bluuebunny/crossref_metadata_2025 huggingface dataset:
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.
Molecular characterization of circulating tumor cells in human metastatic colorectal cancer.
Authors: Barbazan Jorge , Alonso-Alconada Lorena , Muinelo-Romay Laura , Vieito Maria , Abalo Alicia , Alonso-Nocelo Marta , Candamio Sonia , Vazquez Francisca , Vidal Yolanda , Fernandez Beatriz , Abdulkader Ihab , Casares Maria de los Angeles , Gomez-Tato Antonio , Abal Miguel , Lopez Rafael
Published: March 2020

10534

Background: Metastatic colorectal cancer (mCRC) relies on the detachment of aggressive malignant cells from the primary tumor into the bloodstream, being this Circulating Tumor Cells (CTC) the principal source of the further metastasis. Clinically, the presence of CTC is associated with poor prognosis and there exists a clear necessity for more specific and efficient chemotherapies in the treatment of mCRC. Our aim was to overcome this adverse scenario through the massive molecular profiling of the CTC population isolated from mCRC patients. Methods: CTC’s were magnetically isolated by using anti-EpCAM coupled magnetic beads from 6 mCRC patients and 3 healthy controls. The presence of CTCs was evaluated by citokeratins 8, 18 and 19 staining. RNA from CTCs was amplified by a whole transcriptome amplification system (WTA) and resulting material was hybridized onto gene expression arrays. Bioinformatics were used to array analysis. Selected genes were validated by RT-qPCR. Results: 410 transcripts were found to specifically characterise the CTC population after array signals comparison between mCRC patients and controls. Gene-gene interaction analysis generated networks related with cell migration, adhesion or apoptosis resistance. Gene ontology revealed similar functions. Signalling pathways such as RhoA, PKA, ILK, integrins or actin cytoskeleton signalling were found as relevant in CTCs. Eleven genes (TGFB1, APP, TIMP1, CD9, CLU, ITGB5, LIMS1, RSU1, VCL, BMP6 and TLN1) were validated by real-time PCR in 20 mCRC patient and 10 control samples. All genes showed a significantly higher expression in patients (p<0.0001). Except from TLN1 and CD9, all genes had a prognostic value in terms of progression free survival (p<0.05). Conclusions: We described the molecular profiling of CTCs in stage IV CRC patients, characterized by a migratory and invasive phenotype. Specific and sensitive diagnostic/prognostic markers were obtained. Our strategy represents an innovative and promising approach in the clinical management of mCRC patients.
A new medical device for in vivo capturing of circulating tumor cells in breast cancer (BC) patients.
Authors: Murawa Dawid , Herold Stefanie , Kim Phillip Sangwook , Schmitz Arndt , Krahn Thomas , Murawa Pawel , Zabel Maciej , Morgenthaler Nils G. , Nowaczyk Piotr , Luecke Klaus
Published: March 2020

10537

Background: In BC, the number of circulating tumor cells (CTCs) is discussed as a prognostic and stratification biomarker, and could also reflect treatment efficacy. Currently, CTCs are isolated ex vivo from a small volume of blood. Results from a larger volume of blood are scarce. The aim of the study was to assess a functionalized and structured medical wire (FSMW) for in vivo capturing of CTCs directly from the blood stream of BC patients. Methods: The device was inserted in a cubital vein through a standard cannula for thirty minutes. The interaction of target CTCs with the FSMW was mediated by antibodies directed against the epithelial cell adhesion molecule (EpCAM). To confirm binding of CTCs to the wire, the immunohistochemical positive staining against EpCAM as well as negative staining for CD45 was performed. There were 54 applications of the wire in 42 stage I-IV BC patients (12 double applications). Enumeration data from 37 BC patients with 49 applications (5 failed subsequent analyses) were assessed. CTC counts on 23 devices were directly compared to counts by CellSearch. Results: The device was well tolerated in all 54 applications without side effects. We obtained in vivo isolation of CTCs in 44 of 49 applications to BC patients (89.7 %). The sensitivity was similar for early and late stage BC patients. The median (range) of isolated EpCAM-positive CTCs was 5 (0-515). The CellSearch method reached a sensitivity of 18.5%. In all paired samples the number of CTCs detected with the FSMW was higher or equal to CellSearch, regardless of the disease stage. Linear regression of the data of the double application of the FSMW showed a very good concordance (r2 = 0.97, p<0.0001). Conclusions: Whilst well tolerated without side effects, the CTC detection rate of the FSMW in BC patients was nearly 90 %. CTC detection was obtained in 18.5% by the CellSearch. Double application of FSMWs in the same patient indicates ample precision. This proof of concept study may have important clinical implications, as the device may improve early detection, prognosis and therapy monitoring of BC patients. The molecular analysis of the captured CTCs could become a breakthrough in personalized medicine.
Different EGFR/KRAS mutation spectrums in lung cancer between never smokers and heavy smokers.
Authors: Takamochi Kazuya , Oh Shiaki , Suzuki Kenji
Published: March 2020

10548

Background: EGFR mutations are more commonly found in lung adenocarcinomas in never smokers, while KRAS mutations are more frequently present in those in heavy smokers. Although the incidence is low, EGFR mutations are also found in tumors in heavy smokers and KRAS mutations also occur in tumors in never smokers. Therefore, there may be different biological characteristics in EGFR/ KRAS mutated lung cancers according to the smoking status. Methods: This was a retrospective review of 382 patients with surgically resected lung cancers between February 2009 and March 2011. The clinicopathological factors (age, gender, histology, serum CEA level, pathological nodal status, lymphatic permeation, and blood vessel invasion) and EGFR/KRAS mutation spectrums were compared between never smokers (pack-year = 0, n = 161) and heavy smokers (pack-year > 20, n = 167). Results: EGFR mutations were detected in 88 (55%) never smokers and in 33 (20%) heavy smokers. In contrast, K-ras mutations were detected in 7 (4%) never smokers and in 31 (19%) heavy smokers. Both EGFR and KRAS mutations were more frequently observed in female never smokers and in male heavy smokers. The spectrum of both EGFR and KRAS mutation differed according to the smoking status. Minor EGFR mutations other than exon 21 L858R and exon 19 deletions that are activating mutations indicating the efficacy of EGFR tyrosine kinase inhibitors (TKIs) were more frequently found in heavy smokers than in never smokers. G→A transitions were more common KRAS mutations in never smokers and G→T transversions that are thought to be related to exposure to the polycyclic aromatic hydrocarbons found in cigarette smoke were more common KRAS mutations in heavy smokers. Conclusions: The EGFR/KRAS mutation spectrums in lung cancer were quite different in never smokers and heavy smokers. Further study is needed to evaluate the relationship between the efficacy of such molecular targeting agents as EGFR TKIs and the EGFR/KRAS mutation spectrums.
Prediction of late metastasis in node-negative breast cancer.
Authors: Schmidt Marcus , Hellwig Birte , Gehrmann Mathias , Koelbl Heinz , Boehm Daniel , Cadenas Christina , Rahnenfuehrer Joerg , Hengstler Jan G
Published: March 2020

10551

Background: Prediction of late metastasis is of clinical relevance in breast cancer. However, systematic genome-wide studies to identify genes associated with increased risk of metastasis 5 or more years after surgery are scarce. Methods: We examined the natural course of disease in three previously published cohorts (Mainz, Rotterdam, Transbig) including 766 node-negative breast cancer patients with gene array data who did not receive systemic chemotherapy in the adjuvant setting. We established a Cox regression based method adjusted for multiple testing that identified genes predicting late metastasis (5 or more years after surgery). Only those genes were accepted that showed similar results in all three cohorts. Metastasis-free survival (MFS) was analyzed with univariate and multivariate Cox regression. Results: We identified 9 genes [ABCC5 (Hazard Ratio (HR) 2.19, p=0.003), EDDM3B (HR 3.58, p=0.044), RAD23B (HR 0.37, p<0.001), XYLT2 (HR 2.19, p=0.027), DDX18 (HR 0.35, p=0.006), GPBP1L1 (HR 0.20, p=0.018), UBB (HR 9.73, p=0.025), RPS24 (HR 0.20, p=0.050), GPC1 (HR 2.36, p=0.013)] predicting late metastasis. These genes retained their independent prognostic significance after adjustment for established clinical factors (age, tumor size, grade, hormone receptor status, HER2) and biological motives like estrogen receptor, proliferation, B or T cells. These late-type genes are largely associated with resistance to hypoxia, apoptosis and DNA damage, suggesting that they might contribute to persistence of disseminated tumor cells. Conclusions: Genes associated with late metastasis offer a perspective to identify breast cancer patients suitable for additional and prolonged therapies.
Central review of discordant samples for microarray based on ER, PR, and HER2 and local IHC/FISH assessment worldwide from 827 patients.
Authors: Wesseling Jelle , Tinterri Corrado , Sapino Anna , Zanconati Fabrizio , Lutke Holzik Martijn , Nguyen Bichlien , Deck Kenneth B. , Querzoli Patrizia , Perin Tiziana , Giardina C , Seitz Gerhard , Guinebretiere Jean-Marc , Barone Julie , Watanabe Toru , De Snoo Femke , Stork-Sloots Lisette , Cusumano Pino
Published: March 2020

10554

Background: Differences in fixation and IHC and subjective interpretation can substantially affect the accuracy and reproducibility of estrogen receptor (ER), progesterone receptor (PR) and HER2 expression. The commercially available TargetPrint test measures the mRNA expression level of ER, PR and HER2 and is 98% concordant with centrally assessed ER as presented by Viale et al, SABCS 2011. This study compares results from the microarray-based TargetPrint with IHC and FISH (for HER2 IHC2+) generated by local standard procedures. Methods: Fresh tumor samples (core needle biopsies or surgical) were collected for 831 patients diagnosed with breast cancer stage I to IV (Feb 2008 - Jan 2011) from 22 hospitals from Europe, New Zealand, Japan and US. The results of the IHC/FISH assessments performed according to the local standards at the hospitals were compared to the quantitative gene expression readouts with TargetPrint. Discordant cases were centrally reviewed for IHC/FISH assessment. Results: Of the 831 samples, IHC assessment was unknown for 4 ER/ PR samples; HER2 was unknown for 12 samples. Comparison of IHC and gene expression read out by TargetPrint showed a concordance of 95% for ER; 83% for PR and 94% for HER2. In this study, 3% of all IHC ER positive samples were classified negative by microarray, and 11% of IHC PR positive samples were classified negative by microarray. For HER2, 4% of IHC/FISH HER2 positive samples were classified negative by microarray and 2% of IHC/FISH HER2 negative samples were classified positive by microarray. Most notably, all available 5 ER IHC negative/TargetPrint positive samples turned out to be positive with central re-assessment. HER2 IHC2+ samples with discordant classifications for TargetPrint and local assessment are currently being reviewed for FISH/SISH assessment. Conclusions: Microarray based readout of ER, PR and HER2 status using TargetPrint is fairly comparable to local IHC and FISH analysis in 827 analyzed samples in various hospitals worldwide. However, re-assessment of discordant cases –especially IHC ER-/TargetPrint ER+ cases- confirms TargetPrint to be a useful high quality second opinion for local IHC/FISH assessment.
Lymphopenia combined with low TCR diversity to predict overall survival in metastatic breast cancer patients.
Authors: Manuel Manuarii , Tredan Olivier , Bachelot Thomas , Clapisson Gilles , Courtier Anais , Parmentier Gilles , Grives Audrey , Perez Solene , Mouret Jean-Francois , Perol David , Chabaud Sylvie , Ray-Coquard Isabelle , Labidi-Galy Sana Intidhar , Heudel Pierre , Pierga Jean-Yves , Caux Christophe , Blay Jean-Yves , Pasqual Nicolas , Menetrier-Caux Christine
Published: March 2020

10562

Background: Lymphopenia (<1 Giga/L) before initiation of chemotherapy is a predictive factor for toxicity and death in metastatic phase for cancer patients. Combinatorial diversity of T Cell Receptor beta chain (TCR-ß), as a measure of T cell repertoire diversity, was investigated and tested either alone or in combination with lymphopenia as a prognostic factor for overall survival (OS) in first line treatment of metastatic breast cancer (MBC) patients. Methods: Using semi quantitative multiplex PCR, the V-D-J combinatorial diversity of the TCR was measured on cryo-preserved blood samples from 2 cohorts of MBC patients before the initiation of the first line chemotherapy: in an experimental cohort (cohort A, n=66) and in a validation series (cohort B, n=67). A prognostic score, defined NDL (Number & Diversity of Lymphocytes) combining lymphocyte count and TCR diversity was delineated. Univariate and multivariate analysis of prognostic factors for OS were performed in both cohorts. Results: Lymphopenia (<1 Giga/L) was associated with shorter OS for cohort B while TCR diversity ≤33% (called divpenia) was associated with a reduced OS in cohort A. The combination of lymphopenia with low TCR diversity (called lympho-divpenia) was associated with poor OS compared to patients with either lymphocyte count ≥1 Giga/L or diversity >33% or both, in cohort A (median OS: 7.6 vs 24.5 months, p.value =0.0006) and cohort B (median OS 10.6 vs 22.9 months, p.value =0.0035). In a multivariate analysis, including all significant clinical factors from the univariate analysis (PS, liver metastasis, hemoglobin) lympho-divpenia was found to be an independent prognostic factor in the pooled cohort (A+B) (p=0.005) along with triple negative tumors (p=0.011) and hemoglobin level (11.5 g/dL) (p=0.009). Conclusions: NDL score combining lymphopenia and reduced TCR diversity seems to be a strong prognostic factor for OS and could be use to improve care quality of MBC patients.
Detection of EML4-ALK in serum RNA from lung cancer patients using MassARRAY platform.
Authors: Kudo Keita , Nishio Makoto , Sakai Kazuko , Tanimoto Azusa , Sakatani Toshio , Saito Ryota , Kaburaki Kyohei , Yanagitani Noriko , Horiike Atsushi , Ohyanagi Fumiyoshi , Nishio Kazuto
Published: March 2020

10569

Background: The presence of the transforming fusion gene EML4-ALK in non–small cell lung cancer (NSCLC) is a predictive marker for the efficacy of ALK kinase inhibitors. The break apart fluorescence in situ hybridization (FISH) assay has served as the standard test for identification of NSCLC patients with ALK gene rearrangement. Circulating RNA in plasma/serum is an emerging field for noninvasive molecular diagnosis. We previously developed a MassARRAY assay to detect nine types of EML4-ALK fusion gene (variants 1, 2, 3a, 3b, 4, 5a, 5b, 6, and 7). The assay is based upon region-specific PCR followed by specific single-base primer extension reactions; the extended products are resolved using MALDI-TOF mass spectrometry. In this study, we evaluated whether EML4-ALK fusion RNA could be detected in serum obtained from NSCLC patients. Methods: The RNA was extracted from serum obtained from 12 lung cancer patients with ALK rearrangements by FISH analysis. The extracted RNA was reverse transcribed into cDNA, and the resultant cDNA was amplified by nested PCR. The PCR product was subjected to MassARRAY assay to identify EML4-ALK variants. Results: The EML4-ALK RNA (variant 1 and 3) was detected in serum from 2 of 12 patients. These are confirmed by subcloning and sequencing. Conclusions: The detection of EML4-ALK in serum RNA samples by MassARRAY assay is feasible. This noninvasive assay will be useful in patients with insufficient or unavailable tumor specimens. Additional experiments will reveal the sensitivity and specificity of this detection system.
The effect on detection rate of second cancers after the addition of MRI to conventional screening mammography in patients with a history of breast cancer.
Authors: Weinstock Chana , Campassi Cristina , Goloubeva Olga G. , Chumsri Saranya , Bao Ting , Kesmodel Susan , Feigenberg Steven J. , Wooten Kathleen , Ioffe Olga B. , Tkaczuk Katherine Hanna
Published: March 2020

10572

Background: Mammography is currently used in the surveillance of breast cancer survivors, who are at increased risk of developing ipsilateral and contralateral breast cancers regardless of age at diagnosis or time since diagnosis. Several prospective studies have shown the utility of breast MRI in other high risk populations; however, little data exists on the use of MRI for surveillance of breast cancer survivors. We aimed to compare the outcome of surveillance breast MRI vs. mammography in this population. Methods: We identified women <65 with non-metastatic breast cancer or DCIS with at least one MRI performed at our center >11 months after initial diagnosis, along with a mammogram done within 6 months of the MRI. We compared the outcome of MRI and mammography in terms of biopsies performed as well as in detection of new cancers. Results: Of 512 consecutive charts reviewed, 204 patients met inclusion criteria, 105 (51.4%) of whom were African-American. The average number of MRIs per patient was 2.3 (range 2-7), with a total of 474 MRIs performed between 2005 and 2011. MRI resulted in BIRADS scores of 1 or 2 in 73.5% of studies vs. 84.4% for mammography. There were 19 biopsies performed due to MRI findings alone, 7 done due to mammographic findings alone, and 6 biopsies done based on abnormalities seen on both MRI and mammography. There were 7 malignancies identified based on an abnormal MRI, 3 seen on both MRI and mammography, and none identified via mammography alone. The malignancies identified via MRI alone included 1 patient with DCIS, 5 with stage I disease, and 1 with isolated lung metastases. Of the 10 recurrences detected, 5 (50%) were in African Americans. Two patients developed interval cancers within 6 months of normal screening MRI and mammography. Sensitivity and specificity for MRI were 83.3% (95% CI 0.51-0.97) and 92.2% (95% CI 0.87-0.95), vs. 25% (95% CI 0.05-0.57) and 94.8% (95% CI 0.90-0.97) for mammography. Positive and negative predictive values were 40% and 98.9% for MRI vs. 25% and 95.2% for mammography. Conclusions: Gadolinium-enhanced breast MRI is a useful surveillance modality in breast cancer survivors < age 65. Prospective studies are needed in this population.
Correlation of ERCC1 expression on circulating tumor cells with progression-free survival in metastatic non-small cell lung cancer patients treated with platinum-based chemotherapy.
Authors: Riess Jonathan , Das Millie Snigdha , Frankel Paul Henry , Schwartz Erich , Bennis Robyn , Hsieh H Ben , Liu Xiaohe , Ly Janey , Zhou Lisa Ya , Nieva Jorge J. , Bruce Richard , Wakelee Heather A.
Published: March 2020

10574

Background: Biomarkers predicting efficacy of chemotherapy are highly desirable. Fiber array scanning technology (FAST) is a novel method of detecting circulating tumor cells (CTCs) that does not employ an EpCam enrichment step. The purpose of this study was to use FAST to evaluate ERCC1 expression on CTCs to determine whether ERCC1 expression correlates with progression-free survival (PFS) in patients who received platinum-based chemotherapy for metastatic non-small-cell lung cancer (NSCLC). Methods: Peripheral blood from one hundred enrolled patients with metastatic NSCLC was collected by two institutions (Stanford Cancer Institute and Billings Clinic Cancer Center). FAST was used to identify individual CTCs on immunofluorescence by pancytokeratin antibodies. Nuclear localization of ERCC1 expression by immunofluorescence was quantified on individual CTCs. Total patient ERCC1 levels were determined from the average expression of all the CTCs in each patient sample. Fifty-seven of the one hundred patients enrolled received platinum chemotherapy. Seventeen of those fifty-seven patients (30%) had ≥ 2 evaluable intact CTCs and were analyzed retrospectively. Linear regression (F-test) was used to evaluate the correlation between ERCC1 expression and PFS. Kaplan-Meier survival analysis (log-rank test) was used to compare PFS in patients with CTCs with no detectable ERCC1 expression versus patients with CTCs that expressed any level of ERCC1. Results: PFS decreased with increasing ERCC1 expression (P<0.04 F-test, linear regression). Lack of ERCC1 expression was associated with longer PFS (266 days vs. 172 days, log-rank test P<0.02). The difference in survival was statistically significant with a hazard ratio of 4.20 (95% CI 1.25-14.1, p<0.02, log-rank test). Conclusions: In this small study, using FAST to isolate CTCs, low expression of ERCC1 on evaluable CTCs correlated with increased PFS in patients with metastatic NSCLC who received platinum chemotherapy. A larger, prospective study to validate these retrospective results is warranted.
Use of early 18f-fluorodeoxyglucose-positron emission tomography to predict clinical outcome of patients with advanced non-small cell lung cancer on gefitinib treatment versus carboplatin plus paclitaxel.
Authors: Kanazu Masaki , Maruyama Kaoru , Ando Masahiko , Asami Kazuhiro , Ishii Mari , Minomo Shojiro , Matsuda Yoshinobu , Kawaguchi Tomoya , Atagi Shinji , Kusunoki Yoko , Kubo Akihito , Takada Minoru
Published: March 2020

10577

Background: Early prediction of clinical efficacy is of great value in cancer patients in avoiding unnecessary toxicities and giving them another chance for different treatments. This study aimed to assess the 18F-fluorodeoxyglucose-positron emission tomography (FDG-PET) at 3 days on treatment as an early predictor of clinical outcome in patients with advanced non-small cell lung cancer (NSCLC) treated with gefitinib and in those treated with cytotoxic chemotherapy. Methods: This study comprised two groups: patients with stage IIIB or IV NSCLC were treated with gefitinib (250mg) once daily (gefitinib group) or with carboplatin (AUC 6, day 1) plus paclitaxel (200mg/m2, day 1) q21 days (CP group) according to the physicians’ choice. FDG-PET was performed before, 3 days on and 28 days on each treatment. Reduction of tumor FDG uptake was assessed by using standardized uptake value (SUV). Metabolic response was defined as reduction of FDG uptake in the tumor ≥ 25% according to the criteria of the European Organization for Research and Treatment of Cancer. Metabolic response was correlated with clinical outcomes. Results: This study included 38 patients: 19 in gefitinib group and 19 in CP group. Reduction of SUV at 3days on treatment preceded tumor shrinkage more closely in gefitinib group. Metabolic response was significantly correlated with longer progression-free survival (PFS) in gefitinib cohort (median PFS 15.8 months [95% CI 13.2-18.4] vs. 3.7 months [95% CI 0.1-8.0], p < 0.001), but not in CP group (median PFS 5.7 months vs. 2.9 months, p = 0.054). Furthermore, metabolic response was significantly correlated with longer overall survival (OS) in gefitinib group (median OS 28.7 months [95%CI 23.5-33.9] vs. 9.8 months [95% CI 2.1-17.5], p = 0.009), but not in CP group (median OS 13.9 months vs. 10.5 months, p = 0.56). In multivariate analysis using Cox hazards models, metabolic response was a significant predictive factor of PFS and OS. Conclusions: Reduction of SUV levels on FDG-PET at 3 days on treatment may predict response and survival in gefitinib-treated patients with advanced NSCLC.
Combining semiconductor-based sequencing with amplicon-based cancer gene panels: A rapid next-gen approach to clinical cancer genotyping.
Authors: Corless Christopher L. , Neff Tanaya , Heinrich Michael C. , Beadling Carol
Published: March 2020

10591

Background: Bringing next-gen sequencing into clinical (CLIA-licensed) laboratories is an important step in the advancement of personalized cancer care. We have validated a new sequencing approach on the Ion Torrent (IT) PGM using the AmpliSeq Cancer Panel, which covers hotspot regions across 46 commonly mutated cancer genes. Methods: The AmpliSeq panel is comprised of 190 primer pairs that are co-amplified in a single tube to generate amplicons for sequencing. In our testing only 10ng of input DNA was used. Initial PCR was for 20 cycles, after which the amplicons were ligated with sequencing/barcode adapters, amplified for an additional 7 cycles, and then subjected to emulsion PCR. The resulting nanospheres were sequenced on an IT 316 chip. Results: We sequenced 44 samples of FFPE-derived tumor DNA that were previously genotyped on a mass spectroscopy (MS)-based panel. Samples were barcoded and sequenced in batches of 4, yielding an average of 2034 reads per amplicon (range: 95-5162) and an average read length of 76bp. Overall, 95.4% of reads were on target, and 79% of reads were AQ20 or better; 95% of the 190 amplicons had over 500 reads. All 42 known point mutations were accurately identified by the variant caller software. Seventeen in/dels from 4 to 63 bp in length were at least partially visible upon manual inspection of the read alignments, but some were not accurately called by the software. In addition, 22 new mutations were identified in gene regions not covered on our MS-based panel. We demonstrated sensitivity to the level of 5% mutant allele, and the correlation between allelic ratios measured by MS and IT sequencing was excellent (r2=0.81). Two DNA samples from laser-captured tumor worked well with the AmpliSeq Panel. Conclusions: Combining solid-state sequencing with a highly multiplexed PCR method for library construction is a rapid (48 hr) approach for next-gen sequencing of clinical cancer samples. The process is highly scalable and larger, cancer-specific amplicon panels are in development. Automated identification of in/dels remains a challenge in next-gen sequencing output.
The components of progression as explanatory variables for overall survival in the RECIST database.
Authors: Litière Saskia , De Vries Elisabeth , Seymour Lesley , Sargent Daniel J. , Shankar Lalitha , Bogaerts Jan ,   on behalf of the RECIST Working Group
Published: March 2020

10602

Background: Progressive disease (PD) according to RECIST 1.1 (Eisenhauer et al, 2009) is defined as one or more of (1) PD of measurable target lesions, (2) the presence of a new lesion (NL) or (3) the unequivocal PD of non-target disease (NT-PD). We explored the impact of these components, varying over time, on predicting overall survival (OS) in the RECIST database residing at EORTC (Bogaerts et al, 2009). Methods: Data was selected from 12 randomized clinical trials (3530 patients with breast, lung or colorectal cancer). A maximum of 5 target lesions was used to determine the sum of diameters. The following were calculated or assigned at each measurement time t: best response (BR) was best % improvement from baseline up to t (0% if no improvement - 100% if complete response (CR)); tumor growth (TG) was the weekly rate of increase from nadir to t (0 if no increase; irrespective of prior shrinkage), presence of NL (yes/no), and occurrence of NT-PD (yes/no); categories were not mutually exclusive. OS was analyzed by tumor type using a Cox regression model, adjusting for baseline sum, and including BR, TG, presence of NL and NT-PD as time dependent covariates. Results: Thirty-six percent of patients had NL, 26% had NT-PD, 11% achieved CR and 14% did not have shrinkage of target lesions, while 46% experienced TG (median strongest growth per patient of 0.5 mm/week). Regardless of tumor type, the presence of NL (Hazard Ratio (HR) ranging 1.4-2.5), NT-PD (HR 1.2-2.5) and TG (per 1mm/week increase; HR 1.1-1.4) were associated with worse OS, while achieving CR was associated with a longer OS (HR 0.2-0.8). Further analyses exploring the functional shape of the association between BR and TG, and OS are ongoing. This includes putting TG in contrast with the more usual % cutoff defining target PD. Conclusions: All three components of PD according to RECIST are independently strongly associated with OS. Quantification such as this will enable a better understanding of the role of each component (e.g. clinical aspect of NT-PD assessment) in PD evaluation. Work is ongoing to incorporate this information into an updated RECIST with enhanced prediction of subsequent survival.
Anti-AML activity of a novel beta-catenin antagonist BC2059.
Authors: Bhalla Kapil N. , Fiskus Warren , Sharma Sunil , Horrigan Stephen , Mudunuru Uma , Reyes Ruben , Abhyankar Sunil H. , McGuirk Joseph , Aljitawi Omar Salah , Ganguly Siddhartha
Published: March 2020

10605

Background: The canonical WNT-β-catenin pathway is essential for self-renewal, growth and survivalof AML stem and progenitor cells. Deregulated WNT signaling inhibits degradation of β-catenin, causing increased nuclear translocation and interaction of β-catenin with the TCF/LEF transcription factor, which up regulates cyclin D1, Myc and survivin expression in AML progenitor cells. BC2059 (β-Cat Pharmaceuticals) is a potent, small molecule, anthraquinone oxime-analog, which inhibits WNT-β catenin pathway by promoting the degradation and attenuation of β-catenin levels. Methods: We determined the in vitro anti-AML activity of BC2059 (BC) (250 to 1000 nM) against cultured and primary human AML blast progenitors, as well as evaluated the in vivo anti-AML efficacy of BC in NOD-SCID and NOD-SCID-IL2γ receptor deficient (NSG) mice. Results: BC induced cell cycle G1 phase accumulation and apoptosis (40%) of the cultured OCI-AML3, HL-60 and HEL92.1.7 (HEL) AML cells. BC dose-dependently also induced apoptosis of primary AML versus normal progenitors. Treatment with BC resulted in proteasomal degradation and decline in the nuclear levels of β-catenin, which led to decreased activity of the LEF1/TCF4 transcription factor highlighted by reduced TOP-FLASH luciferase activity in the AML cells. This was associated with reduced protein levels of cyclin D1, MYC and survivin. Co-treatment with BC and the histone deacetylase inhibitor panobinostat (PS) (10 to 20 nM) synergistically induced apoptosis of cultured and primary AML blasts. Following tail vein infusion and establishment of AML by OCI-AML3 or HEL cells in NOD-SCID mice, treatment with BC (5, 10 or 15 mg/kg b.i.w, IV) for three weeks demonstrated improved survival, as compared to the control mice (p <0. 001). Survival was further improved upon co-treatment with BC and PS (5 mg/kg IP, MWF). BC treatment (5 or 10 mg/kg IV) also dramatically improved survival of NSG mice with established human AML following tail-vein injection of primary AML blasts expressing FLT3 ITD. Mice did not experience any toxicity or weight loss. Conclusions: These findings highlight the notable pre-clinical in vitro and in vivo activity and warrant further development and in vivo testing of BC against human AML.