tbuckley/cabot-search huggingface dataset:
Embedded tumor cell calibrators (ETC) for normalized quantitative multi-gene expression analysis of micrometastatic cells in blood and bone marrow of cancer patients
Authors: N. Fersis, D. Koliogiannis, L. Sisic, M. Aggarwal, S. Kaul
Journal: Journal of Clinical Oncology (2008)

1065 Background: The purpose of this study was the validation of a new preanalytical enrichment and molecular detection method using embedded tumor cell calibrators (ETC) for quantitative gene expression analysis of circulating tumor cells (CTC) in breast cancer patients. Methods: Samples from every patient were devided in native probes and matched calibrator probes spiked with either 2, 4 or 8 breast carcinoma tumor cells. The high affinity antibodies BM7 (MUC-1) and VU1D9 (EpCAM) were used for immunomagnetic tumor cell enrichment of 10 mL peripheral EDTA-blood of patients with primary breast cancer and metastatic disease. Separated cells were used for mRNA isolation and c-DNA synthesis. A real-time quantitative RT-PCR approach for the markers cytokeratin 19 (CK19), survivin (Sur), mammaglobin 1 (MG1) and prostate-specific ets factor (PSE), HER-2, CD276 and FGFR2 was established using primers and FAM-labeled TaqMan probes selected with the Universal-Probe-Library system (Roche AG, Basel, CH). Results: Positivity rate of ETC controlled realtime RT-PCR on the basis of CK19 and MG1 in blood was 6.9% in 205 patients with primary breast cancer and 61.1% in patients with metastatic disease while 15/104 (14.4%) bone marrow samples were postive. Clonal selection or conversion from a HER2 negative (histology) to a HER2 positive phenotype was determined by qRT-PCR in 17 from 61 (27.8%) patients. During an 18-month follow-up of 92 patients with primary breast cancer, multimarker positivity was determined in 10 patients, and in three of these patients early metastasis was clinically confirmed. Conclusions: For the first time we describe embedded tumor cells (ETC) as internal calibrators for accurate process control and normalization of the complex immunobead quantitative RT-PCR technique. Tumor cell quantification was performed with the tumor identifier CK19 while corresponding expression levels of HER2 and the tumor-related/induced angiogenesis factor CD276 were determined on the basis of spiked calibrator cells. ETC should improve monitoring and gene expression analysis of disseminated tumor cells in bone marrow and circulating tumor cells during therapy. No significant financial relationships to disclose.
Thymidylate synthase polymorphism in the development of Barrett's associated adenocarcinoma
Authors: H. Kuramochi, J. H. Peters, K. Uchida, S. Schneider, D. Vallboehmer, D. Shimizu, P. T. Chandrasoma, K. D. Danenberg, T. R. Demeester, P. Danenberg
Journal: Journal of Clinical Oncology (2004)

9528 Background: Thymidylate synthase (TS), one of the rate-limiting enzymes in the de novo synthesis of DNA, has a unique 28bp tandemly repeated sequence in the promoter region. Patients who are homozygous for the double repeat (2R/2R) of this sequence have been reported to have lower TS expression and better outcome from chemotherapy than patients who are homozygous for the triple repeat (3R/3R). However, loss of heterozygosity (LOH) at the TS locus during tumor development can cause the heterozygous (2R/3R) patients to acquire either the 2R/loss or the loss/3R genotype in their cancer cells, which could affect tumor TS expression as well as clinical outcome. The aim of this study was 1) to verify the relationship between TS mRNA expression and TS genotype in Barrett's associated adenocarcinoma (BA), and 2) to analyze the frequency and timing of LOH at the TS locus in BA and its precursory lesion such as intestinal metaplasia (IM) and high grade dysplasia (HGD). Methods: Sixty-six patients (including 21 with IM, 6 with HGD and 23 with BA) were included in this study. Biopsies were obtained during endoscopy from: (1) normal squamous epithelium at 20cm (HNE); (2) normal squamous epithelium 3cm above the gastroesophageal junction (LNE); (3) IM, HGD or BA. All samples were analyzed for the TS genotype and TS mRNA expression using a quantitative real-time RT-PCR method after laser-capture microdissection. Results: TS mRNA expression from HNE tissue of 3R/3R genotype patients (n=8) was significantly higher than that of 2R/2R genotype patients (1.8-fold; n=14; p=0.0024) and that of 2R/3R genotype patients (1.4-fold; n=44; p=0.0282). Out of 44 patients with heterozygous (2R/3R) genotype in the HNE, no patient lost an allele in the LNE. However, 10 of 18 patients with IM had LOH (55.6%), as had 4/6 patients with HGD (66.7%) and 9/17 patients with BA (52.9%). Conclusions: Our results demonstrate 1) an association between TS genotype and TS expression in normal squamous epithelium and 2) that LOH at the TS locus is a frequent and early event in the IM-BA sequence, and thus tumor and normal genotypes will not be the same in these heterozygous patients. No significant financial relationships to disclose.
K-ras mutational status and its clinical implications in Korean colorectal cancer patients.
Authors: Ho Jung An, Bong-Hyeon Gye, Hyung Jin Kim, Ji Han Jung, Jong Hoon Lee, Sung Whan Kim, Hyun Min Cho, Byoungyong Shim
Journal: Journal of Clinical Oncology (2015)

641 Background: The incidence of K-ras mutation of exon 2 was reported between 30-40% in colorectal cancer, and it is well known predictive biomarker for EGFR monoclonal antibody. However, its prognostic role has not been defined so far, especially in Eastern country. Methods: From January 2007 to September 2013, patients who were diagnosed as colorectal cancer and examed K-ras exon 2 mutation in Saint Vincent’s hospital were retrospectively reviewed. Results: Among 436 patients, 343 patients with sufficient clinical information were analyzed. The median follow up period was 13.0 (0.2-94.8) months. The incidence of K-ras mutation was 37.9% (codon 12 mutation: 28.6%, codon 13 mutaiton: 9.0%, both: 0.3%). Codon 12 p.G12D was most frequent (52.3%), and codon 13 p.G13D was the next (22.3%). The presence of K-ras mutation was associated with old age (p=0.038), female gender (p=0.034), lesser nodal involvement (p&lt;0.001), but not related to stage, tumor site, and histology. There is no significant clinical differences between codon 12 and 13 mutations. The recurrence free survival in patients who received curative resection was worse in patients with K-ras mutation (p=0.001). The prognostic role of K-ras mutation was more prominent in colon cancer, while it lost its prognostic significance in rectal cancer. Conclusions: The prognostic role of K-ras mutation was different according to primary tumor sites in colorectal cancer.
Treatment of hepatocellular carcinoma (HCC) with the tyrosine kinase inhibitor Imatinib
Authors: T. Armbrust, D. Baumhoer, J. Werner, E. Schleyer, G. Ramadori
Journal: Journal of Clinical Oncology (2005)

4210 Background: After having successfully treated a patient with HCC with imatinib (Anticancer Drugs, 2004;15:405) we treated twelve consecutive patients with histologically proven or clinically suspected HCC and Child A-cirrhosis. Methods: Patients were treated with imatinib at dosages from 200mg/d to 400mg/d. Routine chemical values and alpha-fetoprotein (AFP) levels were determined on a regular schedule and imatinib serum concentrations were analyzed by HPLC during the first weeks of treatment. Tumor size was monitored by abdominal ultrasound, or computer tomography. Results: One patient stopped imatinib after ten days due to diarrhea. The patient developed ascites and gastrointestinal bleeding from esophageal varices. Treatment was well tolerated by the remaining 11 patients within the first 6–8 weeks. Laboratory findings remained unchanged and imatinib serum concentrations were within the expected range indicating efficient excretion. However, imatinib metabolites were below the expected range. Eight of the 11 patients developed side effects (nausea, diarrhea, skin rush, fuzzy vision, spasms, edema) during the next 6 months. Treatment was discontinued, side effects disappeared and treatment was restarted at a reduced dosage of 200mg/d that was well tolerated. After 18 months of follow up, one patient has a complete response, two patients have stable disease, and 7 patients developed progressive disease. One patient dropped out of follow up at his own request. To date, 4 patients are alive (33%). Conclusions: Imatinib at a dosage of 200mg/d seems to be safe in patients with liver cirrhosis stage Child-Pugh A. The results suggest that a subgroup of patients with HCC may benefit from imatinib treatment. Efficacy of imatinib treatment in patients with HCC should be tested in a randomized trial. No significant financial relationships to disclose.
A <i>de novo</i> deletional germline mutation in the MLH1 gene resulting in early onset colorectal cancer in a woman with a negative family history: A case report
Authors: D. Zakalik, N. S. Goldstein, W. L. Ducaine
Journal: Journal of Clinical Oncology (2007)

21067 Background: Hereditary non-polyposis colorectal cancer (HNPCC) is a genetic disorder that results in an increased risk of early onset colorectal cancer (CRC). HNPCC is caused by germline mutations in DNA mismatch repair (MMR) genes, including MLH1 and MSH2, and is transmitted in an autosomal dominant manner. De novo germline mutations in MMR genes are exceedingly rare. We now describe a case of a de novo germline mutation in MLH1 associated with early onset CRC in a young woman with a negative family history. Methods: We present a case of a 31-year-old Caucasian female who presented with abdominal pain. Colonoscopy revealed a moderately differentiated adenocarcinoma with focal mucin production involving the sigmoid colon, with a final staging of T 4 N 0 M 0 . Genetic testing was offered because of her young age at diagnosis, having fulfilled the Bethesda guidelines. Microsatellite instability (MSI) testing using a panel of six microsatellite loci was performed on the tumor sample from the affected patient. Immunohistochemistry (IHC) testing for MLH1 and MSH2 was performed. Following counseling and with informed consent, DNA was isolated and sequenced using bi-directional PCR of the MLH1 gene. All exons of MLH1 and MSH2 were analyzed by standard Southern blot methods. Paternity was established using eight genetic loci. Results: The patient's tumor revealed high MSI and complete absence of MLH1 immunoreactivity. MSH2 IHC staining was normal. A large deletional mutation involving exons 5–12 of MLH1 was identified by Southern blot analysis. The patient's parents and siblings were tested and found to have wild type MLH1. Paternity was confirmed with greater than 99.9% certainty. Conclusions: De novo mutations in MMR genes are a rare cause of HNPCC. We report the first case of a large de novo deletion in the MLH1 gene accounting for early onset CRC. Such de novo mutations, albeit rare, must be considered in patients who present with early onset CRC and a negative family history. These results support the use of the Bethesda guidelines to identify individuals who may carry mutations in the MMR genes. No significant financial relationships to disclose.
Radiotherapy for non-small-cell lung cancer: Relationship between loco-regional failure and irradiated volume
Authors: N. Fujimoto, M. Sumi, Y. Ito, A. Imai, Y. Kagami, I. Sekine, T. Tamura, H. Ikeda
Journal: Journal of Clinical Oncology (2005)

7263 Background: The role of elective nodal irradiation for NSCLC patients (pts) treated with thoracic radiotherapy remains unclear. We retrospectively analyzed the relationship between loco-regional failure (LRF) and irradiated volume to reconsider the significance of treating clinically uninvolved lymph nodes (LN). Methods: From 1998 to 2003, pts with IA-IIIB NSCLC were treated with thoracic radiotherapy with or without chemotherapy. Inclusion criteria were pts who were irradiated ≥ 60Gy as a part of initial treatment and those with clinical response better than stable disease. As a typical radiotherapy, 40Gy/20fr was administered to tumor volume (clinical target volume of primary tumor and metastatic LN: CTVp and CTVn, respectively) and bilateral mediastinum and ipsilateral hilum (clinical target volume encompassing subclinical nodal region: CTVs) followed by a reduced off-cord boost to CTVp+n to a total dose 60–68Gy/30–34fr. In pts with LRF, the relationship between the site of recurrence and the irradiated volume was analyzed. Results: 127 pts were identified with a median age of 65 (36–83). A majority pts had stage IIIA (n=59) or IIIB (n=51) disease. 87 (68.5%) pts received platinum-based chemotherapy. Median overall and progression-free survivals were 16.3 (4.2–73.9) and 8.4 (1.1–73.9) months, respectively. At the median follow-up of 13.6 (2.3–73.9) months, first treatment failure was observed in 80 pts (loco-regional: 35, distant: 37, both: 8). Overall, there were 50 pts with LRF (Table). No isolated failure from CTVs was observed. Conclusion: In-field LRF as well as distant metastases was the major site of failure. Significance of prophylactic LN irradiation should be reconsidered to balance local control against toxicity. No significant financial relationships to disclose.
Phase 1 dose escalation study of AQ4N, a selective hypoxic cell cytotoxin, with fractionated radiotherapy (RT): First report
Authors: A. Benghiat, W. P. Steward, P. M. Loadman, M. Middleton, D. Talbot, L. H. Patterson, S. Ford, A. Turner
Journal: Journal of Clinical Oncology (2004)

2091 Background: Most solid tumours contain hypoxic cells which are relatively radioresistant. AQ4N is designed to be non toxic until selectively activated by bioreduction in hypoxic cells to AQ4, a highly potent, stable Topoisomerase II inhibitor. Animal in vivo models have shown enhancement of the effects of radiation by AQ4N, enabling a 50% reduction in the radiation dose for the same antitumour effect. Here we report the first Phase 1 study to determine the pharmacokinetics (PK) and toxicity of AQ4N in humans. Methods:13 patients with advanced esophageal carcinoma (7 adenocarcinoma and 6 Squamous carcinoma) suitable for palliative RT were recruited (ages 55–88 years, M 8, F 5). AQ4N was administered as a 30 min IV infusion on Days 1 and 14, with the first RT fraction given six hours after the second dose of AQ4N. The total RT dose was 20Gy in 5 daily fractions. Sequential plasma samples were taken on day 1. The dose was escalated from 22.5 to 246 mg /m2. Results: There were no drug related deaths. 1 patient died after the first AQ4N dose of a non drug related cause and is not evaluable. The most frequent adverse event was transient blue discolouration of the skin and urine. There were 8 other episodes, in 4 patients, of grade 3 or 4 toxicity possibly related to AQ4N; lymphocytopenia (n=2), fatigue (n=3), hyponatremia (n=3), hyperuricemia (n=1). None of these was clinically significant. PK studies showed a predictable dose related increase in AUC with mean clearance of 2.91 l h m-2 (range 1.84–5.2) and a t 1/2 of 2.9h (range 2.4–5.1). Cmax at 246 mg/m2 was 40.3ug ml-1. A mean 48% of dose was excreted unchanged in the urine within 24 hrs, with metabolites representing <2% of parent compound. Conclusion: AQ4N is generally well tolerated with favourable PK, meriting further investigation. The MTD and DLT have not yet been reached with the RT doses used in this study. No additional normal tissue radiation related toxicity has been observed. (study supported by BTG International, UK) Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Kudos Pharmaceuticals Kudos
Self-renewing resident arterial macrophages arise from embryonic CX3CR1+ precursors and circulating monocytes immediately after birth
Authors: Sherine Ensan, Angela Li, Rickvinder Besla, Norbert Degousee, Jake Cosme, Mark Roufaiel, Eric A Shikatani, Mahmoud El-Maklizi, Jesse W Williams, Lauren Robins, Cedric Li, Bonnie Lewis, Tae Jin Yun, Jun Seong Lee, Peter Wieghofer, Ramzi Khattar, Kaveh Farrokhi, John Byrne, Maral Ouzounian, Caleb C J Zavitz, Gary A Levy, Carla M T Bauer, Peter Libby, Mansoor Husain, Filip K Swirski, Cheolho Cheong, Marco Prinz, Ingo Hilgendorf, Gwendalyn J Randolph, Slava Epelman, Anthony O Gramolini, Myron I Cybulsky, Barry B Rubin, Clinton S Robbins
Journal: Nature Immunology (2015)
Baseline and ontreatment predictors of svr to peginterferon alfa-2a therapy and ribavirin in hcv genotype (GT) 1 treatment naive patients: New insights from the chariot study
Authors: M Weltman, GJ Dore, W Sievert, GW McCaughan, DH Crawford, W Cheng, W Rawlinson, M Yashihara, PI McCloud, B Rizkalla, SK Roberts
Journal: Hepatology (2009)
The additive effects of gamma secretase inhibitor and ionizing radiation in MDA-MD-231 breast cancer cell line
Authors: A. Chi, J. Yun, C. Osipo, P. Rizzo, D. Wyatt, A. Sabou, K. Albuquerque, L. Miele
Journal: Journal of Clinical Oncology (2008)

14594 Background: The Notch signaling pathway is an evolutionarily conserved developmental pathway whose importance has become increasingly recognized in cancer biology. Gamma secretase inhibitors(GSI) are a novel class of agents which prevent the generation of the active domain of Notch molecules, and suppress Notch signaling downstream. GSI has been shown to have synergistic activity against breast cancer in vitro when combined with HER-2 antibodies. This study investigates whether GSI may enhance the effect of radiation on breast cancer cells. Method: The MDA-MD-231 breast cancer cell line has been shown previously to have high Notch activity. The effects of radiation, GSI, and GSI combined with radiation were studied by DNA content analysis and MTT assay after 7 days of 7.5 μM GSI treatment, cells were irradiated after day 1 of GSI treatment with 5 Gy; Cell cycle studies after 5 μM GSI treatment for 48 hrs and 9 Gy 24 hrs after GSI added; Clonogenicity, after exposure to 0, 2, 4, 6, & 8 Gy with or without 7.5 μM GSI for 6 weeks beginning 24 hrs prior to irradiation, was evaluated by soft agar growth assay. Expression of cyclins A, B (Notch targets), and NOXA (inhibited by Notch) were investigated via western blotting. After treated with GSI 7.5 μM for 48 hrs and 5 Gy 24 hrs after GSI added, cells were harvested and lysed. Results: MTT assay and DNA content analysis demonstrated significant additive effects when GSI was combined with radiation. Cell cycle analysis demonstrated increased apoptosis with a decrease in S-phase fraction with combined treatment vs. GSI or radiation alone; enhanced G1 arrest, and a trend toward enhanced G2/M arrest with combined treatment comparing to radiation alone. Soft-agar assay demonstrated decreased clonogenicity with combined 7.5 μM GSI and single-dose radiation exposure compared to radiation alone. By western blotting, GSI alone or combined with radiation was able to attenuate cyclin A expression but no additional increase in NOXA was found under these conditions. Conclusions: This study identified a potential additive effect between GSI and ionizing radiation in breast cancer in vitro. This is at least partially attributed to the inhibitory effect of GSI on cell proliferation pathways. These findings will guide further in vitro and in vivo studies. No significant financial relationships to disclose.
Preliminary results of second-line chemotherapy with vinorelbine and gemcitabine after docetaxel and carboplatin failure in advanced non small cell lung cancer (NSCLC)
Authors: J. Abou Yared, G. Chahine, J. Kattan, F. Farhat, W. Moukadem, F. Nasr, F. Younes, M. Ghosn
Journal: Journal of Clinical Oncology (2006)

17130 Background: To evaluate the efficacy and safety of a doublet platinum-free therapy based on Vinorelbine and Gemcitabine in the salvage treatment of patients with advanced NSCLC, previously treated with Carboplatin and Docetaxel. Methods: We conducted a phase II study with the combination of vinorelbine 30 mg/m 2 and gemcitabine 1000 mg/m 2 d1 d8 / 3w. Eligible were patients with histologically proven advanced or metastatic NSCLC who were refractory or progressed after first-line chemotherapy combining Docetaxel and Carboplatin. Results of this first-line therapy were already reported (Proc. Am. Soc. Clin. Oncol. 2005, abstr 7330). Patients must have measurable disease, PS ≤ 2, life-expectancy ≥ 3 months, adequate hematologic, liver and renal functions. Response to therapy was evaluated according to RECIST guidelines. Toxicities were assessed according to the national cancer institute (NCI) common toxicity criteria 3.0. Results: From August 2004 to September 2005, 28 patients were enrolled. Median age was 63 years (range, 44 to 77) with 18 males and 10 females. A total of 109 cycles were delivered with a median of 4 cycles per patient (range, 1 to 9). Mean metastatic sites were lymph nodes in 9 pts, liver in 6 pts and pleura in 5 pts. 26 patients were evaluable for response (1 patient too early and 1 pt lost of follow-up). 6 patients responded partially (23%), one of them was initially resistant to the first-line therapy. 11 patients had stable disease (42%). Mean objective response duration was 7 months (range, 5 to 10+). Main toxicities (grade 3/4) were: anemia in 4 patients, neutropenia in 7 patients, leucopenia in 8 patients and lymphopenia in 4 patients. Neutropenic fever was encountered in only one patient. Non-hematological toxicities grade 3/4 were universally absent. No dose reduction or treatment delay related to toxicity was necessary. Conclusion: The study is still ongoing and more patients are expected to define time to progression and survival. However, these preliminary results were encouraging with low toxicity profile. No significant financial relationships to disclose.
Thoracic radiation therapy in locally advanced NSCLC patients (pts) with EGFR mutations.
Authors: R. H. Mak, E. Doran, A. Muzikansky, J. Kang, N. C. Choi, H. Willers, D. M. Jackman, L. V. Sequist
Journal: Journal of Clinical Oncology (2010)

7016 Background: NSCLC pts with EGFR mutations have improved outcomes with EGFR-targeted therapy and with chemotherapy, compared to wild-type (wt) pts. There is in vitro and clinical evidence to suggest that EGFR mutations may also confer radiation sensitivity. We examined pts with locally advanced NSCLC and known EGFR mutation status to assess for differences in locoregional recurrence rates (LRR) after thoracic radiation therapy (TRT). Methods: We retrospectively reviewed 1445 pts who underwent EGFR testing at our centers from 2004-09 and identified 109 with locally advanced NSCLC who were treated with TRT. We compared LRR, distant metastases (DM), relapse-free survival (RFS) and overall survival (OS) between EGFR mutant and wt pts. Results: Among 109 pts, 27 (25%) were EGFR mutant and 82 (75%) were wt. Demographics included mean age 61.7 years, 69% female, 92% white, and 84% never/former smokers. Most had stage III disease (IIIA 64%, IIIB 28%), and EGFR mutants had relatively more IIIA than wt (82% vs. 59%; p=0.08). TRT was given as definitive (45%), adjuvant (25%), and neoadjuvant (30%) therapy; more wt than mutant pts received definitive RT (48% vs. 19%). Intensity-modulated RT was given in 48%, and the median TRT dose was 59.4 Gy (range, 28.8 - 74 Gy), with no difference by mutation status. Most patients received concurrent (81%) and/or adjuvant chemotherapy (58%). The median follow-up was 25.4 months. There was a significantly lower rate of LRR at 2 years in the EGFR mutant versus wt pts (19% vs. 46%; p=0.005), which remained significant after adjusting for stage, TRT dose, and TRT timing (HR 0.35, 95% CI 0.15-0.84; p=0.018). Mutant versus wt status was not associated with 2-year RFS (40% vs. 34%; p=0.16) and DM (62% vs. 63%; p=0.15), and the observed difference in 2-year OS (90% vs. 68%; p=0.12) did not reach significance. Conclusions: In NSCLC, mutant EGFR was associated with a decreased risk of LRR compared to EGFR wt tumors, suggesting that EGFR mutations may confer radiation sensitivity. EGFR mutation status was not associated with RFS and DM, and observed differences in OS did not reach significance. No significant financial relationships to disclose.