Intragenic EGFR::EGFR.E1E8 Fusion (EGFRvIII) in 4331 Solid Tumors

Epidermal growth factor receptor variant III (EGFRvIII, the deletion of exons 2-7) is a recurrent intragenic EGFR::EGFR.E1E8 fusion that occurs in high-grade gliomas. The presence of EGFRvIII in other solid tumors has not been well characterized. We retrospectively reviewed advanced malignant solid tumor cases tested by a custom hybrid capture 610-gene next-generation sequencing platform from 2021 to 2022. EGFRvIII was identified in 17 of 4331 (0.4%) cases, including 16 of 238 (7%) brain tumors and 1/301 (0.3%) breast tumors. EGFRvIII-positive brain tumors were all glioblastoma IDH-wildtype, most with concurrent TERT promoter mutation (14 of 16), EGFR amplification (13 of 16), and EGFR mutation (8 of 16). The only EGFRvIII-positive breast lesion was a sarcomatoid neoplasm in a young female patient. A separate breast case tested outside our institution with reported EGFRvIII was noted in a young female patient with a malignant phyllodes tumor with stromal overgrowth. Microscopically, both EGFRvIII-positive breast tumors showed high-grade sarcomatoid morphology with brisk mitotic activity. In summary, EGFRvIII is rare, occurring primarily in glioblastoma and rarely in breast sarcomatoid neoplasm, with no instances identified in other tumor types in our series. This select group of patients may benefit from chemotherapy and/or targeted anti-EGFR therapy.

Single centre experience in transcatheter mitral valve implantation: valve in valve, valve in ring and valve in MAC

Background

Mitral valve replacement/repeair procedures increase year. Redo procedure and severely calcified mitral ring are risk factors for high mortality. Transmitral valve implantation (TMVI) represents a less invasive procedure in high-risk population, but still with increase mortality. We seek to evaluate a one single center experience the safety and efficacy in patients undergoing transeptal TMVI with degenerated bioprostheses or ring and high surgical risk candidates with heavily mitral anulus calcification (MAC).

Methods

One-single centre, retrospective observational analysis, included patientes from 2012 to 2021 treated with a valve in mitral position. Valve-in-valve (ViV), valve in ring (ViR) and valve in MAC were included. Periprocedural, and in-hospital complications were documented and analyzed.

Results

Seventy-nine patients were included. ViV was done in 59 patients, ViR in 8 patients, ViMAC in 10 patients and Valve in native anatomy in 2 patients. Baseline, procedural characteristics and complications and reported on table. No significant statistical difference was observed in baseline characteristics. STS Score was 7.77+5.37 in ViV patients, 5.77+3.02 in ViR patients, 8.70+4.47 in ViMAC patients and 6.29+0.55 in native anatomy (p=0.634). Procedural success was observed in 96.6% of ViV, 87.5% in ViR, 80% in ViMAC and 100% in native anatomy (p=0.124). Procedural related death was observed only in one ViV patient. Conversion to surgery and valve embolisation was observed in one ViV (1.7%) and ViR (12.5%) patient, respectively. In-hospital death was observed in 5.1% ViV patients, 12.5% ViR, 20% ViMAC and none of the native anatomy patients.

Conclusion

TMVI is still challenging but feasible and safe. Carefully planning and heart team approach in experiences centers is important to address this issue and reduce as much as possible any complication.

Funding Acknowledgement

Type of funding sources: None.

Development and Validation of a Gene Signature Classifier for Consensus Molecular Subtyping of Colorectal Carcinoma in a CLIA-Certified Setting

PURPOSE

Consensus molecular subtyping (CMS) of colorectal cancer has potential to reshape the colorectal cancer landscape. We developed and validated an assay that is applicable on formalin-fixed, paraffin-embedded (FFPE) samples of colorectal cancer and implemented the assay in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory.

EXPERIMENTAL DESIGN

We performed an in silico experiment to build an optimal CMS classifier using a training set of 1,329 samples from 12 studies and validation set of 1,329 samples from 14 studies. We constructed an assay on the basis of NanoString CodeSets for the top 472 genes, and performed analyses on paired flash-frozen (FF)/FFPE samples from 175 colorectal cancers to adapt the classifier to FFPE samples using a subset of genes found to be concordant between FF and FFPE, tested the classifier's reproducibility and repeatability, and validated in a CLIA-certified laboratory. We assessed prognostic significance of CMS in 345 patients pooled across three clinical trials.

RESULTS

The best classifier was weighted support vector machine with high accuracy across platforms and gene lists (>0.95), and the 472-gene model outperforming existing classifiers. We constructed subsets of 99 and 200 genes with high FF/FFPE concordance, and adapted FFPE-based classifier that had strong classification accuracy (>80%) relative to "gold standard" CMS. The classifier was reproducible to sample type and RNA quality, and demonstrated poor prognosis for CMS1-3 and good prognosis for CMS2 in metastatic colorectal cancer (P < 0.001).

CONCLUSIONS

We developed and validated a colorectal cancer CMS assay that is ready for use in clinical trials, to assess prognosis in standard-of-care settings and explore as predictor of therapy response.

Abstract 1402: Single cell transcriptomic profiling of ex vivo tumoroid models reveal therapeutic vulnerabilities of pancreatic ductal adenocarcinoma

By 2030, pancreatic ductal adenocarcinoma (PDAC) will likely become the second leading cause of cancer-related death. A lack of actionable mutations continues to be a significant challenge in addressing the disease in a precision medicine setting. As a result, current treatment options are often limited to genotype-independent cytotoxic agents. Patient derived tumor organoid (PDOs) models have gained traction as potential tools for therapeutic stratification. We characterized single cell gene expression profiles of PDOs and applied an in silico therapeutic drug prediction model to identify and validate combinatorial strategies targeting heterogeneous subpopulations. Four established PDOs from PDAC were profiled through single cell RNA-Seq analysis in order to identify subpopulations of cancer cells with differing therapeutic response. The PDOs were then subjected to a high-throughput drug screen of 764 agency approved candidates. Top candidates, including combinatorial drug selections, were orthogonally validated through single cell gene expression analysis and evaluated for efficacy and synergistic interactions. Single-cell transcriptomic profiling of PDOs revealed unique subpopulations of cancer cells with differential expression of DNA Damage response, protein and fatty acid metabolism, and inflammatory related pathways. Effective combinatorial therapies were projected based on pharmacogenomic predictions targeting opposite gene expression patterns of each subpopulation and validated through drug library screens. In a PDO, common sensitivity nodes utilizing epigenetic modifiers were detected among all tumor derived subpopulations. A synergy matrix seeded with PDOs and evaluated using Bliss independence revealed that combinatorial treatment with HDAC-inhibitors and PARP1-inhibitors produced the most profound synergistic result. Mechanistically, HDAC inhibitors limit the activity of DNA repair proteins which in conjunction with PARP-inhibition leads to synergistic outcomes. We have demonstrated the utility of single cell transcriptomic profiling from PDOs in identifying viable treatment options using a pharmacogenomic strategy. The sophisticated heterogeneity of PDOs, revealed the necessity of using combinatorial strategies to target all relevant subpopulations. Furthermore, this strategy revealed an exciting synergistic interplay between HDAC and PARP1 inhibitors, an interaction that has never before been shown in a PDAC case. Looking forward, our model not only may be a vehicle used to discover new drug candidates and elucidate novel mechanisms, but may also be the first step towards the establishment of a true precision medicine paradigm for PDAC.

Citation Format: Vincent Bernard, F. Anthony San Lucas, Jonathan Huang, Reid T. Powell, Paola A. Guerrero, Alexander Semaan, Clifford C. Stephan, Peter Davies, Gauri R. Varadhachary, Matthew H. Katz, Cullen M. Taniguchi, Hector A. Alvarez, Senthil Muthuswamy, Anirban Maitra. Single cell transcriptomic profiling of ex vivo tumoroid models reveal therapeutic vulnerabilities of pancreatic ductal adenocarcinoma [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 1402.

Circulating Nucleic Acids Are Associated With Outcomes of Patients With Pancreatic Cancer

BACKGROUND & AIMS

We aimed to investigate the clinical utility of circulating tumor cell DNA (ctDNA) and exosome DNA (exoDNA) in pancreatic cancer.

METHODS

We collected liquid biopsy samples from 194 patients undergoing treatment for localized or metastatic pancreatic adenocarcinoma from April 7, 2015, through October 13, 2017 (425 blood samples collected before [baseline] and during therapy). Additional liquid biopsy samples were collected from 37 disease control individuals. Droplet digital polymerase chain reaction was used to determine KRAS mutant allele fraction (MAF) from ctDNA and exoDNA purified from plasma. For the longitudinal analysis, we analyzed exoDNA and ctDNA in 123 serial blood samples from 34 patients. We performed analysis including Cox regression, Fisher exact test, and Bayesian inference to associate KRAS MAFs in exoDNA and ctDNA with prognostic and predictive outcomes.

RESULTS

In the 34 patients with potentially resectable tumors, an increase in exoDNA level after neoadjuvant therapy was significantly associated with disease progression (P = .003), whereas ctDNA did not show correlations with outcomes. Concordance rates of KRAS mutations present in surgically resected tissue and detected in liquid biopsy samples were greater than 95%. On univariate analysis, patients with metastases and detectable ctDNA at baseline status had significantly shorter times of progression-free survival (PFS) (hazard ratio [HR] for death, 1.8; 95% CI, 1.1-3.0; P = .019), and overall survival (OS) (HR, 2.8; 95% CI, 1.4-5.7; P = .0045) compared with patients without detectable ctDNA. On multivariate analysis, MAFs ≥5% in exoDNA were a significant predictor of PFS (HR, 2.28; 95% CI, 1.18-4.40; P = .014) and OS (HR, 3.46; 95% CI, 1.40-8.50; P = .007). A multianalyte approach showed detection of both ctDNA and exoDNA MAFs ≥5% at baseline status to be a significant predictor of OS (HR, 7.73, 95% CI, 2.61-22.91, P = .00002) on multivariate analysis. In the longitudinal analysis, an MAF peak above 1% in exoDNA was significantly associated with radiologic progression (P = .0003).

CONCLUSIONS

In a prospective cohort of pancreatic cancer patients, we show how longitudinal monitoring using liquid biopsy samples through exoDNA and ctDNA provides both predictive and prognostic information relevant to therapeutic stratification.

Single-Cell Transcriptomics of Pancreatic Cancer Precursors Demonstrates Epithelial and Microenvironmental Heterogeneity as an Early Event in Neoplastic Progression

PURPOSE

Early detection of pancreatic ductal adenocarcinoma (PDAC) remains elusive. Precursor lesions of PDAC, specifically intraductal papillary mucinous neoplasms (IPMNs), represent a bona fide pathway to invasive neoplasia, although the molecular correlates of progression remain to be fully elucidated. Single-cell transcriptomics provides a unique avenue for dissecting both the epithelial and microenvironmental heterogeneities that accompany multistep progression from noninvasive IPMNs to PDAC.

EXPERIMENTAL DESIGN

Single-cell RNA sequencing was performed through droplet-based sequencing on 5,403 cells from 2 low-grade IPMNs (LGD-IPMNs), 2 high-grade IPMNs (HGD-IPMN), and 2 PDACs (all surgically resected).

RESULTS

Analysis of single-cell transcriptomes revealed heterogeneous alterations within the epithelium and the tumor microenvironment during the progression of noninvasive dysplasia to invasive cancer. Although HGD-IPMNs expressed many core signaling pathways described in PDAC, LGD-IPMNs harbored subsets of single cells with a transcriptomic profile that overlapped with invasive cancer. Notably, a proinflammatory immune component was readily seen in low-grade IPMNs, composed of cytotoxic T cells, activated T-helper cells, and dendritic cells, which was progressively depleted during neoplastic progression, accompanied by infiltration of myeloid-derived suppressor cells. Finally, stromal myofibroblast populations were heterogeneous and acquired a previously described tumor-promoting and immune-evading phenotype during invasive carcinogenesis.

CONCLUSIONS

This study demonstrates the ability to perform high-resolution profiling of the transcriptomic changes that occur during multistep progression of cystic PDAC precursors to cancer. Notably, single-cell analysis provides an unparalleled insight into both the epithelial and microenvironmental heterogeneities that accompany early cancer pathogenesis and might be a useful substrate to identify targets for cancer interception.See related commentary by Hernandez-Barco et al., p. 2027.

Abstract 2599: Circulating nucleic acids as biomarkers of prognosis and chemorefractory status in metastatic pancreatic cancer

Background: Prognostic and therapeutic stratification of pancreatic ductal adenocarcinoma (PDAC) patients remains elusive due to a lack of effective biomarkers, and a predilection towards metastatic disease. Peripheral blood-based liquid biopsies for tumor markers has emerged as a potential minimally invasive strategy for tumor monitoring. We have implemented a liquid biopsy assay utilizing DNA derived from vesicles known as exosomes (exoDNA) and circulating tumor DNA (ctDNA) in the metastatic setting to determine the potential utility of these liquid biopsy compartments in tumor management.

Methods: A total of 318 plasma samples from 123 metastatic pancreatic patients were prospectively collected. ExoDNA and ctDNA were then extracted from matched plasma samples. Digital PCR, was used to identify codon 12/13 KRAS gene mutations. We assessed clinical endpoints in relation to progression free survival (PFS) and overall survival (OS) using univariate and multivariate analyses. In a metastatic PDAC patient, six serial liquid biopsies and seven tissue biopsies taken throughout disease progression underwent whole genome sequencing for detection of copy number events.

Results: Detection rates of KRAS mutations in exoDNA and ctDNA at baseline treatment naïve staus were 61.0% and 52.9%, respectively. On multivariate COX regression analysis, exoDNA KRAS mutant allelic fraction (MAF) ≥ 5% was a significant predictor of poorer PFS (HR 2.28, 95% CI 1.18-4.40, P=0.014) and OS (HR 3.46, 95% CI 1.40-8.50, P=0.007) in metastatic patients. Among 34 patients, liquid biopsy tumor monitoring was performed across 127 serial blood draws during a median followup time of 11.1 months. The presence of an exoDNA MAF peak ≥ 1% during tumor monitoring was significantly correlated to radiological progression (p=0.0003). Specifically, detection of an exoDNA MAF peak ≥ 1% preceded radiological progression by a median of 50 days compared to a median of 0 days for CA19-9 (p=0.03). CtDNA did not emerge as a significant predictor of survival outcomes in our cohort. In a patient with multiple longitudinal liquid biopsies, comprehensive genomic profiling of exoDNA further demonstrated our ability to capture additional mutational events as they emerged during therapy and correlated to progression including amplifications in ERBB2 and MYC and deletions in CDKN2A and SMAD4.

Conclusions: Liquid biopsies in PDAC provide direct evidence of those patients likely to experience poorer outcomes allowing for more effective therapeutic stratification. Liquid biopsies also demonstrate utility in characterization of putative emerging driver events during disease progression.

Citation Format: Vincent Bernard, Dong U. Kim, F. Anthony San Lucas, Jonathan Castillo, Kelvin Allenson, Feven C. Mulu, Bret M. Stephens, Jonathan Huang, Eugene Koay, Cullen M. Taniguchi, Milind Javle, Robert A. Wolff, Matthew H. Katz, Gauri R. Varadhachary, Hector A. Alvarez, Anirban Maitra. Circulating nucleic acids as biomarkers of prognosis and chemorefractory status in metastatic pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2599.

4-1BB Agonist Focuses CD8+ Tumor-Infiltrating T-Cell Growth into a Distinct Repertoire Capable of Tumor Recognition in Pancreatic Cancer

Purpose: Survival for pancreatic ductal adenocarcinoma (PDAC) patients is extremely poor and improved therapies are urgently needed. Tumor-infiltrating lymphocyte (TIL) adoptive cell therapy (ACT) has shown great promise in other tumor types, such as metastatic melanoma where overall response rates of 50% have been seen. Given this success and the evidence showing that T-cell presence positively correlates with overall survival in PDAC, we sought to enrich for CD8+ TILs capable of autologous tumor recognition. In addition, we explored the phenotype and T-cell receptor repertoire of the CD8+ TILs in the tumor microenvironment.Experimental Design: We used an agonistic 4-1BB mAb during the initial tumor fragment culture to provide 4-1BB costimulation and assessed changes in TIL growth, phenotype, repertoire, and antitumor function.Results: Increased CD8+ TIL growth from PDAC tumors was achieved with the aid of an agonistic 4-1BB mAb. Expanded TILs were characterized by an activated but not terminally differentiated phenotype. Moreover, 4-1BB stimulation expanded a more clonal and distinct CD8+ TIL repertoire than IL2 alone. TILs from both culture conditions displayed MHC class I-restricted recognition of autologous tumor targets.Conclusions: Costimulation with an anti-4-1BB mAb increases the feasibility of TIL therapy by producing greater numbers of these tumor-reactive T cells. These results suggest that TIL ACT for PDAC is a potential treatment avenue worth further investigation for a patient population in dire need of improved therapy. Clin Cancer Res; 23(23); 7263-75. ©2017 AACR.

Larger size extracellular vesicle as early biomarker in patients with metastatic pancreatic cancer

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Background: Current research suggests that tumor-derived extracellular vesicles (EVs) play an important role in tumor progression especially with regard to metastasis. Atypically large EVs have been reported to have the ability to transport bioactive molecules through the blood stream. Therefore, EV physical properties such as diameters and concentrations may have a biological impact on tumor progression. However, it has not been described which characteristics are clinically relevant in the longitudinal assessment of tumor progression and chemo-response. Methods: Plasma from 19 metastatic PDAC patients was collected at treatment-naïve baseline and in more than 2 consecutive assessments during chemotherapy between May 2015 and July 2016. EVs from plasma were isolated using a sequential centrifugation protocol, confirmed as described previously and analyzed using the Particle Metrix (Zetaview, Diessen, Germany) and proprietary software. The clinical variables along with concentration and size distribution of EVs were analyzed to identify prognostic factors associated with chemo-response. Results: Mean EV size and concentration were 122.85 nm and 4.13x109/mL plasma at treatment naïve baseline, 123.62 nm and 4.39x109/mL plasma at first response assessment during chemotherapy. Median overall and progression-free survivals were 256 and 165 days, respectively. The change of CA 19-9 (hazard ratio 17.477, p = 0.001, 95% CI 0.995-1.045) and proportion of EVs larger than 150nm (hazard ratio 11.022, p = 0.017, 95% CI 3.183-95.964) was a significant independent predictor of progression-free survival at first response assessment during chemotherapy. In addition, we observed a dramatic increase in the proportion of larger EVs earlier than the increases in CA 19-9. Conclusions: Our data suggests that increases in the amounts of larger EVs are independent predictors of tumor progression and chemo-response in metastatic pancreatic cancer patients. Furthermore, the increases in the amounts of larger EVs may potentially be more clinically useful than CA19-9 in the earlier stages of progression. Concentrations of larger-sized EVs could be a valuable component of more sophisticated diagnostics in liquid biopsies.

Exploiting the neoantigen landscape for immunotherapy of pancreatic ductal adenocarcinoma

Immunotherapy approaches for pancreatic ductal adenocarcinoma (PDAC) have met with limited success. It has been postulated that a low mutation load may lead to a paucity of T cells within the tumor microenvironment (TME). However, it is also possible that while neoantigens are present, an effective immune response cannot be generated due to an immune suppressive TME. To discern whether targetable neoantigens exist in PDAC, we performed a comprehensive study using genomic profiles of 221 PDAC cases extracted from public databases. Our findings reveal that: (a) nearly all PDAC samples harbor potentially targetable neoantigens; (b) T cells are present but generally show a reduced activation signature; and (c) markers of efficient antigen presentation are associated with a reduced signature of markers characterizing cytotoxic T cells. These findings suggest that despite the presence of tumor specific neoepitopes, T cell activation is actively suppressed in PDAC. Further, we identify iNOS as a potential mediator of immune suppression that might be actionable using pharmacological avenues.

Angiographic findigs and prognostic indicators in patients resuscitated from sudden cardiac death

Sixty-four patients with coronary artery disease (CAD) who had been resuscitated from out-of-hospital ventricular fibrillation (VF) underwent cardiac catheterization and angiography. The majority (72%) had a previous history of cardiovascular disease; in the remaining 28%, VF was the first manifestation of CAD. Advanced coronary atherosclerosis was a common finding; 94% of the patients had severe stenoses (70% or greater diameter narrowing) in one or more of the major coronary arteries, and most (70%) had ventricular wall contraction abnormalities. In over half of the patients, coronary anatomy was potentially suitable for complete revascularization. During an average follow-up period of 20.4 months, fourteen of the 64 patients developed a second episode of VF and/or died suddenly (VF/SD). In an attempt to identify characteristics which might be of prognostic value, the clinical, hemodynamic, and angiographic characteristics of this group were compared to those patients who had a single episode of VF and survived during follow-up. Patients who developed recurrent VF/SD had more triple vessel CAD (P less than 0.01), lower ejection fractions (P less than 0.05), and far more severe abnormalities of left ventricular contraction (P less than 0.001). These results indicate that angiographic findings can identify individuals at high risk for recurrent VF and also suggest that myocardial scarring may be an important factor in the initiation of ventricular fibrillation and in its recurrence.