Abstract IA16: Augmenting anti-PD1 activity via an HLA-agnostic, mutation-burden independent, personalized neoantigen vaccine strategy

Neoantigens (neoAg) offer a unique opportunity for directing a patient’s adaptive immune system against tumors while avoiding damage to normal tissues. Current methods for their accurate identification and therapeutic targeting suffer from three main drawbacks: 1) they predict rather than confirm neoAg, 2) their “hit rate” is often too low to be useful in tumors of low to moderate mutational burden such as HNSCC, and, 3) they fail to inform on whether a given mutation is a natural target that can be recognized by CD8+ T cells on tumor cells or by CD4+ T cells on local antigen-presenting cells (APC). This last aspect is perhaps most critical, as a T cell that recognizes a peptide but not a target cell is of little therapeutic value to a cancer patient. We have developed a new unbiased functional approach to neoAg identification that combines bioinformatic analysis of genomic sequence data with functional T-cell assays from a patient’s own PBMC and tumor-infiltrating lymphocytes (TIL). It is based on the concept that, although in silico algorithms may seek to model one or another features of a given mutation’s predicted immunogenicity, the intact immune system can provide proof as to which mutations have been targeted by T cells, and does so according to defined rules of antigen processing and presentation that operate in both cross-presenting antigen-presenting cells (APC) that prime the response and in the tumor cells that express the source antigen. Our approach does not rely on in silico prediction of MHC binding nor any other speculative aspect of peptide immunogenicity and has minimal tissue and peripheral blood requirements. Our preliminary data show it can identify neoAg at a 10x higher rate than current methods and reveals both CD4+ and CD8+ responses. We have performed this analysis for the 4 neoAg identified for the syngeneic murine SCC VII model, and find that the prime/boost vaccination protocol results in significant but incomplete protection from challenge with live SCC VII tumor cells, thus demonstrating that, as a pool, these peptides induce T cells capable of tumor recognition. Furthermore, we have performed preliminary experiments demonstrating that, although SCC VII tumor responds to both PD-1 and CTLA4 blockade immunotherapy, the growing tumors are eradicated much faster in mice that had a pre-existing neoAg-specific T cell response induced in them prior to challenge and treatment. Mice that were vaccinated twice with neoAg peptides + polyI:C but did not receive immune checkpoint blockade showed some initial tumor control that was subsequently lost, leading to progressive growth. A phase 1b clinical trial is now enrolling subjects with advanced cancer that will produce a personalized vaccine for each patient based on our neoantigen identification methodology. The trial combines the vaccine with the anti-PD1 antibody, pembrolizumab, and enrolls patients into 2 consecutive cohorts to elucidate the effects on neoepitope specific T-cell responses of the vaccine versus anti-PD1 targeting. This presentation will summarize our efforts to identify neoantigens, efficacy of a neoantigen-specific vaccine in the murine model, and the current phase 1b study rationale and design.

Citation Format: Ezra Cohen. Augmenting anti-PD1 activity via an HLA-agnostic, mutation-burden independent, personalized neoantigen vaccine strategy [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr IA16.

Adjuncts for the evaluation of potentially malignant disorders in the oral cavity: Diagnostic test accuracy systematic review and meta-analysis-a report of the American Dental Association

BACKGROUND

Oral squamous cell carcinoma is the most common manifestation of malignancy in the oral cavity. Adjuncts are available for clinicians to evaluate lesions that seem potentially malignant. In this systematic review, the authors summarized the available evidence on patient-important outcomes, diagnostic test accuracy (DTA), and patients' values and preferences (PVPs) when using adjuncts for the evaluation of clinically evident lesions in the oral cavity.

TYPES OF STUDIES REVIEWED

The authors searched for preexisting systematic reviews and assessed their quality using the Assessing the Methodological Quality of Systematic Reviews tool. The authors updated the selected reviews and searched MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials to identify randomized controlled trials and DTA and PVPs studies. Pairs of reviewers independently conducted study selection, data extraction, and assessment of the certainty in the evidence by using the Grading of Recommendations Assessment, Development and Evaluation approach.

RESULTS

The authors identified 4 existing reviews. DTA reviews included 37 studies. The authors retrieved 7,534 records, of which 9 DTA and 10 PVPs studies were eligible. Pooled sensitivity and specificity of adjuncts ranged from 0.39 to 0.96 for the evaluation of innocuous lesions and from 0.31 to 0.95 for the evaluation of suspicious lesions. Cytologic testing used in suspicious lesions appears to have the highest accuracy among adjuncts (sensitivity, 0.92; 95% confidence interval, 0.86 to 0.98; specificity, 0.94; 95% confidence interval, 0.88 to 0.99; low-quality evidence).

CONCLUSIONS AND PRACTICAL IMPLICATIONS

Cytologic testing appears to be the most accurate adjunct among those included in this review. The main concerns are the high rate of false-positive results and serious issues of risk of bias and indirectness of the evidence. Clinicians should remain skeptical about the potential benefit of any adjunct in clinical practice.

Abstract CT123: IMvoke010: Randomized Phase III study of atezolizumab as adjuvant monotherapy after definitive therapy of squamous cell carcinoma of the head and neck (SCCHN)

Background: Locally advanced SCCHN is associated with a high risk for local recurrence and distant metastases. Current treatment options include a combination of surgery, radiation therapy and chemotherapy to optimize the chances for long-term disease control and improved survival. As standard of care, patients are monitored after definitive local therapy for local recurrence and/or distant metastases. No effective systemic adjuvant treatment has been identified. Atezolizumab (atezo) is an anti-programmed death-ligand 1 (PD-L1) monoclonal antibody that restores anti-tumor immunity by preventing PD-L1 from binding to its receptors. Efficacy results from a cohort of 32 patients with recurrent/metastatic SCCHN in the Phase I PCD4989g study suggested that atezo offers promising clinical benefit in SCCHN. The objective of IMvoke010 (NCT03452137) is to evaluate the efficacy and safety of adjuvant treatment with atezo in comparison to placebo in patients with locally advanced SCCHN who are at high risk for disease recurrence or progression following definitive curative therapy.

Trial design: IMvoke010 is a global, double-blind, placebo-controlled, randomized Phase III trial currently enrolling patients who have completed definitive local/regional therapy for Stage III human papillomavirus (HPV)-positive oropharyngeal carcinoma or Stage IVA or IVB HPV-negative SCCHN involving the oral cavity, oropharynx, larynx or hypopharynx and are at high risk for disease recurrence or progression. Approximately 400 patients will be randomized 1:1 to receive placebo or atezo 1200 mg every 3 weeks for up to a year (≤ 16 cycles) or until unacceptable toxicity, disease recurrence or progression. Patients with nasopharyngeal carcinoma, metastatic disease or progressive disease during or at completion of definitive local therapy will be excluded. Primary endpoints are independent review facility-assessed event-free survival (EFS) and overall survival. Key secondary endpoints include investigator-assessed EFS, safety and patient reported outcomes. Exploratory biomarkers will also be assessed.

Citation Format: Deborah J. Wong, Jerome Fayette, Ye Guo, Matthew Kowgier, Ezra Cohen, Ricard Mesia Nin, Arunee Dechaphunkul, Kumar Prabhash, Jessica Geiger, Sarwan Bishnoi, Henning Schafer, Christina Matheny, Fairooz Kabbinavar, Alan Sandler, David Raben, Robert Haddad. IMvoke010: Randomized Phase III study of atezolizumab as adjuvant monotherapy after definitive therapy of squamous cell carcinoma of the head and neck (SCCHN) [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 CT123.

Abstract 3420: Integrative tumor profiling beyond panel sequencing

Introduction: Targeted cancer therapies rely on the identification of biomarkers specific to the tumors. Next generation sequencing (NGS) based genomic profiling has informed clinical decision making by identifying somatic alterations such as single nucleotide variants (SNVs), small insertion and deletion mutations (indels), structural variations, tumor mutation burden (TMB), and microsatellite instability (MSI) status. Here, we describe an integrative approach to characterize the genomic complexity of solid tumors using whole genome sequencing (WGS), whole exome sequencing (WES), whole transcriptome sequencing (RNAseq), and tumor only panel sequencing.

Methods: We report on WES for 84 paired tumor normal samples in a variety of tumor types including breast, colon, head and neck, melanoma, cervical, thyroid, glioblastoma, lung, pancreatic, prostate, appendiceal, cholangiocarcinoma, and kidney. A subset of these samples were also sequenced with high depth tumor only gene panel. WGS and RNAseq data were included in the analysis for additional 14 tumor normal pairs. Somatic alteration assessments included SNV, indels, MSI status, TMB, mutational signatures, copy number variations, gene fusions and structural variations.

Results: Analysis using tumor normal WES and RNAseq identified both clinically relevant genes as well as mutational processes. We found a high percentage of germline mutations were misidentified as somatic variants using tumor only panels, further highlighting the importance of paired tumor normal sequencing. In some cases, the putative driver gene or the variant in a cancer gene identified by WES was not included in panel sequencing. For example, mutations in FOXA1 gene were recently implicated as clinically relevant resistance and metastasis marker. Exome wide mutational signature analysis also identified BRCA (Cosmic sig 3) signature in tumors with no alterations in BRCA1/2 genes. WGS analysis and fusion gene detection revealed novel fusion genes as well as important structural alterations. Examples include a novel BRAF fusion in a cholangiocarcinoma devoid of other known driver mutations, a novel NTRK3 fusion partner in a glioblastoma tumor, and numerous tandem duplications in an ovarian cancer.

Conclusion: In contrast to tumor only gene panels, tumor and matched normal whole exome assay examines the entire coding portion of the genome without the limitations of a predefined gene list. This allows for detection of mutations in recently identified cancer drivers, ability to reliably distinguish somatic variants from clonal hematopoiesis or other germline variants, calculate genome wide mutational patterns including TMB, MSI, and identify the underlying mutational processes such as genomic signatures. The addition of WGS sequencing allows the identification of clinically relevant genomic rearrangements and novel structural variations.

Citation Format: Corine K. Lau, Alena S. Harley, Paul Choppa, Janine Cooc, Ainura Kyshtoobayeva, Natalia Jun, Mark Dayrit, Wayne Delport, Mark Saldivar, Yop Jun, Raaj Trivedi, Alexandra E. Gylfe, Travis R. Lacey, Ezra Cohen, Kenneth Bloom, Eve Shinbrot. Integrative tumor profiling beyond panel sequencing [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 3420.

Identifying and engineering TCR specificity against solid tumor neoantigens

Neoantigens (NeoAg) offer attractive therapeutic targets for directing a patient’s immune response to the immunogenic subset of mutations expressed exclusively by their cancer cells. Despite the specificity with which NeoAg enable tumor recognition, the majority of approaches for their identification rely on purely predictive methods such as calculating the ability of mutated peptides to bind to a patient’s set of HLA molecules. These methods have met with limited success in revealing natural targets present on tumor cells. We have developed a novel HLA-agnostic functional approach to NeoAg identification which combines genomic sequencing with bioinformatic analysis to nominate mutations for subsequent functional analysis using patient’s own T cells in an effort to identify natural responses generated under physiologic conditions. Using this, we identified a missense mutation (V205I) in the ribosomal protein RPS2 that is recognized by CD8+ T cells from tumor-infiltrating lymphocytes (TIL) of a metastatic HPV16+ Head and Neck Squamous Cell Carcinoma lesion. We then performed adoptive cellular therapy (ACT) using either unseparated TIL or those enriched for RPS2 V205I-specific CD8+ T cells and found the latter to be superior in controlling outgrowth of tumor of a PDX cell line generated from this lesion in NSG mice. Finally, we used single-cell transcriptomics to isolate the genes encoding the RPS2-specific TCR and show that it recognizes the mutated peptide bound to HLA-B*07:02. These results demonstrate that high-affinity NeoAg-specific T cell responses can be identified in cancer patients, that ACT of these cells can control tumor growth, and that the relevant TCR can be isolated for use in TCR engineering-based immunotherapy.

Protective ventilation with high versus low positive end-expiratory pressure during one-lung ventilation for thoracic surgery (PROTHOR): study protocol for a randomized controlled trial

BACKGROUND

Postoperative pulmonary complications (PPC) may result in longer duration of in-hospital stay and even mortality. Both thoracic surgery and intraoperative mechanical ventilation settings add considerably to the risk of PPC. It is unclear if one-lung ventilation (OLV) for thoracic surgery with a strategy of intraoperative high positive end-expiratory pressure (PEEP) and recruitment maneuvers (RM) reduces PPC, compared to low PEEP without RM.

METHODS

PROTHOR is an international, multicenter, randomized, controlled, assessor-blinded, two-arm trial initiated by investigators of the PROtective VEntilation NETwork. In total, 2378 patients will be randomly assigned to one of two different intraoperative mechanical ventilation strategies. Investigators screen patients aged 18 years or older, scheduled for open thoracic or video-assisted thoracoscopic surgery under general anesthesia requiring OLV, with a maximal body mass index of 35 kg/m2, and a planned duration of surgery of more than 60 min. Further, the expected duration of OLV shall be longer than two-lung ventilation, and lung separation is planned with a double lumen tube. Patients will be randomly assigned to PEEP of 10 cmH2O with lung RM, or PEEP of 5 cmH2O without RM. During two-lung ventilation tidal volume is set at 7 mL/kg predicted body weight and, during OLV, it will be decreased to 5 mL/kg. The occurrence of PPC will be recorded as a collapsed composite of single adverse pulmonary events and represents the primary endpoint.

DISCUSSION

PROTHOR is the first randomized controlled trial in patients undergoing thoracic surgery with OLV that is adequately powered to compare the effects of intraoperative high PEEP with RM versus low PEEP without RM on PPC. The results of the PROTHOR trial will support anesthesiologists in their decision to set intraoperative PEEP during protective ventilation for OLV in thoracic surgery.

TRIAL REGISTRATION

The trial was registered in clinicaltrials.gov ( NCT02963025 ) on 15 November 2016.

Urban young women's preferences for intervention strategies to promote physical and mental health preconception: A Healthy Life Trajectories Initiative (HeLTI)

This study aimed to qualitatively investigate young women's preferences for preconception intervention strategies to promote physical and mental health in a rapidly transitioning, urban setting. Four semi-structured focus group discussions were conducted with young women (n = 29, 18–24 years old) from Soweto, South Africa. Qualitative data were thematically analysed. Two main themes were identified: 1) challenges and needs of intervention beneficiaries; and 2) preferences for intervention strategies (content and delivery). The challenges participants mentioned could be classified as those relating to social pressure, identity, and socioeconomic circumstances. Mental health support appeared to be a greater need than physical health, and this featured in their preferences for intervention content, although a number of physical health topics were also mentioned (healthy eating and contraception). Participants had mixed preferences for intervention materials, ranging from printed to electronic and mobile resources. Their preferences for intervention activities ranged from educational sessions, to fun and interactive practical activities, and activities they could take home. Community health workers (CHWs) were the preferred agent of delivery for interventions, though participants emphasised the importance of CHWs having appropriate interpersonal skills and own life experience. Some women preferred one-on-one sessions with a CHW, while others preferred group sessions. While recognising the value of family sessions, young women were less enthusiastic about this approach. These findings provide valuable formative data for developing effective interventions to optimise young women's preconception health in urban Africa. These contextual realities should be acknowledged when addressing key physical and mental health issues facing young women.

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Social pressure is a major challenge for young women in urban South Africa.

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Mental health should be a key feature of preconception interventions.

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Community health workers are the preferred agent of delivery in this context.

Abstract P6-14-03: Metastatic breast cancer alliance's patient education and access to trials: Perceptions and actions

Background

Those living with metastatic breast cancer (MBC) have distinct and shifting concerns in regard to education and decision making in considering clinical trials as a treatment option. Clinical trials designs, are becoming increasingly complex, and many patients have concerns for biomarker requirements Aims/Research Questions

· What is the status of MBCA advocacy members' and partners' digital information, education and access to metastatic breast cancer trials?

· What plans do MBCA members/partners have for the next 6-18 months to educate and inform their constituents for the 2018 rollout of BreastCancerTrials.org's (BCT)Metastatic Trial Search (MTS) and Metastatic Trial Talk (MTT) and other trial matching systems?

· What are the top 5 barriers regarding trial enrollment?

· What are best practices for MBC trial education?

Research Methodology and Design

A comprehensive analysis was conducted comprising both secondary and primary research to inform these specific aims. Secondary research was conducted using previous capture of MBCA online digital resources and strengthened to include additional research on MBCA members and partners online resources including pages specifically devoted to clinical trials and metastatic clinical trials.

Mixed methods approaches include:

1) An assessment of MBCA members' and partners' digital media presence regarding MBC trials using a standardized form and rating system, and an analysis of MBCA members 2017 use of MTS using BCT secondary data;

2) Structured, recorded interviews with selected MBCA members/ partners, sharing the results of the assessments and querying them regarding their future plans and perceived barriers; and

3) Mixed methods analyses of the interview recordings using DeDoose to assess and articulate key trends and perceptions.

Statistical Methods

Simple frequency percentages and means were used in the assessment rankings of the MBCA members. DeDoose was used to provide mixed method analyses of the MBCA member and partner interviews. Results

Analysis of the MBCA members and partners websites and digital media showed that, increasingly, both groups use the full variety of digital media to educate their constituents regarding MBC clinical trials. The 13 MBCA advocacy members providing online access to BreastCancerTrials' MTS in 2017 provided 97% of the traffic to the MTS trial matching service. System types accessing the MTS widget were 57.3% desktops, 28.6% mobile devices and 14% tablets. Table 1 shows assessment totals of 5 categories of the 13 MBCA advocacy group members' websites using MTS as compared to the 19 MBCA members not using the widget. Table 2 shows the 2017 usage of BCT's MTS with 97% of the page views coming from MBCA members.

Table 1.Assessment Ratings of MBCA Advocacy Partners on Metastatic Trial Education/AccessAwareness of Trials (e.g. explains trial Phases)Knowledge SharingInterest in Metastatic Breast CancerAction Potential for clinical trial access or enrollmentTotal (0-100)13 MBCA Advocate Members with MTS widget22.1523.0024.3124.1593.6219 MBCA Members without MTS widget13.2113.9513.5311.9552.16

Table 2.2017 Use Of Metastatic Trial SearchBCT's Metastatic Trial Search (MTS) Results2017Annual Page views33,360Unique Sessions14,295Show Trials8,100Show Trials by month675Average Time on Site (minutes)3:34Total Engagement Events5,006

Citation Format: Vollmer Dahlke DJ, Smith ML, Han G, Ory MG, Cohen E. Metastatic breast cancer alliance's patient education and access to trials: Perceptions and actions [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 P6-14-03.

Gender differences in homocysteine concentrations, a population-based cross-sectional study

BACKGROUND AND AIMS

High concentrations of homocysteine are considered a risk factor for atherosclerosis and coronary artery disease. The aim of this study was to assess whether or not there are gender differences in the plasma concentrations of homocysteine.

METHODS AND RESULTS

Data were collected from medical records of individuals examined at a screening center in Israel between the years 2000-2014. Cross sectional analysis was carried out on 9237 men and 4353 women. Mean (SD) age of the study sample was 48.4 (9.7) and 47.7 (9.7) years for men and women respectively. Average homocysteine concentrations were 12.6 (5.9) and 9.6 (3.2) μmol/L in men and women respectively (p < 0.001). Prevalence of homocysteine concentrations above 15 μmol/L was found to be significantly higher in men than in women; 15.5% vs 3.9% respectively (p < 0.001). Low concentrations of vitamin (B12 < 200 pmol/L) and low concentrations of folate (<12 nmol/L) were found to be significantly higher in men than in women 20.4% vs. 16.0% and 18.5% vs. 10.8% respectively. Compared to women, men had a significantly higher odds ratio (95% CI) of having homocysteine concentrations above 15 μmol/L: non adjusted model, 4.47 (3.80-5.26); adjusted model for age, smoking status, body mass index, diabetes mellitus, kidney function and low serum concentrations of vitamin B12 and folate, 3.44 (2.89-4.09).

CONCLUSION

Plasma homocysteine concentrations are higher in men than in women. This may be a contributing factor to gender differences for developing atherosclerosis and coronary artery disease.