bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3014: Robust microRNA expression profiling of specific cells in complex archival tissue stained by immunohistochemistry
Authors: Hlubek Falk , Schuster Claudia , Budczies Jan , Kirchner Thomas 
Published: February 2011

Abstract
Molecular diagnostics in modern pathology has been limited by the use of formalin-fixed, paraffin-embedded (FFPE) tissues in current routine diagnostic procedures due to modification and degradation of nucleic acids. In particular, molecular analysis of specific cell types potentially important for basic research and biomarker identification is largely prevented in highly complex, solid tissues routinely used in histopathology. Our objective was to establish a sensitive and robust procedure to quantify miRNA expression in specific cells from complex archival colorectal tumor tissue identified by immunohistochemistry. We combined classical immunohistochemistry and isolation of specific tissue cells by lasermicrodissection with the molecular analysis based on miRNA-preamplification and expression analysis by quantitative real-time PCR. Here we show reliable detection of miRNA expression profiles determined from limited amounts of colorectal cancer FFPE-tissues after routine staining procedure. The combination of routinely used FFPE-specimens stained by immunohistochemistry with the molecular analysis of lasermicrodissected complex tumor tissue resulted in robust miRNA expression patterns exclusively obtained from epithelial tumor cells. This approach allows for a detailed molecular analysis of cancer cells and distinct stromal cell types and their in-situ interaction in solid tumors. The methodology can therefore offer new perspectives for basic research and, by comprehensive use of present archival tissue collections linked to clinical databases, facilitate miRNA biomarker identification in defined tissue cells for future diagnostic and therapeutic strategies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3014.
Abstract 3016: The value of microRNAs in the detection and staging of colorectal cancer
Authors: Ilyayev Nadia , Stojadinovic Alexander , Halle David , Roistacher Marina , Pavlov Vera , Mitrani-Rosenbaum Stella , Nissan Aviram 
Published: February 2011

Abstract
Introduction: MicroRNAs (miRNAs) are a large class of single strand RNA molecules consistent of 18-25 nucleotides, involved in post transcriptional gene silencing. miRNAs show tissue-specific expression and play an important role in carcinogenesis.
The aim of the present study was: A. to identify colorectal cancer (CRC)-specific miRNAs. B. To study the potential value of CRC-specific miRNAs in CRC detection and staging.
Methods: This study was approved by the Institutional Review Board (IRB). RNA was extracted from paired samples of normal and tumor tissue of CRC patients (n=10). miRNA expression was tested using a commercially available array. Differential expression between normal and tumor tissues was identified in 30 human miRNAs and in additional 16 miRNAs identified from database mining. Differential expression was validated by quantitative (real-time) PCR in a larger cohort of samples (n=20). RNA was extracted from sentinel lymph nodes (SLN) of CRC patients. A calibration plot was generated using a CRC cell line (HT29) mixed with peripheral blood lymphocytes (PBL) of healthy donors in a range of concentrations.
Results: After validation, only 8 miRNAs were found to be overexpressed in CRC.
The detection threshold for all 8 miRNAs measured by the calibration plot was 1:1000 (one HT-29 cell in 1000 PBMCs). The expression of the 8 miRNAs was then tested in SLNs (n=86). Fourteen lymph nodes (16.3%) were positive by standard pathological examination (H&E staining) and 25/86 (29.1%) were positive by miRNA expression analysis (p&lt;0.01). miRNA expression was detected in all sera from CRC patients (n=3) and in none of the sera obtained from healthy individuals (n=5, p&lt;0.0001).
Conclusions: A panel of 8 miRNAs was found to be overexpressed in CRC patients. Occult residual disease was indentified in lymph nodes and serum of CRC patients using this miRNA panel.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3016.
Abstract 3017: MicroRNAs as prognostic indicators in gastric cancer
Authors: Kushnir Michal , Hoshen Moshe B. , Purim Ofer , Meiri Eti , Cholakh Hila , Barabash Naama , Goren Yaron , Marshak Gideon , Kundel Yulia , Morgenstern Sara , Halpern Marisa , Niv Yaron , Chajut Ayelet , Brenner Baruch 
Published: February 2011

Abstract
Background: Our ability to determine the prognosis of an individual patient with gastric cancer and thereby to select patients for adjuvant therapy is still limited. Preliminary data suggest that microRNAs may have a prognostic role in this disease. We hence decided to compare the microRNA profiles in the primary tumor of patients with recurrent and non-recurrent gastric cancer and to evaluate the prognostic impact of these molecules.
Patients and Methods: Eligible patients, who underwent curative gastrectomies between 1995 and 2005 and did not receive any pre- or postoperative adjuvant therapy, were identified from the database of the participating institutions. Total RNA was extracted from tumor formalin-fixed paraffin embedded (FFPE) samples using proprietary protocols that preserve the small RNA fraction. Initial profiling using microRNA microarrays identified potential microRNA biomarkers that can be used to predict recurrence of gastric cancer after resection. The expression of differential microRNAs, was verified by qRT-PCR.
Results: Forty-five eligible patients had adequate tumor content and microRNA expression data and were included in the analysis. Of these, 14 (31%) experienced recurrence of disease within three years from surgery (“bad prognosis” group) and 31 (69%) did not (“good prognosis” group). Advanced pathological stage and extensive surgical procedure correlated with bad prognosis. Signal levels of three microRNAs were found to be significantly differentially expressed in tumors from patients with good prognosis vs. patients with bad prognosis. High expression of each of these microRNAs was associated with significantly poorer prognosis for both recurrence and survival. Proprietary microRNA qRT-PCR showed a high correlation to microarrays and similar separation into prognosis groups based on microRNA expression.
Conclusion: We identified a set of microRNAs whose high expression was predictive of tumor recurrence and poor prognosis in patients with gastric cancer. This finding provides a basis for a novel tool for risk stratification in this disease and allows further insight into its pathogenesis. Based on these results, a validation study, on a larger and independent cohort of patients, is planned.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3017.
Abstract 3025: Detection of prostatic fluid micro-RNA species associated with prostate cancer
Authors: Lewis Holly B. , Lance Raymond S. , Drake Richard R. , Kerscher Aurora E. 
Published: February 2011

Abstract
There is a need to develop more accurate and specific biomarkers that can be used in the early detection and determination of aggressiveness of prostate cancers. Collection of expressed prostatic secretions (EPS) in urine can be done following digital rectal exam (DRE) and gentle massage of each side of the prostate gland. This massage stimulates the release and movement of prostatic fluids and detached epithelial cells into the urethra. EPS is currently being used to develop genetic screens for expression of PCA3 non-coding RNA and TMPRSS2/Erg fusion transcripts, and thus could also provide a rich source of prostate-derived microRNAs (miRNAs). This collection is easily obtained, not disruptive to a standard urological exam and can be collected from men at all stages of prostate cancer, thus making EPS an ideal material to develop diagnostic screens for prostate cancer. Proteins and nucleic acids obtained from these fluids are characteristic of the prostate because the fluid is largely devoid of seminal vesicle-derived proteins or sperm. An additional prostatic fluid from cancer patients, termed direct EPS, has been collected via the penis following a vigorous pre-prostatectomy exam while the patient is under anesthesia. Our laboratory has begun to profile the expression of EPS-derived miRNAs to identify novel prostate cancer biomarkers. Large sample numbers of pre-DRE and post-DRE EPS urine specimens from prostate cancer patients and non-cancer controls have been collected to facilitate identification of cancer-specific as well as prostate-specific miRNA biomarkers. We have optimized procedures to isolate and profile the expression of EPS-derived miRNAs using stem-loop RT followed by TaqMan PCR analysis from 0.2-0.5 mls of sample. Several miRNAs linked to cancer progression (i.e., let-7, miR-16, miR-17, miR-21) have been successfully profiled and show differential expression patterns in post-DRE EPS urine samples obtained from prostate cancer patients compared to non-cancer controls. For comparison, we have also identified a subset of miRNA genes that are enriched in prostate cancer cell lines exhibiting invasive metastatic characteristics as well as miRNAs that are enriched in non-invasive prostate cell lines. We are testing if the expression of these miRNA subclasses correlates with the disease states of our patient EPS specimens, with the goal of developing miRNA signatures that could be used as new diagnostic and prognostic biomarkers for prostate cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3025.
Abstract 3027: Plasma microRNA as a potential marker for breast cancer detection
Authors: Ng Enders K.O. , Leung Candy , Au Stephanie , Chan Aaron , Wong Chris , Ma Edmond , Pang Roberta , Chua Daniel , Chu KM , Law WL , Poon Ronnie TP , Kwong Ava 
Published: February 2011

Abstract
Background: Recently, the emergence of small non-protein-coding RNAs, so-called microRNAs (miRNAs), playing important roles in oncogenesis has opened new opportunities for early cancer diagnosis. We have previously shown that microRNAs (miRNAs) in plasma are promising biomarkers for colorectal cancer detection. Here, we investigated whether plasma miRNAs could discriminate patients with and without breast cancer (BC).
Methods: Using TaqMan-based low density miRNA array, miRNAs were profiled from cancerous and adjacent non-cancerous breast tissues, corresponding plasma of 5 BC patients, along with plasma from 5 healthy controls. Marker selection and validation were performed by real-time quantitative RT-PCR on a small set of plasma. Independent set of plasma from 80 BC patients, 20 gastric cancer, 20 lung cancer, 20 colorectal cancer, 20 hepatocellular carcinoma and 50 healthy controls were further validated.
Results: Of the panel of 377 miRNAs analyzed, 8 miRNAs (miR-16, miR-21, miR-27a, miR-141, miR-191, miR-200c, miR-210, miR-451) were up-regulated both in plasma and tissue samples of 5 BC patients. All 8 putative miRNA markers were validated on the plasma of 15 BC patients and 15 healthy controls. Only three miRNAs were significantly elevated in this cohort of BC patients (p&lt;0.0005). The plasma levels of the three markers in those 15 BC patients were significantly reduced after surgery (p&lt;0.05). Further validation with an independent set of plasma samples (n=210) indicated that two markers differentiate BC from normal subjects, colorectal cancer, gastric cancer, hepatocellular carcinoma and lung cancer. These two markers yielded a combined receiver operating characteristic curve area of 88.5%, the sensitivity was 92% and the specificity was 72% in discriminating BC from control subjects.
Conclusions: Plasma miRNAs significantly elevated in BC patients are identified. This can be a novel noninvasive molecular marker for BC screening.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3027.
Abstract 3031: Screening for plasma micro RNAs as biomarkers for breast cancer detection
Authors: Marian Catalin , Bebu Ionut , Kella Danesh , Zhou Xin , Islam Md , Ressom Habtom , Shields Peter , Zheng Yun-Ling 
Published: February 2011

Abstract
Introduction: MicroRNAs (miRNAs) are small, non-coding RNA molecules that play critical roles in a variety of physiological and pathological processes, including carcinogenesis of breast cancer. The research regarding miRNA discovery and characterization is emerging and there is consensus in the literature that miRNAs are excellent candidate biomarkers for human cancer. Cancer specific miRNAs have been detected in tumors as well as in serum, plasma, and other body fluids. However, no extensive profiling of circulating miRNAs in breast cancer patients has been done to date, although several studies investigated a limited number of miRNA panels.
Methods: We investigated the miRNA profile in plasma samples collected before surgery from 10 pathologically confirmed breast cancer patients, one month after surgery from 2 breast cancer patients, and from 10 healthy women controls that were frequency matched to cases on age and race. RNA was extracted from plasma using the mirVana Paris RNA isolation kit (Ambion) and miRNA profiling was done using the TaqMan® Human MicroRNA Array Set v.2.0 (Applied Biosystems), enabling the detection of 667 human mature miRNAs. Plasma miRNA levels were calculated using the well established comparative Ct method (ΔΔCt) relative to the selected controls, and both Wilcoxon rank-sum tests and t tests were used to compare plasma miRNA levels between control subjects and cancer patients. Correlation between miRNAs was assessed separately in cancer and control subjects.
Results: Ten miRNAs (1.5% of total) were detected in plasma of all subjects and 12 miRNAs (1.8% of total) were detected in at least 80% of cases and controls, respectively. Of these, 17 miRNAs presented a significant differential expression in plasma between cases and controls (p&lt;0.05). Only one of these (has-miR-191) was previously described as being differentially expressed in breast cancer tissue compared to normal breast tissue. Based on their ability to discriminate between cancer and controls, their fold change, p values, correlation coefficients and post-surgical levels, we selected 6 candidate miRNAs that will be validated in a larger sample set of 50 cases and 50 controls. The p values of these six candidates ranged between &lt;0.0001 and 0.005 and the fold change between cases and controls ranged from 33.85 to 111.80.
Conclusion: We identified several circulating miRNAs that are differentially expressed between breast cancer patients and normal controls, and therefore could serve as biomarkers for breast cancer detection if confirmed by future studies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3031.
Abstract 3033: Profiling of global changes in microRNA levels during adipocyte differentiation by real-time PCR
Authors: Sebastian Thomas , Dhundia Elica , Yerramilli Subrahmanyam , Lader Eric 
Published: February 2011

Abstract
We have used a novel real time PCR approach to profile global changes in microRNA expression during adipocytic differentiation of 3T3-L1 fibroblast cells. This profiling strategy makes use of a novel two stage screen resulting in a substantial increase in throughput and decrease in reagent use. In the first step, cDNA is prepared from individual samples of undifferentiated fibroblast, and cells at early and late stages of Adipocyte differentiation. A pooled cDNA sample prepared by pooling equimolar amounts of individual cDNAs was used in an initial profiling experiment to identify microRNAs that are expressed at detectable levels in the experimental system. Profiling was performed in triplicate with real time PCR assays for 591 mouse miRNAs (miRBase v12.0). In the second stage of screening, individual cDNA samples were each analyzed in triplicate using the assays for miRNAs that showed expression in the pooled cDNA sample. Expression data was normalized against a panel of small non-coding RNAs and was expressed as x-fold changes relative to expresion in undifferentiated 3T3L1 cells. Our results indicate that 192 (∼32%) miRNAs described in miRBase v12.0 were detectable in resting and differentiated 3T3-L1 cells, and of these, 38 (or 20%) showed differential regulation during adipogenesis (x-fold change&gt;3.0). When compared to data from previous array-based profiling studies, our screen identified additional differentially regulated miRNAs. In addition to profiling changes in mature miRNA levels, miRNA precursor stem loop transcripts were also quantified to gain insight into post transcriptional regulation (if any) of miRNA biogenesis during adipocyte differentiation. The high specificity and sensitivity of the miScript RT-PCR system, together with a novel sample-pooling strategy makes this system a method of choice for miRNA expression profiling. Pooled primary profiling can substantially reduce the total number of PCR reactions which need to be performed and increases assay throughput.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3033.
Abstract 3039: microRNA profiling of gastric cancer patients from formalin-fixed paraffin-embedded (FFPE) samples
Authors: Shimada Yutaka , Okumura Tomoyuki , Osawa Soshi , Sekine Shin-ichi , Moriyama Makoto , Sawada Shigeaki , Nagata Takuya , Takahashi Hiroyuki , Fukuoka Junya , Takano Yasuo , Fukumoto Manabu , Tsukada Kazuhiro 
Published: February 2011

Abstract
InIntroduction: microRNA (miRNA) are small non-coding RNAs which target specific mRNA. Recent progression of RNA extraction technology from formalin-fixed paraffin-embedded (FFPE) tissues enables us to access miRNA profiling using world wide stored specimens. Here, we present miRNA profiling of gastric cancer patients from FFPE specimens.
Method: First, we examined the level of cross-linking caused by formalin and degradation of mRNA and miRNA from day to year levels. Then, we established the criteria of evaluable RNA from FFPE specimens. The miRNA profiling was obtained from 47 gastric cancer patients who received operations from 1997 to 2007 using 3D-Gene human miRNA chip (Toray) which contains 885 miRNA species.
Results: Out of 47 paired samples, 37 pairs (78.8%) were determined evaluable with our criteria. As results, we showed that 30 miRNAs were significantly down-regulated and that 15 miRNAs were up-regulated in gastric cancer in comparison to normal gastric tissue. Of these, 18 miRNAs, including mir-21 and mir-34a, were identified as a prognostic factor of gastric cancer patients. Furthermore, we found 25 miRNAs have association with the recurrence of adjuvant oral Tegaful treatment and 5 miRNAs have association with lymph node metastasis.
Conclusion: We have discovered miRNAs that are associated with prognosis, chemosensitivity and lymph node metastasis in gastric cancer patients. miRNA profiling using FFPE specimens is a useful and promising method of evaluation of world wide stored specimens that accompany may valuable clinical data.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3039.
Abstract 3040: Differential microRNA expression between normal edometrium, endometrioid adenocarcinoma, papillary serous adenocarcinoma, and carcinosarcoma
Authors: Devor Eric J. , Goodheart Michael , DeGeest Koenraad , Bender David , Buekers Thomas , Leslie Kimberly K. 
Published: February 2011

Abstract
This study compares quantitative microRNA expression profiles of normal endometrial tissue and the three primary endometrial tumor types; endometrioid adenocarcinoma, papillary serous adenocarcinoma, and carcinosarcoma, representing a spectrum of tissue involvement, aggressiveness, and prognosis/ recurrence risk.
Methods: Total RNA was prepared directly from primary tissues and microRNA expression was profiled in two ways. Expression levels of 667 human microRNAs were assessed by qPCR using TaqMan microRNA Arrays (Applied Biosystems). In addition, a size-selected small RNA cloning strategy developed in our lab was employed to search for additional microRNAs via deep sequencing on the Illumina/Solexa platform.
Results: A number of recent surveys have implicated a small set of candidate microRNAs in endometrial cancers. Among theses are miR-103, miR-107, miR-141, miR-210, as well as the miR-200 family, particularly miR-200c. Our results confirm these previous studies as well as implicating several additional microRNAs.
Conclusions: Quantitative microRNA expression profiling of endometrial cancers demonstrates differential expression that segregates with tumor type and clinical prognosis. In addition, a number of specific microRNAs appear to be consistently either over- or under-expressed in these cancers compared to normal endometrium. It is these microRNAs, such as miR-210 and miR-200c, that comprise a set of markers for quantitative validation and target ascertainment with the potential to provide important correlates to cancer type and prognosis/ recurrence risk.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3040.