bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and analytical validation of a 523-gene clinical assay for cell-free DNA.
Authors: Harrington Robin , Das Biswajit , Jiang Tingting , LoCoco Jennifer S. , Patidar Rajesh , Peach Amanda , Zhao Chen , Camalier Corinne , Chang Ting-Chia , Chen Alice P. , Chen Li , Forbes Thomas , Katz Sigrid , Nair Nikitha , Sims David J. , O'Sullivan Coyne Geraldine Helen , Takebe Naoko , Williams Paul M. , Karlovich Chris Alan , Doroshow James H.
Published: May 2019

3039

Background: Liquid biopsies are emerging as a powerful complement to tumor biopsies for the clinical management of cancer patients. A large gene panel with robust analytical performance that accurately assesses variants, tumor mutational burden (TMB), and microsatellite instability in plasma would be of high value for immunotherapy studies, monitoring minimal residual disease and early cancer detection. To this end, we have completed the initial validation for the cell-free DNA (cfDNA) assay, TruSight Oncology 500 (TSO500), which interrogates the full coding region of 523 genes plus selected intronic regions for fusion detection in 23 driver genes. Methods: Cell-free DNA was extracted from plasma collected from Streck or EDTA blood tubes and quantitated to achieve an assay input of ≥10 ng. Libraries were constructed using unique molecular identifiers (UMIs) and duplex barcodes for error correction, then enriched by target capture and sequenced on a NovaSeq 6000. Healthy donor (HD) specificity assessment used matched white blood cell results to filter germline and clonal hematopoiesis variants. Contrived specimens were used to evaluate sensitivity. Single nucleotide variants (SNVs) (n = 36), insertion/deletions (indels) (n = 19), copy number variants (CNVs) (n = 6), and fusions (n = 5) were tested in 2 multi-site replicates. Results: Sensitivity of detection at 0.5% variant allele fraction (VAF) was > 95% and > 97% for SNVs and indels, respectively. All expected CNVs were identified at the targeted threshold of ≥1.3X change and showed strong correlation with matched digital PCR results. All fusions were identified at ≥0.4% VAF. Specificity in HD was > 99.99%. In 22 temporally matched tumor and blood samples from late-stage patients, 58% of all reportable mutations in tumor were identified in cfDNA. Preliminary TMB analysis identified one TMB high case with POLE p.P286R observed in both tissue and cfDNA. Conclusions: In this initial validation study the TSO500 cfDNA assay exhibited high sensitivity and specificity consistent with requirements for clinical applications. Ongoing studies will further evaluate TSO500 as a complement or potential alternative to tissue biopsy for the genomic profiling of cancer patients.
Whole-genome cell-free DNA (cfDNA) changes as a dynamic blood-based biomarker for early response assessment of advanced tumors.
Authors: Davis Andrew A. , Iams Wade Thomas , Chan David , Oh Michael S , Lentz Robert William , Peterman Neil , Robertson Alex , Shah Abhik , Srivas Rohith , Lambert Nicole , Wilson Timothy , George Peter , Wong Becky , Tezcan Ayse , Yalamanchili Ram , Nesmith Ken , Spinosa John C , Tezcan Haluk , Chae Young Kwang
Published: May 2019

3041

Background: Liquid biopsies have potential clinical utility as dynamic biomarkers for treatment response. We analyzed serial changes in whole-genome (WG) cfDNA to identify patients with disease progression prior to routine imaging. Methods: We prospectively collected clinical data and blood from 69 advanced cancer patients (28 lung, 25 breast, 16 other). Blood was collected at baseline prior to initiation of a new treatment and at one or two additional timepoints (median 21 and 42 days). We isolated plasma cfDNA and prepared sequencing libraries for WG sequencing or WG bisulfite sequencing (median depth 20X). We quantified changes in the fraction of tumor-derived cfDNA over the initial course of treatment to predict progression vs. no progression. Treatment response at first post-treatment imaging was determined by RECIST 1.1 and clinical assessment. Study endpoints were agreement with first post-treatment imaging and progression-free survival (PFS) by cfDNA prediction. Results: Median age of patients was 70 and 59% were female. Patients were treated with the following therapies: chemotherapy (37), immunotherapy (17), endocrine (9), or targeted therapy (6). Patients with predicted progression by cfDNA (14), indicated by an increase in tumor fraction at either post-treatment blood collection, had shorter PFS (median 63 days) compared to patients without an increase (N = 55; median 255 days), with hazard ratio of 10.3 (95% confidence interval 4.6-23.4, log-rank P = 1x10-11). Positive predictive value was 100% for disease progression and negative predictive value was 78%. These findings were consistent in subset analyses of patients with lung (log-rank P = 2x10-5), breast (log-rank P = 3x10-4), and those treated with immunotherapy (log-rank P = 5x10-6). Conclusions: Our results show the ability to detect early disease progression with high fidelity using WG cfDNA prior to first imaging. These findings were consistent across multiple tumor types and treatments, including immunotherapy patients. Once validated, this dynamic, predictive, blood-based biomarker could aid in clinical decision making for early treatment change as a novel and cost-effective approach.
Cell-free methylated DNA (cfMeDNA) immunoprecipitation and high throughput sequencing technology (cfMeDIP-seq) in patients with clear cell renal cell carcinoma (ccRCC).
Authors: Nuzzo Pier , Spisak Sandor , Chakravarthy Ankur , Shen Shu Yi , Berchuck Jacob E , Nassar Amin , Abou Alaiwi Sarah , Steinharter John A. , Bakouny Ziad , Boccardo Francesco , Sonpavde Guru , Lee Gwo-Shu Mary , Chang Steven Lee , Pomerantz Mark , De Carvalho Daniel , Freedman Matthew , Choueiri Toni K.
Published: May 2019

3052

Background: CfmeDNA is a promising biomarker for non-invasive assessment of solid tumors: i) MeDNA is tissue- and tumor-specific ii) cfDNA methylation changes are stable unlike DNA alterations iii) ‘methylation target size’ is larger than identifying specific genomic alterations and, therefore, more sensitive. CfMeDIP-seq is a sensitive assay for genome-wide bisulfite-free cfMeDNA profiling, that requires 1-10 ng input DNA. We tested the feasibility of cfMeDIP-seq to detect ccRCC across TNM stages. Methods: We evaluated plasma cfDNA collected prior to nephrectomy in 46 pts with ccRCC: 25 stage I, 7 stage II, 6 stage III, 8 stage IV. cfMeDIP-seq involves four steps: 1) cfDNA end-repair, A-tailing, and adapter ligation 2) cfMeDNA immunoprecipitation and enrichment using an Ab targeting 5-methylcytosine (quality control by qPCR to ensure <1% of unMeDNA and >99% reaction specificity) 3) adapter-mediated PCR to amplify cfMeDNA 4) high-throughput NGS for cfMeDNA data. A previously-derived model (Shen et al, Nature, 2018) was used to classify pts as having ccRCC or not based on cfMeDNA. cfMeDIP-seq paired end data was reduced to 300 bp windows of the genome that map to CpG islands, shores, shelves, and FANTOM5 enhancers; a classifier was then built using the top 1,000 most variable fragments between pts with ccRCC and cancer-free controls. Statistical comparisons were performed in the R statistical environment, with the caret package being used for classifier construction and evaluation. Results: The average amount of cfDNA isolated from 1 ml of ccRCC plasma was 19.8±39.8 ng/µL [1.95-260]. Greater than 99% specificity of reaction and <1% of unMeDNA was achieved in 46/46 samples (100%). The previously-derived classifier of ccRCC correctly predicted 46/46 pts (100%) as having ccRCC. Across 3 rounds of 5-fold cross-validation, the classifier performed with a Cohen’s Kappa of 0.93. Conclusions: CfMeDIP-seq is a non-invasive, cost-effective, and sensitive assay to detect cancer-specific cfmeDNA in ccRCC pts prior to nephrectomy. With further validation, cfmeDNA may detect minimal residual disease after nephrectomy for ‘precision’ adjuvant therapy.
Efficacy of tyrosine kinase inhibitors (TKIs) based on the ALK resistance mutations on amplicon-based liquid biopsy in ALK positive non-small cell lung cancer (NSCLC) patients (pts).
Authors: Mezquita Laura , Swalduz Aurélie , Jovelet Cecile , Ortiz-Cuaran Sandra , Planchard David , Recondo Gonzalo , Benitez Jose Carlos , Howarth Karen , Morris Clive D. , Green Emma , Lacroix Ludovic , Odier Luc , Rouleau Etienne , Fournel Pierre , Caramella Caroline , Tissot Claire , Perol Maurice , Friboulet Luc , Besse Benjamin , Saintigny Pierre
Published: May 2019

3055

Background: Acquired ALK resistance mutations (mut.) are the main mechanism of tyrosine kinase inhibitor (TKI) resistance (30-50%). While next-generation TKIs are more active on mut. than earlier TKIs, compound ALK resistance are associated with failure to next-generation TKIs. We evaluated the clinical utility of detecting ALK resistance mutations in blood to predict TKI efficacy. Methods: ALK positive advanced NSCLC pts were prospectively enrolled between Oct. 2015 and Aug. 2018 in 8 French institutions. Prospective samples were collected; ctDNA was analyzed by amplicon-based Inivata InVisionFirst-Lung. Results: A total of 101 pts with advanced ALK positive NSCLC were enrolled and 328 samples collected. In samples collected at TKI failure (N=74), we detected 9 single and 7 complex (≥2) ALK resistance mut. (22%), associated with EML4-ALK variant 3 (38%) vs. variant 2 (13%) vs. variant 1 (none); 30% had other somatic mut. (mainly TP53 and KRAS, PI3KCA, MET, etc.). No mutations were detected in 48% of samples (ctDNA neg). ALK mut. were more frequent after 2nd/3rd generation TKI (43% post-lorlatinib (7), 29% post-2nd gen. (31), 11% post-crizotinib (36)). ALKG1202R was the most common, as single (n=3) or complex mut. (n=4). The median overall survival (mOS) was 100.4 mo. (95% CI 41.9-158.9) and the median progression free-survival (mPFS) to subsequent line was 2.8 mo. (0.7-4.9). Patients with ctDNA neg had mOS of 105 mo. (39.3-172.1) vs. 58.5 mo. (33.1-84.0) if ≥1 ALK mut. vs. 44.1 mo. (20.0-68.2) if others ( P=0.001). Pts with the complex ALK mut. had worse OS compared to singles ALK mut. (mOS 26.9 mo. vs. 58.5 mo., P=0.001); ALK complex mut. were associated with poor efficacy to subsequent therapy (PFS <3 mo. in 57%; no cases with PFS >6 mo.) vs. single mut., with longer PFS (PFS >6 mo. in 56%). Detectable ALKG1202R mut. were associated with shorter median OS (58.3 mo.; 7.9-109.1) vs. overall population; 86% of cases developed rapid PD (PFS <3mo.) to subsequent therapy with only one durable response to lorlatinib (PFS >6mo.). Conclusions: The absence of ctDNA mutations at TKI failure was associated with prolonged OS, whereas complex ALK mutations at TKI failure may predict resistance to subsequent therapy. Larger and specifically designed studies should be performed to validate these findings.
Baseline cfDNA characteristics and evolution of cfDNA profile during treatment with selective FGFR inhibitor TAS-120.
Authors: Moss Tyler J. , Rodon Ahnert Jordi , Oakley Holly D. , Kahle Michael , Karp Daniel D. , Pant Shubham , Jacob Jeena , Raymond Victoria M. , Lanman Richard B. , Kwong Lawrence , Routbort Mark , Soni Nital , Huang Jerry , Javle Milind M. , Meric-Bernstam Funda
Published: May 2019

3056

Background: There is an increasing role for cfDNA in monitoring response and mechanisms of resistance. We performed cfDNA analysis in a subset of patients enrolled on a Phase I trial with an irreversible, selective FGFR1-4 inhibitor, TAS-120. Methods: 58 plasma samples from 17 patients (13 with cholangiocarcinoma) were analyzed on a 73-gene, next-generation sequencing panel. Selected patients(pts) had longitudinal samples. Results: At least one alteration was detected in 46 cfDNA samples, in 16 (94%) of 17 pts – a pt with GBM had no alterations detected. 14 pts had alterations in FGFR2/3 by genomic testing of archival tumor samples, comprising 20 total alterations (18 unique). 10 of 20 FGFR2/3 alterations were also detected by cfDNA testing: 4/5 SNVs, 1/2 amplifications, 5/13 fusions. Three pts had FGFR/FGF alterations not included (thus not detected) in the cfDNA panel: 2 with FGF ligand amplification, and one FGFR4 mutation. 6 pts (35%) had PR, 5 (29%) had SD and 6 (35%) PD as a best response to TAS-120. Four pts had prior FGFRi: 2 had a PR, 1 SD, and 1 PD on TAS-120. Baseline cfDNA mutations became undetectable during treatment in 4/6 pts with PR. 4 of 6 PD pts had other driver mutations at baseline including mutations in PIK3CA, KRAS, IDH1, BRCA2, or amplifications in PIK3CA, PDGFR. 9 pts with cfDNA available at progression after SD/PR: 3 had acquired FGFR2 mutations (one each of V564L, V564F, or N549K). Two also acquired alterations in other candidate resistance genes ( PTEN and MAP2K1). Another pt had low variant allele frequency (VAF) NRAS G12D and BRAF A694T pretreatment and had SD. At progression, cfDNA revealed an increase in NRAS VAF and mutations acquired in the MAPK pathway . One pt with prior FGFRi acquired FGFR2 V564I and V564K detected by cfDNA prior to initiation of TAS-120, and had a PR on TAS-120. There was a drop in FGFR2 V564I VAF with response that subsequently increased with progression. The patient also acquired a FGFR2 V564L mutation at progression. Conclusions: FGFR alterations can be detected by cfDNA. cfDNA may detect potential resistance mechanisms, including PI3K or MAPK pathway alterations and acquired FGFR2 mutations. Patients with gatekeeper mutations in cfDNA at baseline may still respond to TAS-120. Further study is needed to determine the impact of FGFR2 mutations and co-alterations on TAS-120 sensitivity.
No-cost next generation sequencing of advanced cancer patients within the Strata Precision Oncology Network supports clinical trial enrollment.
Authors: Matrana Marc Ryan , Tomlins Scott A. , Kwiatkowski Kat , Mitchell Khalis , Suga Jennifer Marie , Dees Elizabeth Claire , Burkard Mark E. , Khatri Jamil , Safa Malek M. , Yang Eddy Shih-Hsin , Parsons Benjamin , Menter Alex R. , Thompson Michael A. , Gonzalez Anneliese O. , Wassenaar Timothy Robert , Rhodes Dan
Published: May 2019

3073

Background: Widespread integration of systematized next generation sequencing (NGS)-based precision oncology is hindered by numerous barriers. Hence, we developed the Strata trial (NCT03061305), a screening protocol to determine the impact of scaled precision oncology. Methods: We implemented no-cost NGS on formalin fixed paraffin embedded (FFPE) clinical samples for all patients with advanced tumors, a common portfolio of partnered therapeutic clinical trials, and robust infrastructure development across the Strata Precision Oncology Network. Results: Across the network of 17 centers, specimens from 8673/9222 (94%) patients were successfully tested in the Strata CLIA/CAP/NCI-MATCH accredited laboratory using comprehensive amplicon-based DNA and RNA NGS. Patients were tested with one of three StrataNGS test versions; the most recent panel assesses all classes of actionable alterations (mutations, copy number alterations, gene fusions, microsatellite instability, tumor mutation burden and PD-L1 expression). Median surface area of received FFPE tumor samples was 25mm2 (interquartile range 9-95mm2), and the median turnaround time from sample receipt to report was 6 business days. 2577 (27.9%) patients had highly actionable alterations, defined as alterations associated with within-cancer type FDA approved or NCCN guideline recommended therapies (1072 patients), NCI-MATCH trial arms (1467 patients), Strata-partnered therapeutic trials (327 patients), or specific alteration-matched FDA approved therapies in patients with cancers of unknown primary (71 patients). Of the 1467 patients matched to an NCI-MATCH trial arm, 15 enrolled. Of the 327 patients matched to one of nine Strata-partnered clinical trials, 77 (24%) were screen failures, while 250 (76%) have either enrolled or are being actively followed for enrollment upon progression. Conclusions: Through streamlined consent methods, electronic medical record queries, and high throughput laboratory testing at no cost to patients, we demonstrate that scaled precision oncology is feasible across a diverse network of healthcare systems when paired with access to relevant clinical trials. Clinical trial information: NCT03061305.
Comparison of an automated cartridge-based system for mRNA assessment with central immunohistochemistry in the neoadjuvant GeparX trial.
Authors: Denkert Carsten , Link Theresa , Jank Paul , Just Marianne , Hanusch Claus , Brasch Frank , van Mackelenbergh Marion , Küster Willi , Marme Frederik , Karn Thomas , Müller Volkmar , Kümmel Sherko , Nekljudova Valentina , Loibl Sibylle , Blohmer Jens U.
Published: May 2019

3075

Background: Hormone receptors, HER2 and Ki-67 are prognostic values typically determined for breast cancer (BC) outcome and prediction of therapy response. A RT-qPCR based system, the Xpert Breast Cancer STRAT4, can be used to classify BC tissues regarding their hormone receptor status, HER2 and proliferation via Ki-67. We compared mRNA expression analysis of ER, PR, HER2, and Ki-67 by this automated in-vitro diagnostic platform (GeneXpert) (GX) with central immunohistochemistry (IHC) in a large clinical trial cohort. Methods: BC patients from the prospective GBG neoadjuvant trial GeparX (NCT02682693) (still recruiting) were included in this biomarker project. We used formalin-fixed paraffin embedded (FFPE) pretherapeutical core biopsies with a tumor content > 10%. One 4 µm FFPE tissue section was first processed with the Xpert FFPE Lysis Kit, the sample lysate was placed in the STRAT4 cartridge system and then tested on the GX system in which the purification, amplification and real-time detection took place within two hours automatically. Results: A total of 503 (99%) of the 509 samples had a valid measurement of all four genes. 258 samples (51.3%) of the cohort were classified in central pathology as ER positive, 196 (39%) as PR positive and 78 (15.5%) as HER2-positive, and 421 samples (83.7%) were Ki-67-high ( > 20%). The simple kappa coefficient was for ER = 0.7938, PR = 0.6540, HER2 = 0.8172 and Ki-67 = 0.3655. This indicates, that the measurements for ER, PR and HER2 showed a high correlation between both methods, whereas the measurement of Ki-67 does not. The accuracy between the STRAT4 and IHC was 89.7% for ER, 83.3% for PR, 94.6% for HER2 and 86.7% for Ki-67. According to molecular subgroups, highest accuracy regarding Ki-67, was determined in TNBC (96.2%; luminal: 81.1%; HER2-positive: 76.9%). Conclusions: Our results show a high concordance between standardized central IHC and automated mRNA expression analysis for the most important BC biomarkers ER, PR and HER2. For the proliferation marker Ki-67, the concordance is slightly lower. The STRAT4 assay might offer additional option to conventional methods for BC biomarker assessment, in particular in settings where IHC is not feasible. To determine the clinical validity, additional outcome analyses are necessary. Clinical trial information: NCT02682693.
Utility of somatic mutation panel testing in patients with advanced cancer receiving treatment in an Irish teaching hospital.
Authors: Khan Hadia , O' Callaghan Louise , Ahmed Gul , Bird Brian Richard , O'Connor Derbrenn , Murphy Conleth G.
Published: May 2019

3076

Background: Tumor testing for potentially actionable somatic mutations via commercially available panel tests has entered routine clinical practice in many countries. In Ireland the cost of these tests is not covered by insurance companies and must be paid for by patients. Use of these tests is sporadic and depends on patient and clinician factors (including ability to pay). Existing data suggest that such testing results in a direct impact on patient therapy in a minority of patients only. We reviewed the impact of somatic mutation testing on treatment selection and outcomes in patients attending a medical oncology service in a teaching hospital in Ireland. Methods: We performed a retrospective study of patients who had commercial panel testing performed as part of routine oncology care. All patients opportunistically tested between 2013 and 2018 were included. Patients having focused molecular tests for approved therapies (e.g. RAS mutations in colon cancer, EGFR and ALK mutations in non-small cell lung cancer) were excluded.We reviewed medical records to assess the frequency and utility of mutations detected, the impact of testing on next and subsequent lines of therapy, and the effectiveness of therapy. Results: 74 panel tests were performed in 71 patients. 39 tests (53%) detected mutations, of which 21 (28%) were potentially actionable. 36 patients (51%) had further treatment after testing was performed. 9 tests (12%) led to test-based treatment. The mean duration of test-based treatment was 34 days (range 1-90 days). No patients had benefit from test based treatment, defined as tumour response or disease stabilisation on restaging scans. 23 patients died within 90 days of panel tests being requested. Among patients starting and completing a subsequent line of therapy after testing, the mean duration of therapy with test-based treatment was 39 days (range 6-90) and for standard of care treatment was 56 days (range 1-262 days). Conclusions: While testing for tumor-specific somatic mutations with proven predictive benefit is very useful, somatic mutation panel testing for non standard of care genetic alterations is not of utility in this real world setting. Its role in Ireland should be limited to identification of suitable early phase clinical trials. Discussions of panel testing should include frank discussion of expected benefits, and should also address factors such as patient ability to travel for clinical trials. [Table: see text]
Proteomic profile of high-risk luminal A early breast cancers.
Authors: Hajjaji Nawale , Aboulouard Soulaimane , Robin Yves-Marie , Bertin Delphine , Fournier Isabelle , Bonneterre Jacques , Salzet Michel
Published: May 2019

3077

Background: Breast cancer is a heterogeneous disease with a wide range of outcomes. Among the intrinsic breast cancer subtypes, luminal A tumors are considered to have a favorable prognosis. However, molecular studies characterizing the genomic landscape of luminal A tumors revealed a molecular heterogeneity within this subtype, which also translated to variability in survival. A better understanding of the biology of this tumor subgroup is therefore needed to determine the appropriate therapeutic strategy. The aims of the study were to determine the frequency of high-risk luminal A tumors in a real life cohort of early breast cancers and provide a proteomic characterization of this subgroup using a mass spectrometry approach. Methods: 222 early breast cancer patients with hormone receptor positive and HER2 negative tumors treated at our institution had a PAM50-based genomic assay Prosigna to estimate their risk of recurrence. This assay assigned each tumor sample to an intrinsic molecular subtype of breast cancer. Luminal A and B tumors were analyzed with MALDI mass spectrometry imaging combined with microproteomics, a spatially-resolved on-tissue shotgun proteomic technology, to determine the proteomic profiles of both cancer cells and stroma. Results: Among the 129 luminal A breast cancers identified in our cohort, 67 (51%) had a risk of distant recurrence of 10% or more (32% had a 10% to 15% risk, and 19% a risk greater than 15%). High-risk luminal A tumors had a distinctive proteomic profile compared to low-risk luminal A or to luminal B tumors. Overexpression of the methionine biosynthesis pathway was the main differential protein expression observed in cancer cells and stroma of high-risk luminal A. Inflammation mediated by chemokine and cytokine signaling pathway and integrin signaling were also overexpressed in high risk luminal A compared to luminal B. In the stroma of luminal B tumors, EGR signaling, Ras and FGF pathways and angiogenesis were overexpressed compared to high-risk luminal A tumors. Conclusions: Real life data showed a significant proportion of high-risk luminal A breast cancers. MALDI mass spectrometry proteomics revealed distinctive tumor and microenvironment profiles in this breast cancer subgroup.
MET kinase domain rearrangements across 10 cancer types.
Authors: Zhao Jun , Chen Jin , Ma Haitao , Ye Ke , Shi Yue , Yi Yuting , Zeng Xiaoling , Guan Yan-Fang , Wang Jiayin , Yi Xin , Xia Xuefeng
Published: May 2019

3078

Background: MET is a transmembrane receptor tyrosine kinase and deregulated in many kinds of tumors by mutation, rearrangement and amplification. Since the first c onstitutively active MET rearrangement ( TPR-MET) was discovered, many other MET rearrangements have been identified in various tumor types. However, the frequency and characteristic of MET rearrangement in Chinese cancer patients is still unclear. Methods: Targeted sequencing using 1021-gene panel or 59-gene panel was performed on 3952 tissue samples and 5100 blood-based ctDNA samples from 9052 unique patients across 10 cancer types. All MET exons were sequenced, but MET intronic breakpoints were not specifically baited. Results: 24 (0.27%) MET kinase domain rearrangements (KDRE) were identified in 9052 patients. Specifically, 0.25% (16/6284) in non-small cell lung cancer (NSCLC), 0.69% (2/290) in gastric adenocarcinoma, 0.32% (2/897) in colorectal cancer, 0.33% (2/610) in breast cancer, 0.3% (1/330) in hepatocellular carcinoma and 0.69% (1/145) in ovarian cancer, none in 139 pancreatic cancer, 136 thyroid cancer, 111 renal cell carcinoma and 110 esophageal squamous cell carcinoma. Among all of the MET KDRE, 17 were fusions with 5’ identified partner, 3 were kinase domain duplication (KDD) and 4 were probable fusions with unidentified partner. The most common 5 ’partner gene was CAPZA2, followed by CD47 and TES. In the MET KDRE cases in NSCLC, 56.25% (9/16) did not found any clinical actionable variants referring to the NCCN guideline. In addition, MET amplification, EGFR L858R or exon 19 deletion and KRAS mutation co-occurred in 25% (4/16), 18.75% (3/16) and 12.5% (2/16) of NSCLC MET KDRE cases respectively. Conclusions: Our results, for the first time, illustrate the MET KDRE across 10 cancer types among Chinese population and might provide some novel targets to develop new therapies for patients with MET KDRE. MET KDRE across different tumor types. [Table: see text]
Whole transcriptome sequencing in metastatic cancer: A review of expression outliers in 113 metastatic breast cancer patients.
Authors: LeVasseur Nathalie , Csizmok Veronika , Bonakdar Melika , Shen Yaoqing , Zibrik Lindsay , Zhao Eric Yang , Sun Sophie , Gelmon Karen A. , Laskin Janessa J. , Marra Marco A. , Chia Stephen K. L.
Published: May 2019

3080

Background: The genomic profiling of breast cancers has led to a greater understanding of the mutational landscape of metastatic breast cancer (MBC) with potential therapeutic implications. Despite these advances, there is a paucity of data regarding the additive value and relevance of gene expression across histological and molecular subtypes, which represents the majority of informative and actionable findings identified in the BC Cancer personalized oncogenomics program (POG). Methods: Informative findings with potential clinical application from whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) in MBC patients between 2012-2018 were reviewed. Variants observed in pathway genes of potential clinical relevance, as defined by a curated list of genes, were examined across histological subtypes. High and low expression outliers relative to TCGA breast cases, defined as expression greater than 98th percentile and FC > 2 compared to Illumina breast dataset and lower than 25th percentile and FC < -2 compared to Illumina breast dataset, respectively, were then analyzed to establish how many outliers were observed in pathways of potential clinical relevance. Results: A total of 113 cases were included. WGS revealed that TP53 was the most frequent single nucleotide variant (SNV) in triple negative breast cancer (23/30, 77%), whereas PIK3CA (37/78, 47%), PTEN (11/78, 14%) and ESR1 (19/78, 24%) were most frequent in ER positive cases and CDKN2A (2/18, 11%) in HER2 positive cases. Across all subtypes, the mTOR and cell cycle pathways were found to have the highest frequency of SNVs, with the identification of 86 and 71 variants, respectively. Expression data for 113 RNA-sequenced patients revealed a high frequency of expression outliers in the mTOR pathway (26 high expression and 424 low expression outlier genes) and cell cycle pathways (35 high expression and 331 low expression outlier genes), but also in the WNT pathway (96 high expression and 490 lower expression outlier genes) and NOTCH pathway (84 high expression and 564 low expression outlier genes). Conclusions: Frequently identified SNVs across histological subtypes were correlated with expression outliers in pathways of clinical relevance in breast cancer. Additional informative findings, in pathways of potential clinical relevance not historically targeted in breast cancer, were identified with WTS. The clinical utility of these findings warrants further study.
Transcriptome-based cancer type prediction for tumors of unknown origin.
Authors: Michuda Jack , Igartua Catherine , Taxter Tim , Bell Joshua SK , Pelossof Raphael , White Kevin
Published: May 2019

3081

Background: Tumors of unknown origin occur in approximately 5% of newly diagnosed cancers and are difficult to treat without establishing the tissue type from which they derive. Establishing tumor origin guides standard of care treatment for several NCCN targeted therapy guidelines. Leveraging tissue specificity in gene expression profiles, classification models based on RNA expression offer a promising approach to identify the likely primary cancer site in tumors of unknown origin. Methods: In this study, we developed a transcriptome-based cancer type classifier trained on over 10,000 tissue samples annotated by pathologists and sequenced for RNA expression to identify conserved patterns of expression characteristic of 30 tumor types across primary and metastatic tissue sites. The classifier probabilistically ranks cancer of origin. Results: Overall, the accuracy of the most probable cancer prediction was 85%, 88% within primary tumors and 77% within metastatic tumors. The top three cancers types with the highest accuracy were colorectal (accuracy in metastatic: 93%, accuracy in primary tumors: 99%), breast (95%, 96%) and lung (87%, 94%). Classifier performance was lower in low-purity metastatic tumors where the surrounding normal tissue obscures the tumor transcriptional profile, though the classifier still achieves 71% accuracy on metastatic tumors with less than 50% purity. Conclusions: We present a novel method to probabilistically predict tumor type for cancers of unknown origin using RNA-Seq. Our method achieves robust classification that is applicable to primary and metastatic tumors and demonstrates the value of utilizing RNA-Seq to aid cancer diagnosis and treatment decisions.
Machine learning algorithm analysis using a commercial 592-gene NGS panel to accurately predict tumor lineage for carcinoma of unknown primary (CUP).
Authors: Abraham Jim , Heimberger Amy B. , Gatalica Zoran , Korn Wolfgang Michael , Spetzler David
Published: May 2019

3083

Background: The diagnosis of a malignancy is typically informed by clinical presentation and tumor tissue features including cell morphology, immunohistochemistry, cytogenetics, and molecular markers. However, in approximately 5-10% of cancers, ambiguity is high enough that no tissue of origin can be determined and the specimen is labeled as a Cancer of Occult\Unknown Primary (CUP). Lack of reliable classification of a tumor poses a significant treatment dilemma for the oncologist leading to inappropriate and/or delayed treatment. Methods: 40,000 tumor patients with NGS data were used to construct a multiple parameter lineage-specific classification system using an advanced machine learning approach. The dataset for each classifier was split 50% for training and the other 50% for testing. The training task for each classifier was to identify the cases that were similar to the cases it was trained on against a backdrop of randomly selected cases of other histological origins. Results: Tumor lineage classifiers predicted the correct classifications where the primary site was known with accuracies ranging between 85% and 95%. When applied to CUP cases (n = 500), an unequivocal result could be obtained 100% of the time. Conclusions: Lineage predictors can render a histologic diagnosis to CUP cases that can inform treatment and potentially improve outcomes.
Design, engineering, and characterization of a novel long-acting (Pegylated) single isomer human arginase for arginine depriving anticancer treatment.
Authors: Yu Kuo-Ming , Pang Tammy Pui-Shi , Cutler Murray , Lau Johnson Yiu-Nam , Lo Thomas Wai-Hung , Leung Thomas Yun-Chung
Published: May 2019

3090

Background: Arginine deprivation therapy is an attractive strategy to treat arginine-auxotrophic cancers with deficient expression of argininosuccinate synthetase, argininosuccinate lyase or ornithine transcarbamylase. We have designed and engineered a novel human arginase with single site pegylation exerting excellent preclinical pharmacologic profile to serve as a new class of therapy. Methods: Human arginase has three cysteines (at position 45, 168, 303) and none of them is in or close to the active site. Two cysteines were mutated to serines, leaving the only cysteine at 45 for the simple and cost-effective synthesis of a single isoform of pegylated human arginase. Different forms of PEG moieties were evaluated for the selection of a drug candidate (PT01), followed by extensive characterization. Results: Converting Cys at 168 and 303 to serine impacted least on enzymatic activity (with cobalt cation). Pegylation with different sizes and shapes showed that 20 and 40 kDa (linear and branched) had similar PK/PD profile without damaging enzymatic activity. Therefore, arginase modified with a linear 20 kDa PEG was chosen as the candidate. A single 0.4 mg/kg IV dose of PT01 in rats induced 4 days of near complete plasma arginine depletion, while 6–7 days of depletion between 1.2 and 2 mg/kg. Plasma arginine levels were reversible. First-order clearance of both plasma PT01 concentration and activity suggested a terminal half-life of about 20 hours. In vitro assay showed very potent cytotoxicity at sub-nM level against various cell lines of breast, prostate, and pancreas in origins. In two mouse cancer models (hard-to-cure pancreas and castration-resistant prostate), weekly infusion at 5 and 10 mg/kg induced significant tumor growth inhibition of 44-67%. All mice experienced dose-dependent but rapidly reversible weight loss following each weekly dose. Conclusions: A novel single isoform of pegylated human arginase was created, showing excellent enzymatic activity, PK/PD profiles, and cytotoxicity in vitro. Mouse xenograft models showed good tumor growth inhibition activity with tolerable toxicity as manifested on transient weight loss during therapy.
Nanoparticle entrapped docetaxel (CPC634) enhances intratumoral docetaxel exposure compared to conventional docetaxel (Cd) in patients with solid tumors.
Authors: Atrafi Florence , van Eerden Ruben A.G. , van Hylckama Vlieg Marte A.M. , De Hoop Esther Oomen , de Bruijn Peter , Rijcken Cristianne J.F. , Hanssen Rob , Eskens Ferry , Mathijssen Ron H.J. , Koolen Stijn L.W.
Published: May 2019

3096

Background: Failure or resistance to chemotherapy may be caused by sub‐therapeutic intratumoral drug levels. Nanomedicine aim to improve intratumoral drug exposure. CPC634 is a nanoparticle entrapping docetaxel. We hypothesized that CPC634 increases intratumoral docetaxel exposure. Methods: In this randomized cross-over study we assessed intratumoral and plasma pharmacokinetics (PK) of docetaxel after intravenous administration of CPC634 and conventional docetaxel (Cd). The study was powered to identify an 25% increase in intratumoral docetaxel exposure of CPC634 relative to Cd. Patients (≥18 years) were randomized to receive 75 mg/m2 CPC634 in cycle 1 and Cd in cycle 2 or vice versa. After drug administration, patients underwent tumor biopsies during both cycles. Total docetaxel was determined for both drugs and released docetaxel for CPC634 in tumor tissue and in plasma with a validated LC-MS/MS method. PK data were analyzed with mixed model analysis. Results: Sixteen evaluable patients were included. Intratumoral PK revealed a 323% (95% CI: 148,621) higher total docetaxel (p < 0.001) for CPC634. Released docetaxel for CPC634 was comparable to total docetaxel levels for Cd (95% CI: -35-,67) (p = 0.43). Plasma released docetaxel for CPC634 exhibited an 89% (95% CI: 86, 91) lower (p < 0.001) peak plasma concentration (Cmax) and 81% (95% CI: 46, 125) higher (p < 0.001) area under the curve (AUC) relative to Cd. Conclusions: CPC634 resulted in higher intratumoral total docetaxel and comparable released docetaxel levels relative to total docetaxel for Cd. CPC634 had a favorable plasma PK profile with a lower Cmax and prolonged higher systemic exposure relative to Cd. These results indicate that CPC634 could improve intratumoral docetaxel exposure compared to Cd. Additional studies assessing the intratumoral exposure to CPC634 (NCT0371243) and a phase II efficacy study of CPC634 in patients with platinum resistant ovarian cancer (NCT03742713) are currently ongoing.
Patient-derived organoid (PDO), a new personalized therapy selection tool for prompt clinical decision making in metastatic gastrointestinal (mGI) cancer patients.
Authors: Xie Hao , Hogenson Tara L , Horn Isaac P , Almada Luciana , Marks David , Koenig Amanda , Tolosa Ezequiel , Barrett Michael T. , Boyum James H , Mahipal Amit , Hubbard Joleen Marie , Scheffler Hanson Temperance J , Yin Jun , Petersen Gloria M. , Revzin Alexander , Billadeau Daniel D. , Bekaii-Saab Tanios S. , Adjei Alex A. , Ma Wen Wee , Fernandez-Zapico Martin
Published: May 2019

3101

Background: PDO is a promising translational tool that recapitulates the biology and drug response of donor cancer patient. However, an unmet need is to have PDO drug-screening data available for treatment decision making in clinic. We conducted a pilot study to determine whether PDO testing results will be available at critical treatment decision points in metastatic GI cancer patients. Methods: Metastatic GI cancer patients undergoing core-needle biopsy were eligible. Tumor cells isolated from ≤4 fresh biopsy tissues were grown in a Matrigel-based culture. PDO response to anti-cancer drugs were evaluated; and when available, correlated with donors’ clinical response to the same agent(s). PDO response was defined as IC50 < 0.1 × published Cmax of the drug clinically; stable as IC50 between 0.1 to 10 × Cmax. Radiographic response was per RECIST criteria. Results: We enrolled 27 refractory metastatic GI cancer patients (9 colorectal [CRC], 9 pancreas, and 9 biliary tract). Median lines of therapy were 4, 2, and 2; the success rate of organoid establishment was 89%, 44%, and 55%, respectively. The median time from biopsy to availability of drug-testing data was 64 days (range: 24 to 93 days). The median time from biopsy to next CT re-staging in donors was 64 days. The established PDOs shared histological and genomic features with donor clinical tissue. PDO and clinical responses to the same agent(s) were correlated in 2 CRC donors including (1) BRAFV600E-mutated PDO responded to vemurafenib + panitumumab, as did the donor who had partial response (PDO drug-testing data were available 55 days post-biopsy, 23 days prior to restaging scan); (2) KRAS/FGF-dual amplified PDO had stable disease status to regorafenib, as did the biopsied lesion from the donor (73 days post-biopsy, 5 days post-scan). Conclusions: We showed the feasibility of completing PDO drug sensitivity testing in metastatic GI cancer patients within a short time that could impact clinical decision making, particularly in CRC. PDO drug response showed correlation with clinical response. With further refinement, PDO can be a powerful tool for personalizing cancer therapy in metastatic GI cancer patients.
Host transcriptomic signatures associated with dysbiosis in a preclinical model of lung cancer.
Authors: El-Ashmawy Mariam , Wu Benjamin , Tsay Jun-Chieh , Franca Brendan , Perez Luisanny , Sulaiman Sheik Mohammad Imran , Rom William , Wong Kwok-Kin , Segal Leopoldo
Published: May 2019

3107

Background: Enrichment of the lower airway microbiota with oral commensals has been associated with transcriptomic changes affecting several inflammatory pathways associated with non-small cell lung cancer (NSCLC) development and progression. Using a mouse model of NSCLC, we evaluated the effects of lower airway dysbiosis on tumor progression and host transcriptomics. Methods: Preclinical model of lung cancer was constructed by introducing luminescence-tagged Kras mutated cells into C57/B6 mice, causing lung cancer to develop. Lower airway dysbiosis was induced by weekly intratracheal challenge with either PBS or Veillonella parvula in wild type and lung cancer mice. Experiments were repeated twice to evaluate for survival as well as lower airway host response using flow cytometry and RNA sequencing (HiSeq). Sequence data was processed using a validated mouse gene expression signature matrix with cibersort from https://cibersort.stanford.edu and DESeq using FDR correction. Results: In wild type mice, lower airway dysbiosis with Veillonella did not affect the survival, weight gain or airway lumen diameter. Among lung cancer mice, dysbiosis led to increased mortality, weight loss, and tumor burden. Multiple transcriptomic signatures were identified among the dysbiosis groups (both in WT and lung cancer mice). Unsupervised hierarchical clustering of immune cell profiles using cibersort on whole transcriptome showed near perfect separation between the four experimental conditions. Amongst the most differentially enriched immune cell subsets, we identified that lung dysbiosis upregulates genes annotated to Th1 and Th2 cells (p < 0.01, q < 0.2). Using flow cytometry, we identified that PD-1, IL-17, and ROR-gamma are differentially expressed in CD4+ cells in dysbiosis conditions, and these patterns are consistent in whole RNA transcriptome. Conclusions: Transcriptomic signatures reveal immune profiles associated with dysbiosis, an experimental condition associated with worse outcomes in lung cancer. This investigation provides novel insights into how disruption of the lower airway microbiome may contribute to the pathogenesis of NSCLC.
A modeling and simulation study of less frequent dosing of nivolumab 480 mg.
Authors: Peer Cody J. , Goldstein Daniel A. , Ratain Mark J. , Figg William Douglas
Published: May 2019

3115

Background: Nivolumab was originally approved at 3 mg/kg q2w. However, there is abundant evidence that doses as low as 0.1 mg/kg q2w are effective, and a randomized trial in RCC demonstrated equivalence across a dose range of 0.3-10 mg/kg q3w. Modeling and simulation have been used to amend the labeled dosage to 240 mg q2w or 480 mg q4w, with the latter yielding an estimated steady-state trough concentration (Ctrough) of ~50 ug/mL. Given the high cost of nivolumab and the lack of a dose-response relationship, we hypothesized that less frequent dosing of 480 mg would maintain therapeutic serum concentrations. The objective of this study was to use modeling and simulation to develop alternative dosing strategies. Methods: A simulation model was built from a published population pharmacokinetic model, incorporating time-dependent clearance. Various alternative dosing schedules were simulated, beginning with the third dose (doses 1 and 2 were 480 mg at wk 1 and 5). We conservatively chose 4.5 mg/mL as the target concentration (TC), slightly above the mean simulated Ctrough at 0.3 mg/kg q3w (4.1 ug/mL), although even lower levels are likely efficacious. The simulated dose schedules were q8w, q10w, q12w and q14w, beginning with the third dose. Simulations were performed on 50 simulated patients, with each simulation replicated 5 times. Results: The simulated Ctrough following doses 2-4 are presented in the table below. Dosing q12w should maintain TC in > 70% of patients, and q14w dosing should achieve TC in > 55% of patients. Conclusions: Modeling and simulation provide evidence that nivolumab can be effectively dosed q8-14w (after the first 2 doses), resulting in a potential 70% cost savings. As responding patients generally have a 35-45% decrease in clearance over the first 6 months of treatment, even less frequent dosing may be required for subsequent doses. Randomized trials of this interventional pharmacoeconomic strategy are indicated. Similar opportunities may exist for other checkpoint inhibitors. [Table: see text]
Concomitant intake of abiraterone and food to increase pharmacokinetic exposure: Real-life data from a therapeutic drug monitoring program.
Authors: Groenland Stefanie L. , Bergman Andre M. , Huitema Alwin , Steeghs Neeltje
Published: May 2019

3117

Background: Abiraterone acetate is registered for the treatment of metastatic castration resistant prostate cancer. Pharmacokinetic (PK) exposure has been linked to efficacy, since patients with Cmin ≥ 8.4 ng/mL have a significantly longer progression free survival compared to patients with a Cmin below this threshold (7.4 vs. 12.2 months, p = 0.044) (Carton, 2017). At the recommended fixed dose of 1000 mg QD administered in a modified fasting state, 35% of patients do not reach this efficacy threshold (Carton, 2017), providing a strong rationale for therapeutic drug monitoring (TDM). Since a clinically relevant food effect has been established, concomitant intake of abiraterone and food could offer a cost-neutral solution in case of low exposure (Chi, 2015). This study aims to evaluate whether PK-guided abiraterone dosing is feasible and results in an increased proportion of patients with concentrations above the target. Methods: Patients starting regular treatment with abiraterone were included. PK sampling occurred 4, 8 and 12 weeks after start of treatment, and every 12 weeks thereafter. Abiraterone concentrations were measured and Cmin was calculated. In case of Cmin < 8.4 ng/mL and acceptable toxicity, a PK-guided intervention was advised. As a first step, concomitant intake of abiraterone and a light meal or a snack was advised. Results: In total, 35 patients were included, of which 18 patients (51%) had at least one Cmin < 8.4 ng/mL. These patients were advised to take abiraterone concomitantly with food, after which Cmin increased significantly from 5.6 (47%) ng/mL [mean (CV%)] to 40.6 (110%) ng/mL (p = 0.006) without additional toxicities. This intervention led to adequate exposure in 15 patients (83%). Seventeen patients had all Cmin levels ≥ 8.4 ng/mL, in these patients mean Cmin was 31.5 (65%) ng/mL. Conclusions: TDM of abiraterone was applied in clinical practice and proved to be feasible. Concomitant intake with food resulted into a significant increase in Cmin and offers a cost-neutral opportunity to optimize treatment for patients with low PK exposure. Up to 100 patients will be included to evaluate the effect of PK-guided abiraterone dosing on treatment efficacy. Clinical trial information: NL6695.