Aaron James Scott

Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

RNA biomarkers discovered by RT-PCR-based gene expression profiling of archival formalin-fixed paraffin-embedded (FFPE) tissue form the basis for widely used clinical diagnostic tests; however, RT-PCR is practically constrained in the number of transcripts that can be interrogated. We have developed and optimized RNA-Seq library chemistry as well as bioinformatics and biostatistical methods for whole transcriptome profiling from FFPE tissue. The chemistry accommodates low RNA inputs and sample multiplexing. These methods both enable rediscovery of RNA biomarkers for disease recurrence risk that were previously identified by RT-PCR analysis of a cohort of 136 patients, and also identify a high percentage of recurrence risk markers that were previously discovered using DNA microarrays in a separate cohort of patients, evidence that this RNA-Seq technology has sufficient precision and sensitivity for biomarker discovery. More than two thousand RNAs are strongly associated with breast cancer recurrence risk in the 136 patient cohort (FDR <10%). Many of these are intronic RNAs for which corresponding exons are not also associated with disease recurrence. A number of the RNAs associated with recurrence risk belong to novel RNA networks. It will be important to test the validity of these novel associations in whole transcriptome RNA-Seq screens of other breast cancer cohorts.

Apatinib: a promising oral antiangiogenic agent in the treatment of multiple solid tumors.

Aberrant proangiogenic pathways have long been implicated in tumorigenesis and metastasis. Antiangiogenic therapies have shown efficacy in the treatment of a variety of solid tumors including lung, breast, colon, glioblastomas, and other solid tumor types. Apatinib, a small-molecule inhibitor of vascular endothelial growth factor receptor-2 (VEGFR-2), is an orally bioavailable agent currently being studied in multiple tumor types. Apatinib has shown a survival benefit in gastric cancer in a phase III trial and non-small cell lung cancer in a phase II trial. With a favorable side effect profile and improved outcomes, apatinib has demonstrated a substantial potential to augment therapeutic options in a variety of tumor types.

Evaluation of the efficacy of dasatinib, a Src/Abl inhibitor, in colorectal cancer cell lines and explant mouse model

Background Dysregulation of the Src pathway has been shown to be important at various stages of cancer. Dasatinib is a potent Src/Abl inhibitor and has demonstrated to have anti-proliferative and anti-invasive activity in many preclinical models. The objective of this study was to determine the anti-tumor activity of dasatinib using in vitro and in vivo preclinical colorectal (CRC) models. Methods CRC cell lines and patient-derived tumor explant (PDX) models were used to investigate the efficacy of dasatinib. We treated 50 CRC cell lines with dasatinib for 72 hours and proliferation was assayed by a sulforhodamine B (SRB) assay; an IC50 ≤ 0.08 μmol/L was considered sensitive. We treated 17 patient-derived CRC explants with dasatinib (50 mg/kg/day, administered once-daily) for 28 days to determine in vivo efficacy. Tumor growth inhibition (TGI) ≥ 50% was considered sensitive. Results We found that 8 out of 50 CRC cell lines reached an IC50 ≤ 0.08 μmol/L with dasatinib treatment. In addition, of 17 CRC explants grown in the xenograft mouse model, 2 showed sensitivity to dasatinib. The anti-tumor effects observed in this study were a result of G1 cell cycle arrest as the dasatinib sensitive CRC cell lines exhibited G1 inhibition. Moreover, those CRC cell lines that were responsive (0.08 μmol/L) to treatment demonstrated a significant baseline increase in Src and FAK gene expression. Conclusion Dasatinib demonstrated significant anti-proliferative activity in a subset of CRC cell lines in vitro, especially in those with increased Src expression at baseline, but only showed modest efficacy in CRC explants. Dasatinib is currently being studied in combination with chemotherapy in patients with advanced CRC, as its use as a single agent appears limited.

Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

Pancreatic cancers are typically diagnosed at late stage where disease prognosis is poor as exemplified by a 5-year survival rate of 8.2%. Earlier diagnosis would be beneficial by enabling surgical resection or earlier application of therapeutic regimens. We investigated the detection of pancreatic ductal adenocarcinoma (PDAC) in a non-invasive manner by interrogating changes in 5-hydroxymethylation cytosine status (5hmC) of circulating cell free DNA in the plasma of a PDAC cohort (n=51) in comparison with a non-cancer cohort (n=41). We found that 5hmC sites are enriched in a disease and stage specific manner in exons, 3’UTRs and transcription termination sites. Our data show that 5hmC density is reduced in promoters and histone H3K4me3-associated sites with progressive disease suggesting increased transcriptional activity. 5hmC density is differentially represented in thousands of genes, and a stringently filtered set of the most significant genes points to biology related to pancreas (GATA4, GATA6, PROX1, ONECUT1) and/or cancer development (YAP1, TEAD1, PROX1, ONECUT1, ONECUT2, IGF1 and IGF2). Regularized regression models were built using 5hmC densities in statistically filtered genes or a comprehensive set of highly variable 5hmC counts in genes and performed with an AUC = 0.94-0.96 on training data. We were able to test the ability to classify PDAC and non-cancer samples with the Elastic net and Lasso models on two external pancreatic cancer 5hmC data sets and found validation performance to be AUC = 0.74-0.97. The findings suggest that 5hmC changes enable classification of PDAC patients with high fidelity and are worthy of further investigation on larger cohorts of patient samples.

A single-arm, retrospective analysis of the incidence of febrile neutropenia using same-day versus next-day pegfilgrastim in patients with gastrointestinal cancers treated with FOLFOX or FOLFIRI

BackgroundPractice patterns of same-day versus next-day pegfilgrastim vary in numerous practice settings across the country. Current utilization with same-day pegfilgrastim reduced overall visits and reduced treatment time for chemotherapy administration.ObjectiveTo assess the efficacy and safety of same-day versus next-day pegfilgrastim in patients with colorectal cancer.MethodsPatient data was extracted through electronic health records (EHR) search of ICD-9 codes that matched patients with CRC and treated with FOLFOX or FOLFIRI from November 2013 to January 2016. The incidence rates of primary and secondary endpoints were estimated for patients who received either FOLFOX or FOLFIRI and same-day pegfilgrastim with 2-sided 95% confidence intervals. Fisher’s exact test for 2 × 2 contingency tables was used to compare the incidence of primary and secondary endpoints between the two study groups performed at the α = 0.05 significance level. A study by Hecht et al. served as a historical control for next-day pegfilgrastim.ResultsA total of 109 out of an initial 330 patients with appropriate ICD-9 criteria were eligible for study inclusion. The primary endpoint of incidence of FN recorded over 4 chemotherapy cycles with either FOLFOX6 or FOLFIRI occurred in 3.7% of patients (95% CI, 1.1–9.4%). Secondary endpoints also occurred with a relatively low incidence: 13 patients developed grades 3/4 neutropenia (11.9%; 95% CI, 7.0–19.5%); 11 patients required dose reductions because of neutropenia or FN (10.1%; 95% CI, 5.6–17.3%); and 5 patients were hospitalized due to neutropenia or FN (4.6%; 1.7–10.6%). There were 4 reported events of FN (3.2%; 95% CI, 1.0–8.3%) for those who received next-day pegfilgrastim compared to 11 events in the placebo group (9.4%; 95% CI, 5.1–16.4%). The incidence of dose delays or dose reductions due to neutropenia or FN were 5 (4.1%, 95% CI, 1.5–9.4%) in the next-day pegfilgrastim group versus 26 (22.1%, 95% CI, 15.5–30.4%) in the placebo group.LimitationsThe study was retrospective in design and utilized a historical control for the comparator.ConclusionsOur study results suggest that same-day pegfilgrastim administration may be a safe and effective alternative to 24-h post-chemotherapy administration in patients with esophageal, gastric, appendiceal, or colorectal cancer undergoing treatment with FOLFOX or FOLFIRI.

Multiple Myeloma Presenting as Acute Renal Failure in the Absence of Other Characteristic Features

This case report describes a 54-year-old, asymptomatic man who presented with hyperkalemia on routine lab testing who was later found to have acute renal failure, unresponsive to fluid resuscitation, with minimal improvement after hemodialysis. After a comprehensive evaluation ruled out common causes of acute renal failure, the patient underwent testing with a bone survey, urine protein electrophoresis (UPEP), serum protein electrophoresis (SPEP), and immunoelectrophoresis for suspected plasma cell dyscrasia and received plasmapheresis for hyperviscosity syndrome and nephrotoxicity, which resulted in improved renal function. Lab results showed monoclonal gammopathy, elevated serum free light chains, and Bence Jones protein in the urine with a follow-up bone marrow biopsy indicating plasma cell dyscrasia. The patient received a diagnosis of multiple myeloma (MM) and was started on chemotherapy and immunosuppression. In patients presenting with acute renal failure with an evaluation ruling out prerenal and postrenal causes, multiple myeloma should be considered.

The Semantics of Priapism and the First Sign of Chronic Myeloid Leukemia

Priapism is defined as an erection that persists beyond four hours, lasting beyond or unrelated to sexual stimulation (Salonia et al., 2014). Because the risk of ischemic damage and impotence is high with priapism (35%), management guidelines are directed towards rapid treatment of this condition (Salonia et al., 2014). This report describes the rare case of an 18-year-old male who presented to the Emergency Department (ED) three times with recurrent and worsening episodes of sustained penile erections. On the patients third visit, he presented with priapism of greater than six-hour duration that was found to be the result of chronic myeloid leukemia. Clinician awareness of the diagnostic semantics and differential diagnosis surrounding priapism is pivotal in its urgent management.

Abstract P4-02-08: Global quantitative measures using next-generation sequencing for breast cancer presence outperform individual tumor markers in plasma

Background: Analytically and clinically validated non-invasive blood tests that quantify breast cancer burden and clinical drug response/resistance are greatly needed. Many groups have successfully detected tumor markers in blood using a variety of technologies, including next generation sequencing (NGS). We performed a comprehensive NGS study on a small number of patients to evaluate the value of global versus individual markers for the quantitation of tumor-derived cell free DNA (cfDNA) in plasma. Methods: DNA isolated from formalin-fixed primary tumor, buffy coat cells, and plasma from 2 patients with metastatic breast cancer were characterized simultaneously for copy number aberrations (CNAs) and differentially methylated regions (DMRs) using whole genome bisulfite sequencing (WBGS), and targeted sequencing-based genotyping of 346 cancer-associated single nucleotide variations (SNVs). CNA and DMR regions were identified from log normalized, GC content corrected counts and DMR data using Poisson and binomial distribution theory and false discovery rate controlling methods. Percent tumor in cfDNA was estimated from the normalized ratio (plasma: primary tumor) of CNA or DMR compared to buffy coat, aggregating over genomic regions. Sample sets from 8 non-metastatic patients were also profiled using the targeted SNV panel in order to compare SNVs between samples and estimate percent tumor cfDNA. Results: WGBS detected tumor specific alterations in each primary tumor compared to buffy coat. By analyzing the genome using 100 Kb bins, we observed over 1000 bins with detectable CNA signal and, among 56 million CpG sites, over 30,000 DMRs. As expected, 5 or fewer informative somatic SNVs were detected in each patient. Analysis of these somatic changes in plasma revealed that the tumor fraction estimated from SNV detected in cfDNA varied widely between sites originally discovered in the patient’s primary tumor. In contrast, similar estimates of tumor fraction in cfDNA were obtained using CNA and DMR profiles within each patient; both methods yielded similar estimates of over 50% in one patient and less than 10% in the other. For the patient with high tumor fraction, both CNA and DMR profiles contained examples of individual large genomic regions that displayed additional clear aberrations in the plasma compared to the original tumor, such as a striking loss of a >25 Mb region of chromosome 4. Conclusions: Although individual somatic SNV in cfDNA can be detected in metastatic disease, calculated allelic fraction based on individual SNVs varies greatly within the same patient. Measuring and integrating CNA or DMR across the genome provided more consistent and reliable estimates of tumor DNA fraction in plasma, and also revealed alterations in plasma from patients with metastatic disease that were not prominent in the primary tumor. Citation Format: Ellen M Beasley, Richard D Abramson, Gregory E Alexander, David Chan, Kristen Bradley, Francois Collin, Michael Crager, Andrew Dei Rossi, Joseph Dorado, Adam Friedman, William J Gibb, Jennie Jeong, Col Jones, C J Ku, Yan Ma, John Morlan, Kunbin Qu, Aibing Rao, Aaron Scott, Haluk Tezcan. Global quantitative measures using next-generation sequencing for breast cancer presence outperform individual tumor markers in plasma [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-02-08.

Panitumumab in the treatment of colon cancer: A biomarker dilemma.

Panitumumab is a fully human monoclonal antibody targeting epidermal growth factor receptor (EGFR) approved for use in colorectal cancer (CRC). Critical information regarding biomarkers in CRC has been discovered through the investigation of panitumumab treatment. The discovery of anti-EGFR resistance in the setting of Kirsten rat sarcoma viral oncogene (KRAS) and more recently, neuroblastoma RAS viral oncogene (NRAS) mutations in CRC has changed the focus of therapy for metastatic disease to one based on the molecular characteristics of the tumor. This review will give a brief background on panitumumab and its current uses in CRC.