulated immune response in the pathogenesis of this disease. In this study, we analyzed the cargo of EVs isolated from the plasma of patients with COVID-19 for the identifiction of potential biomarkers of disease severity and to explore their role in disease pathogenesis. Plasma-derived EVs were isolated from 53 hospitalized patients with COVID infection and compared according to the severity of the disease. Analysis of inflammatory and cardiovascular protein cargo of large EVs revealed significantly differentially expressed proteins for each disease sub-group. Notably, members of the TNF superfamily and IL-6 family were up-regulated in patients on oxygen support with severe and moderate disease. EVs from the severe group were also enhanced with pro-thrombotic/endothelial injury factors (TF, t-PA, vWF) and proteins associated with cardiovascular pathology (MB, PRSS8, REN, HGF). Significantly higher levels of TF, CD163, and EN-RAGE were observed in EVs from severe patients when compared to patients with a moderate disease requiring supplemental O2. Importantly, we also observed increased caspase 3/7 activity and decreased cell survival in human pulmonary microvascular endothelial cells exposed to EVs from the plasma of patients with severe disease compared to asymptomatic group. In conclusion, our findings indicate alterations in pro-inflammatory, coagulopathy, and endothelial injury protein cargo in large EVs in response to SARS-CoV-2 infection that may be a causative agent in severe illness.

Purpose: Poor preoperative nutritional status is associated with a higher complication rate after radical cystectomy in patients with bladder cancer. Given the short interval between diagnosis and radical cystectomy, we compared the effect of short-term specialized immunonutrition to that of a standard oral nutritional supplement on the acute inflammatory response and arginine status in patients treated with radical cystectomy.Materials and Methods: In this prospective, randomized study in 29 men 14 received specialized immunonutrition and 15 received oral nutritional supplement. Each group drank 3 cartons per day for 5 days before and 5 days after radical cystectomy. The Th1-Th2 balance, plasma interleukin-6 and plasma amino acids were measured at baseline, intraoperatively and on postoperative days 2, 14 and 30. Body composition was measured by dual energy x-ray absorptiometry at baseline and on postoperative days 14 and 30. Differences in outcomes were assessed using the generalized linear mixed model....

Clinical studies have linked usage of progestins (synthetic progesterone) to breast cancer risk. However, little is understood regarding the role of native progesterone (P4), signaling through the progesterone receptor (PR), in breast tumor formation. Recently, we reported a link between PR and immune signaling pathways, showing that P4/PR can repress type I interferon signaling pathways. Given these findings, we sought to investigate whether P4/PR drive immunomodulation in the mammary gland and promote tumor formation. To determine the effect of P4 on immune cell populations in the murine mammary gland, mice were treated with P4 or placebo pellets for 21 days. We found that mice treated with P4 exhibited changes in the mammary gland indicative of an inhibited immune response compared to placebo-treated mice. To assess the effect of PR overexpression on mammary gland tumor development as well as immune cell populations in the mammary gland, a transgenic mouse model was used in which PR is overexpressed throughout the entire mouse. Immune cell populations were assessed in the mammary glands by flow cytometry, which revealed decreased numbers of various immune cell populations. Transgenic mice were also monitored for mammary gland tumor development over a 2-year timespan. Following development of mammary gland tumors, immune cell populations in the tumors and spleens of transgenic and control mice were analyzed by flow cytometry. Upon long-term monitoring, we determined that multi-parous PR overexpressing mice developed significantly more mammary gland tumors than control mice. Additionally, tumors from PR overexpressing mice contained fewer infiltrating immune cells, and RNA sequencing analysis of tumor samples revealed that immune-related gene signatures were lower in tumors from PR overexpressing mice as compared to control mice. Finally, we utilized syngeneic mammary gland tumor models to evaluate the effect of P4 on the growth of PR+ mammary gland tumors in vivo, which revealed that P4 promoted tumor growth and decreased immune cell infiltration of PR+ mammary gland tumors. Together, these findings offer a novel mechanism of P4-driven mammary gland tumor development and provide rationale in investigating the usage of anti-progestin therapies to promote immune-mediated elimination of mammary gland tumors. Citation Format: Lauryn R Werner, Katelin A Gibson, Merit L Goodman, Dominika E Helm, Katherine R Walter, Sean M Holloran, Gloria M Trinca, Richard C Hastings, Howard H Yang, Ying Hu, Junping Wei, Gangjun Lei, Xiao-Yi Yang, Rashna Madan, Alfred A Molinolo, Mary A Markiewicz, Prabhakar Chalise, Margaret L Axelrod, Justin M Balko, Kent W Hunter, Zachary C Hartman, Carol A Lange, Christy R Hagan. Progesterone promotes immunomodulation and tumor development in the murine mammary gland [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-04-07.

TPS209 Background: Lynch syndrome (LS) is the most common inherited colorectal cancer (CRC) syndrome and is responsible for about 3% of newly diagnosed CRC. It is caused by germline mutations in one of the DNA mismatch repair (MMR) genes, and patients with LS carry a lifetime risk of CRC ranging between 10% and 70%. The role of inflammation in driving this malignant transformation is now well established and retrospective studies have revealed a potential chemo-preventative role for omega-3 (ω-3) polyunsaturated fatty acids (PUFAs), possibly via inhibition of inflammatory pathways associated with the development of defective MMR CRC tumors. While patients with LS have the highest risk of developing CRC, the majority of chemoprevention trials are focused on sporadic CRC. Effective interventions to reduce the risk of developing CRC in this population are limited to close surveillance and surgical prophylaxis. There is an unmet need for safe, effective, and non-invasive chemo-preventive interventions in patients with LS. Methods: This pilot study is a single-arm, open-label, phase 2 clinical trial of omega-3 acid ethyl esters (generic Lovasa; 2 grams orally once daily) for adult patients (≥ 18 years of age) with confirmed LS (based on germline testing of the MMR genes panel: MLH1, MSH2, MSHS6, PMS2 or deletion in EPCAM gene). Patients who are not candidate for elective endoscopy and/or with prior history of right sided or pan-colectomy are excluded. Thirty-four patients are expected to enroll, with a primary objective to determine the feasibility (defined as 80% retention rate) of 12 months of treatment with 2 grams capsules of omega-3 acid ethyl esters daily. Secondary endpoints include safety and tolerability of the intervention. Correlative aims include pre and post treatment assessment of colon mucosal tissue proliferation (right sided colon specimens will be evaluated for markers of proliferation (Ki-67) and apoptosis (Caspase-3)), the effect of omega-3 acid ethyl esters on inflammatory markers in serum, urine and feces (PGE-2, COX-2, β-catenin levels, and EPA:AA ratios), and gene expression related to proliferation, apoptosis and cell survival in colon tissue (NF-κB/Wnt pathways). The impact of omega-3 acid ethyl esters on intestinal microbiota will also be assessed (16S rRNA-based profiling). Correlative Colon tissue, serum, urine and feces samples are collected at baseline and at 12 months. The study is actively enrolling with 20 patients enrolled at the time of submission. Clinical trial information: NCT03831698.

Blood pressure data may vary by measurement technique. We performed a technological assessment of differences in blood pressure measurement between non-invasive blood pressure (NIBP) and invasive arterial blood pressure (ABP) in neurocritically ill patients. After IRB approval, a prospective observational study was performed to study differences in systolic blood pressure (SBP), mean arterial pressure (MAP), and cerebral perfusion pressure (CPP) values measured by NIBP arm, ABP at level of the phlebostatic axis (ABP heart) and ABP at level of the external auditory meatus (ABP brain) at 30 and 45-degree head of bed elevation (HOB) using repeated measure analysis of covariance and correlation coefficients. Overall, 168 patients were studied with median age of 57 ± 15 years, were mostly female (57%), with body mass index ≤30 (66%). Twenty-three percent (n = 39) had indwelling intracranial pressure monitors, and 19.7% (n = 33) received vasoactive agents. ABP heart overestimated ABP brain for SBP (11.5 ± 2.7 mmHg, p < .001), MAP (mean difference 13.3 ± 0.5 mmHg, p < .001) and CPP (13.4 ± 3.2 mmHg, p < .001). ABP heart overestimated NIBP arm for SBP (8 ± 1.5 mmHg, p < .001), MAP (mean difference 8.6 ± 0.8 mmHg, p < .001), and CPP (mean difference 9.8 ± 3.2 mmHg, p < .001). Regardless of HOB elevation, ABP heart overestimates MAP compared to ABP brain and NIBP arm. Using ABP heart data overestimates CPP and may be responsible for not achieving SBP, MAP or CPP targets aimed at the brain.

Emerging clinical trial data implicate progestins in the development of breast cancer. While the role for the progesterone receptor (PR) in this process remains controversial, it is clear that PR, a steroid-activated nuclear receptor, alters the transcriptional landscape of breast cancer. PR interacts with many different types of proteins, including transcriptional co-activators and co-repressors, transcription factors, nuclear receptors, and proteins that post-translationally modify PR (i.e., kinases and phosphatases). Herein, we identify a novel interaction between PR and O-GlcNAc transferase (OGT), the enzyme that catalyzes the addition of a single N-acetylglucosamine sugar, referred to as O-GlcNAc, to acceptor serines and threonines in target proteins. This interaction between PR and OGT leads to the post-translational modification of PR by O-GlcNAc. Moreover, we show that O-GlcNAcylated PR is more transcriptionally active on PR-target genes, despite the observation that PR messenger RNA and protein levels are decreased when O-GlcNAc levels are high. O-GlcNAcylation in breast cancer is clinically relevant, as we show that O-GlcNAc levels are higher in breast cancer as compared to matched normal tissues, and PR-positive breast cancers have higher levels of OGT. These data predict that under conditions where O-GlcNAc levels are high (breast cancer), PR, through an interaction with the modifying enzyme OGT, will exhibit increased O-GlcNAcylation and potentiated transcriptional activity. Therapeutic strategies aimed at altering cellular O-GlcNAc levels may have profound effects on PR transcriptional activity in breast cancer.

Background: Recent developments in literature on sample size calculations for time-to-event outcomes involve assumption of Weibull distributed times. These methods require a point estimate of the Weibull shape parameter obtained from historical studies. However, very limited guidance exists in published literature to assess how reliable this point estimate is when it is obtained from published results of a historical study. Methods: We conduct simulations to assess how accurate and reliable the point estimate of the Weibull shape parameter is when it is estimated from published results of median survival time and/or corresponding interquartile range. Accuracy of this estimate is assessed using the criteria of average relative bias, root mean square error, and coefficient of variation for various combinations of sample sizes and censoring rates. Sensitivity of these calculations is assessed first, by increasing the number of survival quantiles used to calculate accuracy, and second, by using the full Kaplan Meier (KM) curve from the historical study. Results: Our simulations suggest that point estimate of the shape parameter is reasonably accurate when estimated from historical studies with sample size ≥ 50 with censoring rate approximately 20%. Knowledge of the median and inter-quartile range seems to be adequate for this purpose. For historical studies with small sample sizes or higher censoring rates, more information needs to be abstracted from the published KM curves to improve accuracy. Conclusions: We conclude that assessing the accuracy of Weibull shape parameter estimate is important before it can be used to conduct sample size calculations for a subsequent trial. Keywords: Censoring, Historical data, KM curves, Sample size, Shape parameter, Weibull

Interventions that relieve vasomotor symptoms while reducing risk for breast cancer would likely improve uptake of chemoprevention for perimenopausal and postmenopausal women. We conducted a pilot study with 6 months of the tissue selective estrogen complex bazedoxifene (20 mg) and conjugated estrogen (0.45 mg; Duavee) to assess feasibility and effects on risk biomarkers for postmenopausal breast cancer. Risk biomarkers included fully automated mammographic volumetric density (Volpara), benign breast tissue Ki-67 (MIB-1 immunochemistry), and serum levels of progesterone, IGF-1, and IGFBP3, bioavailable estradiol and testosterone. Twenty-eight perimenopausal and postmenopausal women at increased risk for breast cancer were enrolled: 13 in cohort A with baseline Ki-67 < 1% and 15 in cohort B with baseline Ki-67 of 1% to 4%. All completed the study with > 85% drug adherence. Significant changes in biomarkers, uncorrected for multiple comparisons, were a decrease in mammographic fibroglandular volume (P = 0.043); decreases in serum progesterone, bioavailable testosterone, and IGF-1 (P < 0.01), an increase in serum bioavailable estradiol (P < 0.001), and for women from cohort B a reduction in Ki-67 (P = 0.017). An improvement in median hot flash score from 15 at baseline to 0 at 6 months, and menopause-specific quality-of-life total, vasomotor, and sexual domain scores were also observed (P < 0.001). Given the favorable effects on risk biomarkers and patient reported outcomes, a placebo-controlled phase IIB trial is warranted.

Why some tumors remain indolent and others progress to clinical relevance remains a major unanswered question in cancer biology. IFN signaling in nascent tumors, mediated by STAT1, is a critical step through which the surveilling immune system can recognize and destroy developing tumors. In this study, we have identified an interaction between the progesterone receptor (PR) and STAT1 in breast cancer cells. This interaction inhibited efficient IFN-induced STAT1 phosphorylation, as we observed a decrease in phospho-STAT1 in response to IFN treatment in PR-positive breast cancer cell lines. This phenotype was further potentiated in the presence of PR ligand. In human breast cancer samples, PR-positive tumors exhibited lower levels of phospho-STAT1 as compared with their PR-negative counterparts, indicating that this phenotype translates to human tumors. Breast cancer cells lacking PR exhibited higher levels of IFN-stimulated gene (ISG) RNA, the transcriptional end point of IFN activation, indicating that unliganded PR alone could decrease transcription of ISGs. Moreover, the absence of PR led to increased recruitment of STAT1, STAT2, and IRF9 (key transcription factors necessary for ISG transcription) to ISG promoters. These data indicate that PR, both in the presence and absence of ligand, attenuates IFN-induced STAT1 signaling, culminating in significantly abrogated activation of genes transcribed in response to IFNs. PR-positive tumors may use downregulation of STAT1-mediated IFN signaling to escape immune surveillance, leading to the development of clinically relevant tumors. Selective immune evasion of PR-positive tumors may be one explanation as to why over 65% of breast cancers are PR positive at the time of diagnosis., This work was supported by the National Cancer Institute (NCI) R00CA166643 (to C.R.H.), Department of Defense Breast Cancer Research Program W81XWH-16-1-0320 (to C.R.H.), Susan G. Komen Foundation CCR16376147 (to C.R.H.), V Foundation V2015-025 (to C.R.H.), National Institutes of Health R01GM114142 (to V.X.J.), U54CA217297 (to V.X.J.), and 1S10OD021805-01 (to Z.L.), the Owens Foundation (to V.X.J.), and NCI Cancer Center Support Grant P30 CA168524 (to C.R.H.).

Sedation practices for pediatric burn patients during dressing changes vary between institutions and providers. To better understand the current trends in pediatric sedation practice, a survey was conducted among the members of the American Burn Association (ABA). Questions asked about nonoperating room sedation and analgesia practices for burn patients (ages 0-17) having dressing changes in the intensive care unit, inpatient unit, and outpatient clinics. ABA members providing sedation for pediatric patients undergoing burn dressing changes are diverse. Physician respondents included surgeons, critical care intensivists, and anesthesiologists. Others included physician assistants, nurse anesthetists, nurse practitioners, and sedation credentialed nurses. Opioids for pain control were prescribed by 100% of respondents, but use of adjuvant nonopioid analgesics was utilized

Why are some early neoplastic lesions identified through immunosurveillance and subsequently destroyed, whereas other tumors evade this clearance step and progress to clinically-relevant tumors? The cancer immunoediting hypothesis highlights that the innate and adaptive immune responses work together to “flag” early neoplastic lesions for immune-mediated elimination. An early mediator of this “elimination” process is activation of type I interferon signaling. Thus, suppression of type I interferon signaling may help developing tumors evade the critical early steps of immune recognition and clearance. As such, female STAT1 knockout mice, lacking the key upstream activator of type I interferon signaling, develop mammary gland adenocarcinomas. Preliminary data from our lab suggest that progesterone, working through the progesterone receptor (PR), may be a key player in tumor immune evasion. The contribution of the ovarian steroid hormone, progesterone, to the development and progression of breast cancer has become increasingly evident, especially in light of recent clinical trial data linking the use of hormonal replacement therapy with breast cancer risk. These highly publicized data showed that women whose hormone replacement therapy (HRT) regimens included synthetic progesterone had a higher relative risk of developing invasive breast cancer. These data underscore the importance of understanding how hormones, particularly progesterone, affect breast cancer initiation and growth. Upon diagnosis, nearly 70% of breast cancers express PR and the estrogen receptor (ER). This is in sharp contrast to what is seen in the normal mammary gland, where only 7-10% of luminal epithelial cells express ER and PR. ER action in breast cancer has been well studied and as a result, ER has proven to be an excellent target for current endocrine-based therapies. However, despite convincing clinical evidence from the aforementioned trials, the role of PR in breast cancer has been largely understudied. Importantly, progesterone is emerging as a potent mitogen in the breast and a significant contributor to breast cancer progression. Despite maintaining receptor (ER/PR) expression, many breast cancer patients eventually progress to hormone-independence, failing current (largely ER/estrogen based) endocrine therapies. Therefore, ER-independent functions of PR are of great clinical interest. PR is a steroid-activated nuclear transcription factor known to regulate context-dependent gene programs in breast cancer. Using Gene Set Enrichment Analysis (GSEA), we analyzed microarray data sets from ligand-treated T47D breast cancer cells stably expressing wt PR (or PR-null). GSEA revealed that genes from multiple inflammatory and interferon-regulated gene sets were significantly enriched in our T47D-wt PR dataset, an effect that was lost in cells lacking PR expression. Leading Edge analysis identified many genes that are transcriptional targets of interferon signaling pathways and key mediators of inflammation (i.e. IFITs, IRF7, OAS1/2 and ISG15) whose regulation is lost in PR-null cells. These genes, classically activated by interferons, are collectively referred to as interferon-stimulated genes (ISGs). Interestingly, in response to treatment with various PR ligands, ISGs are potently transcriptionally repressed. Ligand-activated PR also repressed expression of these genes in response to their classical activator, interferon-alpha. In cells were PR expression has been reduced using si/shRNA, ISG transcriptional repression is lost. Of note, basal levels of ISGs are dramatically upregulated in cells where PR has been knocked-down, indicating that PR also has ligand-independent functions aimed at maintaining low levels of ISG expression. Moreover, we have shown using ChIP assays that all ISGs assayed thus far exhibited PR binding within their proximal regulatory regions, implying direct PR regulation of these genes. Finally, we have data to suggest that PR attenuates canonical (in response to type I interferons, such as interferon-alpha) interferon signaling. Pathway readouts in response to treatment with interferon-alpha, such as STAT1 phosphorylation, are reduced in cells expressing PR, and even further attenuated in PR-positive cells treated with ligand (progesterone). We have detected an interaction between PR and STAT1 that increases in response to ligand; this interaction may explain the observed decrease in phospho-STAT1 in response to interferon-alpha in PR-positive cells. Cumulatively, these data suggest a concerted effort aimed at reducing interferon-signaling through activation of PR. These preliminary data translate to the immune microenvironment in the murine mammary gland. In mice with transgenic overexpression of PR, we observed an immuno-suppressive microenvironment in the mammary gland and the inguinal (draining) lymph node through decreased antigen-presenting cell populations (i.e. dendritic cells and macrophages) and increased T-regulatory cells. We also observe decreases in MHC Class I presentation in PR+ mammary gland epithelial cells, a key step to tumor cell recognition by the immune system. These changes in the immune system suggest that PR can promote immunosuppressive changes in the mammary gland. Moreover, 80% of these mice in a multiparous cohort develop mammary gland tumors. Therefore, early changes in the immune microenvironment in the mammary gland may translate to the development of mammary gland tumors in PR transgenic mice. Together, these data support our hypothesis that PR attenuates the interferon response in breast cancer cells through manipulation of canonical interferon-responsive proteins and transcriptional downregulation of ISGs. This decrease in interferon signaling may be a key step in PR-positive breast tumors evading immune surveillance and clearance, allowing for progression of these tumors. STA1 knockout mouse data shows that inhibition of STAT1 signaling if sufficient to drive tumorigenesis. However, STAT1 knockout is not observed in human tumor. We propose that inhibition of STAT1, through the actions of PR/progesterone, are a driving force behind the development of hormone receptor-positive human tumors. Citation Format: Christy R. Hagan, Lauryn Werner, Emma Helm, Margaret Axelrod, Justin Balko, Zachary Hartman, Kent Hunter, Howard Yang, Prabhakar Chalise, Mary Markiewicz. Progesterone-mediated immune evasion in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr NG15.

Background: Improvements to prognostic models in metastatic castration-resistant prostate cancer have the potential to augment clinical trial design and guide treatment strategies. In partnership with Project Data Sphere, a not-for-profit initiative allowing data from cancer clinical trials to be shared broadly with researchers, we designed an open-data, crowdsourced, DREAM (Dialogue for Reverse Engineering Assessments and Methods) challenge to not only identify a better prognostic model for prediction of survival in patients with metastatic castration-resistant prostate cancer but also engage a community of international data scientists to study this disease. Methods Data from the comparator arms of four phase 3 clinical trials in first-line metastatic castration-resistant prostate cancer were obtained from Project Data Sphere, comprising 476 patients treated with docetaxel and prednisone from the ASCENT2 trial, 526 patients treated with docetaxel, prednisone, and placebo in the MAINSAIL trial, 598 patients treated with docetaxel, prednisone or prednisolone, and placebo in the VENICE trial, and 470 patients treated with docetaxel and placebo in the ENTHUSE 33 trial. Datasets consisting of more than 150 clinical variables were curated centrally, including demographics, laboratory values, medical history, lesion sites, and previous treatments. Data from ASCENT2, MAINSAIL, and VENICE were released publicly to be used as training data to predict the outcome of interestnamely, overall survival. Clinical data were also released for ENTHUSE 33, but data for outcome variables (overall survival and event status) were hidden from the challenge participants so that ENTHUSE 33 could be used for independent validation. Methods were evaluated using the integrated time-dependent area under the curve (iAUC). The reference model, based on eight clinical variables and a penalised Cox proportional-hazards model, was used to compare method performance. Further validation was done using data from a fifth trialENTHUSE M1in which 266 patients with metastatic castration-resistant prostate cancer were treated with placebo alone. Findings 50 independent methods were developed to predict overall survival and were evaluated through the DREAM challenge. The top performer was based on an ensemble of penalised Cox regression models (ePCR), which uniquely identified predictive interaction effects with immune biomarkers and markers of hepatic and renal function. Overall, ePCR outperformed all other methods (iAUC 0·791; Bayes factor >5) and surpassed the reference model (iAUC 0·743; Bayes factor >20). Both the ePCR model and reference models stratified patients in the ENTHUSE 33 trial into high-risk and low-risk groups with significantly different overall survival (ePCR: hazard ratio 3·32, 95% CI 2·394·62, p, European Union within the ERC grant LatentCauses supported the work of C.F and I.K. German Research Foundation (DFG) within the Collaborative Research Centre 1243, subproject A17 awarded to C.F. German Federal Ministry of Education and Research (BMBF) through the Research Consortium e:AtheroMED (Systems medicine of myocardial infarction and stroke) under the auspices of the e:Med Programme (grant # 01ZX1313C) supported the work of D.P.A., P.D., C.F., C.K., I.K., N.K., M.L., H.S. and J.F.S. at the Institute of Computational Biology. NIH Grants RR025747-01, MH086633 and 1UL1TR001111, and NSF Grants SES-1357666, DMS-14-07655 and BCS0826844 supported the work of C.H., J.I., E.L., Y.W., H.Y., H.Z. and J.Z. NSFC Grant Nos. 61332013, 61572139 supported the work of X.L, Y.L, Y.Z., and S.Z. National Natural Science Foundation of China grants [Nos. 61422309, 61379092] was awarded to S.Z. The Patrick C. Walsh Prostate Research Fund and the Johns Hopkins Individualized Health Initiative supported the work of R.Y.C., D.D., Y.D., Z.J., K.R., Z.W. and Y.Z. FCT Ph.D. Grant SFRH/BD/80925/2011 was awarded to S.C. Clinical Persona Inc., East Palo Alto, CA supported the work of L.B. and D.K. The Finnish Cultural Foundation and the Drug Research Doctoral Programme (DRDP) at the University of Turku supported T.D.L. The National Research Foundation Singapore and the Singapore Ministry of Education, under its Research Centres of Excellence initiative, supported the work of J.G. and K.T. A grant from the Russian Science Foundation 14-24-00155 was awarded to M.D.K. A*MIDEX grant (no. ANR-11-IDEX-0001-02) was awarded to P.J.B. NSERC supported the work of R.G. The Israeli Centers of Research Excellence (I-CORE) program (Center No. 4/11) supported the work of E.G. Academy of Finland (grants 292611, 269862, 272437, 279163, 295504), National Cancer Institute (16X064), and Cancer Society of Finland supported the work of T.A. Academy of Finland (grant 268531) supported the work of T.M

Background Extracorporeal photopheresis (ECP), is a cell-based immune-modulatory therapy used in the treatment of steroid refractory chronic graft versus host disease (cGHVD). It is unclear whether ECP is associated with an increased risk of infections compared to alternative treatment. We aimed to study the infectious complications in patients who are on ECP post allogeneic hematopoietic stem cell transplant (alloHSCT). Methods We conducted a retrospective cohort study of adult patients with cGVHD post alloHSCT who were initiated on ECP or second line immunosuppressive agents (SLIS). The study period was from March 1, 2014 to October 1, 2018. Each subject in the ECP arm was matched to the SLIS arm according to gender, age, underlying disease, and date of diagnosis of cGVHD. All subjects were followed for one-year post treatment. The main outcome was incidence of each type of infection (event rate/ person-years). Kaplan Meier analysis was used, evaluating time to infection with log rank test. The spectrum of infectious complications was described. Results Seventy-seven patients were included (36 in ECP and 41 in SLIS arm). Median age was 57.4 years (18.1 -73.4), and 59.7% of patients were male. The most common underlying diseases were acute myeloid leukemia (45.4%), myelodysplastic syndrome (20.8%) and non-Hodgkin’s lymphoma (15.6%). A total occurrence of 94 infections was observed in the ECP arm, compared to 118 in SLIS arm. Bacterial infections accounted for majority of the infections in ECP arm (50%) compared to SLIS arm in which viruses were most common (49.2%). Bacterial pneumonia was the most common clinical syndrome (34% and 27.3%, in the ECP and SLIS arms, respectively). Bacteremia accounted for 12.8% of infections in the ECP arm compared to 16.4% in the SLIS arm. There was no difference in the event rates of infections among the two groups [2.58/ person-years in ECP group vs 3.60/person-years, p = 0.3766], or the probability of infection at any time between the ECP and SLIS group on Kaplan Meier (log rank test, p-value=0.36)(Figure 1). Kaplan-Meier plot of time to the earliest infection diagnosis between ECP and control group Conclusion Bacterial and viral pneumonia were the most common infections in patients undergoing ECP. Overall, ECP does not confer an increased risk of infectious complications compared to second line IS agents. Disclosures Wissam El Atrouni, MD, ViiV (Advisor or Review Panel member)

Why are some early neoplastic lesions identified through immunosurveillance and subsequently destroyed, whereas other tumors evade this clearance step and progress to clinically-relevant tumors? The cancer immunoediting hypothesis highlights that the innate and adaptive immune responses work together to “flag” early neoplastic lesions for immune-mediated elimination. An early mediator of this “elimination” process is activation of type I interferon signaling. Thus, suppression of type I interferon signaling may help developing tumors evade the critical early steps of immune recognition and clearance. Preliminary data from our lab suggest that progesterone, working through the progesterone receptor (PR), may be a key player in tumor immune evasion through downregulation of interferon signaling. In breast cancer cells, we have shown that presence/activation of PR can attenuate interferon-signaling at multiple steps within the signaling cascade: decreased STAT1 phosphorylation, decreased STAT1/STAT2/IRF9 transcriptional complex formation (called ISGF3, required for interferon-alpha signaling), decreased recruitment of ISGF3 to ISG promoter sequences, and decreased transcriptional activation of interferon-stimulated genes (ISG, end point of interferon signaling). These data suggest a concerted effort aimed at reducing interferon-signaling through activation of PR. These data translate to the immune microenvironment in the murine mammary gland. In mice treated with progesterone for 21 days, we see immunosuppressive changes in the mammary gland: increased T-regulatory cells (immunosuppressive), decreased frequency of antigen-presenting cells (decreased ability to present potential tumor-associated antigens to CD8 T-cells), and a decrease in MHC class I presentation in non-lymphoid cells (decreased ability for epithelial cells to present potential tumor-associated antigens). We observe similar phenotypes in mice with transgenic overexpression of PR. These changes in the immune system suggest that PR can promote immunosuppressive changes in the mammary gland. Moreover, 80% of these mice in a multiparous cohort develop mammary gland tumors. Therefore, early changes in the immune microenvironment in the mammary gland may translate to the development of mammary gland tumors in PR transgenic mice. Cumulatively, these data suggest a mechanism through which PR aids early breast cancer lesions in escaping immune surveillance. These data have significant implications for the use of progesterone-containing hormone replacement therapy, as well as underscore the importance of studying anti-progestins as novel chemo-preventative agents for breast cancer. Citation Format: Christy Hagan, Merit Goodman, Gloria Trinca, Katherine Walter, Katelin Gibson, Prabhakar Chalise, Mary Markiewicz. Progesterone promotes immunosuppression in breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-04-20.

Why are some early neoplastic lesions identified through immunosurveillance and subsequently destroyed, whereas other tumors evade this clearance step and progress to clinically-relevant tumors? The cancer immunoediting hypothesis highlights that the innate and adaptive immune responses work together to “flag” early neoplastic lesions for immune-mediated elimination. An early mediator of this “elimination” process is activation of type I interferon signaling. Thus, suppression of type I interferon signaling may help developing tumors evade the critical early steps of immune recognition and clearance. Preliminary data from our lab suggest that progesterone, working through the progesterone receptor (PR), may be a key player in tumor immune evasion through downregulation of interferon signaling. In breast cancer cells, we have shown that presence/activation of PR can attenuate interferon-signaling at multiple steps within the signaling cascade: decreased STAT1 phosphorylation, decreased STAT1/STAT2/IRF9 transcriptional complex formation (called ISGF3, required for interferon-alpha signaling), decreased recruitment of ISGF3 to ISG promoter sequences, and decreased transcriptional activation of interferon-stimulated genes (ISG, end point of interferon signaling). These data suggest a concerted effort aimed at reducing interferon-signaling through activation of PR. These data translate to the immune microenvironment in the murine mammary gland. In mice treated with progesterone for 21 days, we see immunosuppressive changes in the mammary gland: increased T-regulatory cells (immunosuppressive), decreased frequency of antigen-presenting cells (decreased ability to present potential tumor-associated antigens to CD8 T-cells), and a decrease in MHC class I presentation in non-lymphoid cells (decreased ability for epithelial cells to present potential tumor-associated antigens). We observe similar phenotypes in mice with transgenic overexpression of PR. These changes in the immune system suggest that PR can promote immunosuppressive changes in the mammary gland. Moreover, 80% of these mice in a multiparous cohort develop mammary gland tumors. Therefore, early changes in the immune microenvironment in the mammary gland may translate to the development of mammary gland tumors in PR transgenic mice. Cumulatively, these data suggest a mechanism through which PR aids early breast cancer lesions in escaping immune surveillance. These data have significant implications for the use of progesterone-containing hormone replacement therapy, as well as underscore the importance of studying anti-progestins as novel chemo-preventative agents for breast cancer. Citation Format: Merit Goodman, Gloria Trinca, Katherine Walter, Katelin Gibson, Prabhakar Chalise, Mary Markiewicz, Christy R. Hagan. Progesterone receptor promotes immunosuppressive microenvironment in the mammary gland [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2361.

TPS3165 Background: Mutations in p53 contribute to tumor progression. A rational approach is to destabilize mutant (m) p53. The group at the University of Kansas Cancer Center screened compounds that suppress m p53 in a preclinical model. Luciferase-based reporter assay identified statins as suppressors of m p53 expression. In vitro validation assay demonstrated atorvastatin (A) suppressed m p53 level and cell growth selectively; and depletion of mevalonic acid lead to degradation of m p53. These effects were limited to mutations in the conformation of p53, while wild-type and DNA contact mutations were not as sensitive to statin-induced degradation of p53. M p53 xenograft model confirmed that A could suppress tumor growth at a concentration that can decrease LDL level. The primary objective of this trial is to determine if A decreases the level of conformational m p53. The secondary objective is to assess the effects of A on Ki-67 and caspase-3 in conformational m p53 tumors. Methods: This is an open-label, window of opportunity pilot trial to see if A given for 1 to 4 weeks at a dose of 80 mg/day is sufficient to reduce the levels of conformational m p53 in the tumor tissues. Subjects with new diagnosis of malignancy with a planned surgical therapy, and subjects with previously treated AML, in between treatment regimens, are eligible. Tissues from solid tumors, and bone marrow or peripheral blood samples from AML will be used to screen for m p53 by immunohistochemistry (IHC). Subjects will receive A at 80 mg/day po for 1 to 4 weeks. Pharmacokinetics at pre-dose and 1-hour post-dose on Day 1 and on the day of surgery will be done. Mutational analysis using exome sequencing technique will be done on m p53. Using IHC, the amount of p53 in pre-treatment and post-treatment samples will be measured and compared simultaneously. The levels of Ki67 and caspace-3 will be tested and compared between pre-treatment and post-treatment samples in subjects with conformational m p53, between conformational and non-conformational m p53, and in wild-type p53 tumors. The trial is actively enrolling subjects. The results of this trial will determine further investigations on the role of atorvastatin in tumors with p53 mutations in a placebo-controlled, randomized trial. Clinical trial information: NCT03560882.

TPS4168 Background: Attempts to improve therapy for patients with pancreatic adenocarcinoma with traditional chemotherapy have largely failed to meaningfully improve survival. Therefore, there is a critical need for identification of specific molecular changes that define prognosis and potentially guide therapy decisions. Defective DNA damage response pathways in pancreatic cancer represent a targeted opportunity for treatment. PARP inhibitors exert activity in tumor cells that may not be effectively able to repair initially single-stranded and cumulatively double-stranded DNA breaks and can have a heightened susceptibility in tumor cells over normal tissue. This concept is referred to as synthetic lethality. Niraparib is an orally available, potent, highly selective PARP-1 and -2 inhibitor. We are studying the efficacy of Niraparib in pancreatic cancer patients that harbor DNA repair defects. Methods: This study is funded by a research grant from TESARO. Pre-screening of patients to find biomarker positive patients is funded by KU Cancer Center. This is a phase II open label single arm trial in metastatic pancreatic cancer patients with germline or somatic mutations, either already known, or tested after consent to pre-screening tumor tissue analysis in BRCA1/2, PALB2, ATM, NBN, ATR, BRIP1, IDH1/2, RAD51, RAD51B/C/D, RAD54L, CDK12, BARD1, FAM175A, BAP1, CHEK1/2, GEN1, MRE11A, XRCC2, SHFM1, FANCD2, FANCA, FANCC, FANCG, RPA1, ARID1A. Patients are being treated with Niraparib 300mg or 200mg by mouth daily for 28 days (1 cycle = 28 days) (200mg dose is for participants whose baseline weight is < 77 kg [169.756 lbs] or baseline platelet count is < 150,000 µL). The primary objective is to assess antitumor efficacy of niraparib using Objective Response Rate per RECIST 1.1. Secondary objectives include PFS, OS, DCR, DOR, and safety. Eligible patients received > 1 line of therapy, no prior PARP inhibitor(s), have measurable disease, and ECOG PS 0-1. Accrual target enrollment of 18 patients over a period of 24 months with a study duration of 30 months. Correlative studies include assessment of pharmacokinetics, circulating tumor cells and storing samples for future research. The trial is currently enrolling. Clinical trial information: NCT03553004.

Background In most Western nations, the medical oncologist plays a significant role in the administration of systemic therapy for lung cancer. In Japan however, treatment for lung cancer has historically been provided by pulmonologists and thoracic surgeons. A comparison of the management of advanced disease between Japan and other nations has not been described. Methods An online, self-administered, international survey was sent to 3907 active members of the American Society of Clinical Oncology. Eligible participants were degreed physicians who prescribed systemic agents for adult cancer treatment within the past five years. Results In total, 281 respondents answered the questions regarding management of lung cancer. Thorough analysis demonstrated that pulmonologists play a significant role in Japan and the Netherlands, where the role of oncologic specialists is not well established. Of note, all the respondents from the Netherlands reported that pulmonary medicine primarily manages systemic chemotherapy in stage IV, adjuvant chemotherapy, and targeted therapy. Conclusion We found there are several nations where non-oncologic specialists play a critical role in the systemic treatment of lung cancer. We expect this practice pattern to continue until the global adoption of the oncologic specialty role.

In the United States, medical oncologists play a central role in the management of systemic therapy for cancer patients. Medical oncology as a specialty is not as established in Japan and several other European nations according to recent surveys, and little is known about this specialty in developing nations. We aimed to identify global differences in the roles of physicians treating cancer; specifically, how the management of advanced disease differs among nations.In March 2016, a self-administered internet survey was conducted with degreed physicians who prescribed systemic agents for adult cancer treatment within the past 5 years. Physicians were identified from the American Society of Clinical Oncology active member online directory.Among 3907 members in 55 nations, 376 (9.6%) responded to the survey. The 310 respondents who provided an answer to the recognition of medical oncology were dominated by male MDs that have practiced for more than 5 years at academic centers, and ~60% were medical oncologists. A majority of the respondents in all four regions reported that medical oncology was established in their corresponding nations. However, there are several outlying nations where oncologic specialties play a minimal role in the management of systemic therapy.Despite general recognition of medical oncology, the role is not globally established as the primary point of care for delivery of systemic therapy. Nations lacking this specialty should be assisted by the international community to develop medical oncology.

The Cox proportional hazards model is widely used in time-to-event analysis. Two time scales are used in practice: time-on-study and chronological age. The former is the most frequently used time scale in clinical studies and longitudinal observation studies. However, there is no general consensus about which time scale is the best. It has been asserted that if the cumulative baseline hazard is exponential or if the age-at-entry is independent of the covariate, then the two models are equivalent. We show that neither of these conditions leads to equivalency. Variability in the age-at-entry of individuals in the study causes the models to differ significantly. This is shown both analytically and through a simulation study. Additionally, we show that the time-on-study model is more robust to changes in age-at-entry than the chronological age model.

Nicotine improves cognitive enhancement and there are indications that neurodegenerative (age-related) cognitive disorders could be treated with nicotine-based drugs. The zebra finch is a well-recognized model to study cognitive functioning; hence this model could be used to study the effects of nicotine in neurodegenerative cognitive disorders. However, nicotine's in vivo physiological and behavioral effects have never been studied in the zebra finch. Here we present the first in vivo nicotine study in zebra finches. We evaluated the dose-response effects of nicotine on locomotor activity, song production, food intake and body weight. A liquid chromatography tandem mass spectrometry method was developed and validated for quantification of nicotine and cotinine in feces. The subcutaneous nicotine drug regiment (0.054-0.54mg/kg) induced physiologically significant values of nicotine and cotinine. The mid (0.18mg/kg) and high (0.54mg/kg) dose of nicotine promoted the development and expression of a sensitized response of song production and locomotor activity. Food intake and body weight were not affected following nicotine exposure. In conclusion, the zebra finch can be used as an innovative animal model not only in nicotine-related research studying cognitive functioning, but also in studies examining nicotine dependence and addictive mechanisms.

Why some tumors remain indolent and others progress to clinical relevance remains a major unanswered question in cancer biology. Interferon signaling in nascent tumors, mediated by STAT1, is a critical step through which the surveilling immune system can recognize and destroy developing tumors, thereby blocking their progression. We used an unbiased approach aimed at identifying nuclear protein interactions, called RIME, to identify novel progesterone receptor (PR) protein-protein interactions in T47D breast cancer cells. Using this technique, we identified a novel interaction between PR and STAT1. This interaction led to decreased interferon-induced STAT1 phosphorylation, a phenotype that was further potentiated in the presence of PR ligand. In human breast cancer samples, PR-positive tumors exhibited lower levels of phospho-STAT1 as compared to their PR-negative counterparts, indicating that this phenotype translates to human tumors. Breast cancer cells lacking PR expression exhibited higher levels of interferon-stimulated gene (ISG) RNA, the transcriptional endpoint of interferon activation, indicating that unliganded PR alone could decrease transcription of ISGs. Moreover, the absence of PR led to increased recruitment of STAT1, STAT2 and IRF9 (key transcription factors necessary for ISG transcription) to ISG promoters. These data indicate that PR, both in the presence and absence of ligand, attenuates interferon-induced STAT1 signaling, culminating in significantly abrogated activation of genes transcribed in response to interferons. PR-positive tumors may use downregulation of STAT1-mediated interferon signaling to escape immune surveillance, leading to the development of clinically relevant PR-positive tumors. Selective immune evasion of PR-positive tumors may be one explanation as to why over 70% of breast cancers are PR-positive at the time of diagnosis. Citation Format: Merit Goodman, Gloria Trinca, Katherine Walter, Evangelia Papachristou, Clive D'Santos, Tianbao Li, Qi Liu, Zhao Lai, Prabhakar Chalise, Rashna Madan, Victor Jin, Jason Carroll, Christy Hagan. Progesterone receptor attenuates STAT1-mediated interferon signaling in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1800.

Emerging clinical trial data implicate progestins in the development of breast cancer. While the role for the progesterone receptor (PR) in this process remains controversial, it is clear that PR, a steroid-activated nuclear receptor, alters the transcriptional landscape of breast cancer. PR interacts with many different types of proteins, including transcriptional co-activators and co-repressors, transcription factors, nuclear receptors and proteins that post-translationally modify PR (i.e. kinases and phosphatases). Herein, we identify a novel interaction between PR and OGT, the enzyme that catalyzes the addition of a single N-acetylglucosamine sugar, referred to as O-GlcNAc, to acceptor serines and threonines in target proteins. This interaction between PR and OGT leads to the post-translational modification of PR by O-GlcNAc. Moreover, we show that O-GlcNAcylated PR is more transcriptionally active on PR-target genes, despite the observation that PR mRNA and protein levels are decreased when O-GlcNAc levels are high. O-GlcNAcylation in breast cancer is clinically relevant, as we show that O-GlcNAc levels are higher in breast cancer as compared to matched normal tissues, and PR-positive breast cancers have higher levels of OGT. These data predict that under conditions where O-GlcNAc levels are high (breast cancer), PR, through an interaction with the modifying enzyme OGT, will exhibit increased O-GlcNAcylation and potentiated transcriptional activity. Therapeutic strategies aimed at altering cellular O-GlcNAc levels may have profound effects on PR transcriptional activity in breast cancer. Citation Format: Gloria M. Trinca, Merit L. Goodman, Evangelia K. Papachristou, Clive S. D'Santos, Prabhakar Chalise, Rashna Madan, Chad Slawson, Christy R. Hagan. O-GlcNAc-dependent regulation of progesterone receptor function in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1811.

After radical cystectomy (RC), patients are at risk for complications including infections. The expansion of myeloid-derived suppressor cells (MDSCs) after surgery may contribute to the lower resistance to infection. Immune response and postoperative complications were compared in men consuming either specialized immunonutrition (SIM; n=14) or an oral nutrition supplement (ONS; n=15) before and after RC. MDSC count (Lin- CD11b+ CD33+) was significantly different between the groups over time (p=0.005) and significantly lower in SIM 2 d after RC (p0.001). MDSC count expansion from surgery to 2 d after RC showed a weak association with an increase in infection rate 90 d after surgery (p=0.061). Neutrophil:lymphocyte ratio was significantly lower in SIM compared with ONS 3h after the first incision (p=0.039). Participants receiving SIM had a 33% reduction in postoperative complication rate (95% confidence interval [CI], 1-64; p=0.060) and a 39% reduction in infection rate (95% CI, 8-70; p=0.027) during late-phase recovery. The small sample size limits the study findings.Results show that the immune response to surgery and late infection rates differ between radical cystectomy patients receiving specialized immunonutrition versus oral nutrition supplement in the perioperative period.ClinicalTrials.gov NCT01868087.

Background Both genetic and epigenetic factors influence the development and progression of epithelial ovarian cancer (EOC). However, there is an incomplete understanding of the interrelationship between these factors and the extent to which they interact to impact disease risk. In the present study, we aimed to gain insight into this relationship by identifying DNA methylation marks that are candidate mediators of ovarian cancer genetic risk. Methods We used 214 cases and 214 age-matched controls from the Mayo Clinic Ovarian Cancer Study. Pretreatment, blood-derived DNA was profiled for genome-wide methylation (Illumina Infinium HumanMethylation27 BeadArray) and single nucleotide polymorphisms (SNPs, Illumina Infinium HD Human610-Quad BeadArray). The Causal Inference Test (CIT) was implemented to distinguish CpG sites that mediate genetic risk, from those that are consequential or independently acted on by genotype. Results Controlling for the estimated distribution of immune cells and other key covariates, our initial epigenome-wide association analysis revealed 1,993 significantly differentially methylated CpGs that between cases and controls (FDR, q

The search for the underlying heritability ofcomplex traits has led to an explosion of data generation and analysis in the field of human genomics. With these technological advances, we have made some progress in the identification of genes and proteins associated with common, complex human diseases. Still, our understanding of the genetic architecture of complex traits remains limited and additional research is needed to illuminate the genetic and environmental factors important for the disease process, much of which will include looking at variation in DNA, RNA, protein, etc. in ameta-dimensional analysis framework. We have developed amachine learning technique, ATHENA: Analysis Tool for Heritable and Environmental Network Associations, to address this issue of integrating data from multiple “-omics” technologies to identify models that explain or predict the genetic architecture of complex traits. In this chapter, we discuss the challenges in handling meta-dimensional data usinggrammatical evolution neural networks (GENN) which are one modeling component ofATHENA, and a characterization of the models identified in simulation studies to explore the ability of GENN to build complex, meta-dimensional models. Challenges remain to further understand the evolutionary process for GENN, and an explanation of the simplicity of the models. This work highlights potential areas for extension and improvement of the GENN approach within ATHENA.

The Cox proportional hazards model is routinely used to analyze time-to-event data. This model requires the definition of a unique well-defined time scale. Most often, observation time is used as the time scale for both clinical and observational studies. Recently after a suggestion that it may be a more appropriate scale, chronological age has begun to appear as the time scale used in some reports. There appears to be no general consensus about which time scale is appropriate for any given analysis. It has been suggested that if the baseline hazard is exponential or if the age-at-entry is independent of covariates used in the model, then the two time scales provide similar results. In this report we provide an empirical examination of the results using the two different time scales using a large collection of data sets to examine the relationship between systolic blood pressure and coronary heart disease death. We demonstrate, in this empirical example that the two time-scales can sometimes lead to differing regression coefficient estimates but time-on-study model has better predictive ability in general.

Copy number variants (CNVs) have been implicated in many complex diseases. We examined whether inherited CNVs were associated with overall survival among women with invasive epithelial ovarian cancer. Germline DNA from 1,056 cases (494 deceased, average of 3.7 years follow-up) was interrogated with the Illumina 610 quad genome-wide array containing, after quality control exclusions, 581,903 single nucleotide polymorphisms (SNPs) and 17,917 CNV probes. Comprehensive analysis capitalized upon the strengths of three complementary approaches to CNV classification. First, to identify small CNVs, single markers were evaluated and, where associated with survival, consecutive markers were combined. Two chromosomal regions were associated with survival using this approach (14q31.3 rs2274736 p = 1.59 × 10(-6), p = 0.001; 22q13.31 rs2285164 p = 4.01 × 10(-5), p = 0.009), but were not significant after multiple testing correction. Second, to identify large CNVs, genome-wide segmentation was conducted to characterize chromosomal gains and losses, and association with survival was evaluated by segment. Four regions were associated with survival (1q21.3 loss p = 0.005, 5p14.1 loss p = 0.004, 9p23 loss p = 0.002, and 15q22.31 gain p = 0.002); however, again, after correcting for multiple testing, no regions were statistically significant, and none were in common with the single marker approach. Finally, to evaluate associations with general amounts of copy number changes across the genome, we estimated CNV burden based on genome-wide numbers of gains and losses; no associations with survival were observed (p 0.40). Although CNVs that were not well-covered by the Illumina 610 quad array merit investigation, these data suggest no association between inherited CNVs and survival after ovarian cancer.

Variation in drug response results from a combination of factors that include differences in gender, ethnicity, and environment, as well as genetic variation that may result in differences in mRNA and protein expression. This article presents two integrative analytic approaches that make use of both genome-wide SNP and mRNA expression data available on the same set of subjects: a step-wise integrative approach and a comprehensive analysis using sparse canonical correlation analysis (SCCA). In addition to applying standard SCCA, we present a novel modification of SCCA which allows different weighting for the various pair-wise relationships in the SCCA. These integrative approaches are illustrated with both simulated data and data from a pharmacogenomic study of the drug gemcitabine. Results from these analyses found little overlap in terms of genes detected, possibly detecting different biological mechanisms. In addition, we found the proposed weighted SCCA to outperform its unweighted counterpart in detecting associations between the genomic features and phenotype. Further research is needed to develop and assess new integrative methods for pharmacogenomic studies, as these types of analyses may uncover novel insights into the relationship between genomic variation and drug response.

The presence of subterranean conduits within the Woodville Karst Plain is inferred from statistical analysis of several sets of microgravity measurements. In addition to determining the locations of such conduits, their approximate relative depths and sizes are estimated as well. An iterated non-linear least squares method is used to fit observed gravity data to a proposed theoretical model for the conduitgravity relation. The spatial density of the conduits is examined with respect to their relative cross-sectional areas.

Both genetic and epigenetic factors influence the development and progression of epithelial ovarian cancer (EOC). However, there is an incomplete understanding of the interrelationship between these factors and whether they interact to impact disease risk. Given that the development of ovarian cancer is complex, we aimed to identify DNA methylation marks that are candidates for mediating ovarian cancer genetic risk. We used 214 cases and 214 age-matched controls from the Mayo Clinic Ovarian Cancer Study. Pretreatment, blood-derived DNA was profiled for genome-wide methylation (Illumina Infinium HumanMethylation27 BeadArray) and single nucleotide polymorphisms (SNPs, Illumina Infinium HD Human610-Quad BeadArray). We employed a three-step filtering procedure, followed by the Causal Inference Test (CIT), to distinguish CpG sites that mediate genetic risk, from those that are consequential or independently acted on by genotype. Controlling for the estimated distribution of immune cells and other key covariates, we identified 1,993 out of 25,926 (7.7%) CpGs that were significantly differentially methylated between cases and controls (FDR, q < 0.05). The relationship between methylation and case-control status among these 1,993 CpGs was found to be highly consistent with the results of an independent study. Implementation of the CIT test revealed 13 CpG/SNP pairs, comprising 13 unique CpGs and 17 unique SNPs, which represent potential methylation-mediated relationships between genotype and EOC risk. These findings provide additional insight into EOC etiology and may serve as novel biomarkers for EOC susceptibility. Citation Format: Devin C. Koestler, Prabhakar Chalise, Mine S. Cicek, Julie M. Cunningham, Sebastian Armasu, Melissa C. Larson, Jeremy Chien, Matthew Block, Kimberly R. Kalli, Thomas A. Sellers, Ellen L. Goode, Brooke L. Fridley. Integrative genomic analysis identifies epigenetic marks that mediate genetic risk for epithelial ovarian cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 260. doi:10.1158/1538-7445.AM2014-260