bluuebunny/crossref_metadata_2025_split huggingface dataset:
NGS-based targeted RNA sequencing for expression analysis of patients with triple-negative breast cancer using a modulized, 96-gene biomarker panel.
Authors: Lee Byung-In , Oades Kahuku , Vo Lien , Lee Jerry , Landers Mark , Wang Yipeng , Monforte Joseph 
Published: February 2017

56 Background: Gene expression profiling has been shown to be effective in analyzing postoperative tumor samples in various cancers. However, in analyzing small specimens such as core biopsies, the limited amount of available material makes multi-gene analyses difficult or impossible. Microarray-based analyses also provide limited dynamic range. We describe the development of targeted RNA-sequencing methodology which combines the power of a universal RNA amplification with NGS for an ultra-deep expression analysis of multiple target genes, enabling <100 ng of sample input for multi-gene analysis in a single tube format. Methods: The gene expression patterns of triple-negative breast cancer FFPE samples were analyzed using a 96-gene breast cancer biomarker panel across three different platforms: Affymetrix Human Gene ST 1.0 microarrays, a pre-developed OncoScore qRT-PCR panel, and targeted RNA-seq. For targeted RNA-seq analysis, the 96-gene panel was amplified using a universal, single-tube “XP-PCR” amplification strategy followed by sequence analysis using the Ion-Torrent Personal Genome Machine. Results: Targeted RNA-seq provided the most sensitivity in terms of detection rates with <100 ng FFPE RNA input and provides unlimited dynamic range with increased sequencing depth. Expression ratio compression issues typically associated with a high number of pre-amplification cycles in standard multiplex-primed methods were not observed here. Low expressing genes, undetectable by qRT-PCR analysis from 1,000 ng input FFPE RNA, were detected and eligible for expression analysis with a significant number of sequencing reads. Alternative transcription/splicing analysis is also possible from sequence analysis of the target transcripts using targeted RNA-seq. Conclusions: By combining universally primed pre-amplification and NGS in multi-gene expression analysis, targeted RNA-seq provides the most sensitive gene expression analysis methodology.
Evaluating RASSF1 promoter methylation and the 16-gene signature as a prognostic marker in hepatoblastoma.
Authors: Eichenmuller Melanie , Kreuder Michaela , Regel Ivonne , Haberle Beate , Muller-Hocker Josef , von Schweinitz Dietrich , Kappler Roland 
Published: February 2017

63 Background: Hepatoblastoma (HB) is the most common malignant liver tumor in childhood. Although combination of neoadjuvant chemotherapy and surgery has improved the outcome of standard-risk HB-patients up to 94% the outcome of high-risk HB-patients with metastatic tumors or invasion of large hepatic veins is still dismal and only 60% of these patients survive. Therefore, the identification of biomarkers that could help early detection of high-risk HB-patients and lead to risk-adapted therapies is of utmost importance. Methods: Genomic DNA of tumor and normal liver samples from 21 HB patients was extracted with standard procedures and bisulfite-treated using EpiTect Bisulfite Kit (Qiagen). Methylation status of the Ras association (RalGDS/AF-6) domain family member 1 (RASSF1) gene was analyzed by methylation-specific-PCR. cDNA of tumor and normal liver samples was used to determine the 16-gene expression signature according to Cairo et al. (2008, Cancer Cell) using real-time PCR. Association studies of molecular and clinical data were performed with GraphPad Prism Version 3.0 using two-tailed Chi square test. Results: We identified 9/21 HB cases hypermethylated in the RASSF1 promoter region. Interestingly, RASSF1 promoter methylation was significantly associated with metastases (p=0.0166) and occurrence of this epigenetic marker was associated with a reduced overall survival of patients (p=0.0008). Moreover, we discriminated HB tumors in C1 and C2 subclasses by using the 16-gene signature and correlation of these subtypes with the methylation status of RASSF1 showed a significant association (p=0.0037) for aggressive C2 tumors (8/11), but not C1 tumors (1/10). Conclusions: RASSF1 promoter hypermethylation is a strong prognostic marker for metastasis and worse outcome and correlates with an aggressive C2 HB-tumor profile. Since the detection of tumor-derived methylated DNA in the blood stream of cancer patients is nowadays practical, our data advise RASSF1 methylation assays to be used for risk assessment in HB-patients in the future.
A blood-based gene expression signature of early-stage non-small cell lung cancer.
Authors: Rotunno Melissa , Hu Nan , Su Hua , Wang Chaoyu , Bertazzi Pier Alberto , Caporaso Neil , Taylor Phil R. , Landi Maria Teresa 
Published: February 2017

69 Background: Accurate blood-based biomarker for early cancer detection could be an easier and more convenient screening option than monitoring the target organ via tissue or imaging. We recently identified and validated eight genetic biomarkers of early-stage lung adenocarcinoma detectable in both peripheral whole blood (PWB) and lung tissue of smokers. Since biomarkers distinguishing benign disease versus lung malignancy across all cell types are needed in the diagnostic clinical setting, it is important to test the identified biomarkers in other lung cancer histologies, particularly in squamous cell carcinoma (SQCC), the second most common lung cancer histology after adenocarcinoma (AD). Methods: Using Real-Time Quantitative PCR (qRT-PCR), we measured mRNA levels for the eight candidate genes in PWB of 48 randomly sampled stage I SQCC cases, in addition to previously analyzed 82 AD cases and 130 age, sex, and smoking frequency matched healthy controls from the Environment And Genetics in Lung cancer Etiology (EAGLE) case-control study. The qRT-PCR data were analyzed using the 2-ΔΔCtmethod to compare SQCC cases with controls. The area under the receiver operating characteristic curve (AUC) was computed to assess the predictive accuracy of the candidate biomarkers in SQCC separately, and in SQCC and AD together. Results: Expression of TGFBR3, RUNX3, TRGC2, TRGV9, TARP, and TSTA3 genes, significantly differentiated SQCC cases versus controls, while ACP1 and VCAN gene expression did not. The eight genes combined discriminated patients with lung cancer from healthy controls with similarly high accuracy in SQCC and overall (AUC = 0.80 ± 0.1). RUNX3 showed the highest single gene accuracy for SQCC (AUC = 0.78). Conclusions: We showed that the previously identified gene expression signature of early-stage lung AD also differentiated early stage SQCC from healthy controls and demonstrated its sensitivity and specificity as a potential diagnostic lung cancer biomarker. Since lung cancer is the most common cause of cancer mortality worldwide and current smokers are at very high risk, our smoking-specific findings, if confirmed and translated into screening approaches, have the potential to impact public health.
Detecting and classifying circulating tumor cell subclasses from On-Q-ity microfluidic chips using a customized imaging platform.
Authors: Jiang Chunsheng , Tims David , Milutinovic Aladin , Gusyatin Oleg , Merdek Keith D. , Sprott Kam M. , Dong Yi , Stocum Michael , Carney Walter P. 
Published: February 2017

72 Background: Circulating tumor cells (CTCs) have clinical value in cancer diagnosis, prognosis, and treatment prediction. The On-Q-ity Microfluidic Chip (OnQchip) with a gradient design has the advantage of dual size and affinity capture resulting in increased efficiency. Accurately detecting and classifying these rare captured cells in patient blood however is difficult. We present an imaging platform for accurate and reproducible CTC detection, where identified cells and fragments are further classified into several subclasses that may have separate prognostic utilities. Methods: Whole blood from advanced stage cancer patients and non-diseased controls was processed within 36 hours of collection. Blood was run on OnQchips coated with anti-EpCAM antibody. Captured CTCs and cellular fragments were identified by on-chip immunofluorescence. Chips were imaged at 5X magnification on a rapid automated platform. Cytokeratin positive (CK+) events were identified and sorted via an advanced detection algorithm using a set of spatial and spectral features. Events were further validated and separated into subclasses by trained experts using 10X magnification. Results: Greater than 85% capture efficiency was repeatedly achieved in spiked blood with nearly 100% detection sensitivity and 3% false positive rate following automated sorting of CTC candidates. On a cohort of 27 prostate cancer patients and 33 normal subjects a median of 19 CK+events/7.5 ml blood were detected in cancer patients, compared to a median of only 6 in normals. ROC analysis yielded AUC values of 0.62 to 0.77 for separate subclasses of CTCs. An AUC of nearly 0.80 was achieved by combining two or more subclasses. Conclusions: Preliminary evaluation of this imaging platform shows efficient and reproducible CTC detection in spiked and patient samples. Enumeration using subclasses achieved high sensitivities and specificities in separating cancer patients from normals and therefore, makes this technology feasible for both research and clinical studies. Future clinical studies with large sample sizes will be performed to validate clinical significance of CTC subclasses.
Immunomodulatory effects of bevacizumab in metastatic malignant melanoma.
Authors: Mansfield Aaron Scott , Nevala Wendy Kay , Markovic Svetomir 
Published: February 2017

82 Background: Metastatic malignant melanoma is a nearly uniformly fatal disease. Systemic therapy has notable but limited success. Novel therapeutic strategies are urgently needed. To that end, we’ve pursued combinatorial therapeutics using conventional chemotherapy added to an inhibitor of angiogenesis (bevacizumab) with some evidence of clinical benefit. Preliminary analysis of one of our trials suggested a previously unrecognized immunomodulatory effect of bevacizumab when added to chemotherapy in patients with metastatic melanoma, and this may have a potential impact on clinical outcome. Herein we evaluate the immunomodulatory effect of bevacizumab when added to chemotherapy in patients with metastatic melanoma. Methods: We measured levels of peripheral blood mononuclear cell phenotypes in addition to 42 cytokines, chemokines and growth factors in plasma of 55 patients who received albumin-bound paclitaxel and carboplatin (AC) and of 73 patients who received AC with bevacizumab (ACB) on clinical trials N057e and N0775 respectively. The relative percent change in PBMC cell counts and cytokine levels were determined from baseline at their restaging evaluation after two cycles of therapy. The Mann Whitney U test was used to compare responses between the groups. Results: There was a significant increase in CD197+type 1 macrophages in the group that received ACB (35.3%, -11.8-142.7%) compared to AC (-11.6%, -45.9-38.3%; p=0.004). There was a significant decrease in IL-6 in the group that received ACB (-42.4%, -87.7-0.0%) compared to AC (28.4%, -37.4-480%; p=0.0018). Conclusions: The addition of bevacizumab to chemotherapy for the treatment of metastatic melanoma modulates cellular immunity and a pro-inflammatory cytokine. Patients who received bevacizumab had a significant increase in CD197+ type 1 macrophages and a significant decrease in IL-6. Clinical significance of these findings is the subject of ongoing work.
Effect of pericytes on epithelial-to-mesenchymal transition in melanoma.
Authors: Trevino-Villarreal Jose Humberto , Sepulveda Rosalinda , Cotanche Douglas A. , Rogers Rick A. 
Published: February 2017

84 Background: Melanoma-associated stroma cells play an important role in supporting cancer cell proliferation, invasion, and dissemination. Increased invasiveness has been observed in cancer cells undergoing epithelial-to-mesenchymal transition (EMT); however, it is unknown whether EMT is facilitated by stroma cells. We showed that pericytes constitute a predominant stroma subpopulation that promotes melanoma growth by interacting with cancer cells. This study investigates the mechanism by which pericytes facilitate melanoma development. Methods: GFP+ pericytes isolated from tumors and adipose tissue were co-cultured in vitro with B16 melanoma cells at a 3:1 ratio. After 4 days, proliferation of B16 cells and pericytes was assessed. Also, co-cultures were labeled for several markers and analyzed by flow cytometry (FC). Tumorigenicity was investigated by isolating B16 cells from co-cultures by FACS sorting and then injected into SCID mice to measure tumor growth. Results: B16 cells induced pericyte differentiation into FAP+ myofibroblasts. However, no change in the pericyte proliferation rate was observed. B16 cells co-cultured with pericytes, and later separated by FACS sorting, displayed faster proliferation rates in vitro, and induced increased tumor growth rates when injected into SCID mice, compared with naive B16 cells. Pericytes increased B16 cell proliferation rate and induced a change in cell morphology, from cobblestone to fibroblast-like colonies. Interaction between B16 cells and pericytes in co-culture increased pericyte production of TGF-β and increased the expression of the stem cell markers SSEA-1, OCT3/4 and CD271 in B16 cells. In addition, cadherin switching, demonstrated by loss of E-cadherin expression and an up-regulation of the mesenchymal markers N-cadherin and vimentin was observed in B16 cells. Conclusions: Pericyte production of TGF-β promotes B16 cell development of EMT, as shown by loss of E-cadherin expression and up-regulation of the mesenchymal markers N-cadherin and vimentin, resulting in an increase in melanoma cell tumorigenicity. These results suggest that therapies targeting stromal pericytes may be a promising approach for melanoma treatment.
Clinical and genomic analysis of metastatic disease progression in a background of biochemical recurrence.
Authors: Crisan Anamaria , Ghadessi Mercedeh , Buerki Christine , Vergara Ismael A. , Thompson Darby J. S. , Erho Nicholas , Sierocinski Thomas , Haddad Zaid , Zimmermann Benedikt , Sosu-Sedzorme Worlanyo , Harko Sebastian , Black Peter C. , Davicioni Elai , Jenkins Robert B. 
Published: February 2017

90 Background: Biochemical recurrence (BCR) may be an indicator of metastatic prostate cancer; however, it isn't specific enough to differentiate patients who will experience rapid onset of metastases from those who do not. Such lack of specificity leads to overtreatment of men who will likely never experience metastatic disease in their lifetime. We hypothesize that genomic biomarkers, detectable in primary tumor tissue, may better identify rapidly progressing metastatic prostate cancer. Methods: FFPE prostatectomy specimens (n = 309) from the Mayo Clinic tumor registry were profiled using a high-density expression array. Patients were retrospectively classified into three outcome groups: NED (no evidence of disease recurrence); BCR-only (patients that experienced BCR but no metastatic progression); and MET (metastatic disease confirmed by positive CT or bone scans) and were matched on several criteria for analysis . Uni- and multi-variable analyses between outcome groups were used to analyze clinical and genomic variables (adjusting for adjuvant hormone therapy as a confounding factor). Results: Median follow-up was 16.8 years and MET patients were diagnosed a mean of 3.1 years following BCR. Univariable and multivariable analysis of clinical variables failed to show statistically significant differences between NED and BCR-only outcome groups. Differential expression analysis between NED and BCR-only groups showed no significant differences after false discovery correction. Conversely, 6,277 and 52,020 biomarkers were differentially expressed between MET and the BCR-only and NED groups, respectively. Conclusions: Considering the clinical and genomic results together, patients who experienced rapid metastatic disease were significantly different from both the NED and BCR-only groups. However, no significant differences were identified between the BCR-only and NED outcome groups. These results imply that BCR is not a good surrogate for men who are likely to experience rapid onset of metastatic disease and lethal prostate cancer.
Changes in VEGF-A-serum levels after DEBIRI-TACE in patients with liver metastases of chemorefractory colorectal cancer.
Authors: Pluntke Stefan , Dyrda Sven , Malik Amena , Wilke Hansjochen , Stahl Michael , Koch Jens-Albrecht 
Published: February 2017

93 Background: TACE with irinotecan-loaded drug-eluting beads has shown activity in colorectal liver metastases. Among the factors potentially interfering with its effectiveness is a hypothetical neo-angiogenic reaction due to ischemia. Methods: Patients with predominant liver metastases from CRC which were refractory to chemotherapy and documented tumor progression during or shortly after the last chemotherapy, were prospectively treated with irinotecan-loaded drug-eluting beads with a size of 100-300 µm. Therapy was applied by a temporary catheter placed in the liver arteries. Usually each lobe of the liver was according to the recommended DEBIRI treatment algorithm. Each treatment of one liver lobe was performed with 1 vial of the 100-300 µm DC-Beads loaded with 100 mg irinotecan. Blood samples to measure the VEGF serum levels were taken before TACE and at days 7, 14, and 21 after first treatment. Results: Complete blood samples were taken from 15 patients from 2/11 to 2/12. 60% of patients had an increase of the VEGF-A-Level with a median of 107 %, 40% of patients had a decrease of the VEGF-A-Level with a median of – 39% respectively. The relative decrease of the VEGF-A-Levels depends on a prior liver resection (p=0.05), and a significant decrease was found in patients with a prior bevacizumab therapy (p=0.025). A trend to an increase in VEGF-A-Levels was detected in patients with a low count of liver metastases (p=0.087). Conclusions: These findings show different behavior of the VEGF-A-levels after DEBIRI-TACE, suggesting that the occlusion of blood vessels and subsequent ischemia induces neo-angiogenesis due to these growth factors in a subset of 60% of the patients treated with a DEBIRI-TACE. We found a trend for a lower count of liver metastases, prior liver resection and a prior bevacizumab-therapy, respectively influencing the VEGF-A-Level-changes. The trend toward a decrease in patients with a prior bevacizumab therapy may be due to a neoangiogenesis-pathway other than VEGF-mediated. These first results could implicate that antiangiogenic drugs might be effective as an additive therapy to chemoembolization in a subset of patients, e.g., those with no prior bevacizumab therapy.
Preliminary results of a biomarker discovery project for treatment-related brain injury (TRBI) in malignant glioma.
Authors: Yovino Susannah G. , Holdhoff Matthias , Savage William J. , Dulloor Pratima , Grossman Stuart A. , Everett Allen 
Published: February 2017

94 Background: Patients with malignant glioma often develop increased enhancement in the tumor bed after chemoradiation (CRT). Current imaging techniques cannot distinguish if these changes are due to recurrent disease or treatment-related brain injury (TRBI). Serum biomarkers could help noninvasively make this distinction. Brain-specific proteins have been used as markers of the severity of other brain injuries including stroke, hypoxia, and traumatic brain injury. We hypothesized that similar changes could be observed following brain CRT and could provide preliminary data supporting biomarker development for TRBI. Methods: Patients receiving concurrent radiation and temozolomide (TMZ) for malignant glioma were eligible. The study was approved by the institutional review board. Informed consent was obtained from all patients. Serum is sampled before CRT, in the last week of CRT, and at 1 month, 6 mos, and 1 year after CRT. Neurologic exams, cognitive testing, and imaging are performed at the same intervals. Serum samples were tested for glial fibrillary acidic protein (GFAP), neurogranin, ICAM-5, B-syn-nuclein, and brain-derived neurotrophic factor (BDNF). Samples were measured in duplicate using an electrochemiluminescent immunoassay. Results: Data are available for the first 7 patients enrolled in this study. All of the tested markers except GFAP were measurable at baseline and all other time points. None of the markers were consistently elevated during the last week of CRT or at any other time point during follow-up. Three patients had resection of suspected recurrent disease. Two had recurrent tumor and 1 had no evidence of disease. No correlation was apparent with the findings at surgery and serum levels of GFAP, neurogranin, ICAM-5, B-synuclein, or BDNF. Conclusions: This study describes a mechanism for identifying a serum protein marker of TRBI. Preliminary results did not identify elevations in any of the selected markers immediately after CRT when signs of TRBI should be apparent or at other points in the clinical course. Testing of additional serum markers is needed to identify a biomarker of TRBI which would provide valuable information for managing high-grade glioma patients.
Development of open-access mock 510(k) regulatory documents on multiplex proteomic technologies.
Authors: Boja Emily , Hiltke Tara , Kinsinger Chris , Mesri Mehdi , Rivers Robert , Rodriguez Henry ,   Office of Cancer Clinical Proteomics Research
Published: February 2017

99 Background: Proteome-based biomarker science is progressing slowly for a variety of factors, including a lack of dialogue early in the discovery/development process with regulatory agencies such as the Food and Drug Administration (FDA). Although high-throughput multiplex proteomic-based technologies have the potential to accurately measure proteins of clinical significance in complex human matrices, regulatory approval for these analytical technologies have not been explored. Methods: To address this gap, investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) held a forward-thinking workshop, involving clinical laboratories, instrument manufacturers, researchers, and FDA representatives in order to streamline the regulatory approval of protein-based multiplex platforms. Results: Outcomes included a peer-reviewed workshop report published in special proteomics issue of Clinical Chemistry, and first-of-its-kind open access mock 510(k) regulatory documents (based on two most commonly applied quantitative proteomic technologies: multiplex mass spectrometry-based and multiplex affinity-based platforms) as public community resources (also published in Clinical Chemistry). Conclusions: These open-access documents provide a glimpse of the FDA’s perspective of novel approaches to in vitro diagnostics of multiplex protein assays and the process of premarket review. Therefore, these resources should enable others to focus on aspects of the process carefully monitored by the FDA, observe a format that is acceptable to the agency, and understand the iterative nature of review.