bluuebunny/crossref_metadata_2025_split huggingface dataset:
TCR repertoire sequencing of 254 resected non-small cell lung cancers to reveal TCR clonality in normal tissues compared to tumor tissues.
Authors: Reuben Alexandre , Gittelman Rachel , Zhang Jiexin , Yusko Erik , Wu Chang-jiun , Emerson Ryan O , Zhang Jianhua , Tipton Christopher , Vignali Marissa , Fujimoto Junya , Rodriguez-Canales Jaime , Swisher Stephen , Heymach John , Robins Harlan , Lee J. Jack , Futreal Andrew , Wistuba Ignacio Ivan , Zhang Jianjun ,   NSCLC TCR Study Team
Published: September 2018

11500 Background: The mechanisms underlying resistance to immune checkpoint blockade are poorly understood. Major efforts have been made to understand how mutations, through generation of neoantigens, may alter tumor immunogenicity and anti-tumor responses, particularly through T cell responses. However, the T cell repertoire and its interaction with cancers bearing specific molecular alterations have not been systemically studied. Methods: We delineated the landscapes in the T cell receptor (TCR) repertoire, immune infiltration (immunohistochemistry using multiple immune markers), genome (exome sequencing), epigenome (methylation array) and transcriptome (mRNA gene expression array) of 254 resected non-small cell lung cancers (NSCLC), matched normal lung tissues and peripheral blood mononuclear cells (PBMC). We report herein the preliminary analyses of TCR sequencing of NSCLC tumors and matched normal lung tissues. Results: We observed that: 1) Smaller tumors (smaller than median) had a higher T cell infiltrate (p = 0.0016) and higher entropy than larger tumors (p = 0.0098); 2) Tumors from ever/current smokers had higher T cell clonality than former/never-smokers (p = 0.005); 3) TCR clonality was positively correlated with mutational burden (p = 0.0026); 4) Compared to tumors, normal lung tissues demonstrated significantly less T cell infiltration (p = 2.1x10^-11), but a significantly higher clonality (p = 3.9x10^-7). Finally, many T cell clones, including major clones were shared between normal lung tissues and matched NSCLC tumors. Conclusions: Our preliminary data demonstrate the distinct immune microenvironment in different NSCLC tumors may be associated with particular clinicopathological features. The higher TCR clonality in normal lung tissues and overlap of T cell clones between normal lung and NSCLC tumors implies a significant proportion of tumor infiltrating T cells may be a function of constant exposure to mutagens rather than an anti-tumor response. Analysis of the peripheral TCR repertoire, the molecular landscape of these tumors and the association with immune profiling is underway.
Dissecting primary resistance to anti-EGFRs in RAS and BRAF wt metastatic colorectal cancer (mCRC): A case-control study.
Authors: Cremolini Chiara , Morano Federica , Moretto Roberto , Berenato Rosa , Tamborini Elena , Perrone Federica , Rossini Daniele , Gloghini Annunziata , Busico Adele , Zucchelli Gemma , Baratelli Chiara , Tamburini Emiliano , Capone Iolanda , Volpi Chiara , Milione Massimo , Di Maio Massimo , Fontanini Gabriella , De Braud Filippo G. , Falcone Alfredo , Pietrantonio Filippo 
Published: September 2018

11508 Background: Almost half of RAS and BRAFwt mCRC patients do not respond to anti-EGFRs. Different molecular alterations suggested as predictors of resistance have not been validated. Methods: We conducted a case-control study to prospectively demonstrate the negative predictive impact of HER-2 amplification or mutations (mut), MET amplification, NTRK/ROS1/ALK/RET rearrangements, and mut activating MAPKs or PI3K/Akt axis. Patients with RAS and BRAFwt mCRC clearly resistant (cases) or clearly sensitive (controls) to anti-EGFRs were selected. Hypothesizing a prevalence of candidate alterations of 0% and 15% among controls and cases, 47 cases and 47 controls were needed to be able to reject the null hypothesis of equally prevalent alterations, with a- and b- error 0.05 and 0.20. Since hypermutated tumors may hardly rely on a single pathway for their growth, we also evaluated the impact of microsatellite instability. Results: 47 cases and 47 controls were included. Primary endpoint was met: mentioned alterations were reported in 20 (42.6%) cases and 1 (2.1%) control (p<0.001). MSI-high was significantly more frequent among resistant than sensitive tumos (15% vs 0%, p<0.001). Conclusions: This is the first prospective demonstration that the combined assessment of these rare alterations allows to better select patients for anti-EGFRs, while opening the way to other tailored therapies. [Table: see text]
Genomic analysis of circulating tumor DNA in 442 patients with carcinoma of unknown primary: Implications for targeted therapeutics.
Authors: Kato Shumei , Krishnamurthy Nithya , Banks Kimberly , Williams Kirstin Anne , Williams Casey B. , Leyland-Jones Brian , Lanman Richard B. , Kurzrock Razelle 
Published: September 2018

11511 Background: Carcinoma of unknown primary (CUP) is a rare, difficult-to-treat malignancy. To further understand the genomic landscape of CUP, next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) from patient plasma was performed. To our knowledge, this is the largest cohort of patients with CUP interrogated by liquid biopsy. Methods: We evaluated the molecular alterations of 442 patients with CUP using clinical-grade NGS of ctDNA isolated from patient plasma. The test detects single nucleotide variants in 54-70 genes, as well as copy number amplifications, fusions and indels in selected genes. Results: Eighty percent of patients (353/442) had ctDNA alterations with 66% (290/442) harboring at least one characterized alteration; 43.9% (194/442) ≥ 2 characterized alterations. TP53-associated genes were most commonly altered (37.8% [167/442]) followed by genes involved in the MAPK pathway (31.2% [138/442]), PI3K signaling (18.1% [80/442]) and the cell cycle machinery (10.4% [46/442]). Among patients harboring at least one characterized alteration, most (87.9% [255/290]) had distinct genomic profiles, and 99.7% (289/290) had alterations theoretically targetable with either an FDA-approved or investigational agent. The mean number of potentially actionable alterations per patient was 1.7 (range, 0 to 10). Illustrative patients who had dynamic changes in ctDNA content during the course of therapy and responding patients matched on the basis of ctDNA to targeted therapies or immunotherapy will be presented. Conclusions: Evaluation of ctDNA was feasible among individuals with CUP. Most patients harbored a unique somatic profile. The majority of patients had potentially actionable alterations. Serial ctDNA showed dynamic changes in molecular alterations in response to therapy, and several patients have attained responses to targeted or immune therapies chosen on the basis of ctDNA findings. The current report suggests that non-invasive liquid biopsies merit investigation in next generation clinical trials.
Whole exome analysis of patients (pts) with metastatic GIST (mGIST) demonstrating exceptional survival with imatinib (IM) therapy compared to those with short term benefit.
Authors: Ben Ami Eytan , Kamran Sophia C. , George Suzanne , Morgan Jeffrey A. , Wagner Andrew J. , Merriam Priscilla , Thornton Katherine Anne , Jennings Julia , Field Julie , Solomon Sarah , Raut Chandrajit P. , Van Allen Eliezer Mendel , Demetri George D. 
Published: September 2018

11513 Background: Most patients with mGIST initially benefit from IM therapy with durable disease control (DC), i.e. objective responses and stable disease, with median duration of approximately two years. We reported exceptional long-term benefit (LTB) with DC and overall survival (OS) >14 years in a subset of mGIST pts treated with IM. We aimed to characterize tumor and normal genomes of exceptional LTB pts treated with IM and compare with short-term benefit (STB) pts. Methods: Among 87 mGIST pts enrolled between July 2000 and June 2001 in the B2222 trial of IM and followed prospectively at the Dana Farber Cancer Institute, we identified 10 LTB (>14 years of DC) pts, and 6 STB (<2 years of DC) pts on IM. Targeted genotyping ( KIT/PDGFRA)was performed in all tumors (n=16). Whole exome sequencing (WES) was performed on archival FFPE tumor samples from LTB and STB pts prior to any IM treatment. We compared WES results from LTB with STB pts to identify unique features of long-term DC and OS with IM. Results: KIT mutation in LTB pts were as follows: exon 11(6 pts), exon 9 (3 pts), and SDH-deficient with KIT/PDGFRA wild type (1 pt). In STB pts, mutated KITwas found 4 pts (exon 11) and 2 pts (exon 9). WES was successful in six LTB (five exon 11, one exon 9) and three STB (two exon 11, one exon 9) pts. A total of 1211 somatic mutations were observed (546 missense, 37 nonsense, 256 silent, 285 indels, 36 splice mutations). The mean somatic mutational burden was 3.42 mutations/Mb (range 1.18-4.93) and 3.34 mutations/Mb (range 1.06-6.68) among LTB and STB, respectively. Genes mutated in LTB but not in STB were MUC7 (4 pts), H1F0 (3 pts), ZKSCAN1 (3 pts), SLC24A1 (3 pts) and USP4 (2 pts). Conclusions: KRAB domain containing zinc finger (KRAB-ZNF) gene expression signatures have been associated with prediction of response to IM, and a possible role in response modulation to tyrosine kinase inhibitors in GIST. We found variants in ZKSCAN1, a gene encoding a transcriptional regulator of the KRAB subfamily of zinc finger, to be present in LTB but not in STB. KRAB-ZNF family of genes may be linked to LTB and exceptional survival with IM in mGIST; functional analyses will be important to test such hypotheses.
Monitoring of circulating tumor DNA in non-small cell lung cancer patients treated with EGFR-inhibitors.
Authors: Verheijen Remy B , van Duijl Tirsa T , van den Heuvel Michel M , Beijnen Jos H. , Schellens Jan H.M. , van den Broek Daan , Steeghs Neeltje , Huitema Alwin 
Published: September 2018

11535 Background: Epidermal growth factor receptor (EGFR) inhibitors such as erlotinib and gefitinib are routinely used in the treatment of non-small cell lung cancer (NSCLC). Monitoring of EGFR mutations in circulating tumor DNA (ctDNA) derived from plasma has been proposed as an alternative for repeated tumor biopsies. Our aim was to investigate the dynamics of ctDNA in a cohort of NSCLC patients and explore the roles of EGFR driver and resistance mutations in predicting disease progression and progression free survival (PFS). Methods: NSCLC patients treated with either erlotinib or gefitinib as first-line anti-EGFR therapy were included. Clinical data was collected retrospectively from medical records. Plasma samples collected as part of routine care were analyzed. First DNA was isolated from plasma using the QIAsymphony SP (Qiagen). Then EGFR driver (L858R and exon 19 deletions) and resistance (T790M) mutations were quantified using the X100 Droplet Digital PCR and analyzed using QuantaSoft software (Bio-Rad). The dynamics of ctDNA mutations over time and the relationship between copy numbers and progression free survival were explored. Results: 68 NSCLC patients and 249 plasma samples (1-13 per patient) were included in the analysis. In 33 patients, the T790M mutation was detected. The median (range) T790M concentration in these samples was of 7.3 (5.1 - 3688.7) copies/mL. In 30 patients, the L858R or exon 19 deletion driver mutations were found in median concentrations of 11.7 (5.1 – 12393.3) and 27.9 (5.9 – 2896.7) copies/mL, respectively. Using local polynomial regression, the copies/mL of EGFR driver mutations increased several weeks prior to progression on standard response evaluation. In Kaplan-Meier analysis, patients with a detectable T790M mutation during the first 8 weeks of treatment had a shorter PFS (7.6 versus 14.4 months, p < 0.01, log-rank test). Conclusions: Early detection of the T790M mutation in plasma ctDNA is related to poor PFS. Furthermore, an increase in the copies/mL of the EGFR driver mutation over time may predict clinical progression.
Liquid biopsy in the clinic: A prospective study of plasma circulating tumor DNA (ctDNA) next generation sequencing (NGS) in patients with advanced non-small cell lung cancers to match targeted therapy.
Authors: Sabari Joshua K. , Ni Ai , Lee Adrian , Pavlakis Nick , Clarke Stephen John , Tandon Nidhi , Datta Sutirtha , DuBoff Mariel A. , Martinez Andres , Offin Michael D. , Isbell James M. , Rusch Valerie W. , Jones David Randolph , Henderson Samantha , Lim Lee , Raymond Chris , Li Mark , Riely Gregory J. , Rudin Charles M. , Li Bob T. 
Published: September 2018

11536 Background: Liquid biopsy for plasma ctDNA NGS is a rapidly evolving science. Plasma ctDNA assays are commercially available and are increasingly adopted in the community with a paucity of evidence-based guidance. We set out to study the optimal timing and utility of plasma ctDNA NGS in clinic. Methods: Pts with advanced NSCLC who were driver unknown, defined as not having prior tissue NGS or clinical concern for tumor heterogeneity that may affect treatment decisions, were eligible. Peripheral blood was collected in a Streck tube (10mL), DNA extracted, and subjected to a bias-corrected hybrid-capture 21 gene targeted NGS assay in a CLIA lab with unique reads at 3000x and sensitive detection at variant allele frequency above 0.1% (ResolutionBio Bellevue, WA). Pts also had concurrent tissue NGS via MSK IMPACT. Clinical endpoints included detection of oncogenic drivers in plasma, ability to match pts to targeted therapy, concordance and turnaround time of plasma and tissue NGS. Results: Forty-one pts were prospectively accrued. Plasma ctDNA detected an oncogenic driver in 39% (16/41) of pts, of whom 17% (7/41) were matched to targeted therapy; including pts matched to clinical trials for HER2 exon 20 insertionYVMA, BRAF L597Q and MET exon14. Mean turnaround time for plasma was 7 days (4-12) and 28 days (20-43) for tissue. Plasma ctDNA was detected in 56% (23/41) of pts; detection was 40% (8/20) if blood was drawn on active therapy and 71% (15/21) if drawn off therapy, either at diagnosis or progression (Odds ratio 0.28, 95% CI 0.06 - 1.16; p = 0.06). All pts had concurrent tissue NGS; of the 10 samples resulted, there was 100% driver concordance between tissue and plasma in pts drawn off therapy. Conclusions: In pts who were driver unknown or who had clinical concern for tumor heterogeneity, plasma ctDNA NGS identified a variety of oncogenic drivers with a short turnaround time and matched them to targeted therapy. Plasma ctDNA detection was more frequent at diagnosis of metastatic disease or at progression. A positive finding of an oncogenic driver in plasma is highly specific, but a negative finding may still require tissue biopsy.
Biomarker modulation in patients treated with TRC105 in combination with anti-VEGF therapy.
Authors: Liu Yingmiao , Yuan Zhenhua , Zhang Dadong , Starr Mark D. , Brady John C. , Jivani Manoj A. , Adams Bonne J. , Alvarez Delia , Attia Steven , Choueiri Toni K. , Theuer Charles P. , Owzar Kouros , Hurwitz Herbert , Nixon Andrew B. 
Published: September 2018

11546 Background: TRC105, an endoglin-targeting monoclonal antibody with anti-angiogenic and anti-tumor activity, is being evaluated in multiple diseases. Here we report on pharmacodynamic and prognostic biomarkers in patients (pts) treated with both TRC105 and anti-VEGF agents. Methods: Plasma samples were collected from pts on three phase 2 trials combining TRC105 with an anti-VEGF agent: axitinib in metastatic renal cell carcinoma (mRCC), pazopanib in advanced soft tissue sarcoma, and bevacizumab in glioblastoma (GBM). Baseline and on-treatment levels of 22 soluble protein biomarkers were assessed. Results: Soluble endoglin markedly increased after TRC105 treatment in all pts ( p< 0.001) as previously reported. BMP9 (a ligand for endoglin) and TGFβR3 (a type III TGFβ receptor) decreased in sarcoma pts at Cycle 2 Day 1 (C2D1) and generally remained below baseline throughout the course of treatment (BMP9, p= 0.004; TGFβR3, p= 0.003). Although TGFβR3 was decreased at C2D1 in mRCC (p = 0.030), no clear patterns were observed over time. Overall BMP9 levels did not change in response to therapy in either mRCC or GBM. Osteopontin (OPN) levels, a downstream effector of TGFβ signaling, were increased in sarcoma pts [ p= 0.002 at C2D15, p< 0.001 at C4D1 and end of study (EOS)]; however, in mRCC ( p= 0.010) and GBM ( p= 0.003), OPN was only elevated at EOS. Increases in PlGF and VEGFD, and decreases in VEGFR2 were observed across all studies, as previously noted for VEGF inhibitors. In the mRCC trial, 5 of 18 pts exhibited a ≥30% tumor reduction. Lower OPN ( p= 0.026) and higher TGFβR3 ( p= 0.003) levels at baseline correlated with radiographic response to treatment. In the sarcoma trial, 6 of 19 pts responded (CHOI criteria) in which lower baseline levels of ICAM1 ( p= 0.018) and TSP2 ( p= 0.042) correlated with stable disease. Conclusions: In these trials, increases of soluble endoglin in response to TRC105 were observed, independent of the presence of any specific VEGF inhibitor. Differential regulation of BMP9, TGFβR3, and OPN suggests potential disease-specific modulation of key TGFβ signaling molecules in response to dual therapy. Baseline levels of OPN and TGFβR3 showed potential prognostic value in mRCC. Confirmation in larger trials is needed.
Liquid biopsies of plasma exosomal nucleic acids, plasma cell-free DNA, and survival of patients with advanced cancers.
Authors: Moehrmann Lino , Huang Helen J. , Hong David S. , Tsimberidou Apostolia Maria , Fu Siqing , Piha-Paul Sarina Anne , Subbiah Vivek , Karp Daniel D. , Naing Aung , Krug Anne , Enderle Daniel , Priewasser Tina , Noerholm Mikkel , Eng Cathy , Kopetz Scott , Skog Johan , Meric-Bernstam Funda , Janku Filip 
Published: September 2018

11551 Background: Blood-based liquid biopsies offer easy accessible genomic material for molecular diagnostics in cancer. Commonly used cell-free DNA (cfDNA) originates from dying cells. In contrast exosomal nucleic acid (exoNA) originates from living cells, which can better reflect underlying cancer biology. Methods: We isolated exoNA (EXO52) and cfDNA (QIAamp Circulating Nucleic Acid kit) from plasma of patients with progressing advanced cancers and tested for BRAFV600, KRASG12/G13, and EGFRexon19del/L858R mutations using next-generation sequencing (EXO1000), droplet digital PCR (ddPCR, QX200) and BEAMing digital PCR. The results were compared to clinical testing of archival tumor tissue and correlated with survival. Results: Of the 43 patients (colorectal cancer, 20; melanoma, 8; non-small cell lung cancer, 6; ovarian cancer, 2; papillary thyroid cancer, 2; other cancers, 5) 41 had a mutation in the tumor tissue (20 [47%] BRAF mutation, 17 [40%] KRAS mutation and 4 [9%] EGFR mutation). Mutation testing of plasma exoNA from all 43 patients detected 39 (95%) of 41 mutations present in tumor tissue with 100% specificity. Mutation testing of plasma cfDNA from 39 patients using ddPCR detected 33 (89%) of 37 mutations present in tumor and testing of plasma cfDNA from 37 patients using BEAMing detected 34 (97%) of 35 mutations present in tumor tissue; however, both cfDNA methods reported an additional KRAS mutation not present in tumor tissue. Patients with high mutation allele frequency (MAF, > median) had shorter median survival compared to patients with low MAF ( < median) when using exoNA (5.9 vs. 11.8 months, P= 0.006), but not cfDNA ddPCR (6.0 vs. 7.4 months, P= 0.06) or cfDNA BEAMing (6.5 vs. 7.4 month, P= 0.07). High MAF in exoNA was an independent prognostic factor for survival in multicovariate analysis (HR 0.13, P= 0.017). Conclusions: Mutation testing of plasma exoNA for common BRAF, KRAS, and EGFR mutations has high sensitivity compared to clinical testing of archival tumor tissue and better specificity than PCR testing of plasma cfDNA. High MAF in exoNA is the independent prognostic factor for shorter survival.
Tetrahydrouridine-decitabine for non-cytotoxic epigenetic therapy of NSCLC to enhance immunotherapeutic effect of anti-PD1 in vivo.
Authors: Kang Kai , Schrump David S. , Thomas Anish , Schalper Kurt Alex , Saunthararajah Yogen , Velcheti Vamsidhar 
Published: September 2018

11552 Background: NSCLC response to anti-PD1 therapy is ~20%, largely because most NSCLC avoids immune-recognition in the 1stplace, e.g., by epigenetics to suppress neo-antigen expression. DNA methyltransferase (DNMT1) mediates this repression and is depleted by decitabine (Dec). Unfortunately Dec has trivial distribution into solid cancer tissues because of rapid deamination by cytidine deaminase (CDA). Therefore, to improve tissue-distribution of Dec with the low Cmax/long Tmax profile needed for DNMT1-depletion without cytotoxicity, we combined Dec with a CDA inhibitor tetrahydrouridine (THU). Methods: C57/BL6 mice were inoculated with LL3-luc cells via tail vein. After documentation of lung invasion by live-imaging, mice (n = 5/group) were randomized to PBS, THU-Dec (10/0.1 mg/kg sc 3×/wk), anti-PD1 (5 mg/kg ip q5d, DX400 from Merck) or THU-Dec/anti-PD1 combination. Antigen presentation, PD, MDSCs, and T-cells were measured in blood and tumor. Results: THU-Dec or anti-PD1 alone decreased tumor by imaging and increased survival, however, THU-Dec/anti-PD1 combination extended median survival the most and completely regressed tumor in 2/5 mice (median survival days PBS 37, THU-Dec 56, anti-PD1 62, THU-Dec/anti-PD1 77). Rechallenge of cured mice with LL2-luc confirmed immune-memory effect, with no engraftment vs expected engraftment in controls. Consistent with the pharmacologic rationale, THU-Dec produced > 2-fold more DNMT1-depletion in tumor vs PBS. Consistent with non-cytotoxic effect, absolute lymphocyte counts were preserved with THU-Dec, while numbers of G-MDSC decreased (2.9 k/µL PBS vs 0.3 k/µL THU-Dec/anti-PD1, p < 0.01). Expression of neoantigens MAGE-A1 and MAGE-A3 increased > 4-fold with THU-Dec vs PBS (p < 0.01). THU-Dec/anti-PD1 increased tumor infiltrating lymphocytes 6-fold vs PBS (p < 0.01) and decreased regulatory T-cells 2.5-fold vs PBS (p < 0.01). IFNγ expression in tumor increased 2.4-fold with THU-Dec/anti-PD1 vs PBS (p < 0.01). Conclusions: THU-Dec/anti-PD1 produced marked survival improvements and cures in tumor-bearing mice, scientific validation of our clinical trial NCT02664181 combining THU-Dec/nivolumab in 2nd line for NSCLC.