Early changes in tumor-naive cell-free methylomes and fragmentomes predict outcomes in pembrolizumab-treated solid tumors

Early kinetics of circulating tumor DNA (ctDNA) in plasma predict response to pembrolizumab, but typically requires sequencing of matched tumor tissue or fixed gene panels. We analyzed genome-wide methylation and fragment length profiles using cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq) in 204 plasma samples from 87 patients before and during treatment with pembrolizumab from a pan-cancer phase II investigator-initiated trial (INSPIRE). We trained a pan-cancer methylation signature using independent methylation array data from The Cancer Genome Atlas to quantify a cancer-specific methylation (CSM) and fragment length score (FLS) for each sample. CSM and FLS are strongly correlated with tumor-informed ctDNA levels. Early kinetics of CSM predict overall survival and progression-free survival, independently of tumor type, PD-L1, and tumor mutation burden. Early kinetics of FLS are associated with overall survival independently of CSM. Our tumor-naïve mutation-agnostic ctDNA approach integrating methylomics and fragmentomics could predict outcomes in patients treated with pembrolizumab.

Early Cancer Detection in Li-Fraumeni Syndrome with Cell-Free DNA

People with Li-Fraumeni syndrome (LFS) harbor a germline pathogenic variant in the TP53 tumor suppressor gene, face a near 100% lifetime risk of cancer, and routinely undergo intensive surveillance protocols. Liquid biopsy has become an attractive tool for a range of clinical applications, including early cancer detection. Here, we provide a proof-of-principle for a multimodal liquid biopsy assay that integrates a targeted gene panel, shallow whole-genome, and cell-free methylated DNA immunoprecipitation sequencing for the early detection of cancer in a longitudinal cohort of 89 LFS patients. Multimodal analysis increased our detection rate in patients with an active cancer diagnosis over uni-modal analysis and was able to detect cancer-associated signal(s) in carriers prior to diagnosis with conventional screening (positive predictive value = 67.6%, negative predictive value = 96.5%). Although adoption of liquid biopsy into current surveillance will require further clinical validation, this study provides a framework for individuals with LFS.

SIGNIFICANCE

By utilizing an integrated cell-free DNA approach, liquid biopsy shows earlier detection of cancer in patients with LFS compared with current clinical surveillance methods such as imaging. Liquid biopsy provides improved accessibility and sensitivity, complementing current clinical surveillance methods to provide better care for these patients. See related commentary by Latham et al., p. 23. This article is featured in Selected Articles from This Issue, p. 5.

Coronavirus disease 2019 (COVID-19) outbreak on an in-patient medical unit associated with unrecognized exposures in common areas-Epidemiological and whole-genome sequencing investigation

OBJECTIVE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hospital outbreaks have been common and devastating during the coronavirus disease 2019 (COVID-19) pandemic. Understanding SARS-CoV-2 transmission in these environments is critical for preventing and managing outbreaks.

DESIGN

Outbreak investigation through epidemiological mapping and whole-genome sequencing phylogeny.

SETTING

Hospital in-patient medical unit outbreak in Toronto, Canada, from November 2020 to January 2021.

PARTICIPANTS

The outbreak involved 8 patients and 10 staff and was associated with 3 patient deaths.

RESULTS

Patients being cared for in geriatric chairs at the nursing station were at high risk for both acquiring and transmitting SARS-CoV-2 to other patients and staff. Furthermore, given the informal nature of these transmissions, they were not initially recognized, which led to further transmission and missing the opportunity for preventative COVID-19 therapies.

CONCLUSIONS

During outbreak prevention and management, the risk of informal patient care settings, such as geriatric chairs, should be considered. During high-risk periods or during outbreaks, efforts should be made to care for patients in their rooms when possible.

Safety, Immunologic, and Clinical Activity of Durvalumab in Combination with Olaparib or Cediranib in Advanced Leiomyosarcoma: Results of the DAPPER Clinical Trial

PURPOSE

Non-inflamed (cold) tumors such as leiomyosarcoma do not benefit from immune checkpoint blockade (ICB) monotherapy. Combining ICB with angiogenesis or PARP inhibitors may increase tumor immunogenicity by altering the immune cell composition of the tumor microenvironment (TME). The DAPPER phase II study evaluated the safety, immunologic, and clinical activity of ICB-based combinations in pretreated patients with leiomyosarcoma.

PATIENTS AND METHODS

Patients were randomized to receive durvalumab 1,500 mg IV every 4 weeks with either olaparib 300 mg twice a day orally (Arm A) or cediranib 20 mg every day orally 5 days/week (Arm B) until unacceptable toxicity or disease progression. Paired tumor biopsies, serial radiologic assessments and stool collections were performed. Primary endpoints were safety and immune cell changes in the TME. Objective responses and survival were correlated with transcriptomic, radiomic, and microbiome parameters.

RESULTS

Among 30 heavily pretreated patients (15 on each arm), grade ≥ 3 toxicity occurred in 3 (20%) and 2 (13%) on Arms A and B, respectively. On Arm A, 1 patient achieved partial response (PR) with increase in CD8 T cells and macrophages in the TME during treatment, while 4 had stable disease (SD) ≥ 6 months. No patients on Arm B achieved PR or SD ≥ 6 months. Transcriptome analysis showed that baseline M1-macrophage and B-cell activity were associated with overall survival.

CONCLUSIONS

Durvalumab plus olaparib increased immune cell infiltration of TME with clinical benefit in some patients with leiomyosarcoma. Baseline M1-macrophage and B-cell activity may identify patients with leiomyosarcoma with favorable outcomes on immunotherapy and should be further evaluated.

Identifying Mechanisms of Resistance by Circulating Tumor DNA in EVOLVE, a Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer at Time of PARP Inhibitor Progression

PURPOSE

To evaluate the use of blood cell-free DNA (cfDNA) to identify emerging mechanisms of resistance to PARP inhibitors (PARPi) in high-grade serous ovarian cancer (HGSOC).

EXPERIMENTAL DESIGN

We used targeted sequencing (TS) to analyze 78 longitudinal cfDNA samples collected from 30 patients with HGSOC enrolled in a phase II clinical trial evaluating cediranib (VEGF inhibitor) plus olaparib (PARPi) after progression on PARPi alone. cfDNA was collected at baseline, before treatment cycle 2, and at end of treatment. These were compared with whole-exome sequencing (WES) of baseline tumor tissues.

RESULTS

At baseline (time of initial PARPi progression), cfDNA tumor fractions were 0.2% to 67% (median, 3.25%), and patients with high ctDNA levels (>15%) had a higher tumor burden (sum of target lesions; P = 0.043). Across all timepoints, cfDNA detected 74.4% of mutations known from prior tumor WES, including three of five expected BRCA1/2 reversion mutations. In addition, cfDNA identified 10 novel mutations not detected by WES, including seven TP53 mutations annotated as pathogenic by ClinVar. cfDNA fragmentation analysis attributed five of these novel TP53 mutations to clonal hematopoiesis of indeterminate potential (CHIP). At baseline, samples with significant differences in mutant fragment size distribution had shorter time to progression (P = 0.001).

CONCLUSIONS

Longitudinal testing of cfDNA by TS provides a noninvasive tool for detection of tumor-derived mutations and mechanisms of PARPi resistance that may aid in directing patients to appropriate therapeutic strategies. With cfDNA fragmentation analyses, CHIP was identified in several patients and warrants further investigation.

hENT1 Expression Predicts Response to Gemcitabine and Nab-Paclitaxel in Advanced Pancreatic Ductal Adenocarcinoma

PURPOSE

Modified FOLFIRINOX (mFFX) and gemcitabine/nab-paclitaxel (GnP) remain standard first-line options for patients with advanced pancreatic ductal adenocarcinoma (PDAC). Human equilibrative nucleoside transporter 1 (hENT1) was hypothesized to be a biomarker of gemcitabine in the adjuvant setting, with conflicting results. In this study, we explore hENT1 mRNA expression as a predictive biomarker in advanced PDAC.

EXPERIMENTAL DESIGN

COMPASS was a prospective observational trial of patients with advanced PDAC. A biopsy was required prior to initiating chemotherapy, as determined by treating physician. Biopsies underwent laser capture microdissection prior to whole genome and RNA sequencing. The cut-off thresholds for hENT1 expression were determined using the maximal χ2 statistic.

RESULTS

253 patients were included in the analyses with a median follow-up of 32 months, with 138 patients receiving mFFX and 92 receiving GnP. In the intention to treat population, median overall survival (OS) was 10.0 months in hENT1high versus 7.9 months in hENT1low (P = 0.02). In patients receiving mFFX, there was no difference in overall response rate (ORR; 35% vs. 28%, P = 0.56) or median OS (10.6 vs. 10.5 months, P = 0.45). However, in patients treated with GnP, the ORR was significantly higher in hENT1high compared with hENT1low tumors (43% vs. 21%, P = 0.038). Median OS in this GnP-treated cohort was 10.6 months in hENT1high versus 6.7 months hENT1low (P < 0.001). In an interaction analysis, hENT1 was predictive of treatment response to GnP (interaction P = 0.002).

CONCLUSIONS

In advanced PDAC, hENT1 mRNA expression predicts ORR and OS in patients receiving GnP.

In-depth characterization of intratumoral heterogeneity in refractory B-cell non-Hodgkin lymphoma through the lens of a Research Autopsy Program

Intratumoral heterogeneity (ITH) provides the substrate for tumor evolution and treatment resistance, yet is remarkably understudied in lymphoma, due to the often limited amount of tissue that gets sampled during the routine diagnostic process, generally from a single nodal or extranodal site. Furthermore, the trajectory of how lymphoma, and especially non-Hodgkin lymphoma, spreads throughout the human body remains poorly understood. Here, we present a detailed characterization of ITH by applying whole-genome sequencing to spatially separated tumor samples harvested at the time of autopsy (n=24) and/or diagnosis (n=3) in three patients presenting with refractory B-cell non-Hodgkin lymphoma. Through deconvolution of bulk samples into clonal mixtures and inference of phylogenetic trees, we found evidence that polyclonal seeding underlies tumor dissemination in lymphoma. We identify mutation signatures associated with ancestral and descendant clones. In our series of patients with highly refractory lymphoma, the determinants of resistance were often harbored by founding clones, although there was also evidence of positive selection of driver mutations, likely under the influence of therapy. Lastly, we show that circulating tumor DNA is suitable for the detection of ancestral mutations but may miss a significant proportion of private mutations that can be detected in tissue. Our study clearly shows the existence of intricate patterns of regional and anatomical evolution that can only be disentangled through multi-regional tumor tissue profiling.

Methylated circulating tumor DNA (cfMeDIP) as a predictive biomarker of clinical outcome in pan-cancer patients (pts) treated with pembrolizumab (P)

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Background: Bespoke mutation-based circulating tumor DNA (ctDNA) predicts response to P but relies on availability of tumor tissue and presence of mutations. Cell-free methylated immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) may overcome these limitations and be applied to more pts. Methods: Pts with mixed solid tumors divided into 5 cohorts received P 200 mg Q3wks in the investigator-initiated INSPIRE trial (NCT02644369). cfMeDIP-seq was performed at baseline (B), pre cycle 3 (C3) and later cycles. Methylation probability was inferred from read depths in 300 bp bins. cfMeDIP score was the probability-weighted sum of 3270 pan-cancer differentially-methylated regions in the TCGA PanCanAtlas. ctDNA concentration was assayed using tissue-informed bespoke targeted NGS (Signatera). ΔctDNA and ΔcfMeDIP denote the change in ctDNA or cfMeDIP between B and C3, respectively. Association with OS or PFS was assessed using Cox proportional hazards model, adjusting for cohort (aHR). Multivariable analysis (MVA) also included tumor mutation burden and PD-L1 status. Results: 194 plasma samples from 87 pts were analysed with cfMeDIP-seq (84 at B, 55 at C3, 55 at later cycles). Demographics: male 33%; median age = 61 yrs (34–82); Cohorts: triple negative breast (26%), ovarian (25%), head & neck (21%), melanoma (12%), others (15%). Median follow-up = 10.6m (0.6–64.4); Median PFS = 1.9m; Median OS = 10.6m. cfMeDIP at B below median was associated with better OS (aHR = 0.51, 95%CI 0.29-0.91; p = 0.02) in MVA. ΔcfMeDIP was evaluable in 53 pts; any decrease in ΔcfMeDIP was predictive for OS (aHR = 0.36, 95%CI 0.18-0.72; p < 0.01) and PFS (aHR = 0.42, 95%CI 0.22-0.82; p = 0.01). Both ΔctDNA and ΔcfMeDIP were evaluable in 51 pts; decrease in ΔctDNA and ΔcfMeDIP predicted for longer OS (aHR = 0.45, 95%CI 0.23-0.86; p = 0.02 vs aHR = 0.39, 95%CI 0.19-0.80; p = 0.01); and PFS (aHR = 0.44, 95%CI 0.23-0.83; p = 0.01 vs aHR = 0.5, 95%CI 0.25-0.99; p = 0.04), respectively. When both ΔctDNA and ΔcfMeDIP are integrated in MVA, ΔcfMeDIP was predictive for OS (aHR = 0.48, 95%CI 0.23-1; p = 0.05). A decrease in ΔcfMeDIP and/or ΔctDNA was associated with longer OS (aHR = 0.2, 95%CI 0.09-0.45) and PFS (aHR = 0.27, 95%CI 0.13-0.58) compared to an increase in both assays (p < 0.01) (Table). Conclusions: We applied for the first time cfMeDIP-seq and mutation-based ctDNA analysis concurrently in pan-cancer pts treated with checkpoint blockade. ΔcfMeDIP correlated strongly with OS and PFS, representing a promising plasma-based predictive epigenetic biomarker in pts treated with P. ΔctDNA and ΔcfMeDIP can complement each other to predict outcomes, demonstrating that they may capture different biological changes. Clinical trial information: NCT02644369. [Table: see text]

Abstract 2602: Leveraging cell-free methylome markers for early cancer detection

Cancer survival rates are significantly improved when detected at early stages, particularly when the tumor is still localized to the tissue of origin. However, effective screening tools for early cancer detection is currently limited to a subset of cancer types. The early development of human malignancies are difficult to observe as cancers are often detected once it becomes symptomatic, as such many cancer biomarker and evolution studies to date have primarily examined the genomics from solid tumor or liquid biopsies following a diagnosis. Investigating early tumor evolution in the pre-diagnosis context could allow us to better understand how to prevent or detect cancers in the earliest stage when survival rates are significantly higher, however this requires application of new technologies to biologics collected prior to a cancer diagnosis. Here, we leverage blood samples collected from participants in the Canadian Partnership for Tomorrow Project (CPTP), a longitudinal population cohort, prior to the onset of a cancer. Specifically, we utilize hybrid capture approaches to enrich for and characterize early mutations and methylation changes in circulating tumor DNA (ctDNA) of pre-cancer plasma samples collected from patients several months to years prior to clinical diagnosis. Here, we identify the earliest detectability of aberrant genetic and epigenetic events in ctDNA and describe the molecular evolution of these events at various stages prior to clinical detection of cancers. Further, we develop molecular biomarkers and implement machine learning tools to classify individuals with early cancers, and to develop risk scores from survival analyses predictive of cancer development up to 5 years prior to diagnosis. In our current study, we focus specifically on breast, prostate, lung and pancreatic cancer cases, and are extending this to pan-cancer applications in subsequent studies.

Citation Format: Nicholas Cheng, Kimberly Skead, David Soave, Jocelyn Meng, Elias Gbeha, Ilinca Lungu, Bernard Lam, Scott Bratman, Daniel De Carvalho, Philip Awadalla. Leveraging cell-free methylome markers for early cancer detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2602.

Impact of KRAS mutational status on outcomes in patients with pancreatic cancer (PDAC)

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Background: KRAS mutations (m) (KRASm) are present in over 90% of pancreatic adenocarcinomas (PDAC) with a predominance of G12 substitutions. KRAS wildtype (WT) PDAC relies on alternate oncogenic drivers, and the prognostic impact of these remains unknown. We evaluated alterations in WT PDAC and explored the impact of specific KRASm and WT status on survival. Methods: WGS and RNAseq were performed on 570 patients (pts) ascertained through our translational research program from 2012-2021, of which 443 were included for overall survival (OS) analyses. This included 176 pts with resected and 267 pts with advanced PDAC enrolled on the COMPASS trial (NCT02750657). The latter cohort underwent biopsies prior to treatment with first line gemcitabine-nab-paclitaxel or mFOLFIRINOX as per physician choice. The Kaplan-Meier and Cox proportional hazards methods were used to estimate OS. Results: KRAS WT PDAC (n = 52) represented 9% of pts, and these cases trended to be younger than pts with KRASm (median age 61 vs 65 years p = 0.1). In resected cases, the most common alterations in WT PDAC (n = 23) included GNASm (n = 6) and BRAFm/fusions (n = 5). In advanced WT PDAC (n = 27), alterations in BRAF (n = 11) and ERBB2/3/4 (n = 6) were most prevalent. Oncogenic fusions (NTRK, NRG1, BRAF/RAF, ROS1, others) were identified in 9 pts. The BRAF in-frame deletion p.486_491del represented the most common single variant in WT PDAC, with organoid profiling revealing sensitivity to both 3rd generation BRAF inhibitors and MEK inhibition. In resected PDAC, multivariable analyses documented higher stage (p = 0.043), lack of adjuvant chemotherapy (p < 0.001), and the KRAS G12D variant (p = 0.004) as poor prognostic variables. In advanced disease, neither WT PDAC nor KRAS specific alleles had an impact on prognosis (median OS WT = 8.5 mths, G12D = 8.2, G12V = 10.0, G12R = 12.0, others = 9.2, p = 0.73); the basal-like RNA subtype conferred inferior OS (p < 0.001). A targeted therapeutic approach following first line chemotherapy was undertaken in 10% of pts with advanced PDAC: MMRd (n = 1), homologous recombination deficiency (HRD) (n = 19), KRASG12C (n = 1), CDK4/6 amplification (n = 3), ERBB family alterations (n = 2), BRAF variants (n = 2). OS in this group was superior (14.7 vs 8.8 mths, p = 0.04), mainly driven by HRD-PDAC where KRASm were present in 89%. Conclusions: In our dataset, KRAS G12D is associated with inferior OS in resected PDAC, however KRAS mutational status was not prognostic in advanced disease. This suggests that improved OS in the WT PDAC population can only be achieved if there is accelerated access to targeted drugs for pts.

hENT1 gene expression as a predictor of response to gemcitabine and nab-paclitaxel in advanced pancreatic cancer

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Background: Human equilibrative nucleoside transporter 1 (hENT1) belongs to a family of nucleoside transporters critical to entry of gemcitabine into cells. The prognostic and predictive characteristics of this biomarker in pancreatic ductal adenocarcinoma (PDAC) have primarily been evaluated by immunohistochemistry, with conflicting results. We explored the impact of hENT1 gene expression in the Comprehensive Molecular Characterization of Advanced Ductal Pancreas Adenocarcinoma for Better Treatment Selection (COMPASS) trial. Methods: Patients were enrolled on COMPASS from December 2015 to June 2020 and underwent a biopsy for whole genome sequencing (WGS) and RNA sequencing prior to first chemotherapy in the advanced setting. Biopsies underwent laser capture microdissection to enrich for tumour epithelium. Chemotherapy regimen was determined based on clinician preference. The cut-off thresholds for hENT1 expression were determined using the maximal chi-squared statistic. Response rates and overall survival (OS) were computed based on hENT1 expression and chemotherapy regimen. Results: 254 patients were included in the analyses with a median follow-up time of 18 months. 146 patients were treated with modified FOLFIRINOX (FFX), 104 with gemcitabine and nab-paclitaxel (GnP), and 16 received no systemic therapy. Based on gene expression levels, 133 patients were classified as hENT1 high and 121 as hENT1 low. hENT1 expression was significantly associated with the modified Moffitt classifier with higher expression seen in classical tumours (p < 0.001). In the entire cohort, median OS was 10.0 months in hENT1 high vs. 8.3 months in hENT1 low (adjusted HR 0.78, 95% confidence interval 0.59 - 1.03, p = 0.08). In patients receiving modified FFX, there was no difference in response rates (32% vs. 31%, p = 1.00) or OS (10.6 vs. 10.6 months, p = 0.94) between the hENT1 high and hENT1 low groups, respectively. However, in patient treated with GnP, response rates were significantly higher in hENT1 high patients compared to those with hENT1 low tumors (45% vs. 21%, p = 0.035). Median OS in this GnP treated cohort was 9.8 months in hENT1 high vs. 6.1 months hENT1 low (p = 0.003). In an interaction analysis, hENT was predictive of treatment response to GnP (p = 0.0002). Conclusions: Biomarkers predictive of response to GnP and FFX are urgently needed. Here we demonstrate that hENT1 gene expression is a predictor of response to GnP in advanced PDAC.

Prospective observational study and serosurvey of SARS-CoV-2 infection in asymptomatic healthcare workers at a Canadian tertiary care center

Health care workers (HCWs) are at higher risk for SARS-CoV-2 infection and may play a role in transmitting the infection to vulnerable patients and members of the community. This is particularly worrisome in the context of asymptomatic infection. We performed a cross-sectional study looking at asymptomatic SARS-CoV-2 infection in HCWs. We screened asymptomatic HCWs for SARS-CoV-2 via PCR. Complementary viral genome sequencing was performed on positive swab specimens. A seroprevalence analysis was also performed using multiple assays. Asymptomatic health care worker cohorts had a combined swab positivity rate of 29/5776 (0.50%, 95%CI 0.32–0.75) relative to a comparative cohort of symptomatic HCWs, where 54/1597 (3.4%) tested positive for SARS-CoV-2 (ratio of symptomatic to asymptomatic 6.8:1). SARS-CoV-2 seroprevalence among 996 asymptomatic HCWs with no prior known exposure to SARS-CoV-2 was 1.4–3.4%, depending on assay. A novel in-house Coronavirus protein microarray showed differing SARS-CoV-2 protein reactivities and helped define likely true positives vs. suspected false positives. Our study demonstrates the utility of routine screening of asymptomatic HCWs, which may help to identify a significant proportion of infections.

Whole-genome sequencing of cholangiocarcinoma to reveal distinct profiles of patients with underlying cirrhosis or inflammatory disorders

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Background: Cholangiocarcinoma (CCA) is a lethal malignancy with limited treatment options. Molecular profiling of these tumours has revealed a number of actionable mutations and four clusters have been defined through integrative genomic analysis. We sought to explore whole genome sequencing (WGS) data in 20 patients enriched for CCA arising in the setting of cirrhosis or inflammatory disorders. Methods: A previously established Biliary Tract Cancer (BTC) database at the Princess Margaret Cancer Centre (PMCC)/University Health Network (UHN) was used to identify patients of clinical interest including long-term survivors, those with germ-line mutations, and those with chronic inflammatory disorders. WGS and bioinformatic analyses were performed at the Ontario Institute for Cancer Research. Results: The 20 resected samples included 12 patients (pts) with intrahepatic CCA, 7 perihilar CCA, and 1 distal CCA. 8 pts were alive > 8 years post resection and one patient harboured a germline MLH1 pathogenic variant (MLH1 G67R). 3 pts had documented cirrhosis (hepatitis B n = 2, haemochromatosis n = 1); other inflammatory disorders (n = 4) included ulcerative colitis (UC) without documented PSC (n = 1), PSC alone (n = 1), UC with PSC (n = 1), and ankylosing spondylitis (n = 1). The remaining cases were randomly selected. The predominant COSMIC single base substitution (SBS) mutational signatures were 1, 8 and 5, and the median TMB was 1.75 mutations per MB (0.73-33.23). The pt with an MLH1 mutation exhibited a TMB of 33.23 with predominance of SBS26. Actionable variants were enriched in the 8 pts who are alive and disease free including 2 predicted FGFR fusions and mutations in IDH1 (n = 1), BRAF V600E (n = 1), and BAP1 (n = 1). TP53 mutations (n = 7) were present exclusively in patients with cirrhosis or inflammatory disorders and the median survival in the group was 12 months (3 -21 months). Although SBS signatures were similar in this group, in the two cases of UC, SBS17 (unknown etiology) was evident. SBS17 was also dominant in one case where the TMB was 13 mutations per MB and the patient died within 3 months of diagnosis. A somatic case of homologous recombination deficiency, with no causative genetic alteration identified, was evident in a further patient receiving maintenance rituximab for a coexisting stage 4 mantle cell lymphoma. Conclusions: WGS may provide additional biological information in CCA particularly in patients with underlying inflammatory disorders, where TP53 mutations are prevalent and mutational signatures are distinct.

Abstract 5465: HRDetect as a predictive score of platinum response in advanced PDAC

Background: Predictors of response to DNA damaging agents may expand the population of patients who could benefit from platinum and/or PARP inhibition in pancreatic cancer (PDAC). The HRDetect score derived from whole genome sequencing (WGS) incorporates patterns of substitution base signatures and structural variation and is associated with tumours deficient in homologous recombination repair (HRD).

Methods: The prospective COMPASS trial (NCT 02750657) enrolls patients with advanced PDAC prior to systemic treatment for WGS and RNAseq. Choice of combination chemotherapy is at the discretion of the physician. HRD tumours are identified by the presence of a number of known genomic characteristics including evidence of biallelic inactivation of BRCA/PALB2 or the RAD51 family of genes, the presence of signature 3, the number and proportion of indels that are deletions of at least 4 base pairs (bp), and the presence of rearrangement signatures 3 and 5. We ascertained the number of patients with high HRDetect scores (&gt;0.7) and evaluated outcomes and response to chemotherapy including platinum regimens.

Results: As of 1st May 2019 204 eligible patients were enrolled. High HRDetect scores (HRDetecthi ) were present in 26/204 (13%). Only half of these cases were represented by HRD tumours including: 9 germline BRCA1/2 or PALB2 cases with biallelic inactivation and 3 tumours with somatic biallelic inactivation of BRCA2, RAD51C and XRCC2. 1 additional HRD case was of unknown aetiology. All HRD cases were HRDetecthi. Two germline carriers of BRCA2 without a second somatic hit were HR intact with low HRDetect scores. Of the remaining 13 non-HRD tumours identified as HRDetecthi, 6 exhibited a tandem duplicator phenotype (TDP) with tandem duplications ranging from 10Kbp to 1Mbp in size. These tumours did not have any other genomic characteristics of HRD. Notably, of the 204 patients included in this analysis, a TDP was present in 15 (7%), of which 40% were HRDetecthi. In patients treated with modified FOLFIRINOX(mFFX) (n=111, *includes 2 patients treated with cisplatin/gemcitabine) the response rate in HRDetecthi patients (n=16) was 56% vs 20% in HRDetectlo patients (n=95) p=0.005. There was no difference in response rates according to HRDetect score in patients treated with gemcitabine-nab-paclitaxel; HRDetecthi (n=7) 14.3% vs. HRDetectlo(n=71) 32.8%, p=0.42. Median OS in all patients receiving mFFX (n=111) was 10.2 months; in patients with HRDetecthi PDAC, median OS was 15.5 mths vs. 9.9 mths in HRDetectlo PDAC, (HR 0.42, 95% CI 0.24-0.87, p=0.01). In all patients (n=78) receiving gemcitabine based combination treatment the median OS was 8.1 mths; in HRDetecthi patients median OS was 11.5mths vs 7.8 mths in HRDetectlo patients (HR 0.94, 95% CI 0.42-2.13, p=0.8).

Conclusions: In patients with advanced PDAC with high HRDetect scores, response rate to FFX is over 50% and survival is significantly longer compared to patients with PDAC and low HRDetect scores. HRDetect identifies an additional population of patients with non-HRD PDAC who benefit from DNA damaging agents.

Citation Format: Grainne M. O'Kane, Robert E. Denroche, Amy Zhang, Sarah Picardo, Robert C. Grant, MIchael J. Allen, Gun Ho Jang, Yifan Wang, Anna Dodd, Stephanie Rampotar, Shawn Hutchinson, Mustaphe Tehfe, James J. Biagi, Dianne Chadwick, Bernard Lam, Julie Wilson, Faiyaz Notta, Sandra E. Fischer, George Zogopoulos, Steven Gallinger, Jennifer J. Knox. HRDetect as a predictive score of platinum response in advanced PDAC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5465.

Outcomes and Immunogenicity of pancreatic cancer stratified by the HRDetect score

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Background: The HRDetect score uses whole genome sequencing (WGS) to incorporate patterns of substitution base signatures and structural variation to identify tumours deficient in homologous recombination repair (HRD). HRD-tumours, with a higher mutational burden, may be more immunogenic. Methods: We applied HRDetect to 182 resected pancreatic cancers (PDA) and 233 advanced PDA enrolled on the COMPASS trial; both cohorts underwent WGS after tumour enrichment. Patients were classified as high(hi) or low(lo) according to the published score threshold of 0.7; clinical characteristics and survival outcomes were determined. Immunogenicity of the cohorts was explored by analyzing cytolytic activity (CYT) as measured by RNA expression of perforin and granzyme A. Results: 14% of resected (25/182) and 14% of advanced cases (32/233) were considered HRDetecthi . The median age at PDA diagnosis was younger in HRDetecthi vs HRDetectlo (61 vs 66 years, p = 0.005), with no difference in sex between groups. Of the 57 cases identified, 37 (65%) were considered true HRD-PDA with inactivation of BRCA1, BRCA2, PALB2, RAD51C and XRCC2. The remaining 20 cases, were considered false positives for HRD; of these 7 had evidence of a tandem duplicator phenotype with duplications ranging from 10Kbp to 1Mbp in size and 13 had no defining genomic characteristics of the HRD-subtype. In resected PDA, the HRDetect score after adjusting for stage, was not prognostic. In contrast in a multivariable analysis of advanced cases, both HRDetect (HR 0.51, 95% CI 0.30-0.87, p = 0.01) and the Moffitt RNA classifier were highly prognostic (HR 1.99, 95% CI 1.32-3.00, p = 0.0001) with improved survival in HRDetecthi and classical PDA. Of patients receiving platinum in advanced disease (n = 128) HRDetecthi PDA had longer survival compared to the HRDetectlo (15.6 vs. 9.9 months, p = 0.02) although the interaction term between chemotherapy regimen (gemcitabine vs. platinum) and HRDetect score was not significant in this cohort. HRDetecthi tumours had increased cytolytic activity than HRDetectlo PDA; furthermore, within the cohort of HRDetecthi PDA, higher CYT scores were evident in primary lesions compared to metastatic sites sequenced. Conclusions: A high HRDetect score is prognostic in advanced PDA where patients treated with platinum have longest survival. HRDetecthi tumours have increased cytolytic activity with differences observed between primary and metastatic lesions.

Diversity and signature of small RNA in different bodily fluids using next generation sequencing

BACKGROUND

Small RNAs are critical components in regulating various cellular pathways. These molecules may be tissue-associated or circulating in bodily fluids and have been shown to associate with different tumors. Next generation sequencing (NGS) on small RNAs is a powerful tool for profiling and discovery of microRNAs (miRNAs).

RESULTS

In this study, we isolated total RNA from various bodily fluids: blood, leukocytes, serum, plasma, saliva, cell-free saliva, urine and cell-free urine. Next, we used Illumina's NGS platform and intensive bioinformatics analysis to investigate the distribution and signature of small RNAs in the various fluids. Successful NGS was accomplished despite the variations in RNA concentrations among the different fluids. Among the fluids studied, blood and plasma were found to be the most promising fluids for small RNA profiling as well as novel miRNA prediction. Saliva and urine yielded lower numbers of identifiable molecules and therefore were less reliable in small RNA profiling and less useful in predicting novel molecules. In addition, all fluids shared many molecules, including 139 miRNAs, the most abundant tRNAs, and the most abundant piwi-interacting RNAs (piRNAs). Fluids of similar origin (blood, urine or saliva) displayed closer clustering, while each fluid still retains its own characteristic signature based on its unique molecules and its levels of the common molecules. Donor urine samples showed sex-dependent differential clustering, which may prove useful for future studies.

CONCLUSIONS

This study shows the successful clustering and unique signatures of bodily fluids based on their miRNA, tRNA and piRNA content. With this information, cohorts may be differentiated based on multiple molecules from each small RNA class by a multidimensional assessment of the overall molecular signature.

High-temperature high-pressure calorimeter for studying gram-scale heterogeneous chemical reactions

We present an instrument for measuring pressure changes and heat flows of physical and chemical processes occurring in gram-scale solid samples under high pressures of reactive gases. Operation is demonstrated at 1232 °C under 33 bars of pure hydrogen. Calorimetric heat flow is inferred using a grey-box non-linear lumped-element heat transfer model of the instrument. Using an electrical calibration heater to deliver 900 J/1 W pulses at the sample position, we demonstrate a dynamic calorimetric power resolution of 50 mW when an 80-s moving average is applied to the signal. Integration of the power signal showed that the 900 J pulse energy could be measured with an average accuracy of 6.35% or better over the temperature range 150-1100 °C. This instrument is appropriate for the study of high-temperature metal hydride materials for thermochemical energy storage.

The impact of viral hepatitis-related hepatocellular carcinoma to post-transplant outcomes

Hepatocellular carcinoma (HCC) is the most common complication of HCV infection leading to liver transplantation. We evaluated the impact of aetiology of liver disease on patient and graft survival following liver transplantation for HCC. From the Scientific Registry of Transplant Recipients (2002-2011), all adults who underwent liver transplantation for HCC were retrospectively included. Aetiology of liver disease was grouped into HCV, HBV, HCV-HBV co-infection and nonviral liver disease. Of 8,733 liver transplant recipients with HCC, 5507 had HCV, 631 had HBV, 163 were co-infected, and 2432 had nonviral causes of liver disease. In follow-up (48 ± 32 months), 8.2% had graft failure and 29.5% died. The mean rates of graft failure were 9.5%, 4.7%, 6.1% and 6.4% in HCV, HBV, HCV-HBV co-infection and nonviral liver disease, respectively (P < 0.0001). Post-transplant mortality rate in patients with HBV was 20.2%, HCV 31.0%, HCV-HBV 28.5% and nonviral 28.5% (P < 0.0001). This difference was significant starting one year post-transplant and became even more prominent later in follow-up. Five-year post-transplant survival was 64.7% in HCV, 77.7% in HBV, 71.0% in HCV-HBV and 69.1% in nonviral HCC (P < 0.0001). A diagnosis of HCV in patients with HCC was also independently associated with an increased risk of both graft failure (adjusted hazard ratio = 1.84 (1.46-2.33), P < 0.0001) and mortality (1.35 (1.21-1.50), P < 0.0001) in multivariate analysis. Patients with HCV-related HCC are at higher risk of adverse post-transplant outcomes. These patients should be considered for preemptive interferon-free antiviral therapy prior to or immediately following liver transplantation.

The patient's journey with chronic hepatitis C from interferon plus ribavirin to interferon- and ribavirin-free regimens: a study of health-related quality of life

BACKGROUND

Interferon and ribavirin negatively impact health-related quality of life (HRQL) during treatment.

AIM

To compare the impact of interferon and/or ribavirin-containing regimens on HRQL to interferon- and ribavirin-free regimens.

METHODS

HRQL data from nine multinational phase 3 clinical trials of sofosbuvir (SOF)-based regimens with and without ledipasvir (LDV), pegylated interferon (IFN) or ribavirin (RBV) were used. The Short Form-36 (SF-36) HRQL questionnaire was administered to subjects prospectively at baseline, during treatment, and 12 and 24 weeks after treatment cessation.

RESULTS

A total of 3460 CH-C with SF-36 data were included (52.2 ± 10.3 years, 62.6% male, 73.6% treatment-naïve, 15.0% cirrhotic, 68.2% HCV genotype 1 and 20.1% genotype 3). Compared to baseline HRQL, at the end of treatment, severe HRQL decrements were noted in IFN + RBV ± SOF regimens (on average, -3.8 to -24.3 on a 0-100 scale for different HRQL domains), while moderate decrements were noted in SOF + RBV ± LDV (-2.8 to -8.6). In contrast, in SOF/LDV without RBV, HRQL improvements were noted during treatment (+2.3 to +5.2). By 12 weeks post-treatment, HRQL returned to baseline in IFN + RBV ± SOF (P > 0.05) and improved in all IFN-free arms (+2.6 to +7.8). In multivariate analysis, a lower end of treatment HRQL was associated with IFN + RBV + SOF and a higher end of treatment HRQL was associated with SOF/LDV. By post-treatment-12, SOF/LDV was additionally associated with higher mental health scores. These improvements in HRQL scores were maintained 24 weeks post-treatment.

CONCLUSIONS

Removing interferon and ribavirin has led to substantial improvement of health-related quality of life during treatment. This may result in better patient experience and higher adherence to treatment regimen.

Experimental validation of a novel compact focusing scheme for future energy-frontier linear lepton colliders

A novel scheme for the focusing of high-energy leptons in future linear colliders was proposed in 2001 [P. Raimondi and A. Seryi, Phys. Rev. Lett. 86, 3779 (2001)]. This scheme has many advantageous properties over previously studied focusing schemes, including being significantly shorter for a given energy and having a significantly better energy bandwidth. Experimental results from the ATF2 accelerator at KEK are presented that validate the operating principle of such a scheme by demonstrating the demagnification of a 1.3 GeV electron beam down to below 65 nm in height using an energy-scaled version of the compact focusing optics designed for the ILC collider.

Association of hepatitis C with insulin resistance and type 2 diabetes in US general population: the impact of the epidemic of obesity

Studies from tertiary care medical centres have linked hepatitis C virus (HCV) to the development of insulin resistance (IR) and type 2 diabetes. The aim of the study is to assess the relationship between HCV positivity and insulin resistance/diabetes in the US population. Three cycles of the National Health and Nutrition Examination Survey (NHANES) conducted between 1988 and 2008 were used. HCV infection was diagnosed using a positive serologic anti-HCV test. Additionally, diabetes was diagnosed as fasting blood glucose ≥126 mg/dL and/or the use of hypoglycaemic medications. Insulin resistance was defined as a homeostasis of model assessment (HOMA) score of >3.0. Logistic regression was used to estimate the odds ratios (ORs) of each of the potential risk factors for diabetes mellitus (DM). The SUDAAN 10.0 was used to run descriptive and regression analyses. A total of 39 506 individuals from three NHANES cycles (1988-1994, 1999-2004 and 2005-2008) with complete demographic and relevant clinical data were included. Over these three NHANES cycles, prevalence of hepatitis C did not significantly change. During the first NHANES cycle (1988-1994), insulin and diabetes were independently associated with hepatitis C. However, during the later study cycles (1998-2008), these associations were no longer significant. In contrast, other important known risk factors for diabetes and IR (male gender, non-Caucasian race, age and obesity) remained significant over all three NHANES cycles. Although HCV infection was independently associated with an increased risk of diabetes and IR in the US population over a decade ago, assessment of the later NHANES cycles shows that this relationship may have become diluted by the rapid rise of other risks for diabetes, specifically, the prevalence of obesity.

MEDI-573 as a novel approach to IGF-1R and IR-A signaling inhibition by blocking IGF ligands: Phase I PK/PD, safety data, and disease linkage studies in breast cancer

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Background: MEDI-573 is a dual-targeting human antibody that neutralizes IGF-I/-II ligands and inhibits IGF-1R and insulin receptor-A (IR-A) signaling pathways, which play a role in breast and other epithelial cancers. By sparing IR-B and its hybrid receptors, MEDI-573 is expected to achieve antitumor activity without perturbing glucose homeostasis.

Methods: In a 3 + 3 dose-escalation trial ( NCT00816361 ), patients with advanced solid tumors, KPS ≥ 60, received MEDI-573 as a weekly 1-hr IV infusion at 0.5, 1.5, 5, 10, or 15 mg/kg every 21 days. Objectives included determination of MTD, safety profile, pharmacokinetics (PK), pharmacodynamics, and tumor response. In a separate biomarker study, mRNA expression of IR-A and IR-B was compared in HR+/HER- breast cancers.

Results: Patients included 13M/12F (17 evaluable for efficacy at data cutoff); median age 59 yrs (range 37-78). No DLTs, drug-related SAEs, or significant toxicity patterns were reported. Forty-five AEs were considered treatment-related (% of patients): decreased appetite (28%), fatigue (24%), nausea (20%), diarrhea (16%), and anemia (12%). Hyperglycemia occurred in 2 patients, 1 with evidence of prestudy insulin resistance. No other significant changes in plasma glucose levels occurred. MEDI-573 had dose-proportionality, with AUC of 415 ± 165, 597 ± 298, and 1940 ± 904 d*μg/mL at 5, 10, and 15 mg/kg, respectively. Suppression of free IGF-1 and -2 was fully achieved at doses ≥ 5 mg/kg. Stable disease spanning ≥ 12 wks (range 12-36+) was seen in 6/17 patients. No antidrug antibodies were reported. In a study to identify breast cancer subsets that are dependent on IGF signaling, the IR-A:IR-B ratio was significantly higher in HR+/HER2- breast cancer than matched adjacent normal tissues and in proliferative luminal B than in luminal A breast cancer.

Conclusions: MEDI-573 showed acceptable safety and favorable PK profiles without significant changes in glucose levels. The IR-A:IR-B ratio supports a biomarker approach for MEDI-573 patient stratification. A biomarker-rich phase Ib/II study of MEDI-573 with an aromatase inhibitor in patients with advanced HR+/HER2- breast cancer opens in 2011.

The effect of low intensity pulsed ultrasound in a 3D ex vivo orthodontic model

OBJECTIVES

This study investigated the effects of low intensity pulsed ultrasound (LIPUS) on dentoalveolar structures during orthodontic force application using a novel organ culture system.

METHODS

Mandibles were dissected from 28-day-old male Sprague Dawley rats, sliced into 1.5mm and cultured at 37°C and 5% CO(2), prior to application of a 50g force to each mandible slice. Slices were randomly divided into three groups of control, 5 and 10min LIPUS application and cultured for five days before histological and histomorphometrical analysis.

RESULTS

Cementum and predentine thickness and subodontoblast and periodontal ligament cell counts were increased in the ultrasound groups, with increases statistically significant in the 10min treated groups. Odontoblasts remained viable during LIPUS exposure and osteoclast activity was increased by LIPUS.

CONCLUSIONS

LIPUS may influence remodelling of the dentine-pulp complex and associated tissues during orthodontic force application ex vivo.

Early detection of central airway lung cancer in smokers with silicosis

BACKGROUND

Smokers with silicosis are at increased risk of lung cancer.

OBJECTIVE

To evaluate the feasibility of using autofluorescence bronchoscopy after sputum examination for early detection of large airway lung cancer and factors associated with the presence of cancerous and pre-cancerous lesions among smokers with silicosis.

METHODS

Subjects at the pneumoconiosis clinic were recruited if they fulfilled the following criteria: 1) age ≥40 years, 2) smoking history of ≥20 pack-years and 3) confirmed diagnosis of silicosis. Sputum specimens were collected for cytology/cytometry examination and autofluorescence bronchoscopy was performed in subjects with an abnormal sputum result.

RESULTS

A total of 48 subjects were recruited during the study period. The mean age and smoking history were respectively 63 ± 10 years and 51 ± 30 pack-years. Intraepithelial lung cancers and pre-neoplastic lesions (squamous metaplasia or above) were detected in respectively 2 (4.2%) and 14 (29.2%) subjects. The proportions of current smokers (75.0% vs. 40.6%, P = 0.03) and asbestos exposure (37.5% vs. 9.4%, P = 0.04) were significantly higher in subjects with the above lesions compared with those without.

CONCLUSIONS

Sputum examination followed by autofluorescence bronchoscopy may be a useful way of identifying cancerous/pre-cancerous lesions among silicotic smokers. Current smoking and asbestos exposure were associated with these lesions.

Management and prevention of spontaneous pneumothorax using pleurodesis in Hong Kong

BACKGROUND

The practice of pleurodesis for the management and prevention of spontaneous pneumothorax (SP) is uncertain.

DESIGN

A retrospective multicentre analysis of patients admitted to 12 hospitals in Hong Kong with SP in 2004 and who subsequently underwent pleurodesis for the same episode.

RESULTS

Pleurodesis was performed in 394 episodes. Initial medical chemical pleurodesis was performed for 258 (65.5%) patients ('initial medical group'), while 136 (34.5%) underwent initial surgical pleurodesis ('initial surgical group'). Secondary spontaneous pneumothorax (SSP; 237 episodes, 60.2%) was the most common indication for pleurodesis; it was also performed after a first episode of primary spontaneous pneumothorax (PSP) in 22 episodes (5.6%). Tetracycline derivatives (172 episodes, 66.7%) were the most popular sclerosing agents in the initial medical group. Those in the initial medical group were older and were more likely to be males, have SSP, chronic obstructive pulmonary disease and a history of past pleurodesis (P < 0.05) compared to the initial surgical group. Compared to the tetracycline group, more patients who initially received talc slurry had the procedure performed by surgeons, had larger (≥2 cm) pneumothorax or required suction during initial drainage (P < 0.05).

CONCLUSIONS

Despite the availability of international guidelines, there is considerable variation in pleurodesis for SP.