Abstract GS5-05: Resistance to neoadjuvant chemotherapy in triple negative breast cancer mediated by a reversible drug-tolerant state

Approximately 50% of patients with localized triple negative breast cancer (TNBC) have substantial residual cancer burden following treatment with neoadjuvant chemotherapy (NACT), resulting in distant metastasis and death for most of these patients. While genomic and phenotypic intra-tumor heterogeneity are pervasive features of TNBCs at the time of diagnosis, the functional contributions of heterogeneous tumor cell populations to chemoresistance have not been elucidated.

To investigate tumor evolution accompanying NACT, we employed orthotopic patient-derived xenograft (PDX) models of treatment-naïve TNBC, which retain intra-tumor heterogeneity characteristic of human TNBC. We discovered that some PDX models initially exhibited partial sensitivity to standard front-line NACT (Adriamycin plus Cytoxan, AC). Following AC, residual tumors were resistant to chemotherapy but repopulated tumors with chemo-sensitive cells if left untreated, indicating that tumor cells possessed inherent plasticity. To identify the tumor cell subpopulation(s) conferring chemoresistance, we conducted barcode-mediated clonal tracking in three independent PDX models by introducing a high-complexity pooled lentiviral barcode library into PDX tumor cells which were then orthotopically engrafted into recipient mice. Strikingly, residual tumors maintained the same heterogeneous clonal architecture as naïve tumors. Concordantly, whole-exome sequencing revealed conservation of genomic subclonal architecture throughout treatment. These results were corroborated by genomic sequencing of serial biopsies pre- and post-AC obtained directly from TNBC patients enrolled on an ongoing clinical trial at MD Anderson (ARTEMIS; NCT02276443). Together, these studies revealed that genomically distinct pre-treatment subclones were equally capable of surviving AC to reconstitute tumors after treatment.

To identify functional addictions of residual tumor cells, we conducted histologic and transcriptomic profiling. Residual tumors following AC-treatment exhibited extensive fibrotic desmoplasia and tumor cell pleomorphism in both PDX models and in serial biopsies obtained from TNBC patients enrolled on the ARTEMIS trial. Strikingly, these AC-induced features were reverted upon regrowth of residual tumors in PDXs and in patients' tumors. Similarly, residual tumors exhibited unique transcriptomic features, many of which are also de-regulated in cohorts of human TNBCs undergoing chemotherapy treatment. These features were nearly completely reverted after tumors regrew, suggesting that the residual tumor state may be a unique and transient therapeutic window. Gene set enrichment analyses revealed that residual tumors had increased activation of oxidative phosphorylation and decreased glycolytic signaling. Pharmacologic targeting of oxidative phosphorylation with a small-molecule inhibitor of mitochondrial electron transport chain complex I (IACS-010759) significantly delayed the regrowth of AC-treated residual tumors in three independent PDX models. Collectively, these studies reveal that a reversible phenotypic state can confer chemoresistance in the absence of genomic selection and that the residual tumor state is a novel therapeutic window for chemo-refractory TNBC.

Citation Format: Echeverria GV, Ge Z, Seth S, Jeter-Jones SL, Zhang X, Zhou X, Cai S, Tu Y, McCoy A, Peoples M, Lau R, Shao J, Sun Y, Bristow C, Carugo A, Ma X, Harris A, Wu Y, Moulder S, Symmans WF, Marszalek JR, Heffernan TP, Chang JT, Piwnica-Worms H. Resistance to neoadjuvant chemotherapy in triple negative breast cancer mediated by a reversible drug-tolerant state [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr GS5-05.

Abstract GS6-06: Identifying metastatic drivers in patient-derived xenograft models of triple negative breast cancer

Metastases are responsible for the vast majority of deaths due to breast cancer. Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by high rates of metastasis and poor prognosis. We are employing patient derived xenograft (PDX) models of TNBC to identify drivers of metastasis. Tumor samples are obtained from the breast tumors of patients with TNBC and engrafted immediately into the humanized mammary fat pads of immune compromised mice. Lentiviral transduction was employed to express bioluminescent and fluorescent markers in two independent PDX models of TNBC. Using these models, we demonstrated that human breast tumors are capable of completing all stages of the metastatic cascade in mice, and metastatic lesions are observed in organs normally found in patients with metastatic breast cancer including lung, liver, bone, brain, and lymph nodes. Dynamic and reversible epithelial to mesenchymal transition (EMT) was observed as tumors metastasized to lung and were re-passaged to recipient mouse mammary glands. Lung metastases were isolated using bioluminescence imaging and lung metastasis gene expression signatures were generated. Metastasis signatures from two independent PDX models were compared to identify genes that were commonly de-regulated in lung metastases relative to corresponding mammary tumors. Comprehensive gain-of-function screens were then conducted in vivo to identify functional drivers of TNBC metastasis. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) was identified as a metastatic driver in this screen. CEACAM5 mRNA and protein levels were elevated in lung metastases relative to corresponding mammary gland tumors in mice. In addition, we demonstrated that CEACAM5 expression was upregulated in the lung metastases of breast cancer patients, and its expression inversely correlated with patient survival. Our data indicate that the metastatic function of CEACAM5 is to promote growth of breast tumors in the lung by inducing MET (mesenchymal to epithelial transition).

Citation Format: Powell E, Shao J, Picon HM, Ge Z, Echeverria GV, Peoples M, Bristow C, Cai S, Tu Y, McCoy AM, Piwnica-Worms D, Draetta G, Edwards JR, Moulder SL, Symmans WF, Heffernan TP, Liang H, Piwnica-Worms H. Identifying metastatic drivers in patient-derived xenograft models of triple negative breast cancer [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 GS6-06.

Abstract P6-01-08: Identifying metastatic drivers in patient derived xenograft models of triple negative breast cancer

Metastases are responsible for the vast majority of deaths due to breast cancer. Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by high rates of metastasis and poor response to chemotherapy. We are using patient derived xenograft (PDX) models of TNBC to identify drivers of TNBC metastasis. Using these models, we demonstrated that human breast tumors are capable of completing all stages of the metastatic cascade in mice, and metastatic lesions are observed in organs normally found in patients with metastatic breast cancer including lung, liver, bone, brain and lymph nodes. Lentiviral transduction was employed to express both bioluminescent and fluorescent proteins in three distinct PDX models of TNBC. In this way, metastatic lesions can be isolated using bioluminescent imaging and circulating tumor cells (CTCs) are isolated by flow cytometry. A lung metastasis gene expression signature was generated and comprehensive gain-of-function screens are being conducted in vivo to validate this signature and identify functional drivers of TNBC metastasis.

Citation Format: Powell E, Shao J, Tieu T, Peoples M, Bristow C, Manyam G, Cai S, Tu Y, Edwards JR, Heffernan TP, Piwnica-Worms D, Liang H, Piwnica-Worms H. Identifying metastatic drivers in patient derived xenograft models of triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-01-08.

141 DEVELOPMENT OF rLENTIVIRAL VECTORS FOR MALE GERMLINE-SPECIFIC Cre RECOMBINASE EXPRESSION IN LIVESTOCK

Transgenic livestock have been used as biomedical models and have the potential to increase production characteristics. Unfortunately, some of the tools used to confirm genetic modification (transgenesis) are unacceptable in terms of public image. One key component is a fluorescent marker confirming foreign gene insert. The fluorescent protein benefits the researchers producing and selecting transgenic animals but is not required for the enhancement of the animal. Removal of the fluorescent marker can be accomplished by employing the Cre-lox recombination system. By using this system one can produce male genetically modified animals that express the enhanced trait in addition to the fluorescent marker, but their sperm only contain the portion of the transgene that represents the enhanced production trait. As a result, offspring derived from these animals exhibit the desired production trait but not the fluorescent marker. The goal of this research was to develop rlentiviral vectors that use the gamete-specific promoter stimulated by retinoic acid 8 (Stra8) to drive expression of Cre recombinase. The base rlentiviral vector we chose to use was pLB. It is ideal for this research because it has a U6 promoter to drive expression of a short hairpin RNA for an enhanced production trait, as well as Lox P sites flanking a cytomegalovirus-green fluorescent protein (CMV-GFP) expression cassette. Initially we identified and PCR amplified a 400-bp mouse Stra8 promoter and a 1.5-kb promoter region of the pig. The Stra8 promoters were integrated into the pLB vector directly upstream of the green fluorescent protein (GFP). These intermediate vectors should have germline-specific expression of GFP and are the first vectors using a pig Stra8 promoter. Next, we PCR amplified and inserted the coding sequence for Cre recombinase into these vectors for germline-specific Cre expression resulting in the first pig Stra8-Cre expression vector. The Lox P sites of this vector are flanking the GFP expression cassette as well as the Str8-Cre expression cassette. To confirm the functionality of the Cre-lox recombination system, the pLB vectors were transfected into human embryonic kindey 293T cells and fluorescence was measured. After Day 2, a Cre expression plasmid was transfected and 3 days post-Cre transfection, fluorescence was measured again. A decrease in fluorescence and GFP positive cell numbers was observed, thus confirming the functionality of the Cre-lox recombination event for these vectors. These vectors will be used to produce transgenic animals by lentiviral transgenesis. Our laboratory has been successful in using this method to produce transgenic livestock. The transgenic animals will be analysed to confirm male germ-cell-specific expression of Cre as well as removal of the GFP fluorescence. If successful, these will be the first transgenic animals using a pig Stra8 promoter for Cre expression for a novel single rlentiviral vector Cre-lox recombination system.

5 PRODUCTION OF TRANSGENIC LIVESTOCK USING A LENTIVIRUS EXPRESSING MULTIPLE SHORT INTERFERING RNAs TARGETING FOOT AND MOUTH DISEASE VIRUS

One goal of transgenic livestock production is developing animals with enhanced production characteristics. Transgenic animals with resistance to viral disease could greatly reduce economic losses. The use of short interfering RNA (siRNA) or short hairpin RNA (shRNA) targeting viral genomes have shown great promise in vitro for both human and animal applications. However, because of the rapid mutation rate, viruses are able to escape single siRNA inhibition. One method to reduce the chances of a functional escape virus is to target its genome with multiple shRNAs simultaneously. The goal of this research project was to produce a recombinant lentiviral vector that expresses three unique shRNAs targeting different regions of the foot and mouth disease virus (FMDV) and use it to produce transgenic livestock. In these initial experiments we used the goat as our model system. Previously, we confirmed that three distinct siRNAs individually could reduce the ability of the FMDV virion to replicate in vitro. Based upon these results we produced a recombinant lentiviral vector that utilised three bovine Pol III promoters (7sk, H1, U6-2), each transcribing a different effective shRNA targeting FMDV. In addition, the vector also contained the fluorescent marker zsGreen and an antibiotic resistance gene. The lentiviral vector was co-transfected with pCMV and pMDG into 293T cells to produce replication incompetent retroviral particles. The supernatant was collected and ultra-centrifuged (50 000 × g for 1.5 h) to concentrate the viral particles resulting in a high-titer viral preparation (>109 mL–1 infective viral particles). To produce the transgenic caprine offspring, three embryo donors were superovulated and naturally bred. Nineteen zygotes were surgically collected from the oviduct 24 h after mating. Recombinant lentivirus was microinjected into the zygote perivitelline space. Immediately following the injections, four goat embryos were surgically transferred into the oviduct of each synchronized recipient. Pregnancy was determined by ultrasound at Day 30 in 2 of 5 recipients that received embryos. One pregnancy was carried to term resulting in triplets; 1 live birth, and 2 stillborn. The placenta and tissue sample of the live goat both contained a subpopulation of zsGreen positive cells when analysed with fluorescent microscopy. A fibroblast cell line was derived from the tissue sample and placed under antibiotic selection. Results indicate that only the fluorescent cells also expressed a resistance to antibiotic selection. RNA was collected from the fibroblast cells and mature shRNA production was confirmed using the QuantiMir kit (System Biosystems). Expression of all 3 mature shRNAs was verified in these cells. This data further supports that the entire transgene was integrated into the genome. This is the first report of transgenic livestock produced that expresses multiple shRNAs targeting a viral genome.

4 CHARACTERIZATION OF LENTIVIRAL SHORT-HAIRPIN RNA EXPRESSION VECTORS CONTAINING SINGLE OR MULTIPLE BOVINE POLYMERASE III PROMOTERS

Lentiviral vectors have become an important and efficient molecular biology tool to integrate foreign DNA into target genomes. These vectors have been previously used in our laboratory to make cloned transgenic fetuses expressing short-hairpin RNAs (shRNAs) targeting the caprine prion mRNA (Golding et al. 2006 Proc. Natl. Acad. Sci. USA 103, 5285-5290) and bovine myostatin mRNA. Specially designed shRNAs have a robust ability to decrease protein expression by initiating a mRNA destruction pathway or by translational inhibition. However, initial experiments targeting foot and mouth (FMDV) viral RNA have indicated that polymerase (Pol) II promoters may be unable to produce enough mature shRNA particles to significantly knock down viral replication in vitro. The goal of this research project was to identify and utilize bovine Pol III promoters to express shRNAs in lentiviral vectors and to express multiple unique shRNAs from a single lentiviral vector using different Pol III promoters. This goal is particularly important to the successful reduction of FMDV replication in a cell, as it limits random mutations from escaping the shRNA-mediated viral genome destruction. The 3 bovine Pol III promoters we selected were 7sk, U6-2, and H1. They were individually amplified from the same genomic DNA preparation. The promoters were inserted immediately upstream of our shRNA expression sequence, resulting in lentiviral vectors designated GT-b7sk, GT-bU6-2, and GT-bH1.To confirm that the promoters were functional, a luciferase reporter assay was performed in HEK 293T cells, where each vector expressed either a shRNA targeting luciferase (luc) or a non-specific shRNA.All promoters expressing luc shRNA resulted in significant reduction of luciferase activity between 68 and 80% compared with non-targeting controls. In addition, there was no significant difference between Pol III promoters when analyzing reduced luciferase activity. In the second phase of the study, we developed 7 unique combinations of 2 or 3 Pol III shRNA expression cassettes to test individual shRNA function with one shRNA designed to target luciferase and the others non-targeting. In multiple Pol III expression constructs, the U6-2 and 7sk promoters resulted in the greatest reduction of luciferase activity at 89 and 95%, respectively. In addition, luciferase activity was reduced to the greatest extent when the luc shRNA was expressed from the second (82%) or third (87%) Pol III cassette. Overall, bovine Pol III-based promoters are effective at expressing shRNAs from a lentiviral vector. In addition, multiple Pol III shRNA expression cassettes can be inserted into a single lentiviral vector and still achieve significant reduction of target protein. These vectors will be used to create transgenic cattle and pigs that express multiple shRNAs targeting the FMDV genome with hopes of creating animals that are resistant to FMDV.

5 INHIBITION OF FOOT AND MOUTH DISEASE VIRUS IN VITRO USING RNA INTERFERENCE

The use of short-hairpin RNA (shRNA) targeting viral genomes has shown great promise in human medicine and in vitro research in animal agriculture. However, this research has not been extrapolated into livestock applications. Foot and mouth disease virus (FMDV) is a world-wide disease resulting in decreased production and export limitations in countries with endemic FMDV, as well as severe economical impacts if an outbreak occurs in an FMDV-free country. The long-term goal for this project is to produce transgenic cattle that express shRNA targeting the FMDV genome resulting in resistance to infection. As a starting point, five siRNA and one non-targeting control siRNA (Null) were developed targeting different highly conserved regions of a FMDV type-A based replicon. The siRNA were transfected into BHK cells 48 h before viral RNA challenge. Eighteen hours post challenge the cells were lysed and analyzed. Three siRNA targeting the non-structural polymerase protein exhibited severe knockdown of 87, 90, and 92% when compared with the Null siRNA transfected control. The siRNA targeting the VPG3 cap protein reduced activity by 59%, and the siRNA targeting the internal ribosomal entry site had a minimal effect of 15% reduction. Based upon these results, we produced recombinant lentiviral particles designed to deliver the shRNA sequence targeting the FMDV genome and the fluorescent marker, dsRed, into a bovine fetal fibroblast cell line. This transgenic cell line expressing the most effective shRNA (based on initial siRNA screening) was used for somatic cell nuclear transfer to create bovine embryos. One hundred and sixty oocytes were enucleated, of which 149 had successful fusion resulting in 35 blastocysts after in vitro culture. Two embryos per recipient were transferred into five recipients. At Day 40 of pregnancy three of the five recipients had a fetus, but no heart beat could be detected. We are currently in the process of creating another cell line and repeating this experiment. If successful, transgenic calves will be visually and genetically analyzed for expression of dsRed and shRNA targeting FMDV. Transgenic and control animals/tissues will then be analyzed for resistance to infection with FMDV.

177 EXPRESSION PROFILING OF HISTONE-MODIFYING GENES IN BOVINE PREIMPLANTATION EMBRYOS

Global activation of the embryonic genome marks one of the most important aspects of early embryonic development and coincides with both global DNA and histone modifications necessary to control gene expression for further development. In bovine preimplantation embryos, epigenetic reprogramming occurs between fertilization and the blastocyst stage. De novo DNA methylation from the 8-cell stage to the morula represents activation of DNA methyltransferases and histone-modifying genes; however, it is still unclear how these critical events of early development and differentiation are regulated. In this preliminary study, we used quantitative real-time PCR (qRT-PCR) to examine stage-specific expression in bovine gametes (testis and ova) and preimplantation embryos of eight histone-modifying genes: LSH1 (which associates with both DNA and histone methyltransferases), LSD1 (a histone demethylase), SUV39H1, SUV420H1, SETB1, SUZ12, SMYD3, and G9a (all representative histone methyltransferases). Bovine ova and embryos were produced via in vitro maturation, fertilization, and culture from a single pool of ova as per standard laboratory protocol. Testes were harvested from a mature bull and immediately snap frozen in liquid nitrogen. RNA was isolated from testis, and groups of 10–15 in vitro-matured bovine ova or in vitro-produced embryos at the 2-, 8-cell, morula, and blastocyst stages and stored at –80�C until further use. cDNA was generated from each RNA sample using Superscript II" reverse transcriptase (Invitrogen, Carlsbad, CA, USA) under identical PCR conditions. Relative gene expression from each RNA sample was calculated in triplicate using the ΔΔCt method with both SYBR� Green and Taqman� qRT-PCR methods (Applied Biosystems, Foster City, CA, USA) and normalized to endogenous bovine GAPDH expression as per standard protocol. Due to excessive variation in a few of the qRT-PCR reactions, consistent data were collected for only SETB1, SUV39H1, SUV420H1, and G9a. SETB1 and G9a shared a similar expression pattern, with both exhibiting a dramatic relative increase in transcript level near the 8-cell stage and reduction to basal levels thereafter. Also, SUV39H1 and SUV420H1 were similar, showing a gradual increase in relative expression from the oocyte to the 8-cell stage, followed by a drop to low levels by the morula stage. These data indicate that several histone-modifying genes are expressed in distinct patterns during the critical period of zygotic genome activation and establishment of the epigenome in early preimplantation bovine embryos. Continuing studies will determine specific gene function through shRNA-induced silencing of histone-modifying genes and their role in control of gene expression.

Nursing personnel's perceptions of physical restraint use in long-term care

The use of physical restraints as an accepted clinical intervention was dramatically changed by enactment of legislation in the United States. As a result, nursing personnel's notions of restraints as a therapeutic intervention were challenged. This study was initiated to obtain a better understanding of the underlying motivations for restraint use as a clinical intervention and to provide data helpful to nursing staff as they make the transition to restraint-free care. In the study, 124 long-term-care nursing personnel were surveyed regarding their perceptions of restraint use, and were asked whether or not they would recommend using restraints in selected clinical situations. Results of stepwise regression showed that 40% of the variation in the recommendation to use restraints can be explained by the type of nursing personnel (licensed nurse vs. nursing assistant), liability and treatment concerns related to restraint use, age of the nursing staff, and a belief that reducing restraints increases the need for psychoactive medications.