Abstract 6130: Cancer sensitivity to therapy is constrained by apoptosis regulation in cells of origin

Many chemotherapeutic agents target cellular components or processes that are present in all cancers, yet clinical responses to these agents vary greatly between cancer types and even patient age - the basis for these broad-scale differences are unclear. The vast majority of targeted and cytotoxic cancer therapies including ionizing radiation produce pro-apoptotic signaling in exposed cells, suggesting that the mitochondrial apoptosis sensitivity of cancer cells could act as a central signaling “node” to broadly impact therapy outcomes. To test this, we used BH3 profiling and complementary chemosensitivity assays to analyze hundreds of primary cancer specimens across twelve major cancer types. We find that cancers with typically favorable outcomes including certain hematologic malignancies, testicular cancer, and some pediatric cancers contain mitochondria that are highly primed for apoptosis, which renders them hypersensitive to cytotoxic as well as targeted agents and radiation therapy. Priming levels in many epithelial cancers including ovarian cancer and non-small cell lung cancer are highly heterogeneous, mirroring their variability in clinical outcomes. Finally, many tumor types that are typically chemoresistant including adult soft tissue sarcomas, hepatocellular carcinoma and pancreatic cancer are almost completely resistant to pro-apoptotic signaling. By analyzing in vitro and in vivo pancreatic, ovarian, hepatocellular and sarcoma tumorigenesis models, we find that apoptotic priming generally increases during neoplastic transformation, in part due to consistent upregulation of pro-apoptotic proteins BAX and BAK. However, the level of apoptotic priming in cancer cells is constrained by the baseline apoptosis sensitivity of normal cells prior to transformation. Remarkably, we find that apoptotic priming is dynamically regulated by cell lineage and differentiation state but can also be modulated by oncogenes. For instance, Myc activation typically increases apoptotic priming while activation of mutant Ras signaling decreases it - these changes in priming alter the chemosensitivity of cancer cells. Finally, we use inducible mouse tumor models to demonstrate that neoplastic transformation of cells from developmentally immature tissues yields pediatric tumors that are more primed for apoptosis than equivalent tumors arising in adults. This difference in priming causes pediatric tumors to be more sensitive to front-line therapies and BH3 mimetics targeting pro-survival BCL-2 family proteins in vitro and in vivo. Thus, lineage-determined regulation of apoptosis prior to and during neoplastic transformation leads to broad-scale differences in cancer cell chemosensitivity and can be exploited therapeutically by targeting BCL-2 family proteins.

Citation Format: Cameron Fraser, Xingping Qin, Kenichi Shimada, Johan Spetz, Mary Heather Florido, Rumani Singh, Stacey Yu, Adam Presser, Zintis Inde, Gaurav Joshi, Jennifer Guerriero, Francisco Sanchez-Rivera, Alison Karst, Omar Lopez, Chendi Li, Peter Winter, Ying Yue, Peter Sorger, Jingwei Cheng, Izidore Lossos, Aaron Hata, Ronny Drapkin, Adam Palmer, James Decaprio, Manisha Thakuria, Charles Yoon, Ursula Matulonis, Matthew Meyerson, Elizabeth Stover, Diana Cardona, Kris Wood, Shayna Sarosiek, David Kirsch, Joseph Mancias, Andrew Cherniack, Anthony Letai, Kristopher Sarosiek. Cancer sensitivity to therapy is constrained by apoptosis regulation in cells of origin. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6130.

The Translational and Regulatory Development of an Implantable Microdevice for Multiple Drug Sensitivity Measurements in Cancer Patients

OBJECTIVE

The purpose of this article is to report the translational process of an implantable microdevice platform with an emphasis on the technical and engineering adaptations for patient use, regulatory advances, and successful integration into clinical workflow.

METHODS

We developed design adaptations for implantation and retrieval, established ongoing monitoring and testing, and facilitated regulatory advances that enabled the administration and examination of a large set of cancer therapies simultaneously in individual patients.

RESULTS

Six applications for oncology studies have successfully proceeded to patient trials, with future applications in progress.

CONCLUSION

First-in-human translation required engineering design changes to enable implantation and retrieval that fit with existing clinical workflows, a regulatory strategy that enabled both delivery and response measurement of up to 20 agents in a single patient, and establishment of novel testing and quality control processes for a drug/device combination product without clear precedents.

SIGNIFICANCE

This manuscript provides a real-world account and roadmap on how to advance from animal proof-of-concept into the clinic, confronting the question of how to use research to benefit patients.

A phase 2, two-stage study of avelumab and axitinib in patients with mismatch repair proficient (MMR-P) recurrent or persistent endometrial cancer (EC)

TPS5609

Background: Despite significant strides in understanding the molecular pathogenesis of EC, there remain few effective therapies for recurrent disease. Deeper insight into the roles of disordered tumor vasculature and HIF1α- and VEGF-mediated immunosuppressive effects on myeloid-derived suppressor cells, T-cells, and PD-L1 expression contributed to the development of new targeted regimens. Activity of pembrolizumab and lenvatinib was demonstrated in a phase 2 trial in MMR-P EC (NCT02501096). By inhibiting VEGF receptor (VEGFR) and PD-L1 signaling, immunologically “cold” tumors may become inflamed. However, there are concerns regarding the toxicity of pembrolizumab/lenvatinib and alternatives are sought. The combination of the anti-PD-L1 antibody avelumab with axitinib, an inhibitor of VEGFR 1-3 and PDGFR with more potent IC50 inhibitory activity than lenvatinib, has also shown synergistic activity and is FDA approved as first line treatment for patients with renal cell cancer. We therefore hypothesized that this combination would be well tolerated and efficacious in recurrent MMR-P EC. Methods: This is an investigator-initiated, phase 2, two-stage single cohort trial evaluating avelumab with axitinib in recurrent or persistent EC. Participants must have MMR-P EC of any histology and have received at least one chemotherapeutic regimen, with no upper limit on the number of prior lines received. Prior use of immune checkpoint (IC) inhibitors is excluded. Treatment consists of avelumab 800mg IV every 2 weeks and axitinib 5mg orally twice daily. Co-primary endpoints are progression-free survival at 6 months (PFS6) and objective response rate by RECIST 1.1. Translational objectives include characterization of tumor-infiltrating lymphocytes, infiltrating myeloid cells, expression of IC markers, and whole exome sequencing to evaluate mutations in genes related to DNA repair and immunologic response. This is a two-stage design in the method of Sill et al, with 16 participants anticipated in stage 1 and 19 participants in stage 2, for a total of 35 participants. Accrual is ongoing. Clinical trial information: NCT02912572.

A phase 2, two-stage study of mirvetuximab soravtansine (IMGN853) in combination with pembrolizumab in patients with microsatellite stable (MSS) endometrial cancer (EC)

TPS5611

Background: Folate receptor-alpha (FRα) is expressed on endometrial cancer (EC) cells and is associated with poor prognosis. Mirvetuximab soravtansine (ImmunoGen), an antibody drug conjugate (ADC) comprising a FRα-binding antibody, cleavable linker, and the tubulin-disrupting maytansinoid DM4, showed tolerability and single agent activity in a Phase 1 study with dose expansion in FRα+ advanced/recurrent EC (NCT01609556) and also when combined with chemotherapy, bevacizumab as well as pembrolizumab (NCT02606305). In addition to having direct target-mediated cytotoxicity, ADCs also stimulate the local tumor immune microenvironment. Mirvetuximab soravtansine has been shown to activate monocytes and promote phagocytosis of mirvetuximab-treated FRα-positive tumor cells through a mechanism of Fc-FcγR interaction. Further, the combination of ADCs with immune checkpoint inhibitors (ICI) can overcome primary resistance to immunotherapy in murine models. Given the low response of MSS endometrial cancers to PD-1 blockade, we hypothesized that addition of mirvetuximab may enhance response of these tumors to immunotherapy. Methods: This is a Phase 2, single cohort study of mirvetuximab soravtansine with pembrolizumab in recurrent or persistent EC. Patients must have advanced or recurrent MSS serous endometrial cancer with at least 1 and up to 3 prior lines of therapy. Confirmation of FRα expression (with PS2+ staining intensity in ≥ 50% of cells, performed centrally at Ventana Medical Systems, Inc) is required. Prior receipt of ICI is excluded. Patients will receive the combination of mirvetuximab soravtansine 6 mg/kg AIBW IV and pembrolizumab 200 mg IV administered every 21 days. The co-primary endpoint is progression-free survival at 6 months (PFS6) and objective response rate (ORR) by RECIST 1.1. Translational objectives include assessment of tumor infiltrating lymphocytes (TILs), expression of immune checkpoint markers, and whole exome sequencing (WES) for DNA repair pathway mutations, neoantigens, and polymorphisms in immunologically relevant genes. Statistical considerations are for a Simon two-stage optimal design with 16 patients in Stage 1 and 19 patients in Stage 2, to a total of 35. Prespecified activity for the first stage of accrual was met, and second stage accrual began November 2020. Clinical trial information: NCT03835819.

Homologous recombination deficiency real-time clinical assays, ready or not?

Cancers with deficiencies in homologous recombination-mediated DNA repair (HRR) demonstrate improved clinical outcomes and increased survival. Approximately 50% of high-grade serous ovarian cancers (HGSOC) exhibit homologous recombination deficiency (HRD). HRD can be caused by germline or somatic mutations of genes involved in the HR pathway. Given platinum-based chemotherapy and poly (ADP-ribose) polymerase inhibitors (PARPis) are used in HGSOC, double-strand breaks (DSBs) are common. Unrepaired DSBs are toxic to cells as genomic instability ensues and cells eventually die. Thus, tumor cells with DSBs utilize the high-fidelity HRR as one of the central pathways for repair. In tumors that have HRD, an alternate pathway such as non-homologous end-joining (NHEJ) is used and leads to error-prone repair. To date, methods for clinical detection of homologous recombination deficiency (HRD) are limited to genomic changes of HRR genes and genomic mutation patterns resulting from HRD genes involved in HR-mediated DNA repair. However, these tests detect genomic scars that might not always correlate well with PARP inhibitor or platinum sensitivity in the current state. Therefore, a functional HRD assay should be able to more accurately predict tumor response in real-time. RAD51 foci formation has been used as a functional assay to define HRD and closely correlates with chemotherapy and PARPi sensitivity. The inability to form RAD51 foci is a common feature of HRD. DNA damage can also cause transient slowing or stalling of replication forks defined as replication stress. Replication fork stalling can lead to fork degradation and decreased cell viability if forks do not resume DNA synthesis. Fork degradation has been found to lead to chemosensitivity in BRCA-deficient tumors. To determine this fork degradation phenotype, replication fork/DNA fiber assays are utilized. This review will highlight functional assays for HRD in the context of translating these to real-time clinical assays.

Phase II Study of Avelumab in Patients With Mismatch Repair Deficient and Mismatch Repair Proficient Recurrent/Persistent Endometrial Cancer

PURPOSE

Despite the tissue-agnostic approval of pembrolizumab in mismatch repair deficient (MMRD) solid tumors, important unanswered questions remain about the role of immune checkpoint blockade in mismatch repair-proficient (MMRP) and -deficient endometrial cancer (EC).

METHODS

This phase II study evaluated the PD-L1 inhibitor avelumab in two cohorts of patients with EC: (1) MMRD/POLE (polymerase ε) cohort, as defined by immunohistochemical (IHC) loss of expression of one or more mismatch repair (MMR) proteins and/or documented mutation in the exonuclease domain of POLE; and (2) MMRP cohort with normal IHC expression of all MMR proteins. Coprimary end points were objective response (OR) and progression-free survival at 6 months (PFS6). Avelumab 10 mg/kg intravenously was administered every 2 weeks until progression or unacceptable toxicity.

RESULTS

Thirty-three patients were enrolled. No patient with POLE-mutated tumor was enrolled in the MMRD cohort, and all MMRP tumors were not POLE-mutated. The MMRP cohort was closed at the first stage because of futility: Only one of 16 patients exhibited both OR and PFS6 responses. The MMRD cohort met the predefined primary end point of four ORs after accrual of only 17 patients; of 15 patients who initiated avelumab, four exhibited OR (one complete response, three partial responses; OR rate, 26.7%; 95% CI, 7.8% to 55.1%) and six (including all four ORs) PFS6 responses (PFS6, 40.0%; 95% CI, 16.3% to 66.7%), four of which are ongoing as of data cutoff date. Responses were observed in the absence of PD-L1 expression. IHC captured all cases of MMRD subsequently determined by polymerase chain reaction or genomically via targeted sequencing.

CONCLUSION

Avelumab exhibited promising activity in MMRD EC regardless of PD-L1 status. IHC for MMR assessment is a useful tool for patient selection. The activity of avelumab in MMRP/non-POLE-mutated ECs was low.

Genomic biomarkers of recurrence in low-grade, early-stage endometrial adenocarcinoma

5588

Background: Endometrial cancer is the most common gynecologic malignancy in developed countries with over 60,000 new cases diagnosed in the United States each year. Adjuvant therapy is often omitted for low-risk, early-stage disease (FIGO stage IA, grade 1) but 1 in 20 women suffer recurrence after surgery alone. Hence, there is an important need for biomarkers of recurrence in this population to guide therapeutic management. Methods: We retrospectively analyzed 74 patients with FIGO stage 1A, grade 1 endometrial endometrioid adenocarcinoma treated at our institution with hysterectomy alone between 2009-2016. All patients had targeted genomic assessment of their tumors (OncoPanel; somatic mutations, copy number variations and structural variants across 300 cancer genes). The primary outcome of interest was freedom from recurrence (FFR). Outcomes were compared by the logrank test and survival estimates calculated by Kaplan-Meier method. Results: We identified 14 patients who recurred at a median time of 23.6 months after surgery and 60 patients without recurrence at a median follow-up of 38.9 months. Age (median 57 years; log-rank p = 0.91) and BMI (median 31 kg/m2; log-rank p = 0.21) were not associated with risk of recurrence. The median somatic mutation count in the cohort was 8. Patients with more than 8 somatic mutations had a significantly higher risk of recurrence (3-year FFR: 74% vs 90%; log-rank p = 0.004). At the level of individual genes, there were four genes that were significantly associated with recurrence: CTNNB1 (p = 0.046), RHPN2 (p = 0.020), SF1 (p = 0.044), SQSTM1 (p = 0.034). Patients with a mutation in one or more of these four genes had a significantly higher risk of recurrence (3-year FFR: 62% vs 93%; log-rank p = 0.0004). Conclusions: We have identified overall somatic mutation burden and mutations in a subset of four genes ( CTNNB1, RHPN2, SF1, SQSTM1) as determined by a validated 300-gene panel used in routine clinical practice as prognostic biomarkers for patients with low-risk, early-stage endometrial endometrioid adenocarcinoma. These patients may benefit from the addition of adjuvant therapy. Validation with larger cohorts and prospective studies is warranted.

Phase 2, two-group, two-stage study of avelumab in patients (pts) with microsatellite stable (MSS), microsatellite instable (MSI), and polymerase epsilon (POLE) mutated recurrent/persistent endometrial cancer (EC)

5502

Background: This non-randomized phase 2 study evaluated the PD-L1 inhibitor avelumab in two cohorts of EC: i) MSI/ POLE cohort including ECs with immunohistochemical (IHC) loss of expression of at least one of the mismatch repair (MMR) proteins and/or documented mutation in the exonuclease domain of POLE and ii) MSS cohort including ECs with normal IHC expression of all MMR proteins. Methods: Eligibility criteria included measurable disease, unlimited prior therapies, and any EC histology. Co-primary endpoints were confirmed objective response (OR) and progression-free survival rate at 6 months (PFS6). Avelumab 10 mg/kg IV was given every 2 weeks until progression or unacceptable toxicity. In the 1st stage, 16 pts were enrolled in each cohort; if there were ≥2 ORs or ≥2 PFS6 responses, accrual would continue to the 2nd stage with enrollment of 19 additional pts. Overall, if there are ≥4 ORs or ≥8 PFS6 responses, avelumab would be considered worthy of further study in each cohort. Results: As of 12/2018, 33 pts were enrolled. The MSS cohort was closed at the 1st stage due to futility; of 16 pts in the MSS cohort, only 1 pt exhibited an OR and PFS6 response [ORR and PFS6 rate 6.25% (95% CI 0.16%-30.2%)]. Conversely, the MSI/POLE cohort reached the primary endpoint of 4 ORs after accrual of only 17 pts. Two pts in the MSI/POLE cohort did not initiate protocol therapy and were excluded from all analyses. Of 15 pts in the MSI/POLE cohort, 4 pts exhibited OR [1CR+3PRs, OR rate (ORR) 26.7% (95% CI 7.8%-55.1%)] and 6 pts (including the 4 pts with OR) exhibited PFS6 responses [PFS6 rate 40.0% (95% CI 16.3%-66.7%)], 4 ongoing and 3 approaching 2 yrs. Twenty-two pts (71%) reported treatment related toxicities, 6 patients (19%) G3 toxicities; there were no treatment-related G4 and G5 toxicities. In the MSI/POLE cohort, 5 of 6 PFS6 responses were observed in pts with ≥3 lines of prior therapy (p = 0.011) and in tumors who were PD-L1 negative by IHC. Further correlative work will be reported at the meeting. Conclusions: In EC pts stratified by MSI/POLE status, MSI vs MSS status appears to be correlated with avelumab response even in PD-L1 negative tumors. Responses in the MSI/POLE cohort were more frequent in more heavily pretreated patients, a finding that warrants further investigation. Clinical trial information: NCT02912572.

Abstract 1010: Genomic analysis of recurrent ovarian cancer in patient-derived xenografts treated with platinum and taxane chemotherapy

Introduction: Many women with advanced ovarian cancer (OC) are initially sensitive to platinum and taxane chemotherapy, but subsequently develop recurrent disease which is often incurable. OC chemotherapy resistance mechanisms are incompletely understood. We used patient-derived xenografts (PDX) to model OC recurrence following chemotherapy and to analyze genomic evolution of recurrent tumors.

Approach: We leveraged PDX derived from human OC ascites that accurately represent high-grade serous OC. We used two PDX models: PDX-A derived from a chemotherapy-naive patient with WT BRCA1/2; PDX-B derived from a chemotherapy-resistant patient with a BRCA1 mutation. Using luciferase-labeled tumor cells, we generated intraperitoneal disease in multiple recipients. We treated cohorts of 5-10 animals with vehicle, carboplatin, paclitaxel, or carboplatin + paclitaxel (C/T) for 3 cycles followed by observation with bioluminescence imaging of tumor burden.

Results: While vehicle- and paclitaxel-treated animals exhibited rapid disease outgrowth, carboplatin- and C/T-treated animals showed disease regression, followed by recurrence after 90-300 days. Median survival was significantly increased in carboplatin- and C/T-treated animals. Recurrent tumors were histologically similar to vehicle-treated tumors. We performed whole-exome sequencing and whole-transcriptome sequencing on ascites cells from 4 animals in each treatment group. We used a decontamination algorithm to remove stromal mouse reads from our tumor samples, resulting in a highly pure (over 99%) human tumor sequence data. Mutations, insertions/deletions, and copy number alterations were identified and compared among treatment groups. Known TP53 mutations were present at 100% frequency across samples. Average mutation frequencies were similar across all groups. We identified several mutations and copy number variants present in the carboplatin or C/T recurrent tumors that were distinct from the vehicle groups, including putative alterations in chemoresistance pathways such as DNA repair (BRCA1/2), apoptosis (BCL2L1), drug transport (ABC transporters), and PI3K signaling (EEF2K). In model PDX-A, all four carboplatin and one C/T treated recurrent tumors exhibited a similar copy-number profile, suggestive of subclonal expansion, which included an increase in WT copies of PTEN relative to the vehicle tumors. Phylogenetic analysis and whole-transcriptome analysis are ongoing.

Conclusions: Our study models recurrent ovarian cancer in PDX and identifies potential features of in vivo chemotherapy resistance.

Citation Format: Elizabeth Stover, Ali Amin-Mansour, Sangeetha Palakurthi, Sanam Dharma, Qing Zeng, Shan Zhou, Palak Desai, Levi Garraway, Ursula Matulonis, Joyce Liu. Genomic analysis of recurrent ovarian cancer in patient-derived xenografts treated with platinum and taxane chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1010. doi:10.1158/1538-7445.AM2017-1010

Abstract 3037: Dissecting treatment resistance in patients with ovarian cancer and PDX-models using single-cell RNA-sequencing

Background: Ovarian cancer (OvCa) is frequently associated with malignant effusions, which are complex ecosystems with heterogeneous populations of malignant cells and non-malignant cells. Bulk RNA-seq or whole-exome sequencing (WES) only reflect average cellular behavior and thereby mask intrinsic cell diversity with potential relevance for treatment resistance.

Approach: To overcome some of these barriers, we applied single-cell RNA-sequencing (scRNA-seq) to malignant and non-malignant cells isolated from patients with platinum treatment resistant disease. Furthermore, we used patient-derived xenograft (PDX) cohorts, in which we isolated cells for scRNA-seq from vehicle tumors (VEH), treated the other models with carboplatin, and harvested cells at the time of minimal residual disease (MRD) or disease progression (PROG).

Results: To date, we have profiled ~12000 single cells from 12 patients with treatment naïve (n=3) or platinum-resistant disease (n=9), including sequential sampling in 3 patients with resistant disease. We observed significant inter- and intra-individual transcriptional heterogeneity in malignant cells. A recurrent pattern across resistant patients was the differential expression of inflammatory pathways in a subset of cells. In a patient with three consecutive specimens, we observed increasing accumulation of cells expressing a cell state characterized by tumor necrosis factor alpha (TNF-a) signaling, Importantly, these cells were genetically identical to the entire population, supporting the hypothesis that non-encoded mechanisms conferred treatment resistance. In a BRCA-mutant patient, unbiased analysis identified a stemness program in a subpopulation of cells, which was genetically identical to other cells, indicating phenotypic conversion. To systemically interrogate mechanisms of resistance to platinum therapy, sequenced single cells isolated from PDX models at three time points (VEH, MRD and PROG). In a BRCA-WT PDX model, resistant cells isolated at MRD and PROG shared a transcriptional program that was dominated by expression of a STAT3 program. Ex vivo cultures from platinum-resistant patients were exquisitely sensitivity to JAK/STAT3-inhibitor. Live cell imaging revealed that STAT3-inhibition prevented spheroid formation, attachment and clearance through a mesothelial monolayer in vitro.

Conclusion: Our results indicate that non-encoded mechanisms play an important role in the development of treatment resistance in ovarian cancer. Our initial studies indicate an important role of inflammatory pathways in treatment resistance, in particular STAT3 signaling, which can be overcome with specific inhibitors at nanomolar concentrations. These data suggests that single-cell profiling can be performed on clinical ovarian cancer specimens and may yield novel therapeutic avenues for patients with treatment-resistant ovarian cancer.

Citation Format: Benjamin Izar, Itay Tirosh, Elizabeth Stover, Asaf Rotem, Parin Shah, Mike Cuoco, Chris Rodman, Joyce Liu, Ursula Matulonis, Orit Rozenblatt-Rosen, Levi Garraway, Aviv Regev. Dissecting treatment resistance in patients with ovarian cancer and PDX-models using single-cell RNA-sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3037. doi:10.1158/1538-7445.AM2017-3037

Abstract AP19: SINGLE–CELL RNA–SEQUENCING OF PATIENT–DERIVED OVARIAN CANCER CELLS AND PATIENT–DERIVED XENOGRAFT MODELS

BACKGROUND AND PURPOSE: Genetic heterogeneity is a hallmark of ovarian cancer (OvCa) biology and underlies treatment resistance. Macroscopic and or treatment resistant microscopic residual disease (MRD) after debulking surgery and chemotherapy are the source for disease recurrence and death in these patients. Current profiling methods are unable adequately reflect heterogeneity, and transcriptional programs associated with treatment resistance and MRD remain elusive. To elucidate transcriptional heterogeneity and potential mechanisms of drug-resistance, we isolated OvCa cells from patients with malignant ascites using flow-cytometry. We applied single-cell RNA-sequencing (sc-RNA-seq) to ascites-derived cells from patients with OvCa. We picked OvCa spheroids and profiled these separately. To investigate MRD, we used three PDX-models stably expressing mCherry, treated with carboplatin, and harvested tumor cells for sc-RNA-seq at three time points (pre-treatment, at time of MRD as determined by bio-luminescence imaging, and disease relapse).

SUMMARY OF RESULTS: We successfully sequenced 770 single-cell transcriptomes from 6 individuals with treatment-resistant OvCa, including 3 patients with sequential samples. We mapped the landscape of chromosomal aberrations by inferred large-scale copy number variations (CNVs) at a single-cell level. We observed significant inter-tumor heterogeneity and started to deconstruct the genomic architecture of individual patients. Using experimentally validated gene sets, we determined the cell cycle state of individual cells and identified transcriptional programs related to the cell cycle as significant bias in publically available bulk RNA-sequencing data. Principal component analysis revealed the expression of a stem-ness signature, including CD133, ALDH1A and AXL, in a sub-set of non-cycling cells. An important driver of transcriptional heterogeneity common to patients included in this study was the expression of gene sets related to inflammatory pathways, such as the NFkB and JAK/STAT pathways. Hierarchical clustering of 42 spheroid profiles identified four major clusters, including a highly “inflamed” phenotype. Therapeutic inhibition of the STAT pathway abrogated the capacity of spheroid formation on an ultra-low attachment surface, indicating its importance for metastasis. We have successfully isolated thousands of individual cells for single-cell profiling from PDX models treated with carboplatin. These cells were collected at three time points, including at the MRD stage. We have successfully sequenced 100 cells from this collection and were able to generate whole-transcriptome data comparable to that of freshly isolated patient cells and thousands of single cells are currently undergoing sequencing.

CONCLUSION: We have successfully applied single-cell RNA-sequencing to patient-derived ovarian cancer cells and PDX-models. Single-cell transcriptomes enabled inference of genomic information, genetic and transcriptional heterogeneity, cell cycle state, and programs related to stem-ness and inflammation, providing a unique and comprehensive perspective on ovarian cancer cell states. Ongoing profiling of carboplatin-resistant cells captured at the minimal residual disease stage in PDX-models will provide a unique opportunity to understand treatment resistance which ultimately leads to cancer recurrence.

Citation Format: Benjamin Izar, Elizabeth Stover, Itay Tirosh, Asaf Rotem, Parin Shah, Chris Rodman, Sanjay Prakadan, Marc Wadsworth, Mei-Ju Su, Rachel Leeson, Sangeetha Palakurthi, Joyce Liu, Ursula Matulonis, Alex Shalek, Orit Rozenblatt-Rosen, Aviv Regev, Levi Garraway. SINGLE–CELL RNA–SEQUENCING OF PATIENT–DERIVED OVARIAN CANCER CELLS AND PATIENT–DERIVED XENOGRAFT MODELS [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr AP19.

Phase 2, two-group, two-stage, open-label study of avelumab in patients with microsatellite stable, microsatellite instable and POLE-mutated recurrent or persistent endometrial cancer

TPS5615

Background: The Cancer Genome Atlas project identified 2 groups of hypermutated endometrial cancers (ECs): an ultramutated group that harbored mutations in the exonuclease domain of polymerase e ( POLE), and a hypermutated group with microsatellite instability (MSI), the majority of which harbored MLH1 promoter methylation. We (Howitt, JAMA Onc 2015) and others have shown that POLE and MSI ECs are associated with higher number of predicted neoepitopes and tumor infiltrating lymphocytes, which is counterbalanced by overexpression of PD-1/PD-L1, suggesting that they may be excellent candidates for PD-1/PD-L1 blockade. Anti-PD-1 therapy has also demonstrated promising activity in mismatch repair deficient colorectal cancers and collectively in non-colorectal cancers (Le, NEJM 2015). Methods: This is an open-label, two-cohort, two-stage, phase 2 trial, of avelumab, a fully human IgG1 antibody directed against PD-L1, in two cohorts: i) a MSI/ POLE cohort including ECs with immunohistochemical (IHC) complete loss of expression of at least one of the mismatch repair (MMR) proteins and/or documented mutation in the exonuclease domain of POLE and ii) a MSS cohort including ECs with normal IHC expression of all MMR proteins. Key eligibility criteria include measurable disease, no upper limit of prior therapies, and any EC histology. Co-primary objectives include objective response rate and rate of progression-free survival at 6 months. Avelumab is administered at 10 mg/kg as 1-hour IV infusion every 2 weeks until disease progression or unacceptable toxicity; therapy may continue at the investigator’s discretion while awaiting radiologic confirmation of disease progression 4 weeks later. Maximum target enrollment is 70 patients (35 for each cohort). In the first stage, 16 patients will be enrolled in each cohort; if there are at least two objective responses or two patients progression-free at 6 months, accrual will continue to the second stage where 19 more patients will be enrolled for each cohort. Thus far, 16 patients have been enrolled, 13 on the MSS cohort and 3 on the MSI/ POLE cohort. Clinical trial information: NCT02912572.

Association of Polymerase e-Mutated and Microsatellite-Instable Endometrial Cancers With Neoantigen Load, Number of Tumor-Infiltrating Lymphocytes, and Expression of PD-1 and PD-L1

IMPORTANCE

Immune checkpoint inhibitor therapy has shown benefit in various cancers, but their potential in endometrial cancer (EC) is unknown.

OBSERVATIONS

Prediction of neoantigen load was performed using sequencing data from the Cancer Genome Atlas data set. Evaluation of tumor-infiltrating lymphocytes (TILs) and PD-1 and PD-L1 expression was performed in 63 patients with EC referred to our institution. The predicted median (range) neoantigen load (predicted neoepitopes per sample) was proportional to the mutational load: highest in ultramutated polymerase e (POLE) tumors (8342 [628-20 440]), less in hypermutated MSI (541 [146-8063]; P < .001), and lowest in microsatellite-stable tumors (70.5 [7-1877]; P < .001). The POLE and MSI ECs exhibited higher numbers of CD3+ (44.5 vs 21.8; P = .001) and CD8+ (32.8 vs 13.5; P < .001) TILs compared with microsatellite-stable tumors. PD-1 was overexpressed in TILs (81% vs 28%; P < .001) and peritumoral lymphocytes (90% vs 28%; P < .001) of POLE and MSI tumors. PD-L1 expression was infrequently noted in tumor cells but was common in intraepithelial immune cells and more frequent in POLE and MSI tumors (39% vs 13%; P = .02).

CONCLUSIONS AND RELEVANCE

Polymerase e-mutated and MSI ECs are associated with high neoantigen loads and number of TILs, which is counterbalanced by overexpression of PD-1 and PD-L1. Polymerase e-mutated and MSI EC tumors may be excellent candidates for PD-1-targeted immunotherapies.

Importance of early audiologic assessment in distal renal tubular acidosis

Autosomal recessive distal renal tubular acidosis is usually a severe disease of childhood, often presenting as failure to thrive in infancy. It is often, but not always, accompanied by sensorineural hearing loss, the clinical severity and age of onset of which may be different from the other clinical features. Mutations in either ATP6V1B1 or ATP6V0A4 are the chief causes of primary distal renal tubular acidosis with or without hearing loss, although the loss is often milder in the latter. We describe a kindred with compound heterozygous alterations in ATP6V0A4, where hearing loss was formally diagnosed late in both siblings such that they missed early opportunities for hearing support. This kindred highlights the importance of routine audiologic assessments of all children with distal renal tubular acidosis, irrespective either of age at diagnosis or of which gene is mutated. In addition, when diagnostic genetic testing is undertaken, both genes should be screened irrespective of current hearing status. A strategy for this is outlined.

Epidermal growth factor receptor and Ink4a/Arf: convergent mechanisms governing terminal differentiation and transformation along the neural stem cell to astrocyte axis

Ink4a/Arf inactivation and epidermal growth factor receptor (EGFR) activation are signature lesions in high-grade gliomas. How these mutations mediate the biological features of these tumors is poorly understood. Here, we demonstrate that combined loss of p16(INK4a) and p19(ARF), but not of p53, p16(INK4a), or p19(ARF), enables astrocyte dedifferentiation in response to EGFR activation. Moreover, transduction of Ink4a/Arf(-/-) neural stem cells (NSCs) or astrocytes with constitutively active EGFR induces a common high-grade glioma phenotype. These findings identify NSCs and astrocytes as equally permissive compartments for gliomagenesis and provide evidence that p16(INK4a) and p19(ARF) synergize to maintain terminal astrocyte differentiation. These data support the view that dysregulation of specific genetic pathways, rather than cell-of-origin, dictates the emergence and phenotype of high-grade gliomas.

Behavioral prevention is today's AIDS vaccine!

INTRODUCTION

Behavioral prevention is currently the only effective way to stem the further spread of HIV. This article reviews the pro-active programmatic model of behavioral research that has led to the development and testing of successful HIV/STD preventive interventions in the last fifteen years.

OBJECTIVE

To present (1) a model of behavioral prevention adapting phases of clinical trials research: Phase I: Discovery; Phase II: Exploratory; Phase III: Efficacy; and Phase IV: Effectiveness; and (2) a theoretical framework for behavioral prevention; and (3) A Lifespan Model of Health Promotion and Disease Prevention which can be used to design HIV/STD prevention programs across the lifespan, at different levels (e.g., individual, couple, family, community, societal) using different intervention modalities.

CONCLUSIONS

Behavioral prevention is effective with different age groups and at different levels of intervention when the prevention program has a theoretical basis. Behavioral prevention works now and can be mobilized within a community to address all of the factors associated with the rapid development of an epidemic. Behavioral prevention is cost effective and can be delivered in communities that have limited resources.

Cross-Protection of Grapefruit from Decline-Inducing Isolates of Citrus Tristeza Virus

The ability of three mild isolates of citrus tristeza virus (CTV) to prevent natural infection of 84 Ruby Red grapefruit on sour orange rootstock by aphid-transmitted, decline-inducing isolates of CTV was assessed by symptoms and verified by enzyme-linked immunosorbent assay (ELISA) after 16 years. Of 21 trees in each of four treatments protected by the DD 102 bb, Guettler HS, and DPI 1-12-5-X-E mild CTV isolates, 14, 10, and 14% were infected by severe isolates (MCA13 monoclonal antibody reactive) compared with 67% for unprotected control trees. The health of trees protected by the DD 102 bb CTV isolate was significantly better than that of unprotected control trees as measured by decline, tree ratings, and tree height. These data suggest that infection by certain mild isolates of CTV can cross-protect grapefruit trees on sour orange rootstock from decline-inducing isolates of CTV that are prevalent in the Indian River region of Florida.

Animal models recapitulate aspects of HIV/CNS disease

Neurobehavioral and pathological data indicate that the central nervous system (CNS) becomes infected with HIV-1 soon after the virus enters the body. However, neuropathogenesis of HIV-1 infection is difficult to investigate because the brain parenchyma is not accessible to sampling during the course of AIDS. The second compartment of the CNS, cerebrospinal fluid (CSF), is accessible to sampling but how changes in the CSF relate to the changes in the parenchyma is poorly understood. Thus, knowledge of the neuropathogenesis of HIV-1 infection predominantly stems from either postmortem or in vitro studies. This raises the need for animal models of HIV infection of the CNS. Such models have been developed and are briefly reviewed here. The models faithfully recapitulate some aspects of the HIV/CNS disease. Appropriate neuropathological changes and neurobehavioral dysfunction (e.g., cognitive and motor deficits) occur in SIV-infected macaques. Central sensory electrophysiological changes and sleep disturbances occur in FIV-infected cats. Infection of the brain and behavioral changes comparable to some of the changes seen in humans occur in mice infected with a mixture of murine leukemia viruses. Genetically immunodeficient mice (e.g., SCID) accept HIV-infected human organs and or cell grafts. Evidence summarized here indicates that these HuSCID animals undergo neuropathological changes similar to those observed in brains of individuals who died with AIDS. Thus, presently available animal models provide an opportunity to investigate HIV/CNS disease, and to develop and test therapeutic interventions to prevent or cure the disease.

Forensic DNA testing on skeletal remains from mass graves: a pilot project in Guatemala

A reliable method for extracting DNA from teeth was developed and successfully applied to a set of 12 skeletons recovered from two 10-year-old Guatemalan mass graves. Attempts to identify the remains by mitochondrial DNA (mtDNA) testing were hampered by low sequence diversity. Our findings demonstrate the feasibility of using DNA typing to identify victims from mass graves.

Neuroscience findings in AIDS: a review of research sponsored by the National Institute of Mental Health

1. The human immunodeficiency virus (HIV-1) infects cells in both the immune system and the brain, but these effects are not independent. 2. Research funded by the National Institute of Mental Health (NIMH) has been directed at identifying some of the mechanisms by which HIV-1 infects the brain, produces pathology, causes behavioral changes, and alters immune responses. 3. HIV-1-associated peptides have been shown to produce immunological changes without active virus present and there is also evidence that neurological damage may result not from direct viral action, by via excitotoxin production. 4. Rhesus macaque monkeys infected with simian immunodeficiency virus (SIV) are proving to be a useful model of the neurological and behavioral changes identified in human AIDS patients; behavioral changes observed in monkeys are similar to those seen in humans infected with HIV-1. 5. Studies examining the relationship between the brain and immune system are identifying the role that the macrophage cytokine interleukin-1 may play in suppressing T-lymphocyte activity by two pathways, both mediated by corticotropin releasing factor (CRF). 6. One pathway involves the pituitary-adrenal axis and release of glucocorticoids while the other involves direct interaction with the sympathetic noradrenergic nervous system, which has been shown to innervate T-lymphocytes in the spleen and thymus. 7. These observations are relevant because macrophages infected with HIV-1 infiltrate the brain and may release substances that damage the brain. 8. Stress may affect these pathways via the CRF-mediated release of glucocorticoids; a model of stress has also demonstrated that stress can suppress the cellular immune response.

Neurobehavioral outcomes in diseases of childhood. Individual change models for pediatric human immunodeficiency viruses

The growing incidence of human immunodeficiency virus-1 (HIV-1) and acquired immunodeficiency syndrome (AIDS) in children is a major public health problem. Current research emphasizes treatments for ameliorating deleterious effects on the child's neurological and behavioral development. This article outlines approaches to the assessment of individual change that may provide alternatives to more traditional approaches to the assessment of neurobehavioral outcomes in children with chronic diseases. These approaches provide more precise conceptualizations of changes that lead directly to statistical designs and measurement strategies for assessing effects of HIV-1 and AIDS on development. Such assessments can be superimposed on current clinical trial methodologies to evaluate the efficacy of pharmacological and behavioral interventions designed to improve quality of life in HIV-1 infected children.

Neurobehavioral outcomes in diseases of childhood: Individual change models for pediatric human immunodeficiency viruses

The growing incidence of human immunodeficiency virus-1 (HIV-1) and acquired immunodeficiency syndrome (AIDS) in children is a major public health problem. Current research emphasizes treatments for ameliorating deleterious effects on the child's neurological and behavioral development. This article outlines approaches to the assessment of individual change that may provide alternatives to more traditional approaches to the assessment of neurobehavioral outcomes in children with chronic diseases. These approaches provide more precise conceptualizations of changes that lead directly to statistical designs and measurement strategies for assessing effects of HIV-1 and AIDS on development. Such assessments can be superimposed on current clinical trial methodologies to evaluate the efficacy of pharmacological and behavioral interventions designed to improve quality of life in HIV-1 infected children.

Assessment of AIDS-related cognitive changes: recommendations of the NIMH Workshop on Neuropsychological Assessment Approaches

This article presents an extended (7-9 hours) and a brief (1-2 hours) battery designed to evaluate early cognitive changes associated with seropositive, asymptomatic persons. The battery was recommended by an NIMH Workgroup which was guided by 10 principles in its development. The domains assessed by the battery are: (1) Indicators of Premorbid Intelligence; (2) Attention; (3) Speed of Processing; (4) Memory; (5) Abstraction; (6) Language; (7) Visuoperception; (8) Constructional Abilities; (9) Motor Abilities; and (10) Psychiatric Assessment. Although the battery assesses a wide range of psychological functioning, specific emphasis has been placed on divided and sustained attention as well as speed of processing and retrieval from working and long-term memory. Descriptions of both the traditional clinical tests and tasks used in cognitive psychology are provided. Although the Workgroup strongly recommends the use of the extended battery in order to ensure the most sensitivity, it recognizes that there may be situations in which this is not possible. In order to increase the likelihood that neuropsychological tests will identify neurologically affected CDC Stage II and III seropositive individuals, the Workshop recommends that each patient's protocol be rated by two trained neuropsychologists using the same clinical criteria. The Workgroup also recommends that a concerted effort be made to incorporate data from the extended and the brief batteries in some central data bank.

Neuropsychological effects of early HIV-1 infection: assessment and methodology

Studies of neuropsychological performance early in the course of human immunodeficiency virus-type 1, infection are reviewed. The studies differed on reporting the presence and severity of neuropsychological changes, and comparisons among studies are hampered by variations in the study populations, sample sizes, assessment methods, approaches to data analysis, and definitions of thresholds for abnormality. Recommendations that would facilitate comparisons among future studies include using markers for disease state, applying longitudinal designs, using common instruments for assessing neuropsychological status, selecting appropriate controls, controlling for co-factors, reporting raw scores as well as presumed indices of impairment, and relating impairment on neuropsychological tests to affected individuals' daily activities, if possible.