bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplexed genotyping using a novel digitally inscribed bead-based system
Authors: Lipkin S. M. , Yeakley J. , Chao E. , Velasquez J. , Lopez M. , Rhee J. , McDaniel T. , Lewis I. , Chen H. ,   Illumina Genotyping Study Group
Published: March 2020

21089 Background: Genotyping of clinical samples has been limited to low levels of multiplexing, ranging from one to a few dozen single nucleotide polymorphisms (SNPs) per sample. By increasing multiplexing levels, a clinical lab can increase information content per sample, decreasing costs and sample material requirements. Methods: We have adapted the GoldenGate® Assay for simultaneously genotyping 96 to 1,536 SNPs to the BeadXpress™ System, a new high-throughput platform that utilizes digitally inscribed VeraCode™ beads in a compact fluidic instrument. Genotyping on this platform ranges from 96 to 384 multiplexing, using the same GoldenGate Assay that has proven highly robust for millions of genotypes. In preliminary tests, we have observed greater than 99% call rates, and greater than 99.5% rates for reproducibility and heritability. In a test of 96 SNP genotypes chosen for a study of colorectal cancer, a point mutation in the MSH2 gene, previously implicated in predisposition to several cancers, was correctly genotyped when compared to qPCR analysis of the same samples. Conclusion: Together with genotyping data from reference samples, the GoldenGate Assay on the BeadXpress System has yielded highly reproducible and accurate genotypes, suggesting that this approach will prove useful for rapid refinement of SNPs for development of clinical genotyping tests. No significant financial relationships to disclose.
Stem cell markers in gastrointestinal cancer
Authors: Valladares-Ayerbes M. , Díaz Prado S. , Medina V. , Iglesias P. , Rodríguez B. , Haz M. , Reboredo M. , Quindós M. , Alonso-Jaudenes G. , Antón Aparicio L. 
Published: March 2020

21095 Background: Cancer cells with stem cells (CSC) properties have been identified in different tumors. It is suggested that CSC are responsible for the continuous growth of tumors, metastasis and drug-resistance. Markers for stem cells have been described. Oct4 and Nanog are transcription factors required to maintain the pluripotency and self-renewal of embryonic stem (ES) cells. ABCG2 transporter (MDR1) gene expression has been described as surrogate for the side-population phenotype. PTTG1 has also been recently identified as a component of the molecular signature of human (hu) ES cell-lines. Methods: Using Digital Northern we have demonstrated a significant tag counts for PTTG1 and reticulocalbin 2 (RCN2) in 11 huES cell-lines of the CGAP. The objective of our work has been to assess gene expression of these SC markers in a panel of new gastrointestinal cancer (GC) cells lines (CL) developed in our laboratory. Quantitative assessment was obtained by real-time PCR relative to normal bone marrow (BM), colonic mucosa and established cell-lines. GCCLs have been developed from ascitic fluid obtained of pancreatic carcinoma (MBQ-OJC1) and colon cancer (JJPF-OJC4, LCM-OJC5 and JAC-OJC6). GCCLs had been fully characterized by cytomorphology, epithelial and tumor markers (keratins, EGFR, EpCAM, p53), karyotype and tumor spheroids cultures. Results: Expression for ABCG2, Nanog, Oct4, PTTG1 and RCN2 were clearly detected in all the GCCL. Relative levels for each mRNA shown wide variety. For example, ABCG2 mRNA was highly expressed (2–26 fold) in colon cancer CL relative to BM. RCN2 was overexpressed (more than 2 x 102 fold) in 3 GCCL. Conclusions: Our results show that expressions of different “stemness” genes are maintained in cultured cancer cells. These data suggest that CSC are present in metastatic sites and can be maintained in continuous culture. We hypothesized that PTTG1 and RCN2 could be tested as a new cancer stem cells markers. No significant financial relationships to disclose.
Prospective study of a 10-gene molecular assay to predict tissue of origin in patients with carcinoma of unknown primary (CUP)
Authors: Varadhachary G. R. , Talantov D. , Jatkoe T. , Rashid A. , Lenzi R. , Chadha R. , Baden J. , Wang Y. , Abbruzzese J. L. , Raber M. N. 
Published: March 2020

21096 Background: Carcinoma of unknown primary (CUP) where metastatic disease presents without an identifiable primary represents ∼ 3–5% of all cancers. Identifying the origin of the primary tumor in CUP pts can facilitate rational choice of therapeutic regimens. Veridex developed an optimized set of 10 gene markers for a quantitative reverse transcriptase polymerase chain reaction (qRTPCR) assay, and demonstrated high accuracy in predicting the tissue of origin with formalin-fixed, paraffin-embedded (FFPE) metastatic carcinoma samples (J Mol Diagn 2006, 8: 320–9). In this study, the 10-gene assay was prospectively evaluated in CUP pts. Methods: We collected FFPE biopsy tissue specimens from consenting CUP pts at MD Anderson. Eligibile pts met our definition for CUP with adenocarcinoma or poorly differentiated carcinoma. Samples were obtained prior to treatment. 51 pts have been enrolled so far and 11 were ineligible [insufficient samples].Of the 40 pts, qRTPCR assay has been performed on 33 pts. Data on 27/33 is available. A statistical model was used to determine the probability that the metastatic carcinoma tissue assayed originated from 1 of the following 7 categories: lung, pancreas, colon, breast, prostate, ovarian, and other. Subsequently, prediction of the primary by qRTPCR was independently compared with metastatic pattern spread, tumor pathological features, and results of clinical and pathology diagnostic workups. Results: Assay results on 27 prospectively collected CUP patient biopsy specimens are available. In total, CUP tissue of origin prediction by the assay correlated with clinical and pathological assessment in 21 out of 27 evaluated pts (78 %). The most common cancer type predicted by the assay was colon cancer, which correlated with predominantly intra-abdominal metastatic spread in this pt cohort. Conclusions: This prospective study demonstrated the feasibility of conducting gene analysis to predict metastatic carcinoma tissue of origin in FFPE tissue specimens derived from CUP patients. Overall distribution of various primary cancer types as predicted by the assay was consistent with the historical distribution reported for CUP. Assay prediction was concordant with clinical and pathological assessment in 78 % CUP pts. No significant financial relationships to disclose.
Tumor necrosis factor-α is a potent endogenous mutagen that promotes cellular transformation
Authors: Yan B. , Wang H. , Rabbani Z. N. , Dewhirst M. W. , Li C. 
Published: March 2020

21104 Background: It is estimated that chronic inflammation is an important underlying condition for sporadic human tumor development, accounting for approximately 20% of human cancers. TNFa is an inflammation cytokine playing an important role in inflammation- associated cancers. However, the underlying mechanism of how TNFa leads to cancer is not clear. Before we initiated this study, TNFa is not known to have a direct effect on DNA. Methods: We studied genetic mutations, cellular transformation in cells and mice treated with TNFa. DNA damages and genetic aberrations caused by TNFa treatment were measured by gene amplification assay, micronucleus assay, cytogenetic analysis for chromosomal aberrations and immunostaining of 8-OHdG (8-hydroxydeoxyguanine; marker for DNA damage and oxidative stress). Cellular transformation was studied by standard transformation assay using mouse embryo fibroblast cells. Results: In this study, we found that TNFa can cause DNA damages through induction of reactive oxygen species (ROS). Our findings include: (1) The mutagenic effect of TNFa is comparable to that of ionizing radiation. TNFa treatment in cultured cells resulted in increased gene amplification, micronuclei formation and chromosomal instability. (2) Antioxidants significantly reduced TNFa-induced genetic mutations. (3) TNFa also induced oxidative stress and nucleotide damages in mouse tissues in vivo. (4) Moreover, TNFa treatment alone led to increased malignant transformation of mouse embryo fibroblasts, which could be partially suppressed by antioxidants. (5) The mutagenic effect of TNFa is independent that of NF?B which was shown to be a mediator in inflammation-associated cancers. Conclusions: As TNFa is known to be involved in chronic inflammatory diseases such as chronic hepatitis, ulcerative colitis and chronic skin ulcers and these diseases predispose the patients to cancer development, our results suggest a novel pathway through which TNFa promotes cancer development through induction of gene mutations, in addition to the previously reported mechanisms in which NF-?B activation was implicated. No significant financial relationships to disclose.
Gene profiling of tumor tissue in the diagnosis of patients with carcinoma of unknown primary site (CUP): Evaluation of the Veridex 10-gene molecular assay
Authors: Hainsworth J. D. , Talantov D. , Jatkoe T. , Meng C. , Baden J. , Spigel D. R. , Mazumder A. , Wang Y. , Greco F. A. 
Published: March 2020

21109 Background: Standard treatment for most patients with CUP involves empiric chemotherapy. Since specific treatment now exists for most types of advanced carcinoma, precise identification of the primary site could lead to improved therapy. Veridex developed an optimized set of 10 gene markers, for a qRTPCR assay to identify tissue of origin of metastatic carcinoma in formalin-fixed, paraffin-embedded (FFPE) tissue samples (J Mol Diagn 8:320, 2006). The assay includes markers for 6 primary sites: lung, pancreas, colon, breast, ovary, and prostate. In this retrospective study, we evaluated the Veridex assay in patients with CUP. Methods: We obtained FFPE tissue from diagnostic biopsies on 69 CUP patients previously enrolled in empiric chemotherapy studies. The Veridex assay was performed as previously described. Assay results were correlated with clinical features, pathologic features, and response to treatment. Results: The Veridex assay yielded provisional diagnoses in 42 of 69 patients (61%): lung (15), pancreas (11), colon (12 ), ovary (4), breast (0), and prostate, (0 ). Most patients with diagnoses of lung and pancreas cancer had clinical and pathologic features compatible with these diagnoses; response rates to empiric chemotherapy (usually taxane/platinum-based) in patients with these diagnoses were 29% and 9%, respectively. The 12 patients with colon cancer diagnoses had predominantly intra-abdominal metastases (liver, peritoneum); response rate to therapy (usually taxane/platinum- based) was low (8%). The 4 patients with ovarian cancer had atypical clinical and pathologic features, and only 1 of 4 had PR to first-line taxane/platinum therapy. Conclusions: In this retrospective study, the Veridex 10-gene molecular assay was feasible and provided provisional diagnoses in a majority of patients with CUP. The diagnoses made using this assay (except ovarian cancer) were compatible with clinicopathologic features. The efficacy of cancer-specific treatment in patients diagnosed by this assay will be evaluated in prospective studies. No significant financial relationships to disclose.
Triple-negative breast cancer. A clinicopathologic study of 113 cases and comparison with 55 cases with triple positive breast cancer: A matched-control analysis
Authors: El Weshi A. , Tulbah A. , Al Sayed A. , El Twegeri T. , AL Shabanah M. , AL Malik O. , Ajarim D. 
Published: March 2020

21119 Background: Hormone receptor negative breast cancer (BC) is associated with poor outcome. BC patients (pts) with HER2/neu over expression (IHC 3+) are associated as well with poor prognosis. Aim: to further divide breast cancer to prognostic subgroups using interaction between these 2 prognostic factors. Methods: Between January 2002 and May 2004, the clincopathological features as well as treatment results of all non metastatic pts with triple negative BC (TNBC) and those with triple positive BC (TPBC) were reviewed. In all patients the three immunohistochemical markers, ER, PR and HER2/neu were available for review. Results: 113 TNBC pts and 55 TPBC were identified. In the TNBC group; median age was 42y, 76 % were premenopause, 21% with + family history (FH) and 6% were pregnant at diagnosis. Clinical stage (CS): I: 4%, II: 60%, III: 36%. Neo-adjuvant chemotherapy (NACT) was given to 29 %. Modified radical mastectomy (MRM) and breast conservative surgery (BCS) were performed in 49% and 51% respectively. Adjuvant CT (ACT) and radiotherapy (RT) were given to 85% and 84% of the pts. In the TPBC group, the median age was 43y, 71% were premenopause, 16% with + FH, and 2% were pregnant. The CS in the TPBC group was I: 4%, II: 65%, III: 31%. The distributions of NACT, MRM, BCS, ACT and RT in TPBC pts were 35%, 64%, 36%, 60% and 84% respectively. All TPBC pts received adjuvant hormonal therapy and non received adjuvant Herceptin. Relapse rate was 34% in TNBC and 20 % in TPBC (p = 0.04). At a median follow up of 40 months, 72% and 80% of the pts in the TNBC and TPBC groups are alive and disease free respectively. The 4y EFS and OS were 64% and 76% in TNBC and 74% and 89% in TPBC group (p = 0.04 and 0.008 respectively). Conclusions: TNBC is an aggressive neoplasm and has a poor outcome. More aggressive adjuvant chemotherapy and possible biological therapy directed against EGFR, based on previous released information of the prevalence of EGFR in this particular phenotype, should be considered in this group of patients. No significant financial relationships to disclose.
Prognostic significance of immunohistochemical expression of Rb gene product in operable breast cancer
Authors: Song H. , Do Y. , Gang S. , Kwon S. , Kim S. , Lee W. , Lee J. 
Published: March 2020

21121 Background: The aim of this study was to investigate the prognostic significance of the expression of Rb gene product in operable invasive breast cancer by performing immunohistochemical analysis. Methods: Between January 1993 and December 2001, 212 operable invasive breast cancer patients underwent immunohistochemical staining for Rb, and we retrospectively analyzed these results together with the clinical outcomes. Results: The overexpression of p53 was detected in 72.7% of the cases. The overexpression of Rb was correlated with positive hormonal receptor (p=0.000), and inversely correlated with lymph node metastasis (p=0.017) and vascular invasion (p=0.004). The tumor size, tumor histology, histologic grade, and tumor stage were not related to the overexpression of p53. Multivariate Cox regression analysis indicate that lymph node metastasis and tumor size were the significant prognostic factors for overall survival; lymph node metastasis was the significant prognostic factor for relapse free survival. On the subgroup analysis, the Rb expressors showed better 7-year overall survival (98.5% vs. 81.5%, respectively, p=0.005) and relapse free survival (94.1% vs. 77.4%, respectively, p=0.021) than did the p53 non-overexpressors for the patients without lymph node metastasis. However, for the patients with lymph node metastasis, the survival rates were not different for both the Rb expressors and the Rb non-expressors. Conclusions: Immunohistochemical staining of the Rb gene product was an independent prognostic factor for predicting survival of the lymph node negative operable breast cancer patients. No significant financial relationships to disclose.
Expression of matrix metalloproteinases (MMP1, 2, 9, and 11) in metastatic lymph node tissue of breast cancer patients
Authors: Fink-Retter A. , Gschwantler-Kaulich D. , Hudelist G. , Walter I. , Czerwenka K. , Singer C. 
Published: March 2020

21138 Background: Invasive growth requires degradation of extracellular matrix. A number of Zn 2+ -dependent matrix metalloproteinases (MMPs) is associated with this process and leads to local invasion and metastasis in malignant breast tumors. Especially the expression of MMP-2 and MMP-9 has been associated with high potential of metastasis in breast cancer. Methods: We determined the expression patterns of epithelial (E) and stromal (S) MMP-1, MMP-2, MMP-9 and MMP-11 by immunohistochemistry in tissue arrays, containing 50 paraffin-embedded sets of tissues obtained from the malignant tumor of the breast, and 50 paraffin-embedded sets of tissues from metastatic lymph nodes (purchased from Biomax, Biomax Inc, Rockville, MD). Results: MMP2-S and MMP9-S protein expression was significantly higher in lymph node tumor tissue when compared to breast tumor tissue (10% vs. 2%; p=0.005; 78.3% vs. 94.8%, p=0.01 Chi Square test, respectively). MMP9-E showed a borderline significance in lymph node tumor tissue (92.6% vs. 73.5%; p=0.05 Chi Square test). While in breast tumor tissue significant correlations were observed between all MMPs except MMP2-S, these associations were less pronounced in lymph node tumor tissue. Conclusions: We suggest that the expression of MMP-2 and MMP-9 in breast cancer tissue is associated with a high invasive and metastatic potential. This might be confirmed by our finding that MMP2-S, MMP9-S and MMP9-E are increased expressed in metastatic lymph node tissue. This is in line with other studies which showed that MMP-2 and MMP-9 expression in primary breast cancer tissue samples was associated with breast cancer progression and invasion. No significant financial relationships to disclose.
Semi-quantitative gene expression profiling for therapy prediction in a breast cancer neoadjuvant therapy study applying docetaxel/epirubicin/cyclophosphamide
Authors: Vogt U. , Kemming D. , Brandt B. , Bosse U. , Bonk U. , Assen A. v. d. , Muhs H. J. , Schlotter C. M. 
Published: March 2020

21144 Background: More than 28000 curated human genes can be analyzed semi-quantitatively using a chemiluminescent detection technology and 60mer oligonucleotides on a Human Genome Survey Microarray (HGSM, Applied Biosytems). Methods: HGSM expression profiling was performed on biopsy samplesfrom a setting of patients under neoadjuvant treatment. The protocol for a phase II study was elaborated for the treatment of breast cancer patients suffering from a primary tumor > 1,5 cm or inflammatory breast cancer with Docetaxel / Epirubicin/Cyclophosphamide (TEC) prior to surgical treatment. The study was approved by the local ethical committee and 80 patients will be included into the study after written informed consent. 40 patients have been already included in the ongoing study. In this prospective study a biopsy from the tumor is taken before chemotherapy. Therefore, success of treatment is detectable directly at the operated residual tumor. Our results demonstrate a low rate of false-positives (1.2%), a high specificity and quantification accuracy of HGSM system. Comparison of data from HGSM and RT-PCR obtained on mRNA from fresh frozen tissue resulted a Pearson-correlation of 0.92 to 0.63 for the breast cancer genes. Results: Tumour response (pCR, pPR) of more than 70 % can be achieved using neoadjuvant TEC- regimen. 25 % of pCR in this study is comparable with data of other published neoadjuvant trails. First expression profiling results are obtainable showing that a subset of 148 genes indicates patients with complete remission (pCR, no detectable tumor at end of chemotherapy), partial remission (pPR) and progressive disease (pPD). Remarkable, that the expression profile clearly separated pCR and pPD tumors whereas pPR tumors presented with a closer relationship to pPD tumors than to pCR tumors but displayed small specific subprofiles. A comparable separation of the groups could not achieved by established tumor markers, e.g. ER, PgR, HER2, uPA etc. which are measured simultaneously on the HGSM. Conclusions: HGSM expression profiling is promising to have the potential to figure out genes that are related to cancer progression and chemotherapy resistance, especially in PST. No significant financial relationships to disclose.
Clinicopathological features in correlation with epidermal growth factor receptor gene mutations in non-small cell lung cancer (NSCLC)
Authors: Tanaka F. , Matsumoto S. , Takuwa T. , Kondo N. , Okumura Y. , Fukuoka K. , Nakano T. , Hasegawa S. 
Published: March 2020

21148 Background: Mutations in the epidermal growth factor receptor (EGFR) gene are found in 10–30% of non-small cell lung cancer, and are useful to predict the efficacy of EGFR-tyrosine kinase inhibitors (EGFR-TKIs) such as gefitinib and erlotinib. However, it is sometimes difficult to examine such mutations. Thus, prediction of presence or absence of EGFR mutations, correlated with clinical response to EGFR-TKIs, based on clinicopathological characteristics may be important in clinical practice. Methods: We retrospectively assessed EGFR-mutation status in correlation with clinical features including FDG-PET findings and pathological features including presence or absence of bronchioalveolar component (BAC) in adenocarcinoma (Ad) case. A total of 72 consecutive patients (24 females; mean age, 65 years; 40 Ad cases) who received thoracotomy from August 2005 through October 2006 were reviewed Results: Sixteen cases (22%) had EGFR-mutations (8 cases each in exon 19 and exon 21). The incidence of EGFR-mutation was significantly higher in female (42%) or never-smoker (60%) than in male (13%) or smoker (15%). EGFR-mutation was almost exclusively found in Ad; among Ad cases, there was no significant difference in the incidence of EGFR-mutation between BAC-positive (47%) and BAC-negative cases (29%; p=0.33). Among 61 cases who received FDG-PET scan prior to thoracotomy, only 15% of EGFR- mutated cases had higher FDG-uptake, whereas 47% of EGFR-wild cases had higher FDG-uptake (p=0.36); the sensitivity and specificity of lower FDG-uptake to predict the presence of EGFR-mutations were 71% and 53%, respectively. The positive predictive value (PPV) of lower- FDG-uptake for the presence of EGFR-mutations was only 29%, but the negative predictive value (NPV) was as high as 85%. The mean standardized uptake value (SUV) of FDG for EGFR-wild patients and EGFR-mutated patients were 5.7 and 3.3, respectively (p=0.11). The mean SUV for tumors mutated in exon 19 seemed to be lower than that for tumors mutated in exon 21 (1.8 versus4.6). Conclusions: Higher FDG-uptake combined with clinical features (male and smoker) may help to exclude patients with EGFR-wild tumors who may not respond to EGFR-TKIs treatment. No significant financial relationships to disclose.