bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3299: Socio-demographic and lifestyle factors associated with the neutrophil-to-lymphocyte ratio: A systematic evaluation of the United States National Health and Nutrition Examination Survey
Authors: Howard Rachel , Scheiner Aaron , Egan Kathleen M.
Published: August 2019

Background:

The neutrophil-to-lymphocyte ratio (NLR) is an established marker of subclinical inflammation, and a high NLR is associated with poorer clinical outcomes in cancer patients. Despite this, factors that influence the magnitude of NLR independently of disease are poorly understood. Here, we systematically assess the influence of socio-demographic and lifestyle factors on NLR to identify a) potential confounders and effect modifiers in the relationship between NLR and cancer outcomes, and b) possible targets for intervention in patients with high NLR at diagnosis.

Methods:

Based on a total participant cohort of 48,023 adults with available NLR data, we identified 20 factors of interest relating to patient demographics, socioeconomic status and lifestyle that were included in the National Health and Nutrition Examination Survey (NHANES) between 1999 and 2016. Multivariable regression analysis identified factors significantly associated with the magnitude of NLR after adjusting for comorbidities and medications. Interactions between factors of interest were evaluated, and effect modification by demographic characteristics including age, sex and race was quantified.

Results:

Seven demographic and lifestyle factors were found to be significantly and independently associated with NLR: age, sex, race, marital status, physical activity, smoking history and alcohol use. Females, under 60s and non-Hispanic blacks demonstrated significantly lower NLR than males, over 60s and non-Hispanic whites. Participation in vigorous activity for at least ten minutes at a time was associated with decreased NLR, as was never-smoker status. Moderate drinking was also associated with a decreased NLR as compared to complete abstinence from alcohol.

Conclusions:

Multiple demographic and lifestyle factors are independently associated with elevated NLR. For an accurate assessment of the prognostic power of the NLR in the clinical setting, these factors should be routinely adjusted for in studies of the association between NLR and cancer outcomes. The present study reiterates that physical activity may have the potential to improve clinical outcomes by way of reducing systemic inflammation.

Citation Format: Rachel Howard, Aaron Scheiner, Kathleen M. Egan. Socio-demographic and lifestyle factors associated with the neutrophil-to-lymphocyte ratio: A systematic evaluation of the United States National Health and Nutrition Examination Survey [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 3299.
Abstract 3306: Prognostic value of clinical signs at admission in patients with primitive liver cancer at university hospital of Yopougon: Retrospective cohort study
Authors: Tchibozo Djivede Renaud Jutor
Published: August 2019

Introduction: The primitive liver cancer (PLC) is common in Ivory Coast and has a late diagnosis. The PLC has a bad prognosis and few studies have assessed the predictive role of the clinical signs at admission, namely abdominal pain (AD), edematous-ascitic syndrome (OSA), febrile ascites (AF), and Digestive hemorrhage (HD) on the prognosis of patients with PLC .

Objective: To determine the prognostic role of clinical signs in the admission of hospitalized patients for PLC at University Hospital of Yopougon.

Patients And Methods: A retrospective cohort study of 126 patients (average age : 48.2 years, men = 71.4%) hospitalized for PLC at University Hospital of Yopougon from 2012 to 2016 was conducted in the Medicine and Hepato-Gastroenterology Department. For each patient the socio-demographics, clinicals, biologicals and endoscopics data and survival time were collected. These parameters were analyzed by

Kaplan Meier methods and Cox proportional hazards with a significance set at 5%. The risk is expressed in terms of chance ratio (HR) with the confidence interval.

Results: The patients were admitted for DA (32.5%), SOA (50%), AF (7.1%) and HD (10.3). The median duration of follow-up was 0.28 months. The mortality rate was 38.9% (49 of 126 patients) during follow-up. It was 12.7% for AD, 16.7% for SOA, 4.8% for AF and 4.8% for HD. The median overall survival was 0.8 (95% CI: 0.5-1.4) months. It was 0.7 (95% CI: 0.5-2) months for AD, 1.1 (95% CI: 0.4-1.1) months for OSA, 0.3 (95% CI: 0.21-3.6) months for AF and 1.1 (95% CI: 0.6-16.2) months for HD. In multivariate analysis, the predictive factors for mortality were: male sex (HR = 2.12, 95% CI: 1.08-4.17, p = 0.03), AF (HR = 4.51; 95% CI: 1.30 - 15.70, p = 0.02) and the presence of esophageal varicose (HR = 3.43, 95% CI 1.78-6.62, p <0.0001).

Conclusion: Patients suffering from PLC have a higher risk of death due to the presence of febrile ascites or esophageal varicose on admission.

Note: This abstract was not presented at the meeting.

Citation Format: Djivede Renaud Jutor Tchibozo. Prognostic value of clinical signs at admission in patients with primitive liver cancer at university hospital of Yopougon: Retrospective cohort study [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 3306.
Abstract 3315: Workplace program that offers annual fecal immunochemical testing improves adherence to colorectal cancer screening guidelines
Authors: Tong Carmen H. , Satish Anita , Fragala Maren S. , Bare Lance A. , Birse Charles E.
Published: August 2019

Background: Although regular screening reduces the incidence and mortality of colorectal cancer, ~ 35% of eligible adults remain non-adherent to screening guidelines. We asked if a workplace screening program, using a non-invasive fecal immunochemical test (Insure FIT), would improve adherence to guidelines.

Methods: An employer-sponsored program provided eligible employees (age 50-75 years) the opportunity to participate in colorectal cancer screening. InSure FIT collection kits were mailed annually to: (i) newly eligible employees, (ii) new hires, (iii) those who had participated the previous year and (iv) those who requested testing. Employees returned kits by mail for quantitative detection of human hemoglobin in fecal samples. Those with positive test results were contacted by phone and mail with a recommendation to contact their physician for follow up diagnostic testing. Using a limited data set of health plan claims, we identified those employees, with continuous medical coverage over the 5-year study period (2013-2017), who were adherent to current screening guidelines (colonoscopy any year or FIT every year). Colonoscopy procedures were identified in professional services and outpatient event files using current procedural terminology (CPT) codes.

Results: Approximately a third (32.7%; 1,858/5,686) of eligible employees participated in the program. Some 42.7% (794/1,858) of participants underwent colonoscopy over the 5-year study period. An additional 15.9% (296/1,858) were tested with InSure FIT all 5 years. In total 58.7% (1,090/1,858) of participants were adherent to guidelines (colonoscopy any year or annual FIT). In comparison, only 34.6% (1,323/3,828) of non-participants were adherent to guidelines.

ParticipantsNon-ParticipantsTotal1,8583,828Mean age, y (SD)55.9 (4.2)55.7 (4.3)Female, n (%)1,314 (70.7%)2,470 (64.5%)Adherent to screening guidelines, n (%)1,090 (58.7%)1,323 (34.6%)

Conclusion: Participants in an employer-sponsored FIT program had 24% higher adherence to guidelines for colorectal cancer screening compared to non-participants.

Citation Format: Carmen H. Tong, Anita Satish, Maren S. Fragala, Lance A. Bare, Charles E. Birse. Workplace program that offers annual fecal immunochemical testing improves adherence to colorectal cancer screening guidelines [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 3315.
Abstract 3330: Circulating HPV DNA as a biomarker for metastatic cervical cancer detection, genotyping and monitoring
Authors: Kang Zhigang , Stevanović Sanja , Hinrichs Christian , Cao Liang
Published: August 2019

Purpose: Circulating cell-free (cf) human papillomavirus (HPV) DNA is a unique tumor marker for metastatic cervical cancers. We developed a method to genotype and quantify blood circulating HPV DNA in patients with metastatic cervical cancer for patient selection, treatment monitoring, as well as informing data on an experimental T cell therapy.

Patients and Methods: we developed a digital droplet (dd) PCR method for HPV genotyping and quantification with cfDNA. In a retrospective study, HPV cfDNA was measured in serum samples from nine metastatic cervical cancer patients received tumor-infiltrating lymphocyte (TIL) immunotherapy. cfDNA data were aligned with the tumor HPV data, drug treatment, and clinical outcome. In a HPV screening, the genotyping and DNA copy number of HPV cfDNA from 47 cervical cancer patients were measured and the allele frequencies were determined in relative to total genomic cfDNA of each patient.

Results: The ddPCR assay is highly sensitive, specific, and capable of accurate quantification of both HPV16 and HPV18 cfDNA. In the clinical validation, we detected HPV cfDNA from 19/19 (100%) patients with HPV-positive metastatic and recurrent cervical cancer but not in any of the 45 healthy blood donors. The HPV genotype harbored in the patients’ tumors was correctly identified in 87/87 (100%) sequential patient serum samples. Our data showed the use of HPV cfDNA for pharmacokinetic studies, effectiveness on an investigational therapy, and patient monitoring. In three patients who experienced objective responses, a transient HPV cfDNA peak was detected 2-3 days after TIL immunotherapy and a persistent clearance of HPV cfDNA was observed in only two patients with a complete response (CR). Among the HPV positive cases, the median HPV cfDNA allele frequency is above 30% of genomic single copy genes in these cervical cancer patients.

Conclusions: We developed and validated a highly sensitive and specific HPV cfDNA genotyping and quantification method. As a promising non-invasive tumor marker, HPV cfDNA may have value in detecting the efficacy of therapeutic agents and monitoring cervical cancer patients in remission. The cfDNA based HPV genotyping is currently being evaluated for patient selection in an experimental T-cell therapy against a specific HPV antigen. HPV cfDNA may also be a potential biomarker for early diagnosis of cervical cancer.

Citation Format: Zhigang Kang, Sanja Stevanović, Christian Hinrichs, Liang Cao. Circulating HPV DNA as a biomarker for metastatic cervical cancer detection, genotyping and monitoring [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 3330.
Abstract 3334: Predictive therapeutic value of NGS with liquid biopsy in metastatic NSCLC
Authors: Tomao Silverio , Verrico Monica , Rossi Luigi , Stefano Iacobelli
Published: August 2019

Analysis of circulating tumor cells ( CTCs) and circulating cell-free DNA (cfDNA), detected in peripheral blood of patients, is an extraordinary novel strategy to identify and study NSCLC patients, in order to obtain prognostic and predictive molecular informations with a simple, non invasive and sensitive method. Liquid biopsy therefore offers a new source of cancer cells and cancer-derived materials in order to test more personalized treatment. With two PCR-based next generation sequencing (NGS) approaches we evaluated 45 patients with not squamous NSCLC ; in eighteen pts ( 40 % ) almost one genomic mutation was detected among 56 different genes analyzed with NGS. Median age of patients was 69 years ( 55-78) and 14 (73%) were males. Altogether, 11 genes were mutated with a panel of 56 genes analyzed (19,6% ) . The most frequent mutations occurred in KRAS, TP53, MET,KDR, KIT, SMAD4 and MET genes. Several patients expressed many mutations and the most frequent detected concerned gen c-Kit ( 22%). Other mutations concerned the following genes : TP53 ( 16 % ), MET/KDR. / SMAD4/KRas ( 44%). Other genomic alterations concerned the following genes: JACK3 (5%); APC(5%); ERBB4(5%); CTNNB! (5%); EGFR (5%). Altogheter the response to therapy was higher among patients with mutation of Smad 4 gene and lower in patients with mutations of KIT gene. All side effects occurred with target therapy was categorized according to the Common Terminology Criteria for Adverse Events, 4.0 version. An increase of gastroenteric (G3/G4) and hematologic toxicity (G3/G4) was observed in patients with Kit mutations. In our study this correlation was observed mainly during treatment with Tyrosine Kinase Inhibitors (TKIs ).Evaluating Progression Free Survival (PFS) in all the patients recruited in the study, a median PFS of 12.5, 11.5, 4 and 9 months was observed respectively in patients with mutations of KIT, SMAD4, TP53 and MET. In this study, all the genetic alterations analyzed and highlighted were related to the response to chemotherapeutic treatments and possible tyrosine kinase inhibitory treatments in terms of PFS and toxicity.

Note: This abstract was not presented at the meeting.

Citation Format: Silverio Tomao, Monica Verrico, Luigi Rossi, Iacobelli Stefano. Predictive therapeutic value of NGS with liquid biopsy in metastatic NSCLC [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 3334.
Abstract 3349: Collected experiences of young-onset colorectal cancer caregivers
Authors: Newcomer Kimberley L. , Yarden Ronit , Advisory Never Too Young
Published: August 2019

The Colorectal Cancer Alliance launched a survey for caregivers of young-onset colorectal cancer (CRC) patients and survivors. A caregiver of young-onset CRC is an unpaid or paid member of a person's social network who helps them with activities of daily living. Caregivers who participated in our survey (n=427) are diverse: in age, gender, and racial/ethnic group. The majority of them were between the ages of 30-39. The caregivers reported they faced many challenges including lack of resources and information on young-onset disease and the course of the disease progression. Also, many caregivers indicated they had difficulty understanding the different treatment options offered by the physicians as well as the risk and long-term side-effects associated with these aggressive treatments. Only 40 percent of providers talked to patients about genetic testing and explained to the patient's family member their elevated risk of the disease and the associated need for timely screening. The majority of caregivers (59%) reported that their loved one experienced changes in their ability to perform expected social tasks, including those of a spouse, child rearer, friend, or worker. Some caregivers also mentioned the loss of sexuality, depression, pain, despair, lack of sleep, sadness, and stress, along with a loss of faith and hope, which may cause additional strain on their relationships. Thirty-two percent of caregivers reported insufficient psychosocial (66%) and financial support (44%) to effectively care for their patients. Participants also indicated that resources such as transportation, child care, household maintenance, prevention, and surveillance information for family members are limited. Overall, about one in three caregivers reported they were missing 24 hours or more of work each month to care for their loved one. A caregiver stated she needed, “Emotional and basic help around the house with her children and someone responsible enough to stay in the house to understand what we were going through as a family.” Taken together, our survey indicates that additional resources are needed to improve the ability for caregivers to manage everyday tasks, potentially helping caregivers feel more organized and in control. The ability of caregivers to care for themselves and use tools to care for their loved ones will reduce emotional and physical demands involved with caregiving that can cause strain and burnout. The Alliance will use these survey results to learn about and track the self-reported medical, psychosocial, and quality of life experiences of this often overlooked group.

Citation Format: Kimberley L. Newcomer, Ronit Yarden, Never Too Young Advisory. Collected experiences of young-onset colorectal cancer caregivers [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 3349.
Abstract 3364: A study to assess the critical result reporting of the patients diagnosed with cancer at B&C Medical College and Teaching Hospital
Authors: Sharma Sujan
Published: August 2019

Objective: This critical value can occur while performing panels of tests at laboratory by different chemistry or blood analysers with varieties of principles. The main objective of the study was to study the process of critical result reporting and to know the way of communication and documentation done for critical value in the laboratory, ICUs and the wards.Methods: This study was prospective and non-experimental was conducted at B&C Medical College and Teaching Hospital from 14.04.2018 to 14.05.2018 . Total 60 critical values samples were included. The data was collected by means of observing the critical values of inpatient and the process of reporting from the laboratory to the respective wards and ICUs.Results: Out of 60 samples included in our study, there was 100% communication to concerned treating units. For the confirmation of critical value repeat test was done in 68% of cases. In 75% of cases clinicians did follow up. Recording of a critical report in lab was done in 96% of cases and almost all of the critical values 98% were immediately reported to the respective wards by technical staffs. There was no communication in 1.6% of cases to treating units by technical staff. Majority 78% of critical values were communicated by respective wards and ICUs nurses to concerned doctors.Conclusion: Critical value can occur while performing panels of tests at laboratory and reporting such values to treating clinicians or respective wards or ICUs could help heath care providers for effective treatment of the patients and their adequate care.

Note: This abstract was not presented at the meeting.

Citation Format: Sujan Sharma. A study to assess the critical result reporting of the patients diagnosed with cancer at B&C Medical College and Teaching Hospital [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 3364.
Abstract 338: Inhibition of phosphatidylinositol 3-kinase signaling antagonizes paclitaxel-mediated resistance in cervical cancer
Authors: Choi Youn Jin , Jung Yoo Yeon , Liu Jing Jing
Published: August 2019

Paclitaxel is used as an effective treatment against advanced cervical cancer. However, acquired resistance limits its success and results in cancer progression. We investigated whether the inhibition of phosphatidylinositol 3-kinase (PI3K) signaling overcomes paclitaxel resistance in cervical cancer. Two human cervical cancer cell lines (Me180 and HeLa) were used. We established paclitaxel-resistant cell lines (PTX-R Me180/PTX-R HeLa) and confirmed inhibitory concentrations (IC)50 and cell death rates by tetrazolium dye (MTT) and apoptosis assays, respectively, after exposure to a combination of paclitaxel with PI3K inhibitors (LY294002 and BYL-719). Migration and invasive abilities were explored by wound healing and transwell assays, respectively. Western blots were performed to determine the mechanism underlying the antitumor effects of PI3K inhibitors.PTX-R Me180 and PTX-R HeLa cells were gradually established from parental cell lines by stepwise exposure to paclitaxel over 7 months and with stable resistance at under 20 nM. We found that the activation of the PI3K pathway in paclitaxel-resistant lines increased tumor growth and invasiveness, and impeded cell apoptosis. The combination of LY294002 or BYL-719 with paclitaxel significantly enhanced drug sensitivity and synergistic apoptosis through the activation of Bax, caspase-3, and cleaved poly ADP ribose polymerase compared with paclitaxel alone. In addition, PI3K inhibition also suppressed tumor migration and invasive ability by targeting vimentin, matrix metalloproteinase-9 and vascular endothelial cell growth factor.We suggest that a combination of a PI3K inhibitor with paclitaxel may enhance antitumor activity through a cascade of PI3K signaling events.

Note: This abstract was not presented at the meeting.

Citation Format: Youn Jin Choi, Yoo Yeon Jung, Jing Jing Liu. Inhibition of phosphatidylinositol 3-kinase signaling antagonizes paclitaxel-mediated resistance in cervical cancer [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 338.
Abstract 3390: RNA interactome topology perturbation analysis reveals candidate driver mutations in cancer
Authors: Li Yongsheng , McGrail Daniel J. , Xu Juan , Li Junyi , Yi Song , Sahni Nidhi
Published: August 2019

Identification of the driver genomic variants is important for precision therapy of human cancer. Interaction between RNA-binding proteins (RBPs) and RNA plays important roles in regulating cellular function. Decoding genome-wide protein-RNA regulatory networks as well as how cancer-related mutations impair RNA regulatory activities in cancer will help prioritizing candidate driver mutations.

Here, we first explored the genetic alteration patterns of RBPs and found that candidate driver mutations are likely to occur on the surface of RBPs. This observations indicate that the driver mutations may perturb the RBP regulatory network in cancer. We then constructed protein-RNA interactome networks by integration of target binding screens and expression profiles. Regulatory network analysis highlights regulatory principles among interacting RBPs. In addition, somatic mutations selectively target functionally important genes (cancer genes, core fitness genes or conserved genes) in cancer. These regulatory patterns were further validated using independent data. A computational method (MERIT) and a web-based user friendly resource were further proposed to analyze the RBP-gene regulatory network perturbation induced by mutations across cancer types. Pan-cancer analysis also suggests that cancer cells selectively target "vulnerability" genes to perturb protein-RNA interactome that is involved in cancer hallmark-related functions. Based on the expression of perturbed RBP and target genes, we identified three subtypes of liver cancer with different survival rates. Specifically, we experimentally validated four pairs of RBP-gene interactions perturbed by mutations, which play critical roles in cell proliferation.

Taken together, our results provide a valuable resource for characterizing somatic mutation-perturbed protein-RNA regulatory networks in cancer, yielding valuable insights into the genotype-phenotype relationships underlying human cancer, and potential biomarkers for precision medicine.

Note: This abstract was not presented at the meeting.

Citation Format: Yongsheng Li, Daniel J. McGrail, Juan Xu, Junyi Li, Song Yi, Nidhi Sahni. RNA interactome topology perturbation analysis reveals candidate driver mutations in cancer [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 3390.
Abstract 3395: TargetTranslator: Big data identifies non-canonical targets for high risk neuroblastoma
Authors: Almstedt Elin , Wärn Caroline , Elgendy Ramy , Hekmati Neda , Rosén Emil , Larsson Ida , Jörnsten Rebecka , Crona Cecilia , Nelander Sven
Published: August 2019

Despite the many advances in the molecular characterization of neuroblastoma, effective treatments for high-risk patients are currently lacking. Using publically available data, integrated computational analysis offers new opportunities to uncover druggable subgroups. In the TargetTranslator project, we have combined state-of-the-art Big Data techniques to identify new targets in high-risk subgroups of neuroblastoma. Starting with clinical or genomic risk factors, TargetTranslator builds a consensus molecular signature across cohorts. This signature is scored against a massive amount of data from (i) childhood tumor biobanks (TARGET, R2), (ii) drug profiling data from cancer cell models (NIH-LINCS), and (iii) drug targets and pathways (STITCH, STRING, MSIGDB). As output, the system provides ranked lists of compounds, molecular targets and pathways for each risk factor, as well as an aggregated probability score. In a proof-of-concept study, we used TargetTranslator to recommend treatments for high-risk neuroblastoma subgroups, including COG high-risk, MYCN amplification, 11q deletion, and signatures of differentiation and ALK activation. Depending on risk group stratification, we detected between 21 and 680 substances (p<0.001), most of which were strongly associated to approximately 10 key targets. In addition to confirming a key role for the PI3K/mTOR and MAPK pathways, we detected high scoring compounds in non-canonical pathways, including neurotransmission, GLI/SMO, ROCK and PKA. Experimental validation of 11 predicted drugs in patient-derived neuroblastoma lines confirmed our signatures and reduced viability. We also identified four new compounds that significantly (p<0.05) suppressed MYCN protein levels (ROCK inhibitor fasudil, CNR2 agonist GW405833, CDK inhibitor AZD5438, lovastatin) at concentrations non-toxic in zebrafish embryos. By integrating data from patients, drugs, and drug-protein networks, we establish a new computational pipeline that predicts protein targets in specific patient subgroups. The TargetTranslator introduces a way to bridge drug effects with patient data and will be available as a user-friendly web tool on www.targettranslator.org in 2018.

Citation Format: Elin Almstedt, Caroline Wärn, Ramy Elgendy, Neda Hekmati, Emil Rosén, Ida Larsson, Rebecka Jörnsten, Cecilia Crona, Sven Nelander. TargetTranslator: Big data identifies non-canonical targets for high risk neuroblastoma [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 3395.
Abstract 3425: Mutations in DNA repair and microtubule assembly genes found in triple negative breast tumors treated with neoadjuvant chemotherapy
Authors: Grant Michael , Snipes George , Halperin Rebecca , Heaton Paul , Kim Suwon
Published: August 2019

Up to 20% of breast cancer is clinically defined as triple-negative breast cancer (TNBC) lacking estrogen, progesterone, and HER2 receptors. Because no targeted therapy is available, cytotoxic chemotherapy is the primary mode of adjuvant TNBC therapy, but is effective in ~30% patients. In order to determine molecular underpinnings of chemotherapy resistance in TNBC, we analyzed 12 TNBC patient tumor samples collected post neoadjuvant chemotherapy using DNA/RNA sequencing. DNA analysis showed two tumors contained TP53 inactivating mutations and two tumors PIK3CA activating mutations. In addition, a number of mutations in the DNA repair pathway genes were identified including XRCC1, XRCC3, and ATXR, suggesting that DNA damaging nature of chemotherapy agents may have enriched these mutations. In addition, we found mutations in the genes involved in microtubule assembly including BUB3 and APC2, suggesting that these gene mutations may confer resistance to taxol, an anti-microtubule chemotherapy agent. RNA sequencing revealed a true heterogeneous nature of TNBE in that unsupervised clustering did not identify any distinct gene signature correlative of chemotherapy resistance. We are currently evaluating phenotypes related to chemotherapy resistance using cells genetically engineered with the BUB3 or APC2 mutations.

Citation Format: Michael Grant, George Snipes, Rebecca Halperin, Paul Heaton, Suwon Kim. Mutations in DNA repair and microtubule assembly genes found in triple negative breast tumors treated with neoadjuvant chemotherapy [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 3425.
Abstract 3426: Combining cell barcoding and CRISPR sgRNA libraries with targeted gene expression for single-cell genetic analysis of tumor metastasis
Authors: Chenchik Alex , Diehl Paul , Makhanov Mikhail
Published: August 2019

Pooled lentiviral libraries of CRISPR sgRNAs to mediate genome-wide gene knockout have become an invaluable tool for uncovering the functional genetic drivers required for a biological response. Another type of pooled lentiviral library designed with unique DNA sequence tags have also been used to label large populations of cells with unique cell-specific barcodes which allows monitoring changes in sub-populations of cells with distinct phenotypes over time. We have combined cell barcodes with CRISPR sgRNA to construct libraries that enable the identification of multiple occurrences of a common phenotypic response from independent transductions of the same sgRNA effector. Specifically, we demonstrate how this sort of library can be used to identify genes whose activation promotes metastasis of tumors derived from MDA-MB-231 cells engrafted into mice after transduction with a barcoded CRISPR-activation (CRISPRa) sgRNA library. By incorporating multiple barcodes with each sgRNA effector, it is possible to see that, not only are cells in metastatic tumors more likely to have a particular sgRNA targeted to a certain gene, but also that independent transductions of that sgRNA sequence lead to multiple independent metastatic events. With multiple independent clones producing the same phenotype, it is possible to confidently isolate the sgRNA, and by implication, the increased activation of its gene target, as the primary cause of the metastatic phenotype.

Citation Format: Alex Chenchik, Paul Diehl, Mikhail Makhanov. Combining cell barcoding and CRISPR sgRNA libraries with targeted gene expression for single-cell genetic analysis of tumor metastasis [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 3426.
Abstract 3444: Identification of Interleukin-1 (IL-1) induced gene expression pattern in breast cancer (BCa) cells
Authors: Nawas Afshan Fathima , Kanchwala Mohammed , Thomas-Jardin Shayna , Anunobi Vanessa , Wong Ally , Xing Chao , Delk Nikki
Published: August 2019

Breast cancer (BCa) and prostate cancer (PCa) are both hormone driven cancers with similar etiology and tumor microenvironment inflammation promotes BCa and PCa progression. Interleukin-1 (IL-1) is an inflammatory cytokine present in the tumor microenvironment and IL-1 is elevated in BCa and PCa patient tumor and/or blood serum and correlates with poor prognosis. We have shown that IL-1 represses the BCa and PCa therapeutic targets, Estrogen Receptor Alpha (ERa) and Androgen Receptor (AR), respectively, in PCa and BCa cell lines; yet the cells remain viable. Thus, IL-1 may promote treatment resistance and disease progression. The pro-survival protein Sequestome-1 (SQSMT1/p62) is also upregulated in both BCa and PCa cell lines exposed to IL-1, suggesting that BCa and PCa cells have evolved a shared response to IL-1 and hormone receptor loss. RNA sequencing of an IL-1-treated PCa cell line revealed an IL-1-modulated gene suite predicted to confer AR-independent tumorigenicity. We performed RT-qPCR in PCa cell lines for several select genes to confirm the RNA sequencing results and given the similar etiology and IL-1 regulation of ERa, AR, and p62 expression in BCa and PCa cell lines, we presumed that our select genes would be similarly regulated by IL-1 in BCa cells. However, outside of ERa, AR, and p62 expression, our select genes did not show similar IL-1 regulation in BCa cell lines, suggesting that IL-1 regulates a unique set of genes that could contribute to ERa-independent tumorigenicity in BCa cells. Therefore, to identify a BCa-specific IL-1-modulated gene suite, we performed RNA sequencing on an IL-1-treated ERα+ BCa cell line and compared gene expression changes with 1) basal gene expression in an ERa- BCa cell line and 2) our IL-1-modulated PCa-specific gene suite. Our bioinformatics analysis revealed pathways that are predicted to promote ERa-independent tumorigenicity in BCa cells and investigations are underway to demonstrate the functional significance of our gene expression data. Taken together, our studies provide insight into the mechanistic function of IL-1 in PCa and BCa resistance to hormone receptor-targeted therapies and tumor progression.

Citation Format: Afshan Fathima Nawas, Mohammed Kanchwala, Shayna Thomas-Jardin, Vanessa Anunobi, Ally Wong, Chao Xing, Nikki Delk. Identification of Interleukin-1 (IL-1) induced gene expression pattern in breast cancer (BCa) cells [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 3444.
Abstract 3446: STRAP is involved in mutated Apc-induced stemness and tumorigenesis in colon cancer
Authors: Vu Trung
Published: August 2019

Inactivation of the Apc gene is a critical early event in the development of sporadic colorectal cancer (CRC). Loss of its normal function leads to constitutive activation of β-catenin/T-cell factor 4 signaling and hence transcription of Wnt target genes. The signaling scaffold protein STRAP is upregulated in several cancers, where it promotes tumorigenicity and stemness. Here, we tested the effect of conditional deletion of Strap on intestinal tumor formation and growth by crossing ApcMin/+ mice with mice that are null for Strap in the intestinal epithelium, Strapfl/fl;Vil-Cre mice (StrapIEKO). We observed a dramatic decrease in the number of intestinal polyps in the ApcMin/+;Strapfl/fl;Vil-Cre mice (called StrapIEKO;ApcMin/+) compared to mice with intact Strap (Strapfl/fl;ApcMin/+). In an attempt to understand the mechanism of function of STRAP, we have observed that colon tumors from StrapIEKO;ApcMin/+ mice displayed a decrease in β-catenin nuclear localization and downregulation of Wnt targets such as c-Myc, AXIN2, and CCND1. Enteroids prepared from StrapIEKO;ApcMin/+ mice exhibited more budding compared to the ApcMin/+ enteroids, indicating the role of STRAP in stemness. STRAP knockdown in human CRC cells significantly diminished β-catenin/TCF4 transcriptional activity. Specifically, STRAP knockdown impaired the assembly of β-catenin/TCF4 complex and recruitment of the complex to the promoters of β-catenin target genes. Functional proteomic analyses of crypt cells from different genetic mice suggested that the MEK/ERK signaling pathway is suppressed in StrapIEKO;ApcMin/+ mice that is required for the effect of STRAP on Wnt/β-catenin signaling. We have shown that STRAP associates with MEK1/2 and promotes binding between MEK1/2 and ERK1/2 and subsequently induces the phosphorylation of ERK1/2. Given that MEK/ERK signaling is found to promote Wnt/β-catenin signaling, our results suggest that STRAP indirectly induce Wnt/β-catenin signaling through activating MEK/ERK pathway. Importantly, STRAP is found to be a novel target of Wnt/β-catenin

signaling as ChIP assays determined putative binding sites of β-catenin/TCF4 complex on Strap promoter. Finally, we showed that forced expression of STRAP in colon cancer organoids derived from patients with colon cancer can induce the growth of colon tumor organoids through promoting Wnt/β-catenin signaling. Altogether, these results suggest that STRAP is involved in mutated APC-induced tumor initiation through a novel feed-forward STRAP/MEK-ERK/β-catenin/STRAP regulatory axis.

Citation Format: Trung Vu. STRAP is involved in mutated Apc-induced stemness and tumorigenesis in colon cancer [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 3446.
Abstract 3447: APC truncating mutations in Middle Eastern population: Tankyrase inhibitor is an effective strategy to sensitize APC mutant CRC to 5-FU chemotherapy
Authors: Parvathareddy Sandeep K. , Siraj Abdul K. , Bu Rong , Poyil Prateeshkumar , Masoodi Tariq , Padmaja Divya Sasidharan , Concepcion Rica , Begum Rafia , Sabido Maria A. , Melosantos Roxanne , Al-Sanea Nasser , Al-Dayel Fouad , Al-Kuraya Khawla S.
Published: August 2019

Colorectal Cancer (CRC) is the leading cause of cancer related death and the most common cancer affecting Saudi males. Mutation of the adenomatous polyposis coli (APC) gene is considered as the initiating step of transformation in familial and sporadic CRC. The prevalence and prognostic role of APC mutation spectra are not well established in Middle Eastern CRC. Next generation sequencing of 412 CRC tumors was performed to determine mutations in APC. Association with protein expression and clinico-pathological correlation was performed. APC truncating mutation is found at a frequency of 58.2% (240/412) and is significantly associated with superior overall survival, whereas no difference in survival between short truncating and long truncating APC was noted. To test the hypothesis that APC mutations might influence 5- Fluorouracil (5-FU) therapy, which is the first line chemotherapy used in CRC, we compared CRC cell lines and showed that those expressing truncated APC exhibit limited response to 5-FU, unlike cells which were APC wild type. In COLO-320 DM and HCT-15, APC mutated CRC cells, we were able to increase sensitivity of APC truncated cells to 5-FU by inhibiting Tankyrase (TNKs) which are members of PARP family, using XAV939. In conclusion, the study identified the prognostic value of APC truncating mutation in Middle Eastern ethnicity. In vitro data further showed that APC mutation can be used as a molecular biomarker to predict response to 5-FU. Furthermore, Tankyrase inhibitor XAV939 selectively targeting APC-mutated CRC cells can be an effective strategy to overcome 5-FU resistance in these cells.

Note: This abstract was not presented at the meeting.

Citation Format: Sandeep K. Parvathareddy, Abdul K. Siraj, Rong Bu, Prateeshkumar Poyil, Tariq Masoodi, Divya Sasidharan Padmaja, Rica Concepcion, Rafia Begum, Maria A. Sabido, Roxanne Melosantos, Nasser Al-Sanea, Fouad Al-Dayel, Khawla S. Al-Kuraya. APC truncating mutations in Middle Eastern population: Tankyrase inhibitor is an effective strategy to sensitize APC mutant CRC to 5-FU chemotherapy [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 3447.
Abstract 3457: Flubendazole targets STAT3 signaling and distant metasis in triple-negative breast cancer
Authors: Oh Eunhye , Kim Yoon-Jae , Jang Seojin , Cho Tae-Min , Park Soeun , Park Jung Min , Park Minsu , Kim Ji Young , Seo Jae Hong
Published: August 2019

Triple-negative breast cancers (TNBC) with higher cancer stem-like populations are reported to exhibit a more aggressive metastatic phenotype. In the present study, we investigated the effects of flubendazole, a candidate drug for repurposing and its novel mechanism of action with a focus on targeting STAT3 signaling and breast cancer stem-like traits in TNBC. The effect of FLU on TNBC cell lines in vitro was evaluated in terms of cell viability, breast cancer stem cells (BCSC)-like properties and expression of STAT3 signaling-related factors. An orthotopic injection model with BCSC-enriched population was used to examine the effect of flubendazole on tumor growth and metastasis in vivo. Our results showed that the BCSC-enriched populations harbored a higher Aldefluor-positive population and markedly elevated levels of CD49f and ALDH1A1 as well as higher STAT3 activation in vitro. Flubendazole attenuated STAT3 activation, as demonstrated by a significant reduction in phospho-STAT3 levels as well as subsequent downregulation of its downstream effector cyclin D1. Sphere-forming ability was significantly suppressed following two pharmacological STAT3 inhibitor, LLL12 or S3I-201 challenge. Treatment with interleukin-6 (IL-6) was observed to significantly increase the number and volume of mammospheres, while flubendazole abolished this effect. Bioluminescence in vivo imaging (BLI) revealed that the BCSC-enriched populations exhibited enhanced metastasis with higher STAT3 activation, while flubendazole administration inhibited tumor growth and lung and liver metastasis, coinciding with decreased MMP-2 and MMP-9 levels in circulating blood. To our knowledge, these findings are the first to report that flubendazole reduces BCSC-enriched tumor burden and metastasis via STAT3 inactivation, implying that flubendazole treatment may have application in addressing metastasis.

Citation Format: Eunhye Oh, Yoon-Jae Kim, Seojin Jang, Tae-Min Cho, Soeun Park, Jung Min Park, Minsu Park, Ji Young Kim, Jae Hong Seo. Flubendazole targets STAT3 signaling and distant metasis in triple-negative breast cancer [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 3457.
Abstract 3458: Investigation of oxidative stress-related gene signature in cancer-associated cachexia
Authors: Jain Sumeet , Shukla Surendra K. , Dasgupta Aneesha , Singh Pankaj K.
Published: August 2019

About eighty percent of pancreatic cancer patients demonstrate excessive loss of skeletal muscles with or without loss of adipose deposits, a condition known as cancer-associated cachexia. Severe complexities related to cancer-associated cachexia contribute to mortality in one-third of pancreatic cancer patients. Multiple factors, including loss of appetite, systemic inflammation, digestive enzymes, and hormonal imbalance may contribute to the development of cancer-associated cachexia. Poor understanding of the molecular mechanism is the key challenge for targeting cancer-associated cachexia. Hence, to facilitate the identification of new targets for ameliorating cancer-induced muscle loss, we undertook genomic studies. We evaluated differentially expressed gene signatures in muscle tissues of cachectic and non-cachectic human pancreatic cancer patients. To better model the mechanisms of cancer cachexia, we also compared the identified gene signatures to that of orthotopic and spontaneous mice models of pancreatic cancer cachexia. We observed significant alterations in multiple genes related to oxidative stress in muscle tissues from human patients with cachexia and mice cachexia models. We targeted oxidative stress regulatory genes by genetic manipulations or targeted oxidative stress with pharmacological approaches to evaluate the impact of oxidative stress in skeletal muscles on cancer-associated cachexia. Our results suggest that targeting the oxidative stress pathway prevents/reverts cancer-associated cachexia. Moreover, inhibition of oxidative stress also abolished cancer cell-conditioned medium-induced atrophy in C2C12-derived myotubes and diminished the expression of atrophy markers. Overall, our studies revealed the potential role of oxidative stress induced by cancer cells in muscle wasting. Future studies to target tumor-induced oxidative stress in muscle fibers may provide new therapeutic approaches to prevent cancer-associated cachexia.

Citation Format: Sumeet Jain, Surendra K. Shukla, Aneesha Dasgupta, Pankaj K. Singh. Investigation of oxidative stress-related gene signature in cancer-associated cachexia [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 3458.
Abstract 3461: Characterizing the PTEN - p85alpha interaction
Authors: Marshall Jeremy , Mellor Paul , Ruan Xuan , Whitecross Dielle , Moore Stanley , Anderson Deborah
Published: August 2019

Introduction: The phosphatidylinositol 3-kinase (PI3K) pathway plays a key role in regulating cell growth and cell survival and is frequently deregulated in cancer cells. p85α regulates the p110α lipid kinase, and also stabilizes and stimulates PTEN, the lipid phosphatase that downregulates this pathway. We set out to identify residues in both PTEN and p85α that mediate their interaction to better understand the regions important in mediating binding.

Experimental Procedures: We previously showed that the BH domain of p85α is sufficient to mediate binding to PTEN. In this work, a deletion analysis and point mutations were used to mutate each of PTEN and the p85α BH domain to identify residues important for binding, determined using a pull-down analysis. Mutations in the p85α BH domain and in PTEN that reduced their interaction were then used as input data and docking software was used to model possible interaction interfaces for the two the proteins. Further mutagenesis and follow-up binding experiments provided support for our model of the PTEN - p85α BH domain complex.

Results: We identified key residues responsible for mediating PTEN - p85α complex formation. Based on these experimental results, a docking model for the PTEN - p85α BH domain complex was developed that is consistent with the known binding interactions for both PTEN and p85α. This model involves extensive side-chain and peptide backbone contacts between both the PASE (R84, Q87, Y88, E91, E99) and C2 (R189, P190, Q219, C250, D252) domains of PTEN and the p85α BH domains with a buried surface area of 1211 Å2 (PTEN - bovine p85α BH) and 1366 Å2 (PTEN - human p85α BH). The p85α BH domain residues that directly contact PTEN in the two docking models were not identical, however both models implicated p85α residues E212, Q221, K225, R228, H234 and W237. The majority of these p85α BH domain residues were confirmed experimentally as important for PTEN binding. We also verified experimentally the importance of PTEN-E91 in mediating interaction with the p85α BH domain.

Conclusions: These results shed new light on the mechanism of PTEN binding and regulation by p85α.

Citation Format: Jeremy Marshall, Paul Mellor, Xuan Ruan, Dielle Whitecross, Stanley Moore, Deborah Anderson. Characterizing the PTEN - p85alpha interaction [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 3461.