bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression profiles of circulating tumor cells in metastatic breast cancer patients.
Authors: Mostert Bianca , Sieuwerts Anieta M , Kraan Jaco , Bolt-de Vries Joan , Peeters Dieter , Dirix Luc , Seynaeve Caroline M. , Jager A. , de Jongh Felix E , Hamberg Paul , Stouthard Jacqueline , Kehrer Diederik F. S. , Look Maxime P , Smid Marcel , Jiang Yuqiu , Wang Yixin , Gratama Jan W , Foekens John A , Martens John W.M , Sleijfer Stefan 
Published: March 2020

10504 Background: A circulating tumor cell (CTC) count is an established prognostic factor in metastatic breast cancer. Besides enumeration, CTC characterization promises to further improve outcome prediction and treatment guidance. We have previously shown the feasibility of measuring the expression of a panel of 96 clinically relevant genes in CTCs in a leukocyte background, and in the current study, we determined the prognostic value of CTC gene expression profiling in metastatic breast cancer. Methods: CTCs were isolated and enumerated from blood of 130 metastatic breast cancer patients prior to start of first-line systemic, endocrine or chemotherapeutic, therapy. Of these, 103 were evaluable for mRNA gene expression levels measured by quantitative RT-PCR in relation to time to treatment switch (TTS). Separate prognostic CTC gene profiles were generated by leave-one-out cross validation for all patients and for patients with ≥5 CTCs per 7.5 mL blood, and cut-offs were chosen to ensure optimal prediction of patients who might benefit from an early therapy switch. Results: In the total cohort, of whom 56% received chemotherapeutic and 44% endocrine therapy, baseline CTC count (≥5 versus <5 CTCs/7.5 mL blood) predicted for TTS (Hazard Ratio (HR) 2.92 [95% Confidence Interval (CI) 1.71 – 4.95] P <0.0001). A 16-gene CTC profile for all patients and a separate 9-gene CTC profile applicable for patients with ≥5 CTCs were identified, which distinguished those patients with TTS or death within 9 months from those with a more favorable outcome. Test performance for both profiles was favorable; the 16-gene profile had 90% sensitivity, 38% specificity, 50% positive predictive value (PPV) and 85% negative predictive value (NPV), and the 9-gene profile performed slightly better at 92% sensitivity, 52% specificity, 66% PPV and 87% NPV. In multivariate Cox regression analysis, the 16-gene profile was the only factor independently associated with TTS (HR 3.15 [95%CI 1.35 – 7.33] P 0.008). Conclusions: Two CTC gene expression profiles were discovered, which provide prognostic value in metastatic breast cancer patients. This study further underscores the potential of molecular characterization of CTCs.
Circulating DNA analysis and concordance with tumor section analysis in the detection of KRAS and BRAF point mutations from metastatic colorectal cancer.
Authors: Thierry Alain R. , Mouliere Florent , El Messaoudi Safia , Rolet Fanny , Lamy Pierre-Jean , Lopez-Crapez Evelyne , Mollevi Caroline , Bibeau Frederic , Loriot Virginie , Gongora Celine , Del rio Maguy , Molina Franck , Mathonnet Muriel , Pezet Denis , Ychou Marc 
Published: March 2020

10505 Background: We developed a specific method for circulating cell-free DNA (ctDNA) enabling the detection of point mutations. CtDNA exists at high level in patients with different types of cancer, and presents great potential in regards, in particular, to its low invasiveness, rapid data turnaround and cost effectiveness. We described here the first blinded prospective study on the comparison of KRAS and BRAF mutational status data obtained from the analysis of ctDNA and tumor section. Methods: Intplex is a refined Q-PCR-based method specifically designed to analyze ctDNA. IntPlex allows not only the detection of point mutations, but also the determination of tumor-ctDNA concentration and fragmentation index simultaneously. Intplex sensitivity is 0.01% (mutant to WT ratio) and is unprecedented among Q-PCR-based methods. The study was conducted from a multicenter cohort of 79 metastatic CRC patients not having received chemo- or radio-therapy within the month prior to blood sample collection. Results: Mutational status could not be determined in 9 samples with one of the two methods. CtDNA analysis showed 100% specificity and 87% sensitivity for KRAS detection (only three samples are misclassified) as compared to tumor section analysis with 23/70 (33%) positive samples, the concordance value being 96%. For BRAF mutation, the method exhibited a specificity and a sensibility of 100% with 5/70 (7%) positive samples (concordance of 100%). When combining KRAS and BRAF mutations, 100% specificity, 89% sensibility and 98% concordance were determined. The three discordant samples may be explained by the malignant genotype of primary tumor versus metastasis, or by the sensitivity of our detection method. The mutation load (median, 12.4%) expressed as the proportion of mutant allele in ctDNA is highly variable (0.037% to 69%) among mutated samples showing a very high inter-individual heterogeneity. Conclusions: Our blinded prospective multicenter study clearly showed for the first time that tumor section analysis might be advantageously replaced by ctDNA analysis, enlarging personalized medicine power for cancer patients.
Early change in 18-fluorodeoxyglucose (FDG) uptake on positron emission tomography (PET) to predict response to preoperative systemic therapy (PST) in HER2-negative primary operable breast cancer: Translational breast cancer research consortium (TBCRC008).
Authors: Connolly Roisin M. , Leal Jeffrey P , Goetz Matthew P. , Zhang Zhe , Zhou Xian C , Mhlanga Joyce , Jeter Stacie , Walsh Bridget , Powers Penny , Zorzi Jane , Carpenter John T. , Storniolo Anna Maria , Watkins Stanley P. , Fetting John H. , Miller Robert Stephen , Sideras Kostandinos , Khouri Nagi , Gabrielson Edward , Wahl Richard L. , Stearns Vered 
Published: March 2020

10509 Background: PST allows for improved surgical outcomes and response assessment without compromising long term outcomes. PST is an attractive model for assessing surrogate markers of response to therapy. We hypothesized that changes in tumor standardized uptake values corrected for lean body mass (SUL) max on FDG- PET by cycle 1 day 15 (C1D15) of therapy would predict pathological complete response (pCR) to PST in women with stage 2-3, grade 2-3, HER2-negative breast cancer. Methods: TBCRC008 is a multicenter placebo-controlled trial that investigates pCR following 12 weeks of preoperative carboplatin and albumin-bound paclitaxel with or without vorinostat. FDG-PET followed by tumor biopsies were performed at baseline and C1D15. We correlated % reduction in SULmax on FDG-PET (PERCIST 1.0; Wahl RL, J Nuc Med 2009) with pCR (no invasive cancer in breast/axilla). We compared % reduction in SULmax between responders (pCR) and non responders (no pCR) using nonparametric Wilcoxon rank sum test. We explored association of % reduction in SULmax at pre-specified cutoff with response using Fisher’s exact test and logistic regression. We correlated baseline, C1D15, and % change in Ki67 at C1D15 with pCR. Results: Accrual is complete. Of 62 women enrolled (10/2009-11/2011), 40 have completed study PST and surgery (median age 47.5 [range 30-68], ER-positive 67%). Overall pCR was 26%. In an intent to treat analysis (n=39), we observed a significant difference in median % reduction in SULmax between responders vs not (66.6% vs 32.4%, p <0.001). We observed a higher proportion of reduction in SULmax ≥ 60% in responders vs not (80% vs 3.5%, p <0.001). The differences in baseline, C1D15 and % change in Ki67 were not significant between responders and non-responders. Conclusions: Change in SULmax on FDG-PET 15 days after initiating PST was significantly greater in patients with pCR versus no pCR. Future studies will determine whether altering therapy based on early changes in SULmax will improve pCR. Unblinded data from all participants will be presented at the meeting.
Use of nano-immuno assay to generate rapid, quantitative nanoscale proteomic profiling of the hypoxia pathway in renal cell carcinoma clinical specimens.
Authors: Fan Alice C. , Banerjee Prajna , Leppert John , Harshman Lauren Christine , Sabatti Chiara , Brooks James D , Felsher Dean W. 
Published: March 2020

10513 Background: Novel agents that inhibit kinases in the hypoxia pathway [VEGF, PDGF] can achieve response rates of 30-57% in renal cell carcinoma (RCC); however, threshold levels of targets and downstream signaling proteins in patient cells have not been identified as biomarkers to guide treatment. Rapid and quantitative measurements of overall levels and % phosphorylation of proteins in the hypoxia pathway from patient specimens might better enable the development of proteomic biomarkers. Methods: We have developed the use of an automated nanoscale immuno assay (NIA) to profile hypoxia proteins in solid tumors, and now present NIA assays to measure EGFR, VEGF-R, AKT2, GSK3β, CA-9, MEK1 and ERK1/2 proteins in RCC clinical specimens. Furthermore, to decrease the amount of tissue and the invasiveness of the procedure required to obtain specimens for analysis, we have optimized assays to profile RCC specimens acquired by fine needle aspiration (FNA). Results: Unique to NIA technology, we have analyzed percent phosphorylation for phosphorylated proteins and can distinguish differences in even a single phosphorylation in the FNA specimens, allowing us to group tumors based upon different patterns of phosphorylation. In addition, we compared 10-parameter hypoxia profiles in a panel of RCC paired with adjacent non-tumor tissue and will present the proteins that can distinguish tumor from non-tumor tissue. Importantly, we have determined that we can present protein profiles to the clinical team within 8 hours of receiving the specimen (1 hour preparation time, 6 hours of unattended automated instrument time, 1 hour of analysis). Conclusions: NIA is an extremely efficient, quantitative and high-throughput platform that has the potential to be used to rapidly generate proteomic profiles for clinical specimens for the development of novel diagnostic and predictive biomarkers.
Interrogation of polymorphisms in drug metabolism or transport genes and peripheral neuropathy during paclitaxel treatment.
Authors: Hertz Daniel Louis , Dees Elizabeth Claire , Motsinger-Reif Alison A. , Drobish Amy , Roy Siddharth , McLeod Howard L. , Carey Lisa A. 
Published: March 2020

10515 Background: Peripheral neuropathy is the most common severe toxicity in patients treated with paclitaxel. Putative genetic mutations in genes relevant to drug metabolism, distribution, and elimination may explain the differences in risk of neurotoxicity among patients. Using a genotyping platform that interrogates nearly 2,000 known variants in drug exposure genes, we hypothesized that polymorphisms could be identified which modulate a patient’s risk of neuropathy during paclitaxel treatment. Methods: Subjects included in this study were treated for breast cancer with paclitaxel-containing regimens. Clinical data, including patient characteristics and toxicity, was collected prospectively in an observational registry. Blood was collected at diagnosis and genotyped using the Affymetrix DMET Plus chip at Gentris. The primary endpoint was grade 2+ neuropathy as defined by NCI CTC criteria. Statistical analysis was carried out using Fisher’s exact test for each SNP, without assumption of a specific genetic model. For this hypothesis-generating study, a p-value of <0.001 was selected for significance. Results: 412 breast cancer patients treated with paclitaxel were included in the analysis. The median age was 50, 107 (26%) were African-American, and 48 (12%) had preexisting diabetes. The prevalence of grade 2+ neuropathy was 18.5% in the cohort. After exclusion of SNPs based on call rate, Hardy-Weinberg equilibrium, and allele frequency, 564 SNPs were interrogated for an association with grade 2+ neuropathy. Two SNPs, rs3788007 (ABCG1_43706676G>A[Intron]) and rs6163 (CYP17A1_195G>T[S65S]), were associated with grade 2+ neurotoxicity p=0.0003 (OR=3.54, 95% CI: 1.77-7.72) and p=0.0008 (OR=0.35, 95%CI: 0.18-0.66), respectively. Conclusions: We identified two SNPs, both in genes not previously investigated in paclitaxel pharmacogenetic studies, which were associated with modified risk of paclitaxel-induced neuropathy. Both genes are implicated in endogenous steroid biology, which is thought to be relevant to neuropathy development, and one SNP (rs6163) is in high LD (r2=0.93) with a SNP recently reported to be associated with bortezomib-induced neuropathy.
BAP1: The first mutated gene causing familial uveal melanoma.
Authors: Hansson Johan , All-Eriksson Charlotta , Helgadottir Hildur , Edsgard Daniel , Tuominen Rainer , Lundeberg Joakim , Ivanova Ivayla , Emanuelsson Olof , Hoiom Veronica 
Published: March 2020

10521 Background: Uveal melanoma (UM) is a rare malignancy with a poor prognosis. Familial predisposition to UM is rare and accounts for only a few percent of all cases. The genetic background of hereditary UM is unknown and the aim of our project was to identify susceptibility gene(s) for UM. Methods: We identified a family with hereditary predisposition for UM – the proband of which is a young female diagnosed with UM at age 16 who within 6 months developed liver metastases. We also identified two older paternal relatives who were diagnosed with UM at 39 and 44 years of age, respectively. We performed massively parallel sequencing using the Illumina Hiseq2000 technology on germline DNA from the proband, her parents and a healthy sibling. After QC and mapping against the human reference genome the average coverage across the exome was between 35 and 86 for the four sequenced samples. Results: Out of more than 260,000 single nucleotide variants (SNVs) and small insertion / deletion variants (indels), 51 gene variants were filtered out by being novel, shared by the affected proband and her father (considered an obligate mutation carrier), but not by the healthy mother, of predicted functional importance and /or located within strongly conserved regions. The strongest candidate among these was a loss of function-variant in the BAP1 gene, since BAP1 has been suggested as a tumor suppressor in several cancer-related syndromes, including cases of UM. The sequence data indicated an insertion of one base-pair in exon 3 of the BAP1 genecausing a frame-shift and subsequently a truncated protein lacking all its functional domains. The mutation was also present in UM tumor tissue from the two deceased paternal relatives and was found to segregate with the UM phenotype in the family. We also detected loss of heterozygosity in the tumor of the proband, supporting BAP1 as the causative gene in this family. Conclusions: The identification of BAP1 as the gene responsible for this syndrome is the first demonstration of a germline mutation causing UM. This enables us to identify and monitor risk individuals belonging to mutation positive families with predisposition to UM, and possibly other cancer syndromes. We are continuously screening other cases of familial UM for mutations in BAP1.
Next-generation sequencing of FFPE solid tumor specimens for clinical use.
Authors: Yelensky Roman , Wang Kai , Dogan Snjezana , Borsu Laetitia , Frampton Garrett , Lipson Doron , Stephens Philip , Bastian Boris , Klimstra David , Ladanyi Marc , Cronin Maureen T. , Hedvat Cyrus , Berger Michael F. 
Published: March 2020

10524 Background: As more therapies targeting genomic alterations become available, genotyping (e.g., by Sequenom) is increasingly performed in tumor types where mutational status may drive treatment choice. Next-generation sequencing (NGS) technology can expand on genotyping of individual base pairs because it can detect mutations across entire exons, copy changes and fusion genes. However, for NGS to be clinically viable, it must be made compatible with FFPE tissues and shown concordant with best current diagnostic methods. Methods: To explore a potential clinical role for NGS, we selected 120 FFPE specimens (68 NSCLC, 32 CRC, 20 melanoma) previously tested for 97 oncogenic mutations in 8 oncogenes by Sequenom, and sequenced all exons of 182 cancer genes. Genotyping and sequencing were both performed in CLIA compliant labs. DNA was extracted from 4x 10μ unstained sections from the diagnostic FFPE block, followed by library construction and hybridization capture of 3230 exons and 37 commonly rearranged introns. Average coverage of >900X uniquely-mapping reads was obtained. Sequence data were analyzed for all genomic alterations and examined for potentially actionable mutations. Results: High concordance was noted between Sequenom and NGS: 103 and 105 mutations were called by the two technologies, respectively, at mutually tested sites, with 97 mutation calls in common. Notably, mutant allele frequencies in concordant calls ranged as low as 2% by NGS, highlighting the sensitivity of detection enabled by both approaches. Furthermore, in 45/120 (38%) specimens, NGS revealed additional alterations that may confer sensitivity or resistance to approved or experimental targeted therapies and thus plausibly influence treatment decisions. These included 39 copy changes or loss-of-function variants best assayed by an NGS approach. Conclusions: Our results demonstrate technical feasibility and highlight potential benefits of comprehensive cancer gene characterization through next-generation sequencing of clinical FFPE specimens. As NGS is the most practical means to detect all classes of somatic alteration in a small, clinically relevant sample, we suggest that this type of testing will become an essential component of patient care.
Molecular gene expression profiling to predict the tissue of origin and direct site-specific therapy in patients (pts) with carcinoma of unknown primary site (CUP): Results of a prospective Sarah Cannon Research Institute (SCRI) trial.
Authors: Greco Frank A. , Rubin Mark S. , Boccia Ralph V. , Scola Michael A. , Spigel David R. , Raby Samuel , Chirwa Thabiso W. , Quinn Raven , Schnabel Catherine A. , Erlander Mark G. , Hainsworth John D. 
Published: March 2020

10530 Background: Tumor profiling is an emergent technique to determine tissue of origin in CUP patients. However, the value of these predictions in improving treatment efficacy is unknown. In this prospective trial, we used tumor profiling results to direct site-specific therapy for CUP pts. Methods: A 92-gene RT-PCR assay (CancerTYPE ID; bioTheranostics, Inc.) was performed on tumor biopsies from previously untreated CUP pts who consented. When a tissue of origin was predicted, pts who were treatment candidates were assigned standard site-specific first-line therapy. Results: Between 10/08 and 12/11, 289 pts were enrolled, 252 had successful assays performed, and 247 (98%) had a tissue of origin predicted. 224 pts were eligible for treatment; 197 pts received assay-directed treatment. 120 of 224 treated pts (54%) had assay diagnoses of tumor types known to derive substantial benefit from standard site-specific treatment (bladder 27, colorectal 26, NSCLC 24, breast 10, ovary 10, kidney 9, prostate 4, germ cell 4, others 6 (3 sites), while 104 pts (46%) had assay diagnoses of relatively resistant tumors (biliary tract 45, pancreas 12, gastroesophageal 10, liver 7, sarcoma 5, cervix 5, others 20 (8 sites). Median OS for all treated pts was 10.8 months (mos); OS for 197 pts with assay-directed treatment was 12.2 mos (versus 6.0 mos for 27 pts receiving empiric therapy). Median OS was better in the 120 pts with assay diagnoses of more responsive tumor types (12.8 vs 7.4 mos; p = .027). Median OS (mos) in specific subgroups: pancreas 9, kidney 12, colon 12, NSCLC 16, ovary 30. Conclusions: This is the first prospective trial in which molecular profiling has directed site-specific therapy in CUP pts. Assay-directed therapy in 197 pts produced a median OS (12.2 mos) that compares favorably with previous empiric CUP therapy. CUP pts predicted to have more responsive tumor types had longer survival compared to less responsive types, suggesting accurate identification by the assay. These results strengthen the rationale for molecular profiling in CUP management.
Homeobox B9: A potential surrogate marker for bevacizumab in combination with chemotherapy in colorectal cancer.
Authors: Hoshino Yoshinori , Hayashida Tetsu , Hirata Akira , Okabayashi Koji , Ochiai Hiroki , Endo Takashi , Ishii Yoshiyuki , Jinno Hiromitsu , Hasegawa Hirotoshi , Kitagawa Yuko 
Published: March 2020

10531 Background: Homeobox B9 (HOXB9) is known to be overexpressed in human breast cancer and profoundly related to tumorigenicity, lung metastasis and radio-resistance. (Hayashida, PNAS 2010, and Chiba, PNAS 2011). However, little is known about the relation between the expression of HOXB9 and angiogenesis in colorectal cancer (CRC). We aimed to clarify the impact of HOXB9 in CRC and evaluate the importance for bevacizumab treatment. Methods: The expression of HOXB9 in human CRC specimens was analyzed. Then, we introduced HOXB9 construct into human CRC cell lines and examined TGFβ signaling and angiogenic factors. Xenograft model was established by these cell lines either with or without the administration of bevacizumab (5mg/kg, weekly) intraperitoneally. Finally, we examined the mRNA levels of consecutive patients who were treated by chemotherapy with bevacizumab in our institute and calculated the Kaplan- Meier curve with log-rank test. Results: 47 of 69 surgical specimens (67%) showed positive expression of HOXB9 mRNA. The high HOXB9 mRNA levels significantly correlated with poor differentiation and liver metastasis. The HOXB9-overexpressed cell lines showed significantly higher expression of TGFβ signaling target genes and angiogenic factors. HOXB9 overexpression significantly increased tumor volume and burden with higher microvessel density in vivo, even though the cell proliferation decreased in vitro. Notably, HOXB9-overexpressed tumor was dramatically shrunk by administration of bevacizumab (tumor shrinkage rate; 93% vs. 42% in HT29, 83% vs. 27% in HCT116). Patients with high expression of HOXB9 in tumor showed significantly longer progression free and overall survival periods (n=39). Conclusions: Our results demonstrated that patients with high expression of HOXB9 in tumor had better prognosis with bevacizumab treatment but worse without. In vivo and in vitro experiments revealed that HOXB9 might orchestrate angiogenesis and establish positive feedback between cancer cells and microenvironment. Bevacizumab might inhibit the feedback to reduce tumor growth dramatically. Therefore, HOXB9 may work as a potential surrogate marker of bevacizumab treatment in CRC.