Extracellular Vesicle-Based Multianalyte Liquid Biopsy as a Diagnostic for Cancer

Liquid biopsy is the analysis of materials shed by tumors into circulation, such as circulating tumor cells, nucleic acids, and extracellular vesicles (EVs), for the diagnosis and management of cancer. These assays have rapidly evolved with recent FDA approvals of single biomarkers in patients with advanced metastatic disease. However, they have lacked sensitivity or specificity as a diagnostic in early-stage cancer, primarily due to low concentrations in circulating plasma. EVs, membrane-enclosed nanoscale vesicles shed by tumor and other cells into circulation, are a promising liquid biopsy analyte owing to their protein and nucleic acid cargoes carried from their mother cells, their surface proteins specific to their cells of origin, and their higher concentrations over other noninvasive biomarkers across disease stages. Recently, the combination of EVs with non-EV biomarkers has driven improvements in sensitivity and accuracy; this has been fueled by the use of machine learning (ML) to algorithmically identify and combine multiple biomarkers into a composite biomarker for clinical prediction. This review presents an analysis of EV isolation methods, surveys approaches for and issues with using ML in multianalyte EV datasets, and describes best practices for bringing multianalyte liquid biopsy to clinical implementation. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Abstract 4563: Antibody targeting of anaplastic lymphoma kinase induces cytotoxicity of human neuroblastoma

The purpose of this study was to provide the first pre-clinical evidence for antibody targeting of anaplastic lymphoma kinase (ALK) in human neuroblastoma. ALK is a receptor tyrosine kinase expressed by the majority of neuroblastoma tumors. Germline mutations of ALK, shown to account for most cases of familial neuroblastoma, as well as somatically acquired ALK aberrations, induce increased auto-phosphorylation and constitutive ALK activation and increased downstream signaling. Antibody targeting of receptor tyrosine kinases, as monotherapy or together with small-molecule inhibitors, is highly effective in other cancers such as breast and lung cancer. While antibody-mediated immunotherapy targeting of disialoganglioside GD2 has recently been reported to significantly increase 2-year survival in high-risk neuroblastoma patients, over half the patients receiving this therapy ultimately succumb to their disease and therapeutic alternatives are urgently needed to improve survival rates of this devastating pediatric cancer. Therefore, we hypothesized that antibody targeting of ALK in neuroblastoma was a therapeutically appropriate strategy. To first confirm the potential of anti-ALK antibody-mediated immunotherapy, we used in vitro assays to demonstrate enhanced immune-cell induced cytotoxicity of antibody-treated human neuroblastoma-derived cell lines. We next showed that in vitro antibody treatment of neuroblastoma cell lines expressing activated ALK led to growth inhibition and cell death. These effects were enhanced by treatment with PF-02341066, an orally available small-molecule inhibitor of the ALK tyrosine kinase. To identify the mechanism behind this enhanced combined effect, we used flow cytometry to show that PF-02341066 sensitizes cells to antibody treatment by inducing accumulation of cell-surface ALK, thus increasing the accessibility of antigen for antibody binding. Finally, to further predict in vivo cytotoxic mechanisms of dual ALK targeting, we used flow cytometry to demonstrate enhanced apoptosis and proliferation inhibition resulting from combined antibody and inhibitor treatment as compared to either drug alone. Taken together, these findings provide strong evidence for the therapeutic relevance of antibody targeting of ALK in neuroblastoma and argue for the rapid development and further testing of a clinical grade anti-ALK antibody.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4563. doi:10.1158/1538-7445.AM2011-4563

NIMG-45. DISTINGUISHING PROGRESSION FROM PSEUDOPROGRESSION IN GLIOBLASTOMA: COMBINED USE OF 18F-FLUCICLOVINE PET AND MULTI-PARAMETRIC MRI

PURPOSE

Differentiation of tumor progression (TP) from pseudoprogression (PsP) is a major unmet need in post-treatment glioblastoma (GBM). 18F-Fluciclovine is a synthetic amino acid PET radiotracer with higher uptake in tumor tissue vs. areas of treatment-related change. We investigated the value of 18F-Fluciclovine PET for differentiating PsP from TP independent from and in combination with multi-parametric MRI.

METHODS

We prospectively enrolled 30 patients with GBM with a new or enlarging contrast-enhancing lesion on MRI after chemoradiotherapy who were planned for surgical resection of the lesion. Patients underwent pre-operative 18F-Fluciclovine PET and multi-parametric MRI. Following surgery, the relative percentages of viable tumor and therapy-related changes observed in histopathology were quantified. Patients were categorized as TP if viable tumor represented ≥ 50% of the specimen, mixed TP if < 50% and > 10%, and PsP if ≤ 10%.

RESULTS

18 patients had TP, 4 had mixed TP, and 8 PsP. Patients with TP/mixed TP had a significantly higher 40-50 minutes SUVmax (6.64 + 1.88 vs 4.11± 1.52, p=0.009) and an SUVmax cut-off of 4.66 provided 90% sensitivity and 83% specificity for differentiation of TP/mixed TP from PsP (AUC=0.856). A maximum cerebral blood volume (CBVmax) cut-off of 3.67 provided 90% sensitivity and 71% specificity for differentiation of TP/mixed TP from PsP (AUC=0.779). Combining a 40-50 minutes SUVmax cut-off of 4.662 and a relative CBVmax cut-off of 3.67 provided 100% sensitivity and 80% specificity for differentiating TP/mixed TP from PsP (AUC=0.95). The time activity curve patterns and time to peaks were not different between the groups. Normalization of PET parameters to normal brain parenchyma were not helpful to differentiate the groups due to variability in radiotracer uptake in normal brain between subjects.

CONCLUSION

18F-Fluciclovine PET uptake can accurately differentiate PsP from TP in GBM patients, with even more accurate differentiation achieved when combined with MRI.

The identification of reversion mutations in patients with advanced pancreatic cancer and germline or somatic BRCA or PALB2 variants who were treated with maintenance rucaparib

734

Background: Maintenance PARP inhibition (PARPi) extends progression-free survival and improves quality of life for patients (pts) with advanced, platinum-sensitive pancreatic cancer (PC) and BRCA or PALB2 variants. However, most will experience progression. PARPi resistance mechanisms are poorly defined in PC. Cell-free (cf)DNA analysis can detect some known classes of resistance mechanisms, like reversion mutations, and other potentially prognostic and predictive genomic features. Methods: Pts with advanced, platinum-sensitive pancreatic cancer and pathogenic germline or somatic BRCA1, BRCA2, or PALB2 variants were treated with maintenance rucaparib on clinical trial. cfDNA was collected at baseline and progression and analyzed with the GuardantOMNI 500-gene liquid biopsy. Time to event analysis was performed from index date of enrollment until endpoint (PFS, OS, and PFS2). Associations were tested by the log-rank test with adjustment. Results: The trial enrolled 42 pts, of whom 31 have progressed. cfDNA was available for 41 pts at baseline and 30 pts at progression; 88% had baseline detectable cfDNA. Two pts had baseline reversion mutations, 5 had new reversion mutations at progression. Of 21 pts who had tissue NGS, 17 pts had a KRAS variant in the tumor, 12 of whom had detectable cfDNA at either baseline or progression. Of the 41 patients with cfDNA samples, 10 pts had baseline KRAS mutations detected in plasma; an additional 10 pts had a detectable plasma KRAS mutation at progression. Outcomes are shown. Of those who had progressed, pts with acquired reversion mutations had shorter OS (p<0.001) and PFS (p = 0.018) on rucaparib than those without reversion mutations. Of those who received chemo after progression (n=23), PFS2 was shorter for pts with acquired reversions compared to those with no reversions (p = 0.038). KRAS mutation detection at baseline was observed with higher overall somatic allele fraction in cfDNA and a trend toward shorter PFS and OS. Conclusions: Acquired reversion mutations were infrequent but associated with worse outcomes. Other causes of resistance may be dominant. Detection of KRAS mutation in the peripheral blood may be associated with disease burden and clinical outcome. [Table: see text]

A pilot study of galunisertib (LY2157299) plus stereotactic body radiotherapy (SBRT) in advanced hepatocellular carcinoma (HCC)

TPS528

Background: Hepatocellular carcinoma (HCC) is a common and lethal malignancy with few effective treatment options. Inherently aggressive disease biology combined with the immunosuppressive hepatic microenvironment creates a unique therapeutic challenge. TGF-β, the strongest known immunosuppressive cytokine [1, 2], modulates the hepatic immune response to various antigens and to ionizing radiation [3, 4]. TGF-β is constitutively released by liver cells and plays a key role in the early and late pathogenesis of HCC [5-7] by dampening the local T-cell response to the oncogenic hepatitis B and –C viruses [4, 8-11]. TGF-β is activated by ionizing radiation, where it blocks the effector T-cell response to cellular destruction and the release of tumor-specific antigens [4]. Preclinical data demonstrate that neutralizing TGF-β during radiation therapy effectively generates a CD8+ T-cell response to multiple endogenous tumor antigens [4], thereby generating an in-situ vaccine against a tumor [12-17]. We hypothesize that the combination of TGF-β receptor inhibition plus radiation therapy will produce a potent and clinically effective antitumor immune response against HCC. Methods: We have enrolled 9 of 15 planned patients on study NCT02906397. Eligibility criteria include inoperable HCC, Childs Pugh score of ≤7, and either failure of or refusal to take sorafenib. Patients must be 4 weeks from prior therapy and may not be taking immunosuppressants. Patients with major cardiac disease or abnormalities or a predisposition toward aneurysm development are excluded. Patients receive galunisertib on days 1-14 of 28 day cycles. SBRT will be delivered in a single fraction of 18 Gy between days 15-28 of C1. Pre-treatment and on-treatment biopsies are obtained, as well as serial blood collections for circulating tumor material. Immunologic evaluation will include TCR deep sequencing to track T-cell receptor clones, analysis of serum inflammatory cytokines, analysis of myeloid and B cell activation, multiplex flow cytometry of PBMCs to measure percentages and absolute counts of T-cell subsets and tissue assessment of immune markers. Peripheral and tissue levels of TGF-β will be assessed. Clinical trial information: NCT02906397.

Parallelized immunomagnetic nanopore sorting: modeling, scaling, and optimization of surface marker specific isolation of extracellular vesicles from complex media

The isolation of specific subpopulations of extracellular vesicles (EVs) based on their expression of surface markers poses a significant challenge due to their nanoscale size (< 800 nm), their heterogeneous surface marker expression, and the vast number of background EVs present in clinical specimens (10 10 -10 12 EVs/mL in blood). Highly parallelized nanomagnetic sorting using track etched magnetic nanopore (TENPO) chips has achieved precise immunospecific sorting with high throughput and resilience to clogging. However, there has not yet been a systematic study of the design parameters that control the trade-offs in throughput, target EV recovery, and specificity in this approach. We combine finite-element simulation and experimental characterization of TENPO chips to elucidate design rules to isolate EV subpopulations from blood. We demonstrate the utility of this approach by increasing specificity > 10x relative to prior published designs without sacrificing recovery of the target EVs by selecting pore diameter, number of membranes placed in series, and flow rate. We compare TENPO-isolated EVs to those of gold-standard methods of EV isolation and demonstrate its utility for wide application and modularity by targeting subpopulations of EVs from multiple models of disease including lung cancer, pancreatic cancer, and liver cancer.

Abstract PO-071: MYC influences metastatic heterogeneity in pancreatic cancer

Tumor heterogeneity - resulting from genetic and epigenetic alterations acquired during tumor progression - is a critical driver of phenotypic diversity in most cancers. A lethal consequence of tumor heterogeneity is the acquisition of metastatic traits by tumor cells, leading to poor clinical outcomes. This remains a major problem in pancreatic ductal adenocarcinoma (PDAC), which continues to have the worst prognosis of any major cancer type. While most cases of PDAC present with metastatic disease at the time of diagnosis, the patterns and burden of metastasis can vary widely, with some patients exhibiting a limited metastatic burden while others have more extensive spread, which impacts clinical outcomes. However, the biological and functional differences that drive metastatic heterogeneity are poorly understood.

Citation Format: Ravikanth Maddipati, Robert J. Norgard, Timour Baslan, Komal S. Rathi, Amy Zhang, Pichai Raman, Max D. Wengyn, Taiji Yamazoe, Jinyang Li, David Balli, Michael LaRiviere, Ian W. Folkert, Ian D. Millstein, Jonathan Bermeo, Erica L. Carpenter, Scott Lowe, Christine Iacobuzio-Donahue, Faiyaz Notta, Ben Z. Stanger. MYC influences metastatic heterogeneity in pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-071.

Abstract 758: Capture and characterization of circulating tumor cell clusters in patients with metastatic castrate-resistant prostate cancer

Introductory Sentence indicating purpose of study: Circulating tumor cell (CTC) clusters have been shown to have higher metastatic potential than single CTCs in breast, pancreatic, and other cancers, yet these clusters have not been extensively described in metastatic castrate-resistant prostate cancer (MCRPC). Here we sought to determine the feasibility of capturing and characterizing CTC clusters in prostate cancer patients.

Description of Experimental Procedures: Fifty-five blood samples from 29 MCRPC patients, ages 50 to 81 (median age 68), were obtained prior to the patient starting or switching to androgen receptor inhibitor or 17 alpha lyase inhibitor therapies. Eighteen patients received enzalutamide and 11 received abiraterone. The majority of patients had a Gleason score &gt; 7 (22; 75.9%), bone metastases (19; 65.5%), and an ECOG status of 0 (21; 72.4%). All patients had previously undergone, or were receiving at time of enrollment, androgen deprivation therapy. Eleven patients (37.9%) had been on a prior 2nd generation anti-androgen therapy. CTC single cells and clusters (2 or more cells together in one image) were enumerated using the CellSearch system and stained to detect expression of androgen receptor (AR), glucocorticoid receptor (GR), and neuroendocrine (NE) markers.

Summary of Data: Five or more single CTCs, a measure which has previously been associated with an unfavorable prognosis, were detected in 13 of 29 patients (44.8%), and in 19 of 55 blood samples (34.5%). Altogether, a total of 282 CTC clusters was detected, with 1 or more clusters found in 10 patients (34.5%) and 13 samples (23.6%). The number of clusters per 7.5ml of blood ranged from 0-150, and clusters contained anywhere from 2 to 16 cells. Most CTC clusters (268; 95.0%) contained only CTCs and no leukocytes. Just over half the detected clusters (162; 57.4%) contained only 2 CTCs. Cluster staining patterns were fairly homogenous with 29.4% of clusters having uniform expression of either AR, GR, or NE markers, i.e., all CTCs in the cluster expressed the marker of interest. Most clusters (67.7%) were uniformly marker negative and the remaining 2.8% demonstrated a mix of marker positive and marker negative CTCs. Serum Chromogranin A levels, as determined by standard of care clinical blood testing, were found to be positively associated with the number of CTC clusters per 7.5ml of blood (p&lt;0.0001).

Statement of Conclusions: The capture and characterization of CTC clusters in the blood of MCRPC patients can be successfully performed using the CellSearch system. Further investigation into the clinical implications of these clusters is warranted, including whether cluster characteristics are associated with more aggressive disease.

Citation Format: Samantha L. Savitch, Stephanie S. Yee, Devon Soucier, Denis Smirnov, Chandra Rao, Steve Gross, Ravi K. Amaravadi, David J. Vaughn, Naomi B. Haas, Erica L. Carpenter. Capture and characterization of circulating tumor cell clusters in patients with metastatic castrate-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 758. doi:10.1158/1538-7445.AM2017-758

Abstract 4871: New neuroblastoma susceptibility loci at 6q21 within HACE1 and LIN28B

Neuroblastoma is a cancer of the sympathetic nervous system that most commonly affects young children and accounts for approximately 10% of all pediatric oncology deaths. We have reported common SNPs associated with neuroblastoma within LINC00340 at 6p22 (NEJM 2008), BARD1 at 2q35 (Nature Genetics, 2009), LMO1 at 11p15 (Nature, 2010), DUSP12 at 1q23 (PLoS Genetics, 2011), and HSD17B12 at 11p11 (PLoS Genetics, 2011), and one common CNV at 1q21.1 within NBPF23 (Nature, 2009). We have further demonstrated that germline variation in LMO1 and BARD1 not only predisposes to neuroblastoma, but also plays an important role in tumor progression. To identify additional genetic risk factors for neuroblastoma, we expanded our previous genome-wide association study (GWAS) to include 2,841 patients and 7,482 control subjects from three independent case series including two cohorts of European ancestry and one African American cohort. Here, we report two new associations at 6q21, the first within the HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 gene (HACE1; rs4336470 combined P = 3.4 x 10−12; Odds Ratio: 1.27, 95% CI: 1.19-1.36), and the second within lin-28 homolog B (LIN28B; rs17065417 combined P = 8.4 x 10−9; Odds Ratio 1.38, 95% CI: 1.23-1.54). HACE1 is implicated in multiple human cancers as a critical tumor suppressor gene (Nature Genetics, 2009). LIN28B, on the other hand, acts as a repressor of the let-7 family of miRNA, is over-expressed in many human cancers, and promotes cellular transformation (Nature Genetics, 2009). More recently, LIN28B has also been identified as a key regulator of glucose homeostasis (Cell, 2011). Neuroblastoma cell lines homozygous for the LIN28B risk allele showed increased LIN28B mRNA and protein expression and down regulation of the let-7 family of micro RNAs, consistent with the risk allele conferring a growth advantage through increased LIN28B expression. Transcriptome analysis of 251 primary tumors showed that HACE1 is down regulated (p = 3.5 x 10−4) and LIN28B is up-regulated (P = 0.017) in high-risk neuroblastomas compared to more benign forms of the disease. Tumors over-expressing LIN28B showed increased activation of DNA damage response (P = 2.5 x 10−19) and metabolism (P = 3.5 x 10−25) pathways, independent of MYCN amplification. Taken together, we show that common DNA variants in HACE1 and LIN28B influence neuroblastoma susceptibility and our expression analyses suggest that both genes may play an important role in disease progression. Efforts are ongoing to understand the mechanism by which LIN28B and HACE1 influence neuroblastoma tumorigenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4871. doi:1538-7445.AM2012-4871

Improving comprehensive genotyping in patients with newly diagnosed non-squamous NSCLC: Results from a prospective trial of a behavioral nudge intervention

362

Background: Despite current guidelines, less than 50% of patients with metastatic (m) non-squamous (NSq) NSCLC undergo comprehensive molecular genotyping. At our institution, based on improved comprehensiveness of genotyping with use of concurrent tissue (T) and plasma (P) next generation sequencing (NGS), we designed an electronic medical record (EMR)-based “nudge intervention” to auto-generate an order for P NGS at the time of initial consultation, while T NGS was carried out reflexively based on institutional pathways. Methods: A prospective study was conducted at the Abramson Cancer Center and 2 community sites within the University of Pennsylvania Health System after IRB approval. A provider team-focused EMR-based “nudge intervention” was designed to order P NGS at the time of new patient consultation. Eligible patients for the nudge were identified using an EMR based checklist, that included 3 criteria i. newly diagnosed, ii. treatment naïve, iii. mNSq NSCLC. Results from the intervention period (4/2021-12/2021) were compared to baseline data from similar patients treated at our institution between 01/2019 and 03/2021. Categories of NCCN guideline recommended molecular genotyping were defined as: i) comprehensive: EGFR, ALK, BRAF, ROS1, MET, RET, NTRK testing, and ii) incomplete or no testing performed. The proportion of patients with comprehensive molecular genotyping prior to 1st-line therapy were compared in the pre- and post-intervention groups using the chi-square test. Results: 526 patients with mNSq NSCLC were included in this analysis: 381 in the pre-intervention cohort, 145 in the post-intervention cohort. After implementation of the EMR-based nudge, a higher proportion of patients underwent concurrent T+P testing resulting in improved comprehensive molecular genotyping. In addition, a greater proportion of patients had comprehensive genotyping available prior to 1st-line therapy in the post-intervention vs pre-intervention cohort (Table). Conclusions: Across 3 practice sites, a provider team-focused EMR-based nudge intervention was associated with a significantly higher proportion of patients with mNSq NSCLC undergoing comprehensive molecular genotyping, both overall and prior to 1st-line therapy. These findings demonstrate that behavioral, EMR-based nudges can promote guideline concordant diagnostic testing at both community and academic sites and should be studied further as a tool to improve rates of molecular testing in NSCLC.[Table: see text]

Circulating KRAS variant-specific shedding and association with survival in patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) receiving chemoimmunotherapy

2548

Background: Circulating tumor DNA (ctDNA) is increasingly used as a prognostic marker with high ctDNA shedding associated with poor survival. Gene-, but not variant-specific, differences in ctDNA shedding have been reported. Tumor burden, mitotic rate, and cell death rate have been proposed as contributors to ctDNA shedding. Here we investigate associations of ctDNA shedding for the two most common mPDAC KRAS variants, G12D and G12V, with tumor burden, mitotic score, and overall survival (OS). Methods: Pretreatment (baseline) ctDNA was analyzed by droplet digital PCR for 86 (including 44 G12D, 30 G12V) patients with mPDAC receiving front-line chemoimmunotherapy in a randomized open-label Phase II study (NCT03214250). Baseline tumor burden in total, within the pancreas, and distally, was assessed by sum of RECIST target lesion diameters. Tumor tissue variant allele fraction (tVAF) and mitotic score (geometric mean expression of 65 mitosis-associated genes) were calculated from DNA and RNA sequencing. Results: ctKRAS shedding (dichotomized at median mutant copies/mL) was associated with OS for G12D bearing tumors (p = 0.03) but not G12V (p = 0.17, log-rank test). To identify variant-specific features of shedding, we examined the Spearman correlation for total tumor burden and ctKRAS shedding; G12D but not G12V shedding was correlated with tumor burden (p = 0.01 and p = 0.22 respectively). However, the higher tVAF in G12V compared to G12D tumors (p = 0.048, Mann-Whitney test) could result from differences in purity, ploidy, and KRAS copy number. Thus, we used tVAF as a scalar to calculate an adjusted tumor burden which was significantly correlated with both G12D and G12V ctDNA shedding (p = 0.004 and 0.02, respectively). When a patient’s distal vs. pancreatic lesions were analyzed separately, pancreatic tumor burden was not correlated with G12D or G12V shedding (p = 0.10 and 0.33, respectively) but distal burden was correlated with both (p = 0.001 and 0.02, respectively). While there was no difference by KRAS variant for the correlation between adjusted tumor burden and shedding, these results do suggest that, in patients with mPDAC, distal rather than primary tumor burden may drive ctDNA shedding. Finally, tumor mitotic rate was combined with adjusted total tumor burden in a linear regression model; both were significant for predicting G12D shedding (p = 0.007 and p < 0.0001, respectively) but not for G12V (p = 0.045 and p = 0.16, respectively). Conclusions: These data suggest that ctDNA shedding and survival associations may be KRAS variant-specific in mPDAC. Tumor mitotic score and location of tumors may explain some variant-specific differences in shedding. As clinical ctDNA tests become more widely used, further investigation of variant-specific shedding in KRAS and other genes may be key for proper interpretation of ctDNA tests.

Inflammatory and tissue injury marker dynamics in pediatric acute respiratory distress syndrome

BACKGROUNDThe molecular signature of pediatric acute respiratory distress syndrome (ARDS) is poorly described, and the degree to which hyperinflammation or specific tissue injury contributes to outcomes is unknown. Therefore, we profiled inflammation and tissue injury dynamics over the first 7 days of ARDS, and associated specific biomarkers with mortality, persistent ARDS, and persistent multiple organ dysfunction syndrome (MODS).METHODSIn a single-center prospective cohort of intubated pediatric patients with ARDS, we collected plasma on days 0, 3, and 7. Nineteen biomarkers reflecting inflammation, tissue injury, and damage-associated molecular patterns (DAMPs) were measured. We assessed the relationship between biomarkers and trajectories with mortality, persistent ARDS, or persistent MODS using multivariable mixed effect models.RESULTSIn 279 patients (64 [23%] nonsurvivors), hyperinflammatory cytokines, tissue injury markers, and DAMPs were higher in nonsurvivors. Survivors and nonsurvivors showed different biomarker trajectories. IL-1α, soluble tumor necrosis factor receptor 1, angiopoietin 2 (ANG2), and surfactant protein D increased in nonsurvivors, while DAMPs remained persistently elevated. ANG2 and procollagen type III N-terminal peptide were associated with persistent ARDS, whereas multiple cytokines, tissue injury markers, and DAMPs were associated with persistent MODS. Corticosteroid use did not impact the association of biomarker levels or trajectory with mortality.CONCLUSIONSPediatric ARDS survivors and nonsurvivors had distinct biomarker trajectories, with cytokines, endothelial and alveolar epithelial injury, and DAMPs elevated in nonsurvivors. Mortality markers overlapped with markers associated with persistent MODS, rather than persistent ARDS.FUNDINGNIH (K23HL-136688, R01-HL148054).

Corticosteroid-dependent association between prognostic peripheral blood cell-free DNA levels and neutrophil-mediated NETosis in patients with glioblastoma

PURPOSE

Non-invasive prognostic biomarkers to inform clinical decision-making are an urgent unmet need for the management of patients with glioblastoma (GBM). We previously showed that higher circulating cell-free DNA concentration [ccfDNA] is associated with worse survival in GBM. However, the biology underlying this is unknown.

EXPERIMENTAL DESIGN

We prospectively enrolled 129 patients with treatment-naïve GBM with blood drawn prior to initial resection (baseline) and at time of first post-radiotherapy MRI. We performed ccfDNA methylation deconvolution to determine cellular sources of ccfDNA. ELISA was performed to detect citrullinated H3 (citH3), a marker of neutrophil extracellular traps (NETs). Multiplex proteomic analysis was used to measure soluble inflammatory proteins.

RESULTS

We found that neutrophils contributed the highest proportion of prognostic ccfDNA. The percentage of ccfDNA derived from neutrophils was correlated with total [ccfDNA], but only in patients receiving pre-operative corticosteroids. At baseline and on-therapy, [citH3] was significantly higher in the plasma of patients with GBM receiving corticosteroids compared to corticosteroid-naïve GBMs or no-cancer controls. Unsupervised hierarchical clustering of ccfDNA methylation patterns yielded two clusters, with one enriched for patients with the NETosis phenotype and who received corticosteroids. Unsupervised clustering of circulating inflammatory proteins yielded similar results.

CONCLUSIONS

These data suggest neutrophil-mediated NETosis is the dominant source of prognostic ccfDNA in patients with GBM and may be associated with glucocorticoid exposure. If further studies show that pharmacological inhibition of NETosis can mitigate the deleterious effects of corticosteroids, these plasma markers will have important clinical utility as non-invasive correlative biomarkers.

Modeling and optimization of parallelized immunomagnetic nanopore sorting for surface marker specific isolation of extracellular vesicles from complex media

The isolation of specific subpopulations of extracellular vesicles (EVs) based on their expression of surface markers poses a significant challenge due to their nanoscale size (< 800 nm), their heterogeneous surface marker expression, and the vast number of background EVs present in clinical specimens (1010-1012 EVs/mL in blood). Highly parallelized nanomagnetic sorting using track etched magnetic nanopore (TENPO) chips has achieved precise immunospecific sorting with high throughput and resilience to clogging. However, there has not yet been a systematic study of the design parameters that control the trade-offs in throughput, target EV recovery, and ability to discard background EVs in this approach. We combine finite-element simulation and experimental characterization of TENPO chips to elucidate design rules to isolate EV subpopulations from blood. We demonstrate the utility of this approach by reducing device background > 10× relative to prior published designs without sacrificing recovery of the target EVs by selecting pore diameter, number of membranes placed in series, and flow rate. We compare TENPO-isolated EVs to those of gold-standard methods of EV isolation and demonstrate its utility for wide application and modularity by targeting subpopulations of EVs from multiple models of disease including lung cancer, pancreatic cancer, and liver cancer.

Outcomes and clinicopathologic characteristics associated with disseminated tumor cells in bone marrow after neoadjuvant chemotherapy in high-risk early stage breast cancer: the I-SPY SURMOUNT study

PURPOSE

Disseminated tumor cells (DTCs) expressing epithelial markers in the bone marrow are associated with recurrence and death, but little is known about risk factors predicting their occurrence. We detected EPCAM+/CD45- cells in bone marrow from early stage breast cancer patients after neoadjuvant chemotherapy (NAC) in the I-SPY 2 Trial and examined clinicopathologic factors and outcomes.

METHODS

Patients who signed consent for SURMOUNT, a sub-study of the I-SPY 2 Trial (NCT01042379), had bone marrow collected after NAC at the time of surgery. EPCAM+CD45- cells in 4 mLs of bone marrow aspirate were enumerated using immunomagnetic enrichment/flow cytometry (IE/FC). Patients with > 4.16 EPCAM+CD45- cells per mL of bone marrow were classified as DTC-positive. Tumor response was assessed using the residual cancer burden (RCB), a standardized approach to quantitate the extent of residual invasive cancer present in the breast and the axillary lymph nodes after NAC. Association of DTC-positivity with clinicopathologic variables and survival was examined.

RESULTS

A total of 73 patients were enrolled, 51 of whom had successful EPCAM+CD45- cell enumeration. Twenty-four of 51 (47.1%) were DTC-positive. The DTC-positivity rate was similar across receptor subtypes, but DTC-positive patients were significantly younger (p = 0.0239) and had larger pretreatment tumors compared to DTC-negative patients (p = 0.0319). Twenty of 51 (39.2%) achieved a pathologic complete response (pCR). While DTC-positivity was not associated with achieving pCR, it was significantly associated with higher RCB class (RCB-II/III, 62.5% vs. RCB-0/I; 33.3%; Chi-squared p = 0.0373). No significant correlation was observed between DTC-positivity and distant recurrence-free survival (p = 0.38, median follow-up = 3.2 years).

CONCLUSION

DTC-positivity at surgery after NAC was higher in younger patients, those with larger tumors, and those with residual disease at surgery.

Abstract 618: Comparison of mutational spectra in metastatic tumors and cell-free DNA in breast cancer patients

While massively parallel sequencing technology has greatly expanded the number of molecular genetic tests available in oncology, little is known about the spectrum and clinical utility of findings obtained from testing tumors and circulating tumor material in specific patient populations. Here we report findings from the METAMORPH study, in which stage IV breast cancer patients had metastatic tumor biopsies (metDNA) and concurrently collected cell-free circulating tumor DNA (cfDNA). Illumina TruSeq Cancer Panel (for metDNA) and Guardant360 (for cfDNA) were performed. 28 patients had both tests; results are shown in the Table. 68% of patients had at least one alteration in metDNA and 86% in cfDNA. PIK3CA mutations were most common, occurring in 43% and 36% of patients’ metDNA and cfDNA, respectively. Overall, 16 of 28 (57%) of patients had the same alterations identified in both metDNA and cfDNA. Excluding ERBB2 amplifications in HER2+ patients, 43% of patients’ metDNA and 57% of patients’ cfDNA contained pathogenic mutations or variants of uncertain significance (VUS) for which there are approved targeted therapies or clinical trials. Overall, 80 alterations were identified, 23 of which were detected by both assays. Multiple reasons for discordance in calls between metDNA and cfDNA assays were identified. While biological phenomena (e.g. tumor heterogeneity) may contribute to discordance, technical issues played an important role. Additional studies using whole exome sequencing and other platforms to further assess biological evolution of metastatic disease and clinical utility of molecular profiling of metastatic tumors and cell-free DNA are needed.

Table 1

Tumor DNA (metDNA)Cell-free DNA (cfDNA)# pts with alteration (%)19/28 (68%)24/28 (86%)ER+/Her2- (n = 17)10/1715/17Her2+ (n = 4)4/42/4TNBC (n = 7)5/77/7Total # alterations in # genes31 in 7 genes72 in 19 genesGenes w/alterations (total); Bold: genes for which exists a possible targeted therapeuticPIK3CA (13), TP53 (10), ERBB2 (4), EGFR, RB1, SMAD4, STK11PIK3CA (14), TP53 (14), EGFR (9), ERBB2 (6), BRAF (6), MET (6), JAK2 (3), NOTCH1 (2), FBXW7 (2), ARAD, FGFR2, JAK3, KRAS, MYC, NPM1, PROC, RET, SMAD4, SMARCB1Variants only covered by one assay033Variants detected in both but only reported by one assay3 (2 indels, 1 VUS)1 (1 synonymous)Variants detected by only one assay1 amplification at 7-fold; 4 SNVs (AF range 19-75%)2 amplifications at &lt;3-fold; 13 SNVs (AF range 0.1-0.8%)

Citation Format: Kara N. Maxwell, Danielle J. Soucier-Ernst, Erica L. Carpenter, Andrea B. Troxel, Christopher Colameco, Candace Clark, Michael D. Feldman, Bijal Kakrecha, Melissa Langer, Joy Lee, David A. Lewis, David Lieberman, Jennifer Morrissette, Tien-chi Pan, Stephanie S. Yee, Natalie Shih, Lewis A. Chodosh, Angela M. DeMichele. Comparison of mutational spectra in metastatic tumors and cell-free DNA in breast cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 618. doi:10.1158/1538-7445.AM2015-618

Abstract PO-053: MYC Influences metastatic heterogeneity in pancreatic cancer

Tumor heterogeneity - resulting from genetic and epigenetic alterations acquired during tumor progression - is a critical driver of phenotypic diversity in most cancers. A lethal consequence of tumor heterogeneity is the acquisition of metastatic traits by tumor cells, leading to poor clinical outcomes. This remains a major problem in pancreatic ductal adenocarcinoma (PDAC), which continues to have the worst prognosis of any major cancer type. While most cases of PDAC present with metastatic disease at the time of diagnosis, the patterns and burden of metastasis can vary widely, with some patients exhibiting a limited metastatic burden while others have more extensive spread, which impacts clinical outcomes. However, the biological and functional differences that drive metastatic heterogeneity are poorly understood. One barrier to understanding metastatic heterogeneity has been a paucity of model systems that capture this natural variation and allow for direct assessment of paired primary tumors and metastases. We previously developed an autochthonous model of PDAC – the KPCX model – that employs multiplexed fluorescence-based labeling to track the contribution of multiple distinct tumor populations to metastasis. Importantly, this technique allows for ascertainment of primary-metastatic lineage relationships in vivo, so that primary tumor clones with substantial metastatic potential can be distinguished with those having poor metastatic potential. To understand the factors underlying differences in metastatic potential, we analyzed paired primary tumors and metastases in the KPCX model and from a cohort of 398 PDAC patients. Genomic and transcriptomic analysis of murine and human metastatic PDAC revealed an association between the highly metastatic state and gene amplification or transcriptional upregulation of MYC and its transcriptional targets. Functional assessments showed that MYC promotes metastasis by recruiting tumor associated macrophages (TAMs), leading to greater bloodstream intravasation. Consistent with these findings, metastatic progression in human PDAC was also associated of MYC signaling pathways and enrichment for MYC amplification in metastasis. Collectively, these results implicate MYC activity as a major determinant of metastatic burden and heterogeneity in advanced PDA.

Citation Format: Ravikanth Maddipati, Robert J. Norgard, Timour Baslan, Komal S. Rathi, Amy Zhang, Pichai Raman, Max D. Wengyn, Taiji Yamazoe, Jinyang Li, David Balli, Michael J. LaRiviere, Ian W. Folkert, Ian D. Millstein, Jonathan Bermeo, Erica L. Carpenter, Scott Lowe, Christine Iacobuzio-Donahue, Faiyaz Notta, Ben Z. Stanger. MYC Influences metastatic heterogeneity in pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-053.

Abstract 1043: Liquid biopsy signature combining copy number instability and mutant KRAS detection is associated with survival for patients with metastatic pancreatic cancer

Introduction: In the setting of metastatic pancreatic adenocarcinoma (mPDAC), lower baseline plasma KRAS mutation levels have been associated with improved survival. While tissue-agnostic, plasma-based copy number instability (CNI) has been demonstrated as an early indicator of response to immunotherapy for some solid tumors, it has not been assessed for patients with mPDAC, nor in combination with KRAS mutations for patients receiving standard of care chemo/radiotherapy. Here we evaluate the combination of mutant KRAS (mKRAS) and CNI detection in plasma as a predictor of overall and progression-free survival (OS/PFS) in mPDAC patients who received standard of care therapy.

Methods: Cell-free DNA was extracted from plasma and libraries prepared at baseline (Week 0) and weeks 8, 16 and 24 on therapy, and analyzed by next-generation sequencing (CNI) and droplet digital PCR (mKRAS). Descriptive statistics were computed for variables including CNI (score is a measure of circulating tumor DNA) and mKRAS variant allele fraction. Detection was defined as above the limit of detection (mKRAS=0.13%) and above the 95th percentile of the value in normal individuals (CNI=24). Therapy response was assessed by OS and PFS.

Results: 196 plasma samples from 64 mPDAC patients were analyzed. When dichotomized as detectable vs undetectable, CNI alone was significantly associated with OS at all on-therapy timepoints but not baseline, whereas mKRAS was significantly associated with OS for all 4 timepoints (Table 1). Detection of both CNI and mKRAS in combination was strongly associated with worse OS at all timepoints, yielding the highest HR. Similar results were obtained when mKRAS and CNI were dichotomized at their respective median values or with PFS as the clinical endpoint.

Conclusions: Combined CNI and mKRAS detection at baseline and on-therapy may provide a strong and early indication of worse prognosis for patients with mPDAC.

Table 1. Association of CNI and mKRAS with Overall Survival (HazardRatio [95% CI], log-rank p-value) Timepoint CNI mKRAS CNI and KRAS Baseline/Week 0 1.54 [0.89-2.68], 0.1 2.05 [1.12-3.78], 0.02 2.50 [1.46-4.28], 0.0006 Week 8 1.78 [0.99-3.18], 0.05 2.21 [1.19-4.08], 0.01 9.81 [3.40-28.28], &lt;0.0001 Week 16 1.91 [1.03-3.53], 0.04 3.26 [1.60-6.62], 0.0006 11.11 [4.28-28.83], &lt;0.0001 Week 24 2.55 [1.28-5.09], 0.006 4.55 [2.03-10.23], &lt;0.0001 6.42 [2.61-15.84], &lt;0.0001

Citation Format: Samuele Cannas, Jacob E. Till, Kristine Kim, Michael J. LaRiviere, Charles M. Vollmer, Jennifer R. Eads, Thomas B. Karasic, Peter J. O'Dwyer, Charles J. Schneider, Ursina R. Teitelbaum, Kim A. Reiss Binder, Mark H. O'Hara, Douglas T. Ross, Kim McGregor, Kirsten Bornemann-Kolatzki, Ekkehard Schütz, Julia Beck, Erica L. Carpenter. Liquid biopsy signature combining copy number instability and mutant KRAS detection is associated with survival for patients with metastatic pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1043.

Abstract A030: Pancreas-specific circulating cell-free DNA for detection of occult metastases and prognosis in resectable pancreatic ductal adenocarcinoma

Up to 85% of patients with resectable pancreatic ductal adenocarcinoma (PDAC) experience metastatic relapse after curative intent surgery with many recurring early. Detection of such occult metastases (those thought to be below the level of detection of standard of care imaging at the time of resection) could steer patients to a different treatment course rather than delaying systemic therapy until after recovery from inappropriate surgery. Here we investigate the potential of pancreas-specific circulating cell-free DNA (cfDNA) as a biomarker for the detection of occult metastatic disease and as a prognostic biomarker. Blood specimens were collected from 53 patients (15 negative control healthy subjects, 11 positive control metastatic PDAC patients, and 27 resectable PDAC patients prior to resection), processed to plasma, and banked. Plasma cfDNA was extracted, quantified, treated with bisulfite, and used as template for PCR amplification of 9 marker loci that are uniquely unmethylated in DNA of pancreatic acinar or duct cells. Following deep sequencing of PCR products, the fraction of cfDNA molecules derived from the pancreas was determined and multiplied by the total cfDNA concentration to yield pancreas-specific cfDNA. Recurrence and survival data were abstracted from the medical record and receiver operator curve analysis was utilized to determine statistical significance. Metastases were categorized as overt (present at diagnosis), occult (discovered during or within 4 months of curative intent surgery), or two-year (discovered during or within two years of curative intent surgery). Pancreas-derived cfDNA was significant for the detection of occult or overt metastases in our full cohort (18 of 52 evaluable subjects) with an area under the curve (AUC) of 0.86 (95% Confidence Interval, 0.74-0.80) and 0.91 (0.83-1.00) for liver-specific occult or overt metastases (15 of 52). It was borderline significant for the detection of occult metastases in the resectable sub-cohort (7 of 27) with an AUC of 0.71 (0.47-0.96) but significant for the detection of occult liver-specific metastases (5 of 27) with an AUC of 0.79 (0.62-0.96). Further, detection of overt metastases or two-year metastases (28 of 50) was significant with an AUC of 0.85 (0.74-0.96). In the resectable sub-cohort, it was also significant for the detection of two-year metastases (17 of 25) with an AUC of 0.79 (0.60-0.97) and prognostic for 2-year overall survival (12 of 24) with an AUC of 0.81 (0.62-1.00) in the resectable sub-cohort. Liver-derived cfDNA was also analyzed and was always outperformed by pancreas-specific cfDNA. In this pilot cohort, enumeration of pancreas-specific cfDNA shows promise as biomarker of occult metastatic disease, two-year metastatic progression, and two-year overall survival in resectable PDAC. Further investigation of a larger cohort and potential combination with other known markers like CA19-9 and tumor size is underway; results for an additional ~40 patients will be available by the time of the meeting.

Citation Format: Jacob E. Till, Roni Ben-Ami, Ruth Shemer, Kristine Kim, Aseel Abdalla, Samuele Cannas, Charles M. Vollmer, Mark H. O'Hara, Ben Z. Stanger, Yuval Dor, Erica L. Carpenter. Pancreas-specific circulating cell-free DNA for detection of occult metastases and prognosis in resectable pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A030.

A phase I clinical trial of stereotactic body radiotherapy with atezolizumab and bevacizumab in advanced hepatocellular carcinoma

TPS626

Background: Systemic therapy with atezolizumab and bevacizumab (atezo/bev) has improved outcomes for advanced HCC, but results in objective responses in fewer than 30% of patients. Stereotactic body radiotherapy (SBRT) is currently used for small HCC tumors that do not require systemic therapy but has also been shown in a number of clinical trials of other solid tumors to enhance the anti-cancer immune response. Of particular interest, our prior experience with SBRT in a 17Gy fraction has demonstrated the ability to restore sensitivity to immunotherapy in advanced solid tumors, even those previously refractory to immunotherapy. We hypothesize that repeated high dose fractions of radiation will act as an immune booster and will improve on outcomes of patients with advanced HCC. Since the combination of SBRT and atezo/bev has not yet been tested prospectively in patients with HCC, and because bevacizumab is a known radiosensitizer, we are conducting a phase I trial to evaluate the safety of repeated SBRT doses. Methods: This is a single-site phase I clinical trial utilizing a Rolling 6 design to determine the safety of 1, 2, or 3 doses of SBRT fractions in combination with atezo/bev. Up to 18 total patients will be enrolled (n=6 per cohort). Patients must be naïve to systemic therapy with Child-Pugh A or B liver function, at least one lesion amenable to radiation, and a measurable lesion that will not receive radiation. Patients with uncontrolled ascites or hepatic encephalopathy are excluded. Atezo/bev is administered at the standard doses every 21 days. SBRT will start 1 week after the first infusion of this combination. Patients will receive 1, 2, or 3 17Gy fractions of SBRT at 4-week intervals (cohorts 2 and 3 only). Patients will undergo serial collections of circulating cell-free DNA (ccfDNA), methylated DNA, and peripheral blood mononuclear cells to investigate the application of these markers as a predictor of response. Following completion of SBRT, patients will continue with atezo/bev until disease progression, unacceptable toxicity, or withdrawal of consent. The primary endpoint is the proportion of patients experiencing dose-limiting toxicities (grade 3 or higher radiation-related toxicities graded by the Common Terminology Criteria for Adverse Events, Version 5). Secondary endpoints are overall survival, progression-free survival, objective response rate, duration of response, and toxicity rates. Enrollment began 9/2022 and complete accrual is expected by June 2024. NCT05488522. Clinical trial information: NCT05488522 .