Abstract TBD

Learning Objectives

1. Discuss Neoantigen Mechanisms: Gain a comprehensive understanding of the mechanisms by which neoantigens are generated and recognized by the immune system, including the processes of antigen presentation and immune activation.

2. Evaluate Current Strategies: Gain insights into cutting-edge approaches for identifying and targeting neoantigens in cancer immunotherapy, including advancements in vaccine development and adoptive cell therapies. Discover the emerging potential of circular RNA as a novel platform for cancer vaccines, emphasizing its enhanced stability and efficacy in presenting neoantigens to the immune system for more robust therapeutic responses.

3. Explore Manufacturing and Quality Control: Understand the critical manufacturing strategies and quality control processes necessary for the successful development and production of neoantigen-based therapies, ensuring consistency, safety, and efficacy.

The upcoming webinar series will focus on the latest innovations in PCR (Polymerase Chain Reaction) applications, one of the most versatile and widely used techniques in molecular biology. Our webinar is designed to delve into a specific area of PCR research, providing participants with valuable insights into recent advancements and applications. The webinars will feature leading experts from the field, who will share their knowledge and expertise by presenting cutting-edge breakthroughs, innovative methodologies, and practical best practices that can be applied in your research. Whether you're new to PCR or looking to refine your techniques, the webinars will offer relevant, up-to-date content that supports your growth as a researcher.

Key Learnings:

 - Discover cutting-edge advancements in direct PCR technology for faster and more efficient target detection. 

- Overcome challenges with different sample types, eliminating the need for DNA purification.

 - Gain valuable tips to optimize your direct PCR reactions for better results.

Next-generation sequencing (NGS) allows the simultaneous analysis of multiple genomic alterations with therapeutic implications, paving the way for precision medicine and transforming cancer care. However, having more data comes with its own problems. Increased NGS testing has caused an exponential rise in detected variants that, coupled with the sporadic nature of somatic cancers, challenges labs to quickly and confidently identify the most clinically relevant mutations for treatment decisions. Approximately 50% of oncologists in the United States find NGS results sometimes or often difficult to interpret. Meanwhile, 31% of small- to medium-sized labs in Europe view a lack of knowledge and exposure to routine analyses and interpretation as the most critical bottleneck in NGS testing.

Genomic analysis of cancer cells revealed comprehensive mechanism of tumorigenesis in human patients. Among the abnormalities discovered so far, CNVs accounted for a great portion of all the frequently observed pathogenic variants, and serve as important biomarkers for early-detection, diagnosis, prognosis and follow-up patient care. OncoScan CNV assays, as one of the most common CNV analysis tool for solid tumor samples, displayed robust ability in detecting gain, loss and LOH that play an essential role in cancer origination, progression and metastasis. It has the advantage of processing highly degraded and/or low quality samples, which is frequently observed in solid tumor samples. In this talk, we will focus on its development history and current application in research setting to decipher the molecular and cytogenetic mechanisms in a few representative types of solid tumors.
 
Learning Objectives:
 
The audience will go through the history/development of cytogenetics/cytogenomics
The audience will get familiar with current cytogenetic analysis tools
The audience will understand the advantages of OncoScan compared to other array/NGS platforms
The audience will know what types of tumor samples OncoScan could be used for analysis

De novo gene synthesis and protein expression are established technologies that can give access to nearly any target DNA or protein sequence, allowing for engineering of biologics. In this presentation we demonstrate how considering more than codon usage in gene optimization can boost protein expression. Advanced mammalian expression systems can further enhance antibody yields by getting more product from the same culture volumes. Customer examples demonstrate the benefits of a continuous workflow, from gene to protein, to accelerate discovery and early development.

Learning Objectives:

1. Explain how Enhancing Protein Expression: optimize gene synthesis techniques beyond codon usage can significantly improve protein expression rates, facilitating the engineering of biologics.

2. Summarize how Maximizing Antibody Yields: utilize advanced mammalian expression systems can increase antibody yields, extracting more product from identical culture volumes to accelerate discovery and early-stage development processes.

Cancer neoantigens arise from protein-altering somatic mutations in tumor and rank among the most promising next-generation immuno-oncology agents when used in combination with immune checkpoint inhibitors. We previously developed a computational framework, REAL-neo, for identification, quality control, and prioritization of both class-I and class-II human leukocyte antigen (HLA)-presented neoantigens resulting from somatic single nucleotide mutations (SNMs), small insertions and deletions (INDELs), and gene fusions. In this study, we developed a new module, SPLICE-neo, to identify neoantigens from aberrant RNA transcripts from two distinct sources: 1) DNA mutations within splice sites and 2) de novo RNA aberrant splicings. Using SPLICE-neo, we identified abundant splicing neoantigens in four cancer types in The Cancer Genome Atlas (TCGA): BRCA, LUAD, LUSC, and LIHC. In addition to their substantial contribution to neoantigen load, several splicing neoantigens were bench validated as potent tumor antigens with stronger bindings to HLA compared to the positive control of antigens from flu virus. SPLICE-neo is the first tool to comprehensively identify and prioritize splicing neoantigens from both DNA splice-site mutations and de novo RNA aberrant splicings. There are two major advances of SPLICE-neo. First, we developed novel logic models that assemble and prioritize full-length aberrant transcripts from DNA splice-site mutations. Second, SPLICE-neo can identify exon-skipping events involving more than 2 exons, which account for a quarter to one third of all skipping events.

Learning Objectives:

• Describe the basic steps of computational identification of neoantigens
• Differentiate the two sources of splicing neoantigens
• Identify a potential therapeutic benefit of recurrent neoantigens

Pancreatic ductal adenocarcinoma (PDAC) is characterized clinically by poor survival and mechanistically by KRAS- and autophagy-dependent growth. We and others previously demonstrated that inhibition of the KRAS-RAF-MEK-ERK pathway enhanced autophagic flux and dependency in several PDAC models. Furthermore, we demonstrated that concurrent treatment with the only FDA-approved autophagy inhibitors chloroquine/hydroxychloroquine (CQ/HCQ) and ERK MAPK inhibitors synergistically blocked PDAC growth. However, CQ is limited in terms of specificity and potency, and we therefore aimed to identify more efficacious anti-autophagy strategies. To this end, we performed a CRISPR-Cas9 loss-of-function screen in PDAC cell lines that identified the lipid kinase PIKfyve as a gene necessary for PDAC proliferation. PIKfyve is a lipid kinase that is essential for the production of PI(3,5)P2, and critical for the proper regulation of lysosome recycling. We evaluated the effects of PIKfyve inhibition on growth and autophagic flux in PDAC cell lines and tumors. We demonstrated that PIKfyve inhibition by the small molecule apilimod resulted in durable growth suppression, with much greater potency than CQ treatment. PIKfyve inhibition also impaired autophagy as demonstrated by robust accumulation of autophagy-related proteins and significantly impaired autophagic flux. This was likely due to impaired lysosome function, demonstrated by accumulation of LAMP1 positive vacuoles that exhibited impaired cargo degradation and lack of normal acidity. We next showed that PIKfyve inhibition blocked the compensatory increases in autophagic flux associated both with MEK inhibition and with direct RAS inhibition. Accordingly, combined inhibition of PIKfyve and either the ERK-MAPK pathway or RAS itself showed robust growth suppression across a panel of KRAS-mutant PDAC models. Growth suppression was due, in part, to potentiated cell cycle arrest and induction of apoptosis following loss of IAP proteins. We conclude that concurrent inhibition of RAS and PIKfyve is a synergistic, cytotoxic combination that may represent a novel therapeutic strategy for PDAC.

Learning Objectives:

• Identify the effects of PIKfyve inhibition on autophagic flux and tumor growth in pancreatic cancer.
• Analyze the efficacy of combining PIKfyve inhibitors with RAS or ERK-MAPK pathway inhibitors in KRAS-mutant PDAC.
• Describe the mechanisms through which PIKfyve inhibition enhances cell cycle arrest and apoptosis in PDAC cells.

Genomic research has long been skewed toward European populations, leading to significant underrepresentation of Non-European groups in both research studies and genomic databases. This bias results in genomic annotations that are less effective at identifying clinically relevant variants in these underrepresented populations. As a consequence, Non-European populations exhibit rates of variants of unknown significance (VUS) up to two times higher than their European counterparts.

The overrepresentation of VUS in Non-European populations is a crucial challenge in addressing health disparities. These variants, which are currently classified without clear clinical relevance, may hold significant potential for improving healthcare outcomes. By prioritizing research on VUS in these populations, there is an opportunity to discover clinically actionable insights that could lead to better diagnostic and therapeutic strategies.

Key topics to be covered:

Disparities in Genomic Research: The historical bias towards European populations and its impact on genomic data interpretation. VUS Rates and Clinical Implications: The heightened prevalence of VUS in Non-European populations and its role in exacerbating healthcare inequities. Opportunities for Health Equity: How focusing on the study of VUS can help close health disparity gaps, by offering new, clinically actionable genomic insights. This presentation aims to highlight the importance of increasing diversity in genomic databases and research to ensure equitable healthcare advances for all populations.

Learning Objectives:

• Identify factors that contribute to health disparities.
• Distinguish differences in genetic variation across populations.
• Define variants of unknown significance.

The 21st Century Cures Act, along with the FDA's Real-World Evidence (RWE) framework, has established a foundation for incorporating real-world data (RWD) into regulatory decision-making processes. Among the various sources of RWD, Electronic Health Records (EHRs) have emerged as a crucial asset, providing rich insights into treatment responses across diverse patient populations in real-world settings. These insights are essential for generating robust and meaningful RWE. In this presentation, I will introduce a comprehensive pipeline for generating reproducible and generalizable real-world evidence (RWE) on longitudinal disease outcomes by leveraging electronic health record (EHR) data. The pipeline links EHR data with registry information and uses algorithms based on longitudinal EHR features to evaluate the outcomes for chronic diseases. The practical application of this pipeline will be illustrated through a case study focused on predicting the risk of renal cell carcinoma (RCC) recurrence.

Learning Objectives:

• Identify the role of Electronic Health Records (EHRs) in generating real-world evidence for chronic disease outcomes.
• Describe the steps of the pipeline that links EHR data with registry information for predicting disease recurrence.
• Discuss the application of EHR-based algorithms in predicting renal cell carcinoma recurrence risk.

Immunotherapy has changed the landscape of oncology, improving survival rates for many patients across a variety of malignancies. Two antibody-based immunotherapies, immune checkpoint inhibitors (ICI) and targeted immunotherapy, are among the most successful clinical modalities. However, response rates remain incomplete with many patients exhibiting primary or acquired resistance. Our studies have identified host genetics as a contributor to response variation. Most preclinical research utilizes inbred mouse models, which fail to recapitulate the genetic diversity of humans. We have developed a unique approach utilizing F1 crosses of inbred mice with the genetically heterogeneous Diversity Outbred (DO) and Collaborative Cross (CC) mouse models, producing cohorts of mice with variable genetics that reliably accept tumor lines syngeneic to the inbred strain. In both ICI and targeted immunotherapy studies, we show that germline genetics influence anti-tumor immunity and response to immunotherapy against genetically identical tumors. Genetic linkage analysis pinpoints genomic loci that associate with response, revealing candidate causal genes. These loci are then validated in CC F1 models where the CC mice are selected for positive or negative driver genetics at our loci of interest. Single-cell RNA sequencing (scRNAseq) of tumor immune infiltrates is used to evaluate expression patterns of genes in each locus. Comparison to publicly available human scRNAseq datasets indicates similar expression patterns, supporting the translational potential of our findings. Additional work is underway to determine if our candidate genes/pathways contribute to cancer disparities. Collectively, our goal is to unveil novel actionable targets to improve immunotherapy outcomes, and to discover key biomarkers to guide clinical decision-making.

Learning Objectives:

• Discuss the role of host genetics in cancer immunotherapy
• Introduce new candidate mechanisms of cancer immunotherapy resistance
• Consider the choice of animal models for cancer immunology research

To determine efficacy of specific complementary therapies to advance evidence-based, integrative healthcare, the complementary modality should first be introduced to stakeholders to determine interest, feasibility, relevant disease sites and patient populations, appropriate means of delivery, and potential impact. To address these points, a nursing-based holistic biofield modality, Healing Touch (HT), was introduced in a Survivorship Clinic at an NCI designated Comprehensive Cancer Center to patients, caregivers, survivors, and staff. The program was led by a Healing Beyond Borders (HBB) Certified HT Practitioner. HT was offered twice a week for 3 hours each day and participants received a 30-minute HT chair session in a group setting delivered by hospital volunteers trained in HBB Level I HT.

Stakeholders' demographic data, affiliation, associated disease site/clinic, and department was collected. A mixed methods approach was used (10-point scale) to assess how they were feeling pre and post HT, along with other qualitative comments.

In the first year, 760-30-minute sessions were performed. Over 350 participants came to the clinic. Participants were active cancer patients, caregivers, survivors, and staff coming from come a variety of disease sites, were older, mostly employed, married, women, and self-referred. Ninety-eight percent of participants increased at least 1 point on the scale from baseline assessment, with 80% increasing between 2-5 points. Clinics most represented included Breast, Gyn Onc, and BMT. Physical, mental, emotional, and spiritual comments were obtained, but most focused primarily on cancer related symptom relief and feeling relaxed.

HT was feasible, well received by our stakeholders, and delivered successfully in 30 minutes by our volunteers. HT has been incorporated in several additional programs at our institute. Additional wellness programs, including another biofield modality, Reiki, are currently available to our patients.

Learning Objectives:

• Describe the concept and impacts of nursing-based holistic biofield modalities
• Examine the efficacy of complementary therapies in cancer treatment
• Evaluate appropriate means of delivery and potential impace of complementary therapies

Engineered immune cell therapies offer the promise of more tailored interventions than traditional systemic checkpoint blockades, but so far remain ineffective across the majority of clinical settings, especially solid tumors. To overcome the slew of resistance mechanisms cancers present, various screening modalities have nominated numerous gene knockouts, gene overexpression, and synthetic CAR and TCR sequences to further refine T cell therapies. But among this abundance of gene targets, effective methods to directly compare large numbers of potential clinical constructs to engineer immune cells are lacking. Further, the association of these synthetic genetic sequences with the functional phenotype they impart on an engineered cell is costly, time consuming, and low throughput. Here, we developed Modular Pooled Knockin Screening (ModPoKI), a highly scalable platform to rapidly associate large pools of T cell genetic modifications with high dimensional single cell phenotypes across diverse cancer immunotherapy contexts. We built libraries of transcription factors (TFs) and natural and synthetic surface receptors, including numerous proposed constructs under clinical investigation. Over 20 ModPoKI screens across dozens of healthy human donors in both TCR and CAR T cells in diverse conditions built a high dimensional genotype x phenotype map which benchmarked existing clinical constructs and nominated unique novel cell therapy targets for further clinical development which overcame cancer resistance mechanisms and showed improved in vitro and in vivo performance. Analysis across these diverse functional contexts identified a transcription factor AP4 (TFAP4) construct that enhanced long-term T cell fitness and anti-cancer function in vitro and in vivo. ModPoKI’s modularity further allowed us to generate a ∼10,000-member library of TF combinations, revealing unexpected functional relationships within CAR T cells with synthetic transcriptional programs. Non-viral knockin of a combined BATF-TFAP4 polycistronic construct further enhanced function in vivo. ModPoKI facilitates scalable discovery of complex gene constructs to program and improve engineered immune cell functions tailored to specific cancer resistance mechanisms.

Learning Objectives:

• Describe the ModPoKI platform’s role in identifying gene modifications for improving T cell therapies.
• Compare the effectiveness of synthetic and natural genetic constructs in overcoming cancer resistance mechanisms.
• Analyze how transcription factors, such as TFAP4, enhance T cell function and long-term fitness in cancer immunotherapy.

Solute carriers include numerous uptake transporters that serve as major regulators of drug absorption, disposition, and clearance. Indeed, drug interactions or genetic variation that alter solute carrier activity can impact patient outcome by modifying drug pharmacokinetics to yield changes in efficacy or toxicity. Our group has recently shown that many tyrosine kinase inhibitors (TKIs), which are a class of small molecule drugs used to treat a variety of diseases that include cancer, rheumatoid arthritis, pulmonary fibrosis, and macular degeneration, can inhibit the function of a variety of uptake transporters through a novel non-competitive mechanism. For example, numerous reports of clinical drug interactions among TKIs and substrates of the hepatic solute carrier known as the organic anion transporting polypeptide OATP1B1 transporter have been reported, where systemic concentration of OATP1B1 substrates, along with the severity of their toxicity, are elevated. This presentation will outline our efforts in clarifying how TKIs that inhibit the tyrosine kinase known as LYN will alter OATP1B1 activity resulting in diminished hepatic uptake and elevated systemic concentrations of various substrates, ultimately leading to potentially life-threatening toxic risks. Overall, these findings serve to better predict dangerous drug interactions or guide drug development in avoiding particular off target kinases. Moreover, this session will serve to highlight the potential of TKIs to similarly impact the activity of other solute carriers through altered kinase activity, as well as outline possible clinical strategies that can be developed to improve patient outcome with this knowledge.

Learning Objectives:

• Identify risk of Tyrosine Kinase Inhibitor Drug Interactions with OATP1B substrates
• Describe the regulation of solute carriers by tyrosine kinase activity/phosphorylation and its sensitivity to tyrosine kinase inhibitors
• Interpret the benefit of using tyrosine kinase inhibitors to manipulate solute carriers involved in platinum toxicity

There are known health outcome disparities among those with pancreatic neuroendocrine tumors (pNET) of minority race and those living with adverse social determinants of health (SDOH) (rurality, unmarried) influencing overall survival compared to their peers. The potential biologic mechanism of these factors is unknown. Our lab explores differential epigenetic expression of pnet tumors based on environmental exposures including race/ancestry and exposure to adverse social determinants of health. Our preliminary data show significant biologic changes are seen in pNET gene expression of patients living in neighborhoods characterized by adverse SDOH. The pathways most effected center around suppressed immune response and heightened catabolism. These changes may be linked to disparate outcomes among minorities.

Learning Objectives:

• Discuss the disparities that exist within pancreatic neuroendocrine tumors
• Discuss the epidemiology of pancreatic neuroendocrine tumors in the United States
• Review how environmental factors can alter tumor epigenome