tbuckley/cabot-search huggingface dataset:
Validation of a comprehensive cancer genomic profiling assay based on massively parallel DNA sequencing.
Authors: Yuanyuan Hong, Weizhi Chen, Huiting Yan, Linlin Yan, Xuexia Zeng, Yipeng Song
Journal: Journal of Clinical Oncology (2019)

e13138 Background: Validation is very important for diagnostic assays, here we describe a validation process of a comprehensive cancer genomic profiling assay based on massively parallel DNA sequencing. This assay can detect base substitutions, short insertions and deletions, copy number alterations, tumor mutation burden (TMB) and microsatellite instability (MSI) across 543 cancer-related genes from tumor specimens or plasma. Methods: Analytical validation was conducted with 20 cell line pools whose mutation were verified by digital droplet PCR (ddPCR). Clinical validation was conducted with Proficiency Test samples and clinical samples whose mutation were verified by ddPCR. Sensitivity, positive predictive value (PPV) and precision of tumor specimens and plasma were assessed across the reportable range of the assay. For measurement of TMB， NGS libraries of a cohort of tumor samples were tested by whole exosome panel (WES) and this assay respectively. And clinical tumor tissue samples whose MSI status were identified by fluorescent PCR-capillary electrophoresis were also tested by this assay. Results: The SNV/Indel LOD 95 was 0.6% for hot-spot variants, and 1.3% for panel-wised variants of tumor tissue samples with high specificity (PPV &gt;99%). The SNV/Indel LOD 95 was 0.4% for hot-spot variants, and 1.1% for panel-wised variants of plasma samples (cfDNA≥15ng), with PPV &gt;99%. LOD 95 of CNV was 2.2-2.3, with PPV&gt;99%. Precision of CNV was higher than 95%, precision of SNV/Indel was higher than 97%. Concordance between TMB results tested by WES and this assay was 0.94. MSI results identified by this assay was the same as fluorescent PCR-capillary electrophoresis method. Conclusions: In summary, we present the analytical and clinical validation of a comprehensive NGS-based diagnostic assay for comprehensive tumor genomic profiling.
Exosomal microRNA-199b-5p as a potential circulating biomarker to predict response of preoperative chemoradiotherapy for locally advanced rectal cancer.
Authors: Dong Won Baek, Kyung Hwa Kim, Byung Woog Kang, Hye Jin Kim, Soo Yeon Park, Jun Seok Park, Gyu Seog Choi, Jin Ho Baek, Keun Hur, Jong Gwang Kim
Journal: Journal of Clinical Oncology (2019)

e15161 Background: Preoperative chemoradiotherapy (CRT) followed by total mesorectal excision has become the standard treatment for locally advanced rectal cancer (LARC). However, the effect of CRT varies from complete response to complete resistance, and predicting response to CRT have not been well characterized yet. Previous studies have shown the potential of micro-RNA (miRNA) based approaches to enhance tumor radiation response. Accordingly, the present study attempted to identify biomarkers to predict response for preoperative CRT using comprehensive miRNA analysis in patients with LARC. Methods: This study included 65 rectal cancer tissues and 90 serum samples from patients who diagnosed with LACR and received preoperative CRT at Kyungpook National University Chilgok Hospital. Tissue specimens and serum samples were collected before CRT to evaluate the biologic differences between the good CRT response group and the poor CRT response group. For discovery of specific miRNAs, 800 miRNAs were analyzed using NanoString in 30 rectal cancer tissues. Thereafter, a total of 65 tissues, and 90 serum samples were investigated using real-time PCR for validation. Results: The median age was 59 years (range, 30-82), and the ratio of male to female was 3.05 to 1. The pathologic stages after preoperative CRT were as follows: pathologic complete response (n=13, 14.4%), pathologic stage I (n=13, 14.4%), pathologic stage II (n=27, 30.0%), pathologic stage III (n=28, 31.1%), and pathologic stage IV (n=9, 10.0%). In the discovery set, 16 target miRNAs were detected. In the validation set with tissue specimens, expression of 3 miRNAs (miR-199a/b-3p ( p=0.032), miR-199a-5p ( p=0.023), miR-199b-5p ( p=0.005)) was significantly upregulated which was associated with better response of CRT. Moreover, among the 3 candidate miRNAs, miR-199b-5p level was significantly upregulated in serum, and it was also found to be related with better response of CRT in LARC (pathologic stage 0/I versus II/III/IV, p=0.027). Conclusions: In the present study, high level of exosomal miR-199b-5p was associated with better response, suggesting it to be a promising non-invasive biomarker to predict response of CRT in patients with LARC. Accordingly, specific miRNAs can be predictive biomarker or therapeutic target to overcome radiotherapy resistance in LARC with a functional study.
Blood-based next-generation sequencing analysis of neuroendocrine tumors.
Authors: Walid Labib Shaib, Ali Roberts, Katerina Mary Zakka, Mehmet Akce, Christina Wu, Olatunji B. Alese, Bassel F. El-Rayes, Pashtoon Murtaza Kasi, Jason Scott Starr
Journal: Journal of Clinical Oncology (2019)

4110 Background: Neuroendocrine tumors (NET) comprise around 2% of all malignant tumors of the gastrointestinal system. The genomic landscape of NET has not been well studied. The aim of this study was to confirm the feasibility of next generation sequencing (NGS) using ctDNA in NET and characterize common alterations in the genomic profile. Methods: Molecular alterations in 114 plasma samples from 114 patients with NET using clinical-grade NGS of ctDNA (Guardant360 Ò ) across multiple institutions were evaluated. The test detects single nucleotide variants in 54-73 genes, copy number amplifications, fusions, and indels in selected genes. Results: A total of 114 NET patients were evaluated, of which 64 (56.1%) were female. Mean age was 59.7 years with a range between 23-89 years. ctDNA NGS testing was performed on 114 plasma samples; 1 patient had testing performed twice. Genomic alterations were defined in 94 (n = 94/114, 82.5%) samples with a total of 289 alterations identified after excluding variants of uncertain significance (VUSs) and synonymous mutations. Alterations were identified in at least one sample from 83 patients; TP53 associated genes were most commonly altered (n = 83/289, 28.7%), followed by KRAS (n = 22, 7.6%), PI3CA (n = 15, 5.2%), CCNE1 (n = 15, 5.2%), BRAF (n = 13, 4.5%), MYC (n = 12, 4.1%), ERBB2 (n = 11, 3.8%), APC (n = 10, 3.5%), EGFR (n = 10, 3.5%), MET (n = 10, 3.5%), PTEN (n = 9, 3.1%), RB1 (n = 9, 3.1%), CDK6 (n = 7, 2.4%), AR (n = 5, 1.7%), ARID1A (n = 5, 1.7%), FGFR1 (n = 5, 1.7%), and PDGFRA (n = 5, 1.7%). Other genomic alterations of low frequency, but clinical relevance included: CDK4 (n = 4, 1.3%), NF1 (n = 4, 1.3%), RAF1 (n = 4, 1.3%), GNAS (n = 3, 1.0%), KIT (n = 3, 1.3%), BRCA2 (n = 2, 0.7%), CCND2 (n = 2, 0.7%), CTNNB1 (n = 2, 0.7%), JAK2 (n = 2, 0.7%), NRAS (n = 2, 0.7%), SMAD4 (n = 2, 0.7%), and TERT (n = 2, 0.7%). Alterations in AKT1, ALK, ATM, BRCA1, CCND1, CDKN2A, FGFR2, MTOR, RHOA, SMO and STK11 were all reported once (n = 1, 0.3%). Conclusions: Evaluation of ctDNA is feasible among individuals with NET. Liquid biopsies are not invasive and can provide personalized options for targeted therapies in NET patients.
Immune gene signatures and integrative spatially-resolved digital profiling of prognostic biomarkers for mesothelioma.
Authors: Sarah Elizabeth Church, Carmen Ballesteros-Merino, Amy H Sullivan, Andrew M White, Michael D Bailey, Shawn M Jensen, John R Handy, Rachel E. Sanborn, Carlo Bruno Bifulco, Sarah Warren, Joseph M Beechem, Bernard A. Fox
Journal: Journal of Clinical Oncology (2019)

e20071 Background: Malignant mesothelioma has been an incurable disease with few effective therapies. While PD-1 targeted therapies have elicited some patient responses, the overall response rate for mesothelioma is low. Since mesothelioma is derived from the mesothelium of the lung, we hypothesize that immune cells in the tumor microenvironment (TME) may behave differently than other solid tumors that are responsive to immunotherapy. Here we characterize prognostic immune gene signatures and spatial protein expression in the mesothelioma TME. Methods: 50 FFPE mesothelioma samples were analyzed using the NanoString PanCancer IO360 assay which measures expression of 770 genes, including the abundance of 14 immune cell types and of 32 IO signatures. All genes and signatures were correlated with overall survival (OS). GeoMx digital spatial profiling (DSP) was performed on 40 samples assessing the protein expression along 12 geometric circular regions-of-interest (ROI). Tissue slides were stained with a combination of fluorescent-labeled antibodies (pan-cytokeratin, CD3, CD68) and a panel of 38-antibodies each conjugated to a unique UV-photocleavable DNA barcode. UV light was applied to the defined ROI, which releases the DNA barcodes for quantitation on the nCounter platform. Results: Unsupervised clustering of samples based on gene signatures showed two distinct groups; one, with low expression of lymphocyte activation/exhaustion signatures and the second, with moderate expression of immune signatures. Two samples had high expression of all immune gene signatures, also confirmed by DSP had increased expression of T cell markers. Tumor proliferation (p &lt; 0.001), hypoxia (p = 0.04), glycolysis (p &lt; 0.001), B7-H3 (p = 0.007) and TGF-β (p = 0.001) signatures were significantly associated with shorter OS. Additional DSP profiling of these mesothelioma samples showed both T cell excluded and desert TMEs. Conclusions: We show that the mesothelioma TME has distinct immune biology associated with OS. Tumors from patients with poor survival had expression profiles previously described to be associated with immune excluded and desert phenotypes. We show that gene expression and DSP identifies unique targets for immunotherapy and we hypothesize that these findings may guide the development of combination trials that will be effective against mesothelioma.
Real-world data (RWD) and patients reported outcomes (PRO) in breast cancer (BC): Physical, emotional side effects (S/E), financial toxicity (FT), and complementary usage (CM) relations.
Authors: Daniel A. Vorobiof, Eliran Malki, Irad Deutsch, Lior Hasid
Journal: Journal of Clinical Oncology (2019)

e18060 Background: RWD denotes data accumulated via electronic health records as well as cutting edge technology paired with consumer mobile devices. Artificial intelligence (AI) incorporates the use of algorithms and machine learning (ML) software to analyze complex medical data, improving the knowledge of cancer journeys. PRO on 256 BC patients (pts) survey repliers, users of Belong.life, a worldwide social media application for cancer pts, are presented. Methods: From 11/2018 to 01/2019, 256 pts replied to a 37 questions’ survey which included information regarding clinical and emotional S/E, FT and CM use. Results: 98 pts (38%) were &lt; 50 years of age, 158 (62%) &gt; 50 years. Most of the pts (163, 64%) were diagnosed within 2017-8. Most pts had Stage 1 (83 pts,32%) and 2 (94 pts,37%) and 71 pts (28%) had Stage 3-4. 154 (61%) had neo-adjuvant anthracyclines-based treatments, followed by a taxane (docetaxel/paclitaxel). 149 of 256 pts (58%) reported clinical S/E: nausea and vomiting in 77 pts (52%), fatigue in 63 pts (42%), hair loss in 42 pts (28%) and body pain and neuropathy in 13 pts each (8.8%). 90 pts (35%) described various emotional symptoms: depression in 32 pts (35.6%), anxiety 13 (14.4%), ‘up and down’ feelings in 20 pts (22 %). FT was experienced by 100/208 pts (48%). FT was most prevalent in ages 35-50 (51/85pts, 60%) than in 51-65 (41/100pts, 41%). Main reported causes in both groups were loss or absence from work (33% and 51%) and treatment copayments (40% and 21%). CM use was reported by 42/256 pts (16.4%). Most common CM were nutritional, multivitamins, supplements and CBD oil use. ML documented a strong relationship between BC recurrence in 55/256 pts (21.5%), FT in 25/55 pts (45.5%) and CM use in 9/25 pts (36%) vs no FT in 3/30 pts (10%). Conclusions: 256 BC users of the Belong application reported on clinical and emotional S/E, FT and CM use. The high incidence of emotional S/E stresses the need for individualized attention. FT was most prevalent in the younger age group (35-50yrs) due to work loss and treatment copayments. A significant relationship was determined by ML techniques on those patients experiencing BC recurrence, FT and CM use.
AR changes in circulating-tumor DNA (ctDNA) in patients with metastatic castration-resistant prostate cancer (mCRPC) treated with high-dose testosterone.
Authors: Marcus W. Moses, Elisa Ledet, Charlotte Manogue, Patrick Cotogno, Brian E. Lewis, A. Oliver Sartor, Pedro C. Barata, Jodi Lyn Layton
Journal: Journal of Clinical Oncology (2019)

5058 Background: High-dose testosterone (HDT) is active in mCRPC pts and may allow successful re-sensitization to previously utilized androgen-axis targeted therapies. The relationship of genomic alterations in AR gene to HDT responsiveness is unclear. Methods: Analysis of consecutive pts treated with ≥1 dose of HDT (testosterone cypionate q 2-4 weeks n = 29; continuous gel n = 4). Baseline characteristics, ctDNA data (Guardant360), and clinical outcomes were assessed. Presence of genomic AR alterations included amplifications (amps) and mutations (muts); all muts had allele fraction ≥0.3%. PSA response rates included PSA declines of &gt; 30% or ≥50%. PSA-progression-free survival (PSA-PFS) was defined as HDT start date to PSA ≥ 25% over baseline after a second confirmed PSA rise. Results: Between May 2016 and Feb 2018, 33 mCRPC pts had median age 73 (58-85), 39% Gleason 8-10, 100% bone mets, 24% nodes + bone, and median baseline PSA level 36.1 ng/mL (0.04-1290). HDT was given post-median of 2 (1-10) CRPC therapies. 73% (24/33) of pts previously received abiraterone (n = 14), enzalutamide (n = 4), or both sequentially (n = 6) prior to HDT for a median of 10.5 months (0.7-56.8). Baseline ctDNA showed 42% AR alterations (amps = 8, muts = 4, both = 2); 33% TP53, and 6% DNA repair (ATM n = 1; BRCA2 n = 1). With median follow-up 4.4 months, HDT given for median of 4.2 months (95% CI, 3.6-4.8); 29% had PSA ≥50% response and 45% PSA ≥30% response. Median PSA-PFS is immature at 5.5 months (95% CI, 1.5-9.5); 14 pts still on HDT treatment. Grade ≥3 AEs were observed in 6% of pts (G4 thrombocytopenia = 1; G4 asthenia = 1). For pts with baseline AR alterations and HDT treatment, repeated ctDNA assays (n = 7) showed that 100% had decreased AR alterations. No relationship between PSA response and baseline ctDNA AR characteristics are discerned at this time. Conclusions: HDT was safe and active in a subset of mCRPC. Responses were clearly noted for men receiving continuous daily testosterone gels, thus continuously high testosterone levels are active in addition to injection-induced bipolar changes. Further understanding of the genomic alterations predicting responsiveness to HDT in mCRPC is required.
Bispecific NKG2D-CD3 and NKG2D-CD16 fusion proteins for induction of NK and T cell reactivity against acute myeloid leukemia
Authors: Melanie Märklin, Ilona Hagelstein, Samuel P. Koerner, Kathrin Rothfelder, Martin S. Pfluegler, Andreas Schumacher, Ludger Grosse-Hovest, Gundram Jung, Helmut R. Salih
Journal: Journal for ImmunoTherapy of Cancer (2019)

Monoclonal antibodies (mAbs) mediate their effects in great part by inducing ADCC of NK cells, and multiple efforts aim to increase this function by engineering mAbs optimized Fc-parts. Even more potent antitumor immunity can be induced by strategies to stimulate T cells with their profoundly higher effector potential. However, upon increased immunostimulatory potential, the necessity to target highly tumor-specific antigens becomes critically important to reduce side effects. We here report on bispecific fusion proteins (BFP) that target ligands of the immunoreceptor NKG2D (NKG2DL), which are widely expressed on malignant cells but generally absent on healthy tissue. They consist of the extracellular domain of NKG2D as targeting moiety fused to Fab-fragments of CD3 (NKG2D-CD3) or CD16 (NKG2D-CD16) antibodies. NKG2D-CD16 displayed increased affinity to the FcγRIII on NK cells compared to engineered Fc-parts, which are contained in optimized mAbs that presently undergo clinical evaluation. In line, NKG2D-CD16 induced superior activation, degranulation, IFN-γ production and lysis of acute myeloid leukemia (AML) cell lines and patient AML cells. NKG2D-CD3 in turn potently stimulated T cells, and comparison of efficacy over time revealed that NKG2D-CD16 was superior upon short term application, while NKG2D-CD3 mediated overall more potent effects which manifested after longer times. This can be attributed to treatment-induced proliferation of T cells but not NK cells. Taken together, we here introduce novel "antibody-like" BFP that take advantage of the highly tumor-restricted expression of NKG2DL and potently activate the reactivity of NK cells or T cells for immunotherapy of AML.
EATON: An open-label, multicenter, phase I dose-escalation trial of nazartinib (EGF816) and trametinib in patients with EGFR-mutant non-small cell lung cancer – preliminary data on safety and tolerability.
Authors: Sebastian Yves Friedrich Michels, Lucia Nogova, Barbara Deschler-Baier, Enriqueta Felip, Delvys Rodriguez-Abreu, Rafael Rosell, Martin Sebastian, Martin H. Schuler, Martin Wermke, Rieke Nila Fischer, Sophia Koleczko, Diana S.Y. Abdulla, Richard Riedel, Matthias Scheffler, Jana Fassunke, Martin Hellmich, Sabine Merkelbach-Bruse, Reinhard Buettner, Juergen Wolf
Journal: Journal of Clinical Oncology (2019)

e20577 Background: Multiple mechanisms of resistance to EGFR TKIs therapy in EGFR-mutant non-small cell lung cancer (NSCLC) have been described, most often including the acquisition of the secondary resistance mutations in exon 20 of EGFR. Preclinical models and clinical findings have also shown that co-occurring activation of the RAS/MEK pathway may result in reduced EGFR dependency, which may be overcome by co-inhibition of MEK. We thus hypothesize that the combined inhibition of EGFR and MEK may restore sensitivity to EGFR inhibition in patients with acquired resistance to EGFR inhibition and may as well prolong the acquisition of resistance in treatment-naïve patients. Methods: EATON is an international, multicenter, phase I, dose escalation investigator-initiated trial investigating the recommended phase 2 dose (RP2D), safety and preliminary efficacy of the combination of the third-generation EGFR inhibitor EGF816 with the MEK inhibitor trametinib (NCT03516214). Eligibility criteria: Advanced NSCLC harboring EGFR del19 or p.L858R, first-line or after failure of any EGFR TKI including osimertinib, independently of p.T790M status. Patients with high-level MET amplification are excluded. Dose level escalation will be based on a modified traditional cumulative 3+3 design, i.e. “up and down” (dose level 1: 100 mg nazartinib (EGF816) QD + 1 mg trametinib QD). A total number of 24 patients is planned to be enrolled in 8 trial sites in Germany and Spain. At a first stage, 18 (6´3) patients will be treated and evaluated. Exploratory endpoints aim at the identification of potential mechanisms of resistance to the trial treatment by massively parallel sequencing (MPS), FISH, phospho-protein analyses and whole exome/genome sequencing of baseline and PD biopsy tumour tissue. Additionally blood samples for MPS of cell free DNA will be collected throughout the trial treatment. Results: At the time of data-cut off for this abstract, one patient received treatment at dose-level 1. Treatment was withdrawn due to a serious, bacterial soft tissue infection of the hand outside the DLT period. Conclusions: Data on safety and tolerability of the combination of nazartinib and trametinib is premature. Updated results will be presented at the conference. Clinical trial information: NCT03516214.
Development of a plasma cell-free DNA chromosome instabilities assay for early cancer detection and treatment response monitoring of multiple tumor types.
Authors: Yang Yang, Wei Yin, Nan Li, Wensheng Xu, Fei Ma, Xiaosong Chen, Wen-Ming Cao, Wangjun Yan, Jiandong Wang, Dongxing Nai, Chenjie Qin, Qian Ziliang
Journal: Journal of Clinical Oncology (2019)

e13072 Background: Tumor cells keep shedding DNA into blood stream. Here we present a retrospective study to investigate the potential of CIN in plasma cell-free DNA (cfDNA) as a minimal-invasive biomarker for early cancer detection and cancer treatment responses monitoring. Methods: To characterization cfDNA CIN, 160 plasma samples from non-cancer individuals and 569 from cancer patients, including tumors from the brain, respiratory tract, gastrointestinal tract, urinary tract, liver, gallbladder, female reproductive system, prostate, breast and sarcoma. cfDNA was extracted and sent to low-coverage whole genome sequencing by the Illumina X10, followed by CIN analyses by a customized workflow Ultrasensitive Chromosomal Instability Detector (UCAD). Results: In non-cancer individuals, increased CIN in cfDNA was found associated with active EBV infections(P&lt;0.01) and HBV infection (P=0.042). No statistical significances were found for the other parameters, including age, hypertension, diabetes, chronic kidney diseases, family history of cancer and etc. cfDNA CIN increased along with the development of lung cancer lesions, from adenocarcinoma in-situ, minimal invasive adenocarcinoma, invasive adenocarcinoma (P=0.034) to relapsed cancer (P&lt;0.01). The sensitivity of early lung cancer detection was 30.7%, 37.5%, 45.5%, 50.0% and 98.1% for AIS, MIA, IAC, SCC and relapsed lung cancer, at a specificity of 75%. cfDNA CIN levels did not show statistical differences regarding metastases sites. cfDNA CIN were further increased in relapsed breast cancer (P&lt;0.01). The sensitivity of relapsed breast cancer detection was 73.3%, 94.4%, 89.6% and 80.0% for HER2+, Luminal A, Luminal B and triple negative breast cancer, at a specificity of 90%. In primary liver cancer, cfDNA CIN decreased after curative therapies, including R0 resections and liver transplant. R0 resections showed similar performance as compared to liver transplant (P=0.35) in terms of cfDNA CIN decreasing. Furthermore, cfDNA CIN was higher in patients after R0 resections (P=0.003) and liver transplant (P=0.03) than that of HBV-positive cancer-free patients, indicating the potential risk of disease relapses. For advanced stage patients, continuously increasing cfDNA CIN level was found associated with worse survival, and a decreasing trend predicting better prognosis vice versa. Conclusions: Plasma cfDNA CIN analysis might be a useful tool for cancer management.