Panel Of Tumors Research Articles

6981 Atypical hypoglycemia in a teenage boy with prediabetes

Abstract Disclosure: N. Shahid: None. C. salgado: None. N. Gurtunca: None. Background: Hypoglycemia in teenagers is seen less commonly than in younger children. Overweight children with prediabetes presenting with hypoglycemia symptoms are often considered to have reactive post-prandial hypoglycemia due to the degree of hyperinsulinemia with insulin resistance seen in these children. We present a 13-year-old boy with prediabetes, who presented with episodes of altered mental status and was found to have hypoglycemia due to a solitary insulin secreting tumor. Case presentation: A 13-yr old boy with pre-diabetes presented to the ER with altered consciousness and non-ketotic, non-acidotic hypoglycemia [25 mg/dl] & trace ketonuria in the setting of Influenza A infection. Weight and BMI above the 99th%ile and acanthosis nigricans in the skin creases. No access to oral hypoglycemic agents. Urine toxicology was negative. EEG was normal. Euglycemia and level of consciousness restored after IV dextrose & this was considered a possible hypoglycemic seizure episode secondary to poor oral intake. 4 months later he had another episode of altered mental status, jittery movements and was found to be hypoglycemic [41 mg/dl]. He was admitted for further workup of recurrent hypoglycemia. Adrenal insufficiency was ruled out and a diagnostic fast was started. After 15 hours, he developed non-ketotic hypoglycemia [<50 mg/dl]. Critical sample [Table 1] and Glucagon challenge [Table 2] at the termination of the fast confirmed hyperinsulinemic hypoglycemia. Given the unusual age and presentation, an MRI abdomen was done which showed a 1.6 cm lesion in the pancreatic body [Fig 1]. Dotatate whole body PET scan confirmed the insulinoma with no evidence of nodal or distant metastasis [Fig 2]. He underwent surgical enucleation of the insulinoma. Intraoperative secretin showed no evidence of pancreatic duct dilatation or leakage. Hereditary endocrine tumor panel including multiple endocrine neoplasia [MEN] gene analysis was negative. The postoperative course was complicated by a persistent pancreatic leak and pancreatitis eventually requiring an ERCP and stent placement 2 months post operatively. Conclusion: Insulinomas are very rare neuroendocrine tumors in pediatric population, with a prevalence of one in 250,000 and median age at presentation of 45-50 years. About 90% insulinomas are benign and less than 10% are associated with MEN-1 syndrome. Chronic hypoglycemia irrespective of the underlying insulin resistance of prediabetes can be seen with insulinoma and can cause hypoglycemia unawareness as seen in our patient. This has also been reported in literature to be misdiagnosed as refractory epilepsy or psychiatric disorders. Hypoglycemic symptoms at any age should be promptly worked up. Ruling out associated neuroendocrine hereditary tumor syndromes is crucial and prognosis of benign solitary insulinomas after surgical removal is mostly favorable. Presentation: 6/3/2024

Genomic Alterations in Molecularly Defined Oligodendrogliomas.

Oligodendrogliomas are defined by IDH1/2 mutation and codeletion of chromosome arms 1p/19q. Although previous studies identified CIC, FUBP1, and TERTp as frequently altered in oligodendrogliomas, the clinical relevance of these molecular signatures is unclear. Moreover, previous studies predominantly used research panels that are not readily available to providers and patients. Accordingly, we explore genomic alterations in molecularly defined oligodendrogliomas using clinically standardized next-generation sequencing (NGS) panels. A retrospective single-center study evaluated adults with pathologically confirmed IDH-mutant, 1p/19q-codeleted oligodendrogliomas diagnosed between 2005 and 2021. Genetic data from formalin-fixed, paraffin-embedded specimens were analyzed with the NGS Solid Tumor Panel at the Johns Hopkins Medical Laboratories, which tests more than 400 cancer-related genes. Kaplan-Meier plots and log-rank tests compared progression-free survival (PFS) and overall survival by variant status. χ2 tests, t-tests, and Wilcoxon rank-sum tests were used to compare clinical characteristics between genomic variant status in the 10 most frequently altered genes. Two hundred and seventy-seven patients with molecularly defined oligodendrogliomas were identified, of which 95 patients had available NGS reports. Ten genes had 9 or more patients with a genomic alteration, with CIC, FUBP1, and TERTp being the most frequently altered genes (n = 60, 23, and 22, respectively). Kaplan-Meier curves showed that most genes were not associated with differences in PFS or overall survival. At earlier time points (PFS <100 months), CIC alterations conferred a reduction in PFS in patients (P = .038). Our study confirms the elevated frequency of CIC, FUBP1, and TERTp alterations in molecularly defined oligodendrogliomas and suggests a potential relationship of CIC alteration to PFS at earlier time points. Understanding these genomic variants may inform prognosis or therapeutic recommendations as NGS becomes routine.

Unusual PEComa With PRCC :: TFE3 Fusion Mimicking Sinonasal Tract Melanoma.

We report a nasal cavity unusual perivascular epithelioid cell tumor (PEComa) mimicking mucosal melanoma. Immunohistochemistry was performed using BenchMark Ultra and panel of antibodies. The Ion Torrent platform and Ion AmpliSeq cancer hotspot panel were utilized for DNA genotyping. Target-specific RNA libraries for the detection of fusion transcripts were constructed using Archer Universal RNA Reagent Kit v2 and Archer FusionPlex Solid Tumor panel and sequenced on the MiSeqDx instrument. The tumor, diagnosed in 46-year-old female, was composed of spindle cells, and lacked pigmentation. Immunohistochemically, it showed a patchy HMB-45 positivity. Other melanocytic markers (S100 protein, Melan-A, SOX10) were negative. The tumor cells were weakly positive for KIT (CD117) while negative for smooth muscle actin, pancytokeratin cocktail (AE1/AE3), and synaptophysin. Diagnosis of primary sinonasal tract mucosal melanoma was favored. Additional molecular studies detected PRCC :: TFE3 fusion as the sole genetic change, and suggested the diagnosis of unusual PEComa. Previously, TFE3 fusions were reported in a subset of PEComas but not in melanomas, while PRCC involvement has only been documented once in an ocular PEComa. Immunohistochemistry revealed strong nuclear TFE3 expression concordant with the molecular findings. This report emphasis the importance of molecular testing in the differential diagnosis between PEComa and melanoma, especially when the tumor arises in a site typical of melanoma but showing an unusual morphology and immunophenotype. The detection of TFE3 fusion transcripts suggested the diagnosis of SNT PEComa, although it cannot be excluded that this and similar tumors represent a distinct diagnostic category.

In Situ Protein Expression Analysis of Melanocyte Differentiation Antigen TRP1 (Tyrosinase-Related Protein-1).

Melanocyte differentiation antigens refer to molecules expressed in cells of melanocytic lineage such as gp100/PMEL, tyrosinase, and Melan-A. Corresponding antibodies such as HMB45, T311, and A103 have become key immunohistochemical tools in surgical pathology for the diagnosis of pigmented and related lesions. Little is known about tyrosinase-related protein 1 (TRP1), another melanocyte differentiation antigen, which is an enzymatic component of melanogenesis and known as the brown locus in mice. In this study, we tested several commercial reagents to TRP1 and identified one clone, EPR13063, which we further characterized by testing its specificity and usefulness for surgical pathology. Subsequently, we analyzed the expression of TRP1 in panels of normal tissues and tumors. TRP1 is regularly expressed in normal skin and in cutaneous nevi predominantly present in junctional and to a lesser extent in dermal nevocytes. In melanoma, TRP1 is present in 100% and 44% of primary and metastatic melanomas, respectively. TRP1 was absent in 5 desmoplastic melanomas but heterogeneously present in 9 of 11 PEComas/angiomyolipomas. No TRP1 was found in neoplasms of nonmelanocytic lineage. We demonstrate that EPR13063 is a valuable reagent for the analysis of TRP1 expression in archival surgical pathology material. The TRP1 expression pattern in melanocytic and related lesions appears to parallel other melanocyte differentiation antigens with a higher incidence in primary and a lower incidence in metastatic melanomas.

NURS-23. THE ROLE OF THE ADVANCED PRACTICE PROVIDER IN THE PAIRED NORMAL SPECIMEN PROCESS AT A TERTIARY CARE CENTER

Abstract BACKGROUND Paired tumor - normal specimen testing is standard of care to improve the timing and knowledge of genetic variations present in the brain tumor cell and germline. A new process was developed to ensure the paired normal specimen (PNS) testing was completed. METHODS The Neuro-Oncology Advanced Practice Provider (APP) is integral in the process of ordering and obtaining the PNS. RESULTS In the last 15 months, this tertiary care center has performed more than 90 pediatric brain tumor biopsies and/or resections. APPs identify patient surgery dates via the neurosurgery calendar. On the day of surgery a PNS is ordered for the Solid Tumor panel (predetermined by pathology and neuro-oncology) and “Include germline variant resolution information if applicable?” is answered as “No”. The laboratory runs the next generation sequencing (NGS) on PNS and tumor but the findings remain blinded until a second order is placed to “unblind” the specimen. By doing so, the treating physician collaborates with a genetics counselor prior to discussing with the family. Initial difficulty included patient identification, ordering, and collecting PNS. The APPs developed a shared list with patient identifiers, surgery date, order and collection date of PNS which has ensured less than 5% of PNS have been missed. Challenges include weekend surgeries, APPs out of office, and communication to nursing to collect PNS. Updated protocol includes ordering PNS, messaging shift nurse with order explanation and request to collect. Additionally, the pathology team now messages the APPs if a PNS is not submitted and the tumor is undergoing NGS. CONCLUSIONS Comprehensive processes ensure that paired normal – tumor testing is completed in a timely manner and during the same admission with surgery to ensure better insurance coverage and less cost to families, as well as earlier results of somatic and germline variants.

Abstract B012: Predicting targetable paralog synthetic lethalities and functional redundancies in cancer genomes

Abstract Paralogs are prevalent in the human genome and are considered a rich source of synthetic lethality due to functional redundancy. For a cancer cell carrying a gene with Loss-Of-Function (LOF) mutation, inactivation of its paralog using gene editing can induce a selective decrease in viability, leaving normal cells that do not harbor the mutation unharmed. Previous studies have exploited this vulnerability of cancer genomes. However, the cancer-specificity of such synthetic lethality limits its application across different cancer types. Furthermore, the role of functional redundancy which can explain the cancer specificity has remained largely unexplored. In this study, we computationally predicted synthetic lethal paralogs along with mechanistically important functional redundancies between them in a cancer-specific manner. We applied our prediction method to publicly available data for an aggressive subtype of breast cancer called triple-negative breast cancer (TNBC), which lacks the expression key biomarkers and hence has the worst prognosis among other breast cancer subtypes. TNBC is characterized by the highest mutational load and the largest fraction of genome altered among the breast cancer subtypes providing a rich mutational landscape to identify LOF genes. Using the CRISPR inactivation screen data for cancer cell lines obtained from the Cancer Dependency Map (DepMap) project, we predicted sets of synthetic lethal paralogs that show a significantly greater viability decrease if a gene carries LOF and its paralog is inactivated, compared to the viability decrease due to the inactivation of only one of the paralogs. Consistent with previous findings of context-dependent synthetic lethality, we found that a relatively small fraction of TNBC-specific synthetic lethal paralogs overlapped with those found across other cancer types. To uncover the mechanistically important functional redundancies between paralogs, we analyzed the genomics and transcriptomics data from multiple sources: TNBC panel of primary tumors and patient-derived xenografts, Pan-Cancer Analysis of Whole Genomes (PCAWG), and the Cancer Cell Line Encyclopedia (CCLE). The functional redundancies varied across cancer types based on (1) mutual exclusivity of LOFs, (2) backup compensation of deleterious mutations, (3) backup upregulation, and (4) dosage balance. Overall, our findings show a strong context-dependency of synthetic lethal paralogs and estimates of functional redundancy, emphasizing the importance of such cancer-specific predictions in identifying targetable paralog synthetic lethalities. Collectively, the computational method and sets of targetable paralogs are a unique resource for developing precision oncology therapeutic strategies against TNBC and other cancers more broadly. Citation Format: Rohan Dandage, Elena Kuzmin. Predicting targetable paralog synthetic lethalities and functional redundancies in cancer genomes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B012.

Biomarker development from functional precision medicine datasets via explainable machine learning.

10061 Background: Genomics precision medicine, deployed via tumor panel sequencing, now assists in deploying targeted therapies to cancer patients. Numerous clinical trials have investigated the utility and benefit of genomics precision medicine in multiple cancer indications. Current large-scale studies report actionability rates from ~35% to ~60%, although clinical benefit rates have been shown to be closer to 10%. While this has positively impacted patients in need, the gap between actionability and benefit remains a clinical challenge attributed to multiple factors including the complex, multi-factorial relationship between molecular status and response to therapy. These differences go beyond simple disease states and may be reflective of multiple clinically relevant features including age, sex, and race/ethnicity. Methods: We implemented a functional precision medicine (FPM) program where patients with advanced pediatric cancers were prospectively profiled via high-throughput drug sensitivity testing (DST) of FDA-approved agents on patient-derived tumor cells as well as genomics testing. The objective was to investigate the clinical utility and benefit of FPM guidance in the treatment of pediatric cancer and elucidate the relationship between molecular status of patients’ diseases and treatment responses. We generated DST data (n = 21 patients) and genomic profiling data (n = 20 patients) on pediatric cancer patients in Miami, FL, as well as post-hoc whole exome and transcriptome sequencing data (n = 13 patients) and investigated three specific relationships. Results: We analyzed the relationship between racial/ethnic background and functional response to anti-cancer agents, determining potential differences in response to therapeutic classes. Next, we examined relationships between functional response and cancer type, identifying an unanticipated lack of clustering between disease indications in patients with advanced pediatric cancers. Finally, we applied an explainable machine learning (xML) framework to the functional genomic dataset to develop multi-omics biomarker hypotheses for the chemotherapy agent idarubicin, pinpointing a potential multi-cancer relationship between response to idarubicin and known disease mechanisms in acute myeloid leukemia (AML), the sole indication where idarubicin is approved. We further present additional proof-of-concept studies generating biomarker hypotheses via xML, demonstrating a framework for development of multi-omics biomarkers. Conclusions: We are now expanding our pan-pediatric cancer functional genomics dataset through an NIMHD-funded expansion cohort (NCT05857969, n = 65 patients) to further investigate multi-omics relationships between functional and molecular characteristics and understand the role of race/ethnicity in the complex relationship.

Phase 1b Trial Evaluating Tolerability and Activity of Targeted Fibroblast Growth Factor Receptor Inhibition in Localized Upper Tract Urothelial Carcinoma.

We initiated a biomarker-informed preoperative study of infigratinib, a fibroblast growth factor receptor (FGFR) inhibitor, in patients with localized upper tract urothelial carcinoma (UTUC), a population with high unmet needs and tumor with a high frequency of FGFR3 alterations. Patients with localized UTUC undergoing ureteroscopy or nephroureterectomy/ureterectomy were enrolled on a phase 1b trial (NCT04228042). Once-daily infigratinib 125 mg by mouth × 21 days (28-day cycle) was given for 2 cycles. Tolerability was monitored by Bayesian design and predefined stopping boundaries. The primary endpoint was tolerability, and the secondary endpoint was objective response based on tumor mapping, done after endoscopic biopsy and post-trial surgery. Total planned enrollment: 20 patients. Targeted sequencing performed using a NovaSeq 6000 solid tumor panel. From May 2021 to November 2022, 14 patients were enrolled, at which point the trial was closed due to termination of all infigratinib oncology trials. Two patients (14.3%) had treatment-terminating toxicities, well below the stopping threshold. Responses occurred in 6 (66.7%) of 9 patients with FGFR3 alterations. Responders had median tumor size reduction of 67%, with 3 of 5 patients initially planned for nephroureterectomy/ureterectomy converted to ureteroscopy. Median follow-up in responders was 24.7 months (14.9-28.9). In this first trial of targeted therapy for localized UTUC, FGFR inhibition was well tolerated and had significant activity in FGFR3 altered tumors. Renal preservation was enabled in a substantial proportion of participants. These data support the design of a biomarker-driven phase 2 trial of FGFR3 inhibition in this population with significant unmet clinical needs.

1237 The Mutational Landscape of Molecularly Defined Oligodendrogliomas

INTRODUCTION: Oligodendrogliomas are molecularly defined by IDH1/2 mutation and codeletion of chromosome arms 1p/19q. Prior studies identified capicua transcriptional repressor (CIC), far upstream binding protein (FUBP1), and the promoter region of telomerase reverse transcriptase (TERTp) as commonly mutated in oligodendrogliomas. However, prognostically relevant molecular signatures have yet to be identified. METHODS: A retrospective single-center study evaluated adults with pathologically confirmed IDH-mutant and 1p/19q co-deleted oligodendrogliomas that underwent surgery between 2005 and 2021. Genetic data from formalin-fixed, paraffin-embedded specimens were analyzed with the NGS Solid Tumor Panel at the Johns Hopkins Medical Laboratories, which tested over 400 genes. Kaplan-Meier curves and log-rank tests were used to compare progression-free survival (PFS) and overall survival (OS). Chi-squared tests compared clinical characteristics between mutation status in the ten most frequently mutated genes. RESULTS: From 277 patients with IDH-mutated, 1p/19q co-deleted oligodendrogliomas, 95 patients with NGS were included. Ten genes had 9 or more patients with a mutation, with CIC and FUBP1 being the most frequently mutated genes (n = 60 and n = 23, respectively). Kaplan-Meier curves showed that most genes were not associated with differences in PFS or OS. CIC conferred a reduction in PFS in patients with a PFS &lt;100 months (p = 0.038), though this significance was lost when including all PFS durations (p = 0.52). While no biomarkers had sufficient statistical power, our analysis showed trends in shortened survival in patients with TP53 (p = 0.01) and PIK3CA (p = 0.03) mutations. CONCLUSIONS: Oligodendrogliomas harbor frequent mutations in CIC, FUBP1, and TERTp, but most patients typically have minimal additional alterations. As NGS becomes routine, understanding these mutations may inform therapeutic and prognostic recommendations or the development of novel targeted therapies. Additional molecular assays beyond mutation analysis with NGS may reveal prognostically relevant biologic subgroups of oligodendrogliomas.

Abstract 4250: Adherent and spheroid cell models of patient-derived xenograft for drug development and translational research

Abstract Introduction: The development of new drugs in cancer therapy comprises toxicity and efficacy tests with increasing complexity. First and foremost, in vitro experiments are performed with well-established cancer cell lines, which are subsequently validated in animal experiments as prerequisite for clinical trials. Until a few years ago, there were gaps in the complexity chain between in vitro and in vivo experiments. Ethical considerations have led to use of systems like organ on a chip or mini-organ 3D in vitro models. In cancer research, cell cultures or organoids are generated from patient tumor material. However, these cultures only reflect the tumor of one patient, which is why panels of patient tumors should be used to evaluate the effectiveness of drugs on different patients. In vivo panel screens of patient derived xenografts (PDX) mouse models need high numbers of animals and takes several months. A pre-screen with in vitro models generated from in vivo PDX tissues allows large scale and faster pre-screens complementing in vivo systems for more focused in vivo analyses. Methods: Currently we have a pool of more than 600 established PDX models of 21 tumor entities. From this pool, cancer tissues of glioblastoma, mesothelioma, gastric, head/neck, lung and breast cancer were processed in single cell suspensions and cultured under defined conditions to obtain adherent cells or spheroids. The generated PDX in vitro cultures were analyzed for cellular impurities, cancer stem cell content and perpetuation of in vivo PDX characteristics. FACS analyses for tumor specific markers, chemo sensitivity assays and growth characteristics of the PDX derived cell lines (especially for glioblastoma) were analyzed. Results: From PDX tissues used, 90% grew as adherent and/or spheroid PDX derived in vitro cultures, in which mouse cells were entirely depleted. A high percentage of these cultures showed enriched cancer stem cell features and stem cell marker expression. Tumor marker expression and standard drug sensitivity data correlate to the in vivo PDX and derived in vitro cell culture models. RNAseq data were used to predict drug sensitivities in silico for untested drugs and drug combinations on our newly established PDX derived glioblastoma cell lines. Initial screens with predicted candidates were performed. Promising conditions were successfully repeated in corresponding animal PDX models. Conclusion: The newly developed technology for establishment if in vitro cell cultures from PDX efficiently generates stably growing cell lines possessing all key features of the original PDX. These cell lines can be used for initial pre-screens to optimize and improve selection of pharmacologically active drugs or drug combinations before initiating in vivo PDX studies. Citation Format: Lars Winkler, Joshua Alcaniz, Maria Stecklum, Wolfgang Walther, Jens Hoffmann. Adherent and spheroid cell models of patient-derived xenograft for drug development and translational research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4250.

Abstract 1627: Persistence and dynamics of mutation, selection, and epistasis during the somatic evolution of low-risk, high-risk, and metastatic prostate cancer

Abstract Driver genes and mutations responsible for prostate cancer tumorigenesis have been identified, but research has not previously quantified the effects of prostate cancer driver mutations, or how the magnitude of those effects vary with cancer stage and epistatic interactions among genes. Using 2699 prostate cancer tumor exomes, genomes, and panel sequences (1648 primary tumors and 1051 metastatic samples), we calculated the cancer effect size (CES)—the each mutation confers to lower-risk (Grade Group 1/2) and higher-risk (Grade Group 3/4/5) tumorigenesis and metastasis. The lower-risk, higher-risk, and metastatic tumors exhibited similar neutral rates at which mutations were introduced into DNA, with these underlying gene mutation rates generally increasing from lower-risk to higher risk to metastatic tumors. However, lower risk, higher risk, and metastatic tumors noticeably differed in the genes and specific somatic variants that were most highly selected for within each group. Therefore, to assess whether differences in natural selection that we observed among low-risk, high-risk, and metastatic tumor types were at least partly due to epistatic interactions, we applied a model of pairwise epistasis that quantified the effect of the presence or absence of a mutation in one gene on the selection for mutations in another gene. We found significant evidence of epistatic effects among driver genes. Our results indicate a very early role for SPOP in the development of prostate cancer: strength of selection for SPOP mutations is tightly associated with the degree to which the mutation ablates contact with the BRD3, and these disruptive mutations in turn increase the selection for mutations in several other tumor suppressors and oncogenes such as RHOA. Previously identified gene-gene interactions such as that between SPOP and PIK3CA were supported by this analysis, and we also identified novel gene-gene interactions such as those between AR and MUC16 occurring during metastasis. In conclusion, we have demonstrated that rates of mutation and strengths of selection on these driver mutations vary dynamically along the trajectories to lower-risk, higher-risk, and metastatic prostate cancer, and that powerful selective epistasis among driver genes provides an explanation for these differences. Because precision therapeutic targeting of somatic variant genes is fundamentally targeting the selective benefit obtained from that variant at the time of treatment, understanding these changes in stage-specific and somatic genotype-specific selective strengths will enable better therapeutic targeting in translational and clinical science. Citation Format: Moein Rajaei, Alexander Yang, Christopher N. Cross, J Nick Fisk, Elizabeth B. Perry, Jeffrey D. Mandell, Stephen G. Gaffney, Takafumi N. Yamaguchi, Julie Livingstone, Vincent L. Cannataro, Peter Humphrey, Jose Costa, Paul C. Boutros, Jeffrey P. Townsend. Persistence and dynamics of mutation, selection, and epistasis during the somatic evolution of low-risk, high-risk, and metastatic prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1627.

Abstract 330: FusionPlex™-HT and VariantPlex™-HT: Automation ready solutions for anchored multiplex PCR

Abstract Introduction: Anchored Multiplex PCR (AMP™) assays, VariantPlex and FusionPlex are amplicon-based, next generation sequencing (NGS) workflows that identify genomic variations present in DNA or RNA input, respectively. AMP reagents are available in a lyophilized format which are user-friendly and convenient to store. However, lyophilized reagents are not suitable for liquid handlers or high-throughput environments. Thus, we developed AMP reagents in liquid format to satisfy the need for a platform-agnostic method of high-throughput (-HT) AMP library preparation. Methods: The performance of our liquid reagent-based VariantPlex-HT and FusionPlex-HT workflows were evaluated relative to legacy lyophilized reagents using several input of varying quantity, quality and type. In addition, we examined liquid reagent performance across multiple AMP panels, which target solid tumor and blood cancers variants. Prepared libraries were then sequenced and analyzed using Archer™ Analysis v7.0 software. Results: When using 50ng SeraSeq® Myeloid DNA input (LGC Clinical Diagnostics, Inc.) and the VariantPlex Core Myeloid panel (37 gene targets), both the lyophilized VariantPlex and VariantPlex-HT detected 100% (22/22) known variants ranging from 3.8% to 20.4% allele frequency (AF). When using low-quality FFPE and the VariantPlex Complete Solid Tumor panel (430 gene targets), both workflows captured 28/28 (AF: 1.4%-20.2%) and 11/11 (AF:1.2%-18.9%) single nucleotide variants (SNVs) and Insertion and Deletions (InDels) when 50ng of SeraSeq compromised FFPE or 200ng Horizon Severe FFPE was used as input, respectively. The FusionPlex-HT workflow consistently showed increased library complexity using the FusionPlex Lung V2 panel with 20ng or 50ng of Seraseq RNA Fusion Mix v4 input. This, coupled with greater on-target percentage resulted in an average increase in fusion supporting reads of 1.95x ± 0.53 and 2.2x ± 0.41 for 20ng and 50ng input, respectively. Next, we prepared a dilution series of SeraSeq RNA Fusion Mix v4 FFPE material at 100%, 25%, 10% and 5% dilutions. We utilized our FusionPlex Pan Solid Tumor panel (137 gene targets) which covers all expected fusions in this input material. At 100% and 25% dilutions, all expected fusions were detected by lyophilized FusionPlex and FusionPlex-HT workflows. However, at 10% and 5% dilutions FusionPlex-HT detected 100% and 91% of expected fusions, respectively, while legacy lyophilized reagents detected 80% and 60% of expected fusions. Citation Format: David Knupp, Christine Troutman, Allison Hadjis, Dhruti Legare, Paula Kalavakur, Michael Washburn. FusionPlex™-HT and VariantPlex™-HT: Automation ready solutions for anchored multiplex PCR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 330.

Benchmarking mismatch repair testing for patients with cancer receiving immunotherapy.

179 Background: Mismatch repair deficiency (MMR-D) serves as a theranostic marker for directing immune checkpoint inhibitor (ICI) treatment across various cancer stages and tumor types. The College of American Pathologists endorses immunohistochemistry (IHC) as the primary approach for assessing mismatch repair (MMR) testing in colorectal (CRC) and endometrial cancer (EC) patients. An alternative method involves genetic evaluation of microsatellite instability (MSI). Previous studies have shown that resistance to immune checkpoint inhibitors (ICIs) may occur due to inaccurate MSI or MMR IHC status determination. Accurate assessment of MMR status is critical for treatment decision-making. Methods: We hypothesized that tumor-only next generation sequencing (NGS) for MMR mutation signature assessment for identification of MMR-D tumors is more sensitive than MMR IHC testing. Using a standardized, clinically validated, tumor-only NGS mutation signature pipeline in place in the Oncopanel assay at DFCI/BWH, we compared the concordance in MMR determination between NGS and IHC. We then evaluated a subset of ICI-treated patients to assess the clinical implications of these findings. Results: 1655 colorectal cancer (CRC) and endometrial carcinoma (EC) patients who had both NGS MSI (NGSd = deficient or NGSp = proficient) and MMR IHC (IHC- = absent or IHC+ = intact) assays performed were assessed. Discordant NGSd/IHC+ results were identified in 1% of CRC and 5% of EC cases that were IHC+. Importantly, patients with discordant NGSd/IHC+ (median OS: not reached [NR], 95% CI, 9.9 months-NR; median TTF: 44.4 months, 95% CI, 4.1-NR) and concordant NGSd/IHC- results, showed a similar overall survival and time to treatment failure with ICI treatment (p=non-significant) which contrasted with results for patients with concordant NGSp/IHC+ results (median OS: 14.9 months, 95% CI, 7.3-24.6, p-value 0.0025 and &lt; 0.0001; median TTF: 5.0 months, 95% CI, 3.2-7.3; p-value 0.0014 and &lt; 0.0001). Patients with EC or CRC and discordant NGSd/IHC+ results had better survival when treated with ICI-based regimens, compared to those who received non-ICI treatments (p= 0.054 and 0.017). Conclusions: In 2022, 151,030 new CRC and 65,950 new EC cases were diagnosed in the USA. Extrapolating our findings to this larger population, use of NGS mutational signature analysis instead of IHC would amount to about 1510 additional MMR-D CRC cases and 3297 additional MMR-D endometrial cases identified each year for whom first-line ICI therapy is preferred. Our findings support revisiting guideline recommendations for diagnostic testing of MMR to incorporate both IHC and targeted NGS tumor panel testing using sensitive and specific mutation signature calling algorithms. Larger prospective studies are warranted to confirm these findings in patients with mCRC and mEC treated with ICIs. Evaluation of this approach in other cancer types is also warranted.

Abstract C104: Dual primary pancreas cancers – Related or independent lesions?

Abstract Background: Not infrequently, an apparent second pancreas ductal adenocarcinoma (PDAC) is identified either synchronously or metachronously. To date, it remains unclear whether these individual PDACs represent intrapancreatic metastases or a new primary PDAC. Here, we sought to understand the clinicogenomic features of this patient population to provide insights on the underlying biology and management implications. Methods: Memorial Sloan Kettering Cancer Center (MSK) institutional databases were searched for patients with two PDAC diagnoses and at least one pancreatic resection or patients who had undergone completion/total pancreatectomy and then manually curated. Detailed demographic and clinical information were abstracted from the medical record. Metachronous patients excluded if previous surgical margin positive for invasive or pre-invasive carcinoma. All patients were either consented to MSK IMPACT for somatic and germline sequencing (N=16), were approved for de-identified genomic analyses by IRB (N=3), or were excluded from genomic analysis (N=2). KRAS wild-type (WT) tumors were interrogated for targetable fusions with Archer FusionPlex solid tumor panel. Results: N=21 patients (pts) identified, N=6 synchronous, N=15 metachronous. Mean age at diagnosis of first PDAC (PDAC1): 67.1y (51.2–79.1y). PDAC risk factors: 52% (10/19) smoking history, 15% (2/13) with first degree relative with PDAC, 85% (11/13) with first degree relative with any malignancy, and 40% (8/20) with history of premalignant pancreas lesion. N=2 pts with pathogenic germline mutation in ATM. By morphology, 80% (4/5) of synchronous and 65% (11/17) of asynchronous lesions indistinguishable. Two lesions, both metachronous, demonstrated divergent histology while remaining cases demonstrated focal differences. Genomically, 40% (10/25) samples with mKRAS G12V, G12R (16%), G12D (12%), Q61H (8%), G12C (4%); 20% KRAS WT. Of available paired tumor samples, 71% (5/7) with identical KRAS alleles and additional driver mutations. N= 1 pt with different KRAS alleles also had divergent TP53 alleles and CDKN2A/B loss occur in metachronous lesions 14 m apart. N=1 pt with KRAS WT tumor had an actionable fusion involving FGFR2. For metachronous lesions, median interval PDAC1 to PDAC2: 5.1 y (1.1 – 15.2 y). At median follow-up of 7.2 y (0.2 – 15.4 y) from PDAC1, 90% (19/21) have undergone completion/total pancreatectomy and N=16 (76%) alive with 5-year survival rate of 93% (14/15). Conclusions: The clinical, pathologic, and genomic data strongly suggest that two PDAC, independent of disease interval, most often represent the same phylogenetic entity. KRAS allele variant adjudication was the single most important discriminator and was in concordance with other driver oncogenes. Pathogenic germline variants were rare and limited to gATM; notably no gBRCA/PALB2. Acknowledging the highly selected nature of this cohort, solitary intrapancreatic metastases demonstrate a more favorable biology and these patients may benefit from personalized management approaches beyond traditional paradigms. Citation Format: Joshua D. Schoenfeld, Hulya Sahan-Ozkan, Nadeem Bilani, Michael I. D'Angelica, William R. Jarnagin, Jeffrey Drebin, Diane Reidy-Lagunes, Alice C. Wei, Sree B. Chalasani, Anna M. Varghese, Fiyinfolu Balogun, Wungki Park, Kenneth H. Yu, Olca Basturk, Eileen M. O'Reilly. Dual primary pancreas cancers – Related or independent lesions? [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C104.

Importance of Patient Health Insurance Coverage and Out-of-Pocket Costs for Genomic Testing in Oncologists' Treatment Decisions.

Use of genomic testing, especially multimarker panels, is increasing in the United States. Not all tests and related treatments are covered by health insurance, which can result in substantial patient out-of-pocket (OOP) costs. Little is known about oncologists' treatment decisions with respect to patient insurance coverage and OOP costs for genomic testing. We identified 1,049 oncologists who used multimarker tumor panels from the 2017 National Survey of Precision Medicine in Cancer Treatment. Separate multivariable ordinal logistic regressions examined associations of oncologist-, practice-, and area-level characteristics and oncologists' ratings of importance (very, somewhat, or a little/not important) of insurance coverage and OOP costs for genomic testing in treatment decisions, adjusting for oncologist years of experience, sex, race and ethnicity, specialty, use of next-generation sequencing (NGS) tests, region, tumor boards, patient insurance mix, and area-level socioeconomic characteristics. Among oncologists, 47.3%, 32.7%, and 20.0% reported that patient insurance coverage for genomic testing was very, somewhat, or a little/not important, respectively, in treatment decisions. In addition, 56.9%, 28.0%, and 15.2% reported that OOP costs for testing were very, somewhat, or a little/not important, respectively. In adjusted analyses, oncologists who used NGS tests were more likely to report patient insurance and OOP costs as important (odds ratio [OR], 2.00 [95% CI, 1.16 to 3.45] and OR, 2.12 [95% CI, 1.22 to 3.68], respectively) in treatment decisions compared with oncologists who did not use these tests, as were oncologists who treated solid tumors, rather than only hematological cancers. More years of experience and higher percentages of Medicaid or self-paid/uninsured patients in the practice were associated with reporting insurance coverage (OR, 1.43 [95% CI, 1.09 to 1.89]) and OOP costs (OR, 1.51 [95% CI, 1.13 to 2.01]) as important. Oncologists in practices with molecular tumor boards for genomic tests were less likely to report coverage (OR, 0.63 [95% CI, 0.47 to 0.85]) and OOP costs (OR, 0.72 [95% CI, 0.53 to 0.97]) as important than their counterparts in practices without these tumor boards. Most oncologists rate patient health insurance and OOP costs for genomic tests as important considerations in subsequent treatment recommendations. Modifiable factors associated with these ratings can inform interventions to support patient-physician decision making about care.

Application of WHO CNS Fifth Edition Criteria for Glioblastoma Multiforme Diagnosis: A single center study

Abstract Introduction/Objective The fifth edition of the WHO classification of the tumors of the central nervous system (WHO CNS 5) published in 2021 introduced major changes that incorporate molecular diagnostics in CNS tumor classification along with histology and immunohistochemistry. Glioblastomas (GBM) were diagnosed based on the histologic features of diffuse and astrocytic glioma in adults, if there is microvascular proliferation and /or necrosis. Isocitrate dehydrogenase 1 (IDH) R132 H immunohistochemical stain expression and /or mutation analysis results were used to further classify GBMs as IDH mutant or IDH wild type. In WHO CNS 5 all IDH mutant diffuse astrocytic tumors are considered a single type (Astrocytoma, IDH mutant) and graded 2, 3, or 4. Glioblastoma IDH wild type is diagnosed in the setting of an IDH wild type diffuse and astrocytic glioma with microvascular proliferation or necrosis or TERT promoter mutation or EGFR gene amplification or +7/-10 chromosome copy number changes. In this study, we analyze how the change in diagnostic criterion would affect the classification of GBMs diagnosed in our institution retrospectively. Methods/Case Report The pathology database was searched for all diffuse gliomas diagnosed as GBM between 01/2019 and 12/2021. Age of the patient, gender, location of tumor, histologic features, IDH status and molecular alterations ( Onkosight Advanced solid tumor panel, 50 genes) were reviewed. Results (if a Case Study enter NA) A total of 74 adult high grade glial neoplasms were identified out of which 25 were GBMs. The age of the patients ranged from 40 to 87 years. 14 were men and 11 were females. All tumors had histologic features of GBM such as necrosis and microvascular proliferation. 24 (96%) tumors were IDH negative by immunohistochemistry and mutation analysis, and 1 (4%) was IDH strongly positive by immunohistochemistry. Molecular studies were not performed on this tumor. Conclusion 96% of GBMS diagnosed during the time period conformed to the WHO CNS 5 diagnostic criteria. The one IDH positive tumor would be reclassified as diffuse astrocytoma, IDH mutant, Grade 4. Like previous WHO classifications, WHO CNS 5 is a work in progress attempting to introduce new knowledge into the classification hoping to provide practical guidance to pathologists and neuro-oncologists and to benefit the patients with CNS tumors.

Role of the S1P Signaling Pathway in the Pathogenesis of Angioimmunoblastic T-Cell Lymphoma

Peripheral T cell lymphomas (PTCLs) are a group of aggressive lymphoid malignancies originating from mature T cells. Angioimmunoblastic T-cell lymphomas (AITL) represent 20% to 30% of all PTCL diagnoses and are associated with autoimmune features, poor response to chemotherapy, and dismal prognosis. Molecular profiling of AITL has identified T-follicular helper (TFH) cells as the cell of origin of AITL, while mutational analysis has identified frequent alterations in epigenetic regulators ( TET2, DNMT3A, and IDH2) and elements of the TCR pathway as drivers of AITL transformation. Our group identified the highly recurrent RHOA G17V mutation as a defining hallmark of AITL and other T-cell lymphomas of TFH-cell origin (Palomero et al., 2014). Using a novel conditional knockin mouse model, we demonstrated that expression of Rhoa G17V in CD4+ T-cells induces TFH cell specification and promotes AITL lymphomagenesis in the context of loss of Tet2 (Cortes et al., 2018). Recently, we have identified that Rhoa G17V regulates the expression of the sphingosine-1-phosphate (S1P) receptor 1 (S1PR1) one of the five members of the receptor family of S1P, which plays an essential role in immune response and lymphocyte trafficking. During thymic T-cell development, expression of Rhoa G17V in CD4+ cells inhibited S1PR1 downregulation after the double positive stage leading to altered positive selection, reduced CD4+ single positive cell numbers and premature thymic egress of autorreactive T-cells which results in the development of systemic inflammation and autoimmunity. In our Tet2 −/− RHOA G17V AITL tumor model, constitutive activation of S1P receptors supported activation of the STAT3 and NFkB pathway and enhanced migration of malignant cells to peripheral organs. Mechanistically, expression of Rhoa G17V in mature CD4+ T-cells impaired re-phosphorylation of the Ezrin-Radoxin-Moesin (ERM) complex independently of ROCK signaling and led to the activation and increased migration of CD4+ T-cells. Importantly, blockade of S1PR1 signaling by fingolimod induced anti-tumor activity in Tet2 −/− RHOA G17V lymphoma-bearing mice in vivo with significant reductions in tumor burden associated with increased apoptosis and decreased STAT3 phosphorylation. Furthermore, analysis of a panel of primary tumors from AITL patients using a multiplexed staining panel and PhenoImager platform revealed significantly higher S1PR1 expression in AITL tumor cells than normal TFH cells from benign reactive lymph nodes. Our findings highlight the role of S1P signaling pathway in the pathogenesis of RHOA G17V-driven AITLs and the potential therapeutic benefit of targeting this pathway.

Characterization of DNA Damage Response-Associated Somatic Mutations in Borderline Resectable and Locally Advanced Pancreatic Cancer

The role of radiation for pancreatic cancer remains controversial, with recent studies showing conflicting results, highlighting the need to develop biomarkers of radiation response. Despite its potential utility in predicting radiosensitivity, the landscape of somatic mutations in borderline resectable pancreatic cancer (BRPC) and locally advanced pancreatic cancer (LAPC), as related to DNA damage response (DDR), has not been well characterized. This study aimed to characterize the frequency of such mutations in a cohort of patients with BRPC/LAPC treated with neoadjuvant chemotherapy and stereotactic body radiotherapy (SBRT). Mutational data was collected from patients with BRPC/LAPC treated at a single institution with neoadjuvant chemotherapy and SBRT, followed by surgical resection from 2016-2021. Chemotherapy consisted of modified FOLFIRINOX or gemcitabine/nab-paclitaxel, and patients were treated with SBRT in 33 Gy in 5 fractions. Genomic data was obtained from either endoscopic biopsy or surgical specimens, and next-generation sequencing was performed either in-house with a Solid Tumor Panel or with FoundationOne CDx. Specific emphasis was placed on the characterization of double-strand DNA break (DSB) repair genes, as this is the type of tumor cell damage traditionally induced by radiation therapy. Genes associated with the two main pathways of DSB repair, non-homologous end joining (NHEJ) and homologous repair (HR), were analyzed. Specific HR pathway mutations assessed were BLM, BRCA1/2, MRE11, NBN, PALB2, RAD50, RAD51B-D, and RAD54L, while PRKDC mutations were assessed for the NHEJ pathway. Mutations in ATM, an important initiator of DDR pathways, were also analyzed. Additionally, the frequency of mutations in TP53, CDKN2A and SMAD4 in patients with concomitant KRAS mutations was assessed. Eighty-five patients were included in the study. Five (5.9%) patients had mutations in the NHEJ pathway of the PRKDC gene. Twenty (23.5%) patients had mutations in the HR pathway, including BRCA2 (10/85; 11.8%), PALB2 (5/85; 5.9%), BRCA1 (3/85; 3.5%), and RAD50 (1/85; 1.2%). Six (7.1%) patients had mutations in ATM. No patients were found to have mutations in BLM, RAD51B-D, RAD54L, or NBN. Amongst patients with KRAS mutations (72/85), concomitant mutations were observed in TP53 (47/85; 55.3%), CDKN2A (16/85; 18.8%), and SMAD4 (9/85; 10.6%). Herein, we characterized the frequency of somatic mutations associated with DSB repair genes in patients with BRPC/LAPC. Data analysis on outcomes related to radiation response in patients with mutations in DDR pathways is ongoing, but will likely also benefit from multi-institutional efforts to increase the power to answer this question.

Pathway Mutations are Associated with Clinical Outcomes in Localized Pancreatic Cancer Treated with Neoadjuvant Chemoradiation Followed by Surgery

The purpose of this study was to determine if mutations in biological pathways are associated with clinical outcomes in patients with localized pancreatic cancer who undergo neoadjuvant chemoradiation followed by surgical resection. Patients treated with neoadjuvant chemoradiation followed by oncologic resection from 2015-2019 who also underwent next generation sequencing (NGS) of the primary tumor were included in this retrospective analysis. NGS was done using either Foundation One (n = 20), in-house Solid Tumor Panel (n = 121), or Tempus XT (n = 1). Genes were included in pathway analysis if at least one patient harbored a mutation in the gene. Pathways were defined from the Molecular Signatures Database Hallmark, KEGG, and Reactome gene sets. A pathway was deemed mutated if at least one gene within the pathway was mutated. Univariable Cox regression was performed to determine the association between pathway mutation status and overall survival (OS) as well as progression-free survival (PFS). In total, 142 patients met criteria for study inclusion. For pathway analysis, 329 genes met inclusion criteria. Patients were typically treated with neoadjuvant chemotherapy (either 5-fluorouracil-based or gemcitabine-based) followed by radiation. Patients received SBRT (n = 104, most commonly 33 Gy in 5 fractions) or conventionally fractionated radiation (n = 38, most commonly 50.4 Gy in 28 fractions). For clinical variables, worse OS was significantly associated with T stage (p = 0.036), N stage (p = 0.044), and lymphovascular invasion (LVI, p = 0.011); worse PFS was significantly associated with T stage (p = 0.0008), N stage (p = 0.022), LVI (p = 0.026), and conventional RT (p = 0.007). Mutations in major pathways were associated with worse OS, notably hedgehog signaling (p = 0.001), chromatin modifying enzymes (p = 0.002), WNT/beta-catenin signaling (p = 0.005), mismatch repair (0.006), E2F targets (p = 0.008), FLT signaling (p = 0.012), VEGF signaling (0.025), innate immune system (p = 0.026), and NOTCH signaling (p = 0.029). Pathway mutations associated with worse PFS included mismatch repair (p = 0.007) and hedgehog signaling (p = 0.013). For pancreatic cancer patients that undergo neoadjuvant chemoradiation followed by oncologic resection of the primary tumor, mutations in key biological pathways are associated with OS and PFS. Characterizing the importance of common pathway mutations may become increasingly valuable to help categorize less commonly mutated genes assayed by NGS.

P02.12.B UNDERSTANDING THE ROLES OF EPHRIN A5 IN GLIOBLASTOMA AND ITS POTENTIAL AS A THERAPEUTIC TARGET

Abstract BACKGROUND Glioblastoma (GBM) is the most common and aggressive malignant primary brain cancer and is associated with very poor patient outcomes. GBM has been classified into three cell subtypes (proneural (PN), classical (CL), and mesenchymal (MES)), which have been further defined into four plastic cell states (neural-progenitor-like (NPC-like), oligodendrocyte-progenitor-like (OPC-like), astrocyte-like (AC-like), and mesenchymal-like (MES-like)). Existing treatment options have had limited success in improving overall survival, with the extreme heterogeneity present in GBM presenting a major barrier to effective therapy. Thus, there is an urgent need to develop more effective therapeutic strategies which better capture heterogeneity and delay tumour relapse. Several erythropoietin-producing human hepatocellular (Eph) receptors and ephrin ligands have been shown to be functionally overexpressed in cancer and have become attractive therapeutic targets. EphA3 has previously been shown to be a functional, tumour-specific target, frequently elevated in the MES subtype. We identified ephrin A5, the high-affinity ligand of EphA3, to be frequently co-expressed with EphA3 in GBM tumours. However, unlike EphA3, the mechanisms of ephrin A5 in GBM remain understudied. We therefore believe that ephrin A5 serves as an attractive synergistic target for the treatment of GBM. MATERIAL AND METHODS We examined the expression of ephrin A5 in a panel of GBM patient specimens. A panel of GBM tumours were also selected for immunohistochemical and spatial transcriptomics analysis. For in vitro functional studies, ephrin A5 was overexpressed in several GBM primary cell lines. Assays examining proliferation, stemness and differentiation were performed. RESULTS Expression of ephrin A5 was comparable to EphA3 in GBM. 64% of GBM tumours analysed showed higher levels of ephrin A5, relative to the highest normal brain specimen. Initial immunohistochemistry analysis suggests EphA3 and ephrin A5 to be expressed discretely on over 75% of the total tumour mass. Spatial transcriptomics analysis suggests ephrin A5 to be enriched in cells of the AC-like cell state. In vitro overexpression of ephrin A5 was shown to reduce neurosphere formation and induce differentiation of GBM cells. CONCLUSION EphA3 and ephrin A5 are overexpressed in a portion of GBM tumours. Critically, there was a strong mutually exclusive expression to different compartments of the GBM tumour, covering the vast majority of the total tumour mass. Our data suggests that ephrin A5 overexpression drives a less aggressive, more differentiated AC-like tumour phenotype. Thus, dual targeting of EphA3 and ephrin A5 in GBM could provide an opportunity to better capture tumour heterogeneity and achieve more durable therapeutic responses.