Abstract P2-13-06: Pancreatic nutrition program (PNP): A novel weight reduction program for breast cancer survivors

BACKGROUND: Breast cancer survivors have a high prevalence of metabolic dysfunction—characterized by high glucose and weight gain. Regardless of menopausal status, overweight and obese women are at increased risk for developing breast cancer and those who are diagnosed with breast cancer experience adverse cancer-related outcomes. The underlying principle of the Pancreatic Nutrition Program (PNP) is that bio-individualized healthy food choices—eating the correct foods and food combinations for an individual's body—can minimize fluctuations in insulin by keeping blood glucose regulated (70-100 mg/dL) and this will promote sustained weight loss, improved health, and quality of life. METHODS: The primary endpoint was change in body weight at 24 weeks post-PNP. The study was powered to detect a 10% loss of weight from baseline. Secondary endpoints included change in: glucose levels, insulin resistance, body composition, body chemistry, physical fitness, biological markers, quality of life, and compliance. Postmenopausal, non-diabetic breast cancer survivors (stages I-III) within 5 years of completion of treatment who had a body mass index of 25-33 kg/m2 were recruited. For the first 12 weeks, patients wore a glucometer (Abbott), which recorded glucose every 15 minutes continuously, and kept a food journal. During weekly meetings, glucometer data was reviewed with journal entries to identify food choices and combinations that would kept the subject's glucose levels between 70-100 mg/dL. At the end of the 12-weeks, the weekly meetings and glucometer were discontinued and patients were expected to maintain the PNP for an additional 12 weeks. Study endpoints were measured at baseline, 12-week and 24-week visits. RESULTS: Of the 21 patients enrolled in the study, 12 were non-Hispanic Caucasian, 5 were Hispanic, 2 were African-American, and 2 were Asian. The median age was 56 years (43-76 years). Twenty were estrogen-receptor positive, 18 progesterone-receptor positive, and 8 were HER2/neu positive. The mean body weight at baseline was 170.9 lbs (±20.4 lbs). Two patients dropped out prior to 12-weeks and 1 developed recurrent disease. Among the 18 eligible women who completed the first 12 weeks, the median weight loss at 12-weeks was 10.1 lbs (1.5-19.6 lbs). The median waist circumference lost was 2.5 inches (gain of 0.4 inches-loss of 5.5 inches). Among the women whose total cholesterol was above 200 mg/dL, 71% reduced their cholesterol below 200 mg/dL by 12-weeks. All women who had triglyceride levels above 150 mg/dL reduced their levels below 150 mg/dL by 12-weeks. Likewise, among women who were identified as being pre-diabetic based on fasting glucose or hemoglobin A1c levels, all were within normal range at 12-weeks. 6-month testing will be completed in August. Among the 15 women eligible for 6-month testing, 8 (53%) completed the testing. Of those, 7 (88%) maintained their positive results. CONCLUSIONS: Bio-individualized food choices based on glucose response combined with culturally-sensitive nutrition counseling may provide a feasible mechanism for sustainable weight loss in a population at high-risk of metabolic dysfunction. However, to increase adherence, a tapering strategy should be developed after the first 12-weeks of health counseling.

Citation Format: Clague DeHart J, Rosen C, Wong L, Moore S, Flores S, Salehian B, Mortimer J. Pancreatic nutrition program (PNP): A novel weight reduction program for breast cancer survivors [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-13-06.

YaliBricks, a versatile genetic toolkit for streamlined and rapid pathway engineering in Yarrowia lipolytica

Effective metabolic engineering of microorganisms relies on balanced expression of both heterologous and endogenous genes to channel metabolic flux towards products of interest while achieving reasonable biomass buildup. To facilitate combinatorial pathway engineering and facile genetic operation, we engineered a set of modular cloning vectors compatible with BioBrick standards, called YaliBricks, to allow for rapid assembly of multigene pathways with customized genetic control elements (promoters, intronic sequences and terminators) in the oleaginous yeast Yarrowia lipolytica. We established a sensitive luciferase reporter and characterized a set of 12 native promoters to expand the oleaginous yeast genetic toolbox for transcriptional fine-tuning. We harnessed the intron alternative splicing mechanism and explored three unique gene configurations that allow us to encode genetic structural variations into metabolic function. We elucidated the role of how these genetic structural variations affect gene expression. To demonstrate the simplicity and effectiveness of streamlined genetic operations, we assembled the 12 kb five-gene violacein biosynthetic pathway in one week. We also expanded this set of vectors to accommodate self-cleavage ribozymes and efficiently deliver guide RNA (gRNA) for targeted genome-editing with a codon-optimized CRISPR-Cas9 nuclease. Taken together, the tools built in this study provide a standard procedure to streamline and accelerate metabolic pathway engineering and genetic circuits construction in Yarrowia lipolytica.

Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression

Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5'UTR, terminator and trans-activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5'UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans-activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.

Renal transplantation outcomes following heart and heart-lung transplantation

BACKGROUND

Chronic kidney disease is a frequent complication following heart and combined heart-lung transplantation. The aim of this study was to analyse the outcome of a subsequent renal transplant in heart, lung and heart-lung transplantation recipients.

METHODS

All heart, lung and heart-lung transplant recipients who received a subsequent renal transplant over a 27-year period in a national heart and lung transplant centre were included in this study.

RESULTS

A total of 18 patients who had previously undergone heart (n = 6), lung (n = 7) and heart-lung (n = 5) transplantation received a renal transplant. The mean duration to development of end-stage kidney disease (ESKD) was 115 ± 45.9 months. The most common contributor to ESKD was calcineurin inhibitor nephrotoxicity. The 5-year patient survival and graft survival rates were 91.7 and 85.6%, respectively. The median creatinine level at the most recent follow-up was 123 μmol/L, IQR 90.8-147.5.

CONCLUSIONS

The overall outcome of renal transplantation following previous non-renal solid organ transplantation is excellent considering the medical complexity and co-morbidities of this patient population. Renal transplantation represents an important treatment option for ESKD in non-renal solid organ transplant recipients.

Data from a pre-publication independent replication initiative examining ten moral judgement effects

We present the data from a crowdsourced project seeking to replicate findings in independent laboratories before (rather than after) they are published. In this Pre-Publication Independent Replication (PPIR) initiative, 25 research groups attempted to replicate 10 moral judgment effects from a single laboratory's research pipeline of unpublished findings. The 10 effects were investigated using online/lab surveys containing psychological manipulations (vignettes) followed by questionnaires. Results revealed a mix of reliable, unreliable, and culturally moderated findings. Unlike any previous replication project, this dataset includes the data from not only the replications but also from the original studies, creating a unique corpus that researchers can use to better understand reproducibility and irreproducibility in science.

Abstract PD6-05: Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response

Although defects in cancer susceptibility genes within the DNA-damage response (DDR) machinery including BRCA1 and BRCA2 account for only 5-10% of all breast cancer cases, these defects are highly penetrant and significantly increase the risk of breast (60-80%) and also ovarian (35%) cancers [1]. Together with defects in the DNA-damage sensor ATM, apoptosis effector TP53, and PTEN and CDH1 with roles in regulation of DDR, these account for considerable proportions of sporadic breast (63%) and ovarian (85%) cancers. To compensate for these DDR defects and to avoid cell death triggered from a genomic catastrophe, cancer cells rewire their DDR network while also selecting (during clonal expansion) the optimal combination of oncogenic events. Deciphering these combinations of events would aid in mapping the vulnerabilities of cancer cells harbouring defects in DDR.

While there have been several studies screening for essentiality of genes across DDR-deficient cell-lines, the essential genes so identified are either restricted only to these cell-line models or are not frequently (over)expressed in cancers. Here, we observe that oncogenic events that are mutually exclusive to DDR defects in large proportions of cancers constitute the (clonally) selected combinations that are amenable to cancer-cell survival, and therefore by systematically mining for these events, we infer vulnerability genes that if targeted in conjunction with DDR defects could induce a genomic catastrophe and trigger cancer-cell death.

Using data from DNA copy-number and mRNA-expression profiles we infer vulnerability genes that are mutually exclusive to defects in six DDR genes ATM, BRCA1, BRCA2, CDH1, PTEN and TP53 across four cancers (total 3980 samples) – breast (2029), prostate (623), ovarian (828) and uterine (500) from The Cancer Genome Atlas. Interestingly, across the four cancers these vulnerability genes form the most combinations with BRCA2 (59.02%), followed by CDH1 (24.59%), PTEN (8.20%) and TP53 (8.19%) at p<0.01 (1-hypergeometric test), whereas these show distinct patterns within the individual cancers: combinations dominated by CDH1 (90%) in breast, PTEN (78.38%) and BRCA2 (16.82%) in prostate, and BRCA1 (71.94%) and TP53 (16.21%) in ovarian cancers. Validation using GARP (Gene Activity Rank Profile)-score data from essentiality screens [2] from ten breast cancer cell lines (HCC1143, HCC1187, HCC1395, HCC1419, HCC1428, HCC1500, HCC1806, HCC1954, HCC38, MCF7) which harbour defects in at least one of the six DDR genes shows remarkable agreement between the GARP rankings and our inferred vulnerabilities. Our inferred genes are significantly enriched (p<0.0001 X2 test) in the top quartile of the entire set of profiled (∼16000) essential genes in these screens. Moreover, Kaplan-Meier analysis using survival data from 1000 breast cancer patients shows considerable overexpression of these genes (e.g. TLK2 in 37% luminal cases) which correlates significantly (TLK2: p<0.0006; Grade 3 hazard ratio 2.5) with poor prognosis. Experimental validation of these genes using single- and double knockout with DDR in breast cancer cell lines is currently underway.

[1] Liu & Srihari et al., Nucl Acids Res 2014, 42(10):6106-27.

[2] Marcotte et al., Cancer Discov 2012, 2(2):172-89.

Citation Format: Srihari S, Singla J, Wong L, Simpson PT, Khanna KK, Ragan MA. Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD6-05.

Abstract P4-10-05: Changes in metabolic syndrome components in breast cancer patients receiving neoadjuvant or adjuvant chemotherapy

Purpose. We sought to determine the impact of (neo)adjuvant chemotherapy on metabolic syndrome (MetS) components and related anthropometric and metabolic biomarkers among premenopausal and postmenopausal early stage breast cancer patients.

Methods. Eighty-six women with early stage (I-III) breast cancer who were free from clinically diagnosed MetS (defined as 3 out of 5 components of MetS) and were planning to undergo chemotherapy, enrolled in the study. Participants were tested for MetS (blood pressure; BP, waist circumference; WC, fasting blood glucose; FBG, high-density lipoprotein cholesterol; HDL-C, and triglycerides; TG), anthropometrics (body weight; BW, percent body fat; BF, fat mass; FM), lipid profile (total cholesterol; TC, low-density lipoprotein cholesterol; LDL-C), glucose metabolism (insulin, homeostatic model- insulin resistance; HOMA-IR, glycosylated hemoglobin; HbA1c), and inflammation (C-reactive protein; CRP) within one week before and following the completion of chemotherapy. Fasting (12-hour) venous blood samples of the antecubital vein were drawn to measure glucose, insulin, lipid profile (TC, HDL-C, LDL-C, and TRI), HbA1c, and CRP. Blood samples were analyzed at the City of Hope Clinical Pathology Laboratory. Insulin resistance was calculated using the HOMA index: [(fasting glucose (mg/dL) x fasting insulin (mg/dL)/405]. Height, BW, and BP measurements were obtained by the nursing staff during pre-chemotherapy physical exams. Body composition (BF and FM) was measured using a portable hand-held bioelectrical impedance device (Omron®; Hoffman Estates, IL). WC was measured, using a fabric measuring tape, as the distance around the waist using the umbilicus as the reference point.

One-way analysis of covariance (ANCOVA) using SPSS version 18.0 was used to compare means adjusting for covariates such as age, race, type of chemotherapy, duration of chemotherapy, BMI at baseline, and menopausal status.

Results. The majority of the 86 women enrolled were Caucasian (44%) or Hispanic (30%), nonsmoking (96%), employed (84%), and well-educated (90%), with a mean age of 48.2 years. Women were most commonly undergoing Cytoxan/Adriamycin + Taxol (42%) or Taxotere/Cytoxan (36%) chemotherapy regimens, lasting on average 15.3 (±2.7) weeks. Overall the population was sedentary, averaging 7.2 (±5.8) minutes of physical activity/week.

Following chemotherapy, all MetS components and overall MetS score (out of 5) significantly increased (p<0.01). Additionally, BW, BF, FM, lipids (TC, LDL), glucose metabolism (HOMA-IR, insulin, HbA1c), and inflammation (CRP) significantly increased (p<0.01).

Conclusion. In women without MetS, (neo)adjuvant chemotherapy negatively altered MetS components, related anthropometrics, and biomarkers of glucose metabolism and inflammation, within 12 -18 weeks. Studies that test the impact of lifestyle interventions, such as diet and exercise, should be explored in this population of breast cancer patients to reduce the onset of MetS.

Citation Format: Dieli-Conwright CM, Wong L, Waliany S, Bernstein L, Salehian B, Mortimer JE. Changes in metabolic syndrome components in breast cancer patients receiving neoadjuvant or adjuvant chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-10-05.

Abstract P1-10-23: Bladder symptoms in women with newly diagnosed breast cancer

Background: Changes in bladder function are recognized effects of aging and menopause but have not generally been reported in women treated for breast cancer. We initiated a prospective trial to assess the impact of (neo) adjuvant therapy on women with early stage breast cancer.

Methods: Women with newly diagnosed invasive breast cancer who were to initiate (neo) adjuvant chemotherapy or endocrine therapy were approached for study participation. At baseline a urinalysis, urine culture, and self assessment quality of life questionnaires were completed. The Urogenital Distress Inventory (UDI-6) assesses bladder symptoms and the Incontinence Impact Questionnaire (IIQ-7) assesses the impact of bladder symptoms on quality of life. Three months after initiation of (neo)adjuvant therapy, the quality of life questionnaires were repeated. We report the results of the pretreatment questionnaires.

Results: Between February and June, 2015, forty-nine women with newly diagnosed breast cancer were enrolled on study. The median age was 54 (Range 25-78); 21 were premenopausal and 28 postmenopausal. Twenty nine (59%) were treated in the adjuvant setting; 12 with chemotherapy and 17 with endocrine therapy. Twenty patients, (41%) were treated in the neoadjuvant setting with chemotherapy. Prior to initiation of therapy, " Frequent urination" was reported in 38 (65%), " Leakage related to urgency" in 5 ( 10%), " Leakage with physical activity" in 32 (55%) and "Small amounts of leakage" in 32 (55%). Bladder symptoms impacted the ability to perform household chores in 8 (16%), Physical recreation in 10 (20%), social activities in 9 (18%), and Emotional health in 5 (10%).

Conclusions: Symptoms of bladder dysfunction are common in women with newly diagnosed breast cancer even before therapy is initiated.

Citation Format: Wong L, Chung C, Flores S, Mortimer J. Bladder symptoms in women with newly diagnosed breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-10-23.