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Supplementary Figure from PD-1 Blockade in Solid Tumors with Defects in Polymerase Epsilon

Supplementary Data from PD-1 Blockade in Solid Tumors with Defects in Polymerase Epsilon

Missense mutations in the polymerase epsilon (POLE) gene have been reported to generate proofreading defects resulting in an ultramutated genome and to sensitize tumors to checkpoint blockade immunotherapy. However, many POLE-mutated tumors do not respond to such treatment. To better understand the link between POLE mutation variants and response to immunotherapy, we prospectively assessed the efficacy of nivolumab in a multicenter clinical trial in patients bearing advanced mismatch repair–proficient POLE-mutated solid tumors. We found that only tumors harboring selective POLE pathogenic mutations in the DNA binding or catalytic site of the exonuclease domain presented high mutational burden with a specific single-base substitution signature, high T-cell infiltrates, and a high response rate to anti–PD-1 monotherapy. This study illustrates how specific DNA repair defects sensitize to immunotherapy. POLE proofreading deficiency represents a novel agnostic biomarker for response to PD-1 checkpoint blockade therapy.Significance:POLE proofreading deficiency leads to high tumor mutational burden with high tumor-infiltrating lymphocytes and predicts anti–PD-1 efficacy in mismatch repair–proficient tumors. Conversely, tumors harboring POLE mutations not affecting proofreading derived no benefit from PD-1 blockade. POLE proofreading deficiency is a new tissue-agnostic biomarker for cancer immunotherapy.See related video: https://vimeo.com/720727355This article is highlighted in the In This Issue feature, p. 1397

Missense mutations in the polymerase epsilon (POLE) gene have been reported to generate proofreading defects resulting in an ultramutated genome and to sensitize tumors to checkpoint blockade immunotherapy. However, many POLE-mutated tumors do not respond to such treatment. To better understand the link between POLE mutation variants and response to immunotherapy, we prospectively assessed the efficacy of nivolumab in a multicenter clinical trial in patients bearing advanced mismatch repair–proficient POLE-mutated solid tumors. We found that only tumors harboring selective POLE pathogenic mutations in the DNA binding or catalytic site of the exonuclease domain presented high mutational burden with a specific single-base substitution signature, high T-cell infiltrates, and a high response rate to anti–PD-1 monotherapy. This study illustrates how specific DNA repair defects sensitize to immunotherapy. POLE proofreading deficiency represents a novel agnostic biomarker for response to PD-1 checkpoint blockade therapy. Significance: POLE proofreading deficiency leads to high tumor mutational burden with high tumor-infiltrating lymphocytes and predicts anti–PD-1 efficacy in mismatch repair–proficient tumors. Conversely, tumors harboring POLE mutations not affecting proofreading derived no benefit from PD-1 blockade. POLE proofreading deficiency is a new tissue-agnostic biomarker for cancer immunotherapy. See related video: https://vimeo.com/720727355 This article is highlighted in the In This Issue feature, p. 1397

Mutational signatures accumulate in somatic cells as an admixture of endogenous and exogenous processes that occur during an individual’s lifetime. Since dividing cells release cell-free DNA (cfDNA) fragments into the circulation, we hypothesize that plasma cfDNA might reflect mutational signatures. Point mutations in plasma whole genome sequencing (WGS) are challenging to identify through conventional mutation calling due to low sequencing coverage and low mutant allele fractions. In this proof of concept study of plasma WGS at 0.3–1.5x coverage from 215 patients and 227 healthy individuals, we show that both pathological and physiological mutational signatures may be identified in plasma. By applying machine learning to mutation profiles, patients with stage I-IV cancer can be distinguished from healthy individuals with an Area Under the Curve of 0.96. Interrogating mutational processes in plasma may enable earlier cancer detection, and might enable the assessment of cancer risk and etiology.

In consideration of the recent ICH Quality Discussion Group (QDG) recommended revision to the ICH series of stability guidelines, the IQ Consortium (International Consortium for Innovation and Quality in Pharmaceutical Development) Science- and Risk-based Stability Working Group conducted a comprehensive review of ICH Q1A, Q1B, Q1C, Q1D, Q1E, and Q5C to identify areas where the guidelines could be clarified, updated, and amended to reflect the potential knowledge gained from current risk-based predictive stability tools and to consider other science- and risk-based stability strategies in accordance with ICH Q8-12. The recommendations propose a holistic approach to stability understanding, utilizing historical data, prior knowledge, modeling, and a risk assessment process to expand the concept of what could be included (or would be acceptable) in the core stability data package, including type and amount of stability evidence, assignment of retest period and shelf-life for a new product, and assessment of the impact of post-approval changes.

Context: Polymerase epsilon (POLE) gene missense hotspot mutations can generate pathogenic (p) proofreading defects resulting in hypermutated genomic profiles. Aim: Determine the prevalence, genomic consequences and immunotherapy sensitivity of advanced POLE mutated tumors according to mutation site, primary tumor and tumor mutational burden (TMB). Results: Pan-Cancer TCGA & MSKCC databases genomic analyses found a prevalence of non-pathogenic POLE mutations (POLEnp) of 3.4% with median TMB of 11 mutations/Megabase (mt/Mb, IQR 3-34). Pathogenic POLE mutations (POLEp) prevalence was 0.4% with median TMB of 215 mt/Mb (IQR 107-324), predominantly in colorectal and endometrial cancers. Prevalence dropped to 0.1% in metastatic cancers. We assessed prospectively the efficacy of PD-1 blockade in mismatch repair proficient advanced solid tumors harboring POLE missense mutations (phase II ASCe Nivolumab trial; NCT03012581). Variants were categorized prospectively by a molecular board as POLEp, POLEnp or Variants with Unknown significance (VUS). The primary endpoint was the Overall Response Rate (ORR) at 12 weeks according to RECIST 1.1, and secondary endpoints included survival analyses according to POLE variants pathogenicity. Among 61 screened patients, 21 were eligible and 20 received Nivolumab and 19 were assessable for response (table 1). The 12-week ORR was 37% for patients harboring POLEp and VUS and resulted in major survival improvement compared to POLEnp patients (HR=0.1 ; CI95% 0.02-0.7); see results in Table 1. Among patients POLEp tumors, while higher TMB was not predictive of response, higher proportion of POLE-related mutational signature correlated with improved benefit. In silico exonucleasic POLE domain analyses confirmed that all POLEp and 2 VUS clustered in the DNA binding or the Catalytic site. Recategorizing the VUS according to the location within the exonucleasic domain improved the prediction of survival outcomes. Impact: This study gives new insights on how DNA repair defects, mutational burden and signatures sensitize to PD-1 blockade and may offer emerging tumor agnostic biomarkers for benefit to checkpoint blockade. POLE variant pathogenicity All(N=21) POLEnp(N=5) VUS(N=4) POLEp(N=12) Age, years ± SD 57 ± 16 64 ± 10 56 ± 16 54 ± 17 Sex, Male (%) 12 (57) 5 (100) 2 (50) 5 (42) PS (ECOG)=1 (%) 16 (75) 4 (80) 2 (50) 10 (83) Primary tumor Colorectal 9 (43) 2 (40) 2 (50) 5 (42) Endometrial 6 (29) 0 (0) 0 (0) 6 (50) Gastric 2 (9) 2 (40) 0 (0) 0 (0) Glial 1 (5) 0 (0) 0 (0) 1 (8) Biliary tract 1 (5) 0 (0) 1 (25) 0 (0) Pancreas 2 (9) 1 (20) 1 (25) 0 (0) Number of previous treatments 2.4 ± 2 5 ± 2 1.8 ± 1 1.5 ± 1 TMB (mt/Mb, Min-Max)(N=16) 36.2 (2-385) 5 (4-9) 3 (2-4) 114 (25-385) ORR at 12 weeks (CR+PR) 37%(N=7/19) 0%(N=0/5) 50%(N=2/4) 46%(5/10) DCR at 12 weeks (CR+PR+SD) 58%(N=11/19) 0%(N=0/5) 75%(N=3/4) 80%(8/10) Median Progresssion-Free survival (months) 5.6 2.3 10.3vs POLEnp: HR=0.2 IC95% 0.1-0.7 Median Overall Survival (months) 9.1 5.0 Not Reachedvs POLEnp:HR=0.1 IC95% 0.02-0.7 Citation Format: Benoît Rousseau, Ivan Bieche, Eric Pasmant, Nadim Hamzaoui, Nicolas Leulliot, Lucas Michon, Aurelien de Reynies, Mike Foote, Julien Masliah-Planchon, Magali Svrcek, Romain Cohen, Victor Simmet, Paule Augereau, David Malka, Antoine Hollebecque, Damien Pouessel, Carlos Gomez-Roca, Rosine Guimbaud, Amandine Bruyas, Marielle Guillet, Muriel Duluc, Sophie Cousin, Christelle de la Fourchardiere, Frederic Rolland, Sandrine Hiret, Esma Saada-Bouzid, Olivier Bouche, Thierry Andre, Diane Pannier, Farid El Hajbi, Stephane Oudard, Christophe Tournigand, Jean-Charles Soria, Drew Gerber, Dennis Stephens, Michelle Lamandola-Essel, Steven B Maron, Bill Diplas, Guillem Argiles, Asha Krishnan, Neil Segal, Andrea Cercek, Nathalie Hoog-Labouret, Frederic Legrand, Clotide Simon, Assia Lamrani-Ghaouti, Luis A. Diaz, Pierre Saintigny, Sylvie Chevret, Aurelien Marabelle. PD-1 blockade in solid tumors with defects in polymerase epsilon [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT021.

Circulating cell-free DNA (cfDNA) from blood plasma of cancer patients can be used to interrogate somatic tumor alterations non-invasively or when adequate tissue is unavailable. We have developed and clinically implemented MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), an NGS assay for detection of very low frequency somatic alterations in select exons and introns of 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance and utility of MSK-ACCESS, we report results from the first 681 prospective blood samples (617 patients) that underwent clinical analysis to guide patient management. Somatic mutations, copy number, and/or structural variants were detected in 73% of the samples, and 56% of these circulating-tumor DNA (ctDNA) positive samples had clinically actionable alterations. The utilization of matched white blood cell sequencing allowed retention of somatic alterations while filtering out over 10,000 germline and clonal hematopoiesis variants, thereby greatly enhancing the specificity of the assay. Taken together, our experience illustrates the importance of analyzing a matched normal sample when interpreting cfDNA results and highlights the potential of cfDNA profiling to guide treatment selection, monitor treatment response, and identify mechanisms of treatment resistance.

Summary Increased neoantigens in hypermutated cancers with DNA mismatch repair deficiency (dMMR) are proposed as the major contributor to the high objective response rate in anti-PD-1 therapy. However, the mechanism of drug resistance is not fully understood. Using tumor models defective in the MMR gene Mlh1 (dMLH1), we show that dMLH1 tumor cells accumulate cytosolic DNA and produce IFN-β in a cGAS-STING-dependent manner, which renders dMLH1 tumors slowly progressive and highly sensitive to checkpoint blockade. In neoantigen-fixed models, dMLH1 tumors potently induce T cell priming and lose resistance to checkpoint therapy independent of tumor mutational burden. Accordingly, loss of STING or cGAS in tumor cells decreases tumor infiltration of T cells and endows resistance to checkpoint blockade. Clinically, downregulation of cGAS/STING in human dMMR cancers correlates with poor prognosis. We conclude that DNA sensing within tumor cells is essential for dMMR-triggered anti-tumor immunity. This study provides new mechanisms and biomarkers for anti-dMMR-cancer immunotherapy.

BACKGROUND: Liquid biopsy for plasma circulating tumor DNA (ctDNA) next-generation sequencing (NGS) is commercially available and increasingly adopted in clinical practice despite a paucity of prospective data to support its use. METHODS: Patients with advanced lung cancers who had no known oncogenic driver or developed resistance to current targeted therapy (n = 210) underwent plasma NGS, targeting 21 genes. A subset of patients had concurrent tissue NGS testing using a 468-gene panel (n = 106). Oncogenic driver detection, test turnaround time (TAT), concordance, and treatment response guided by plasma NGS were measured. All statistical tests were two-sided. RESULTS: Somatic mutations were detected in 64.3% (135/210) of patients. ctDNA detection was lower in patients who were on systemic therapy at the time of plasma collection compared with those who were not (30/70, 42.9% vs 105/140, 75.0%; OR = 0.26, 95% CI = 0.1 to 0.5, P

State legislatures in the U.S. are becoming increasingly involved in utility regulation. While state utility legislation can expand regulator authority, for example in the case of renewable energy or energy efficiency standard administration, it can also reduce it. Given the challenging nature of for-profit monopoly regulation, state utility legislation often reduces regulator authority unintentionally. This editorial begins with an examination of the outcomes of state legislation related to baseload generation in the U.S. and the resulting impacts to customers, shareholders, and state economies. The record indicates that utility regulation through state legislation has caused significant economic harm, generally by encouraging for-profit utilities to make riskier investments. A description of more recent state legislation involving distribution grids is presented, along with evidence that increases in grid investment encouraged by state legislation has not improved the reliability of U.S. for-profit utilities. The authors claim that features common to state utility legislation, particularly the requirement that utilities provide investment plans to regulators in advance, practically eliminates cost disallowance risk. This, in turn, reduces regulator authority despite legislative provisions intended to protect consumers. The authors hypothesize that the practical elimination of cost disallowance risk, combined with information and expertise asymmetry among regulators and stakeholders, encourages for-profit monopoly utilities to make grid investments that are not cost effective. The editorial concludes that legislators should avoid utility regulation through legislation, thereby preserving regulator authority, whenever possible. The authors also present their fifth annual Customer Value Ranking of U.S. investor-owned electric utilities. The ranking represents a comparison of the benefits utilities deliver to customers (measured by reliability performance and customer satisfaction) to the costs customers pay (measured by O&M and capital spending per customer).

Programmed cell death protein-1 (PD-1) blockade therapies have demonstrated durable responses and prolonged survival in a variety of malignancies. Treatment is generally well tolerated although immune-related adverse events (irAEs) can occur. Autoimmune thyroid dysfunction is among the most common irAE, but an assessment of the clinical, mechanistic, and immunologic features has not been previously described.Patients with advanced non-small-cell lung cancer (NSCLC) treated with pembrolizumab at Memorial Sloan Kettering Cancer Center (n = 51) as part of KEYNOTE-001 (NCT01295827) were included. Thyroid function test and anti-thyroid antibodies were assessed prospectively at each study visit, beginning before the first treatment. Frequency of development of thyroid dysfunction, association with anti-thyroid antibodies, clinical course, and relationship with progression-free survival and overall survival to treatment with pembrolizumab was evaluated.Of 51 patients treated, 3 were hypothyroid and 48 were not at baseline. Ten of 48 [21%, 95% confidence interval (CI) 10% to 35%] patients developed thyroid dysfunction requiring thyroid replacement. Anti-thyroid antibodies were present in 8 of 10 patients who developed thyroid dysfunction, compared with 3 of 38 who did not (80% versus 8%, P 0.0001). Thyroid dysfunction occurred early (median, 42 days) in the pembrolizumab course, and a majority (6 of 10 patients) experienced brief, transient hyperthyroidism preceding the onset of hypothyroidism; no persistent hyperthyroidism occurred. Both hyperthyroidism and hypothyroidism were largely asymptomatic. Overall survival with pembrolizumab was significantly longer in subjects who developed thyroid dysfunction (hazard ratio, 0.29; 95% CI 0.09-0.94; P = 0.04).Thyroid dysfunction during pembrolizumab treatment of NSCLC is common and is characterized by early-onset, frequently preceded by transient hyperthyroidism, closely associated with anti-thyroid antibodies, and may be associated with improved outcomes. The presence of antibody-mediated toxicity in T-cell-directed therapy suggests an under-recognized impact of PD-1 biology in modulating humoral immunity.

Purpose The enucleation rate for retinoblastoma has dropped from over 95% to under 10% in the past 10 years as a result of improvements in therapy. This reduces access to tumor tissue for molecular profiling, especially in unilateral retinoblastoma, and hinders the confirmation of somatic RB1 mutations necessary for genetic counseling. Plasma cell‐free DNA (cfDNA) has provided a platform for noninvasive molecular profiling in cancer, but its applicability in low tumor burden retinoblastoma has not been shown. We analyzed cfDNA collected from 10 patients with available tumor tissue to determine whether sufficient tumorderived cfDNA is shed in plasma from retinoblastoma tumors to enable noninvasive RB1 mutation detection. Methods Tumor tissue was collected from eye enucleations in 10 patients diagnosed with advanced intra‐ocular unilateral retinoblastoma, three of which went on to develop metastatic disease. Tumor RB1 mutation status was determined using an FDA‐cleared tumor sequencing assay, MSK‐IMPACT. Plasma samples were collected before eye enucleation and analyzed with a customized panel targeting all exons of RB1. Results Tumor‐guided genotyping detected 10 of the 13 expected somatic RB1 mutations in plasma cfDNA in 8 of 10 patients (average variant allele frequency 3.78%). Without referring to RB1 status in the tumor, de novo mutation calling identified 7 of the 13 expected RB1 mutations (in 6 of 10 patients) with high confidence. Conclusion Plasma cfDNA can detect somatic RB1 mutations in patients with unilateral retinoblastoma. Since intraocular biopsies are avoided in these patients because of concern about spreading tumor, cfDNA can potentially offer a noninvasive platform to guide clinical decisions about treatment, follow‐up schemes, and risk of metastasis., Cancer Medicine, 9 (17), ISSN:2045-7634

Background: Cell-free DNA (cfDNA) is a promising tool to noninvasively profile the cancer genome and track response to treatment. Its utility in adult cancers has been widely demonstrated; however, evidence in pediatric cancers is relatively limited. To address that, we performed targeted sequencing to screen for actionable mutations in plasma, and evaluated the utility of shallow whole-genome sequencing (sWGS) as (i) a tool to estimate cfDNA tumor fractions to guide data interpretation in plasma, and (ii) a mutation-agnostic approach to monitor treatment responses and at the same time screen for actionable somatic copy number alterations from cfDNA, in pediatric cancer patients with neuroblastoma (NB), osteosarcoma (OS), and Wilms’ tumor (WT). Methods: In the first part of the study, we analyzed cfDNA by a ~400 gene targeted sequencing assay, MSK-IMPACT, and found mutations in 62% (31/50) of patients. In parallel, we performed sWGS (~0.1x) in the same cfDNA samples to estimate the fraction of tumor-derived DNA (cfDNA tumor fraction), which is established based on global copy number alterations and distinct tumor-derived cfDNA size profiles as features, that we learned in an independent adult cancer dataset using logistic regression model. Then we further evaluated the utility of sWGS-estimated tumor fractions to track responses in 28 patients (18 OS, 7 WT, and 3 NB) for whom longitudinal plasma samples were available. Results: Plasma samples with an estimated high tumor fraction tend to show better agreement between tumor and plasma. Among the three cancer types, MSK-IMPACT targeted sequencing analysis of cfDNA from relapsed neuroblastoma revealed actionable mutations, including alterations in ALK, NRAS, and TSC1. Wilms’ tumor cfDNA revealed prognostic biomarkers, such as somatic mutations in TP53 and 1q gains, which are associated with worse prognosis and require more aggressive therapy. The sWGS analysis also revealed somatic focal copy number amplifications that are potentially actionable such as CDK4 and MDM2 from the OS patients. When analyzing longitudinal plasma samples, we found that sWGS-derived cfDNA tumor fractions closely tracked the dynamics of disease response to treatment and surgical resection. In two OS patients where no mutations were detected by targeted sequencing but cfDNA tumor fraction was high, we performed exome sequencing on the cfDNA and found BRCA signature, which is potentially actionable in OS. Conclusions: Our results show that plasma profiling reveals actionable alterations across different types of pediatric cancers. Gene-panel targeted sequencing can reveal important somatic mutations, and low-pass sWGS allows longitudinal monitoring of tumor responses and detects clinically relevant copy number alterations. It also helps to identify cfDNA samples that have sufficient tumor-derived DNA for more comprehensive molecular profiling such as exome sequencing to screen for mutational signature that has clinical implication. Citation Format: Prachi Kothari, Julie Yang, Caitlin Stewart, Erika Gedvilaite, Dennis Stephens, Michael F. Berger, Michael V. Ortiz, Neerav Shukla, Emily Slotkin, Shakeel Modak, Dana W. Y. Tsui. Cell-free DNA for noninvasive molecular profiling and response monitoring in pediatric cancers [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A25.

Summary The early detection of relapse following primary surgery for non-small cell lung cancer and the characterization of emerging subclones seeding metastatic sites might offer new therapeutic approaches to limit tumor recurrence. The potential to non-invasively track tumor evolutionary dynamics in ctDNA of early-stage lung cancer is not established. Here we conduct a tumour-specific phylogenetic approach to ctDNA profiling in the first 100 TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy (Rx)) study participants, including one patient co-recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and perform tumor volume limit of detection analyses. Through blinded profiling of post-operative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients destined to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastases, providing a new approach for ctDNA driven therapeutic studies

A noted clinical application for liquid biopsy is as a non-invasive method of detecting and monitoring of minimal residual disease (MRD) in patients with cancer. The low concentration of circulating tumor DNA in blood, especially in early stage cancers, however, complicates the detection of tumor-derived cell-free DNA. To address this challenge, we have developed MSK-ACCESS (Analysis of Circulating cfDNA to Examine Somatic Status), a custom NGS assay covering selected exons from 129 cancer related genes for high-sensitivity detection of somatic mutations from plasma. Using ultra-high depth sequencing, with duplex unique molecular indexing (UMI), unique dual sample barcodes, and background error suppression, MSK-ACCESS is able to detect low-frequency (0.1%) variants with high confidence. The design of MSK-ACCESS leverages our dataset of more than 30,000 tumors profiled by our institutional tumor sequencing assay, MSK-IMPACT, ensuring that the majority of patients harbor multiple mutations that can be tracked in plasma. We have validated MSK-ACCESS using plasma samples collected from 40 healthy individuals and 70 cancer patients harboring a range of somatic mutations in 11 genes. Greater than 95% of mutations at allele fractions >0.1% were empirically detected, and we established the performance characteristics of the assay through intra- and inter-assay reproducibility tests and dilution experiments. We have initiated clinical trials in multiple tumor types to evaluate the benefit of early therapeutic intervention in patients where MSK-ACCESS can detect circulating tumor DNA following surgery. Tumor mutations revealed by MSK-IMPACT in surgically resected specimens will be monitored at regular intervals as evidence of MRD. As a proof of concept, we have applied MSK-ACCESS to monitor variants known from tissue tumor sequencing in pre- and post-surgical cfDNA samples from 9 colon adenocarcinoma patients. All samples were sequenced to an average total depth of approximately 20,000X coverage and subsequently collapsed to consensus sequences exhibiting an average noise level less than 0.0006%. Circulating tumor DNA was detected in 66%(6/9) of the pre-surgical samples. Of these samples, ctDNA was also detected in 50% (3/6) of the post-surgical samples. Overall, this study shows that MSK-ACCESS can be used to successfully detect MRD. Citation Format: Maysun M. Hasan, Juber Patel, Ian Johnson, Fanli Meng, Grittney K. Tam, Xiaohong Jing, Julie L. Yang, A. Rose Brannon, Jayakumaran Gowtham, Dennis P. Stephens, Monica Diosdado, Ryma Benayed, Ahmet Zehir, Chin-Tung Chen, Martin R. Weiser, Dana Tsui, Brian Houck-Loomis, Michael Berger. Tracking minimal residual disease in post-operative cell-free DNA using MSK-ACCESS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1387.

Background: The ERBB2/HER2 gene has long been known as an important oncogene in human cancer. Overexpression of HER2 influences the development of various cancers, and amplification of the gene is often found in aggressive forms of breast cancer, leading it to be an important biomarker in many targeted therapies. The goal of our study is to (i) detect the presence of HER2 amplification in plasma cell-free DNA (cfDNA) using two approaches: shallow Whole Genome Sequencing (sWGS) and digital droplet PCR (ddPCR). Methods: Tumor biopsy DNA from 3 patients was collected from surgeries performed either at diagnosis, disease progression, or relapse prior to enrollment on the trial. Plasma and matched control (buffy coat) were collected from patients before treatment (baseline) and at disease progression. The time of collection between tumor and baseline plasma was 71-913 days. Tumor specimens were analyzed using MSK-IMPACT, a comprehensive 468 gene platform, while plasma cfDNA and matched buffy coat DNA was analyzed using sWGS, ddPCR (using an assay previously reported that detection HER2 amplification by targeting regions on HER2 and a reference region 17q21.31), and a deep targeted sequencing assay that interrogate 60 frequent cancer drivers. Results: MSK-IMPACT revealed HER2 amplifications (1.5-15.4 fold) in all tumor samples. DdPCR analysis revealed HER2 amplification in all matched plasma samples (1.25-29.82). SWGS analysis of cfDNA detected HER2 amplifications in 5 of the 6 samples (2 baseline and all progression), and missed in one sample, which later confirmed to have the lowest low mutant allele fraction (MAF) among all samples analyzed: deep targeted sequencing analysis of that particular sample reveals a APC X215 mutation at 3% at baseline which later increased to 25% at disease progression, accompanied by the detection of HER2 amplification. In that particular patient, deep sequencing data reveal distinct dynamics of TP53, APC and PIK3CA, indicating the underlying tumor molecular evolution is highly heterogeneous. Conclusions: These results confirm that the detection of gene amplification in cfDNA is dependent on both the magnitude of amplification and the amount of tumor-derived MAF in the particular plasma sample. Noninvasive analysis of cfDNA allows the tracking of gene amplification and the dynamics of multiple cancer drivers during targeted therapies. Citation Format: Erika Gedvilaite, Caitlin Stewart, Julie Yang, Jonathan Reichel, Dennis Stephens, Michael D. Offin, Xiaohong Jing, Fanli Meng, Daoqi You, Michael F. Berger, Bob Li, Dana WY Tsui. Noninvasive profiling of molecular dynamics in patients receiving HER2 targeted therapies by cell-free DNA analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-228.

e21234Background: Liquid biopsy of circulating tumor DNA (ctDNA) by next generation sequencing (NGS) is widely adopted in clinical practice. ctDNA shedding across different lung cancer histologies,...

Canceling journal subscriptions has become an unhappy serials management routine. Identifying proposed titles for non-renewal is a topic of continuing interest in academic libraries, where faculty advice on the journal list is an important practical and political consideration. This workshop discusses a Web-based approach to faculty review and prioritization of journal titles used during spring 1999 at the University of Alaska Fairbanks. The software methods used to create the database-driven Website are described.

The human T-cell leukemia virus type I (HTLV-I) and HTLV-II Tax proteins are potent transactivators of viral and cellular gene expression. Using deletion mutants, the downstream parathyroid hormone- related protein (PTHrP) promoter is shown to be responsive to both HTLV- I and HTLV-II Tax as well as the AP1/c-jun proto-oncogene. Transactivation of PTHrP by Tax was seen in T cells but not in B-cell lines or fibroblasts. A carboxy terminal Tax deletion mutant was deficient in transactivation of both the PTHrP and IL2R alpha promoters but not the HTLV-I long terminal repeat (LTR). Exogenous provision of NFkB rescued IL2R alpha expression but not the PTHrP promoter. Thus, HTLV-I Tax, HTLV-II Tax, and c-jun transactivate PTHrP and may contribute to the pathogenesis of hypercalcemia in adult T-cell leukemia.

Lactate oxidase (EC 1. 1. 3. 2) catalyzes the oxidation of lactate to pyruvate with the concurrent reduction of oxygen to hydrogen peroxide. An oxygen electrode (−650 mV vs Ag/AgCl) was prepared with an immobilized lactate oxidase membrane. L-Lactate was determined by monitoring the decrease in oxygen concentration from the enzyme reaction. The initial rate of decrease was proportional to the concentration in the range tested (70–340 μM, RSD 3.2%, det. limit 6 μM). Recovery from a spiked placebo was 102% and D-lactate did not give a significant response. Results from testing two pharmaceutical products indicated that one was manufactured with racemic lactate (L-lactate 49.4 % of label claim) and one was manufactured with enantiomerically pure L-lactate (L-lactate 102% of label claim).

Coordinated collection development and management planning in Alaska is based on the Conspectus. Conspectus data is used for collection development in individual libraries, among groups of local libraries, and for statewide coordination and policy-making.

8064 Background: Patients with ALK + non-small cell lung cancer (NSCLC) initially respond to crizotinib, but eventually develop resistance. Treatment of patients with ALK positive lung cancer with HSP90 inhibitors leads to clinical and radiographic response. We hypothesized that treatment of patients with ALK rearranged NSCLC with crizotinib and ganetespib, an HSP90 inhibitor, would be safe. Methods: All patients had ALK rearranged metastatic non-small cell lung cancer not previously treated with crizotinib. Prior chemotherapy was allowed. Patients were treated with crizotinib 250 mg bid continuously; ganetespib was administered intravenously on days 1 and 8 of a 21-day cycle. In a standard 3+ 3 design, ganetespib was explored at 3 different dose levels. The primary objective was to determine the maximum tolerated dose of the combination of crizotinib and ganetespib. Secondary objectives included establishing the safety profile (CTCAE v4) of the combination in patients with ALK+ lung cancer, exploring the...

A production-scale manufacturing process has been developed for polyanhydride/gentamicin sulfate implants for the treatment of osteomyelitis. Gentamicin sulfate was first dried to an acceptable moisture level by using a tumble vacuum dryer. Dried gentamicin sulfate powder and polyanhydride granules were separately fed into the twin-screw extruder at a pre-determined metering rate using a gravimetric feeding device. The extruded molten mixture was solidified to form strands which were subsequently cut into pellets by using a pelletizer. The pellets were characterized with respect to copolymer molecular weight and drug content uniformity. The pellets were later fed into production-scale injection-molding equipment for implant fabrication. The injection-molding cycle was developed and evaluated in terms of cycle reproducibility. Implants were tested and shown to yield an oriented skin-core structure exhibiting a desirable in-vitro drug release profile.

A case is presented to demonstrate the use of computerized axial tomography (CAT) to develop precise registration of incisal edges for comparison to bite marks. Emphasis is drawn to the availability of CAT Scanning equipment and the importance of understanding its use as an adjunct or alternative to already accepted methods of incisal registration.