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Serial analysis of gene expression of lobular carcinoma in situ identifies down regulation of claudin 4 and overexpression of matrix metalloproteinase 9
Dengfeng Cao, Kornelia Polyak, Marc K Halushka, Hind Nassar, Nina Kouprina, Christine Iacobuzio-Donahue, Xinyan Wu, Saraswati Sukumar, Jessica Hicks, Angelo De Marzo, Pedram Argani
Breast Cancer Research , 2008, DOI: 10.1186/bcr2189
Abstract: We analysed the comprehensive gene expression profile of a unique case of mass-forming LCIS using serial analysis of gene expression (SAGE). This SAGE library is publicly available online. By comparing the gene expression profile of LCIS to that of benign breast epithelium and stroma, we identified several genes up and down regulated in LCIS. Differential expression of selected genes not previously studied in LCIS was validated at the protein level by immunohistochemistry and at the RNA level by quantitative reverse transcriptase PCR (RT-PCR).We identified down regulation of claudin 4 and overexpression of matrix metalloproteinase 9 in LCIS relative to normal breast epithelium and stroma. We validated these findings by immunohistochemistry in a separate series of 11 and 19 LCIS cases, respectively. Overexpression of matrix metalloproteinase 9 was further confirmed by quantitative RT-PCR analysis of the index case.We have created the first global gene expression profile of LCIS, and demonstrated down regulation of cell junction proteins (an expected result) and overexpression of matrix metalloproteinase 9 (an unexpected result). Additional analysis of this data made available as an online resource should facilitate further molecular characterisation of LCIS.Lobular carcinoma in situ (LCIS) is characterised by small, discohesive epithelial cells that fill, distend and distort the terminal duct lobular units of the breast [1,2]. LCIS cells, which are cytologically identical to those of invasive lobular carcinoma, frequently contain mucin vacuoles, imparting a signet-ring cell appearance. At the immunohistochemical level, the hallmark of LCIS is loss of the expression of the E-cadherin protein, which results in the loss of cohesion of the cells. Unlike ductal carcinoma in situ (DCIS), a localised proven precursor to invasive breast carcinoma, LCIS tends to be multifocal and bilateral, and typically is neither calcified on mammography nor mass forming on clinical or gros
Comprehensive serial analysis of gene expression of the cervical transcriptome
Ashleen Shadeo, Raj Chari, Greg Vatcher, Jennifer Campbell, Kim M Lonergan, Jasenka Matisic, Dirk van Niekerk, Thomas Ehlen, Dianne Miller, Michele Follen, Wan L Lam, Calum MacAulay
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-142
Abstract: We have sequenced 691,390 tags from four L-SAGE libraries increasing the existing gene expression data on cervical tissue by 20 fold. One-hundred and eighteen unique tags were highly expressed in normal cervical tissue and 107 of them mapped to unique genes, most belong to the ribosomal, calcium-binding and keratinizing gene families. We assessed these genes for aberrant expression in CIN III and five genes showed altered expression. In addition, we have identified twelve unique HPV 16 SAGE tags in the CIN III libraries absent in the normal libraries.Establishing a baseline of gene expression in normal cervical tissue is key for identifying changes in cancer. We demonstrate the utility of this baseline data by identifying genes with aberrant expression in CIN III when compared to normal tissue.Approximately 500,000 women are diagnosed with cervical cancer worldwide each year and more than half of them will die from this disease [1]. The highest incidence rates are observed in developing countries where it is the second most prevalent cancer in women and remains a leading cause of cancer related death [1]. Widely implemented screening programs have been responsible for the much lower incidence and mortality rates seen in the developed world. Present day screening methods primarily identify precancer lesions termed cervical intraepithelial neoplasia (CIN). CIN lesions are classified into three subgroups, CIN I, CIN II and CIN III, corresponding to mild, moderate and severe dysplasia/carcinoma in situ (CIS), respectively. CIN III lesions have a high likelihood of progression to invasive disease if left untreated [2]. Human Papillomavirus (HPV) has long been established as a necessary but not sufficient cause for cervical carcinoma development. HPV is detected in 99% of invasive disease, 94% of CIN lesions and 46% of normal cervical epithelium [2]. The high risk strains HPV 16 and HPV 18 are most prevalent in invasive disease.A comprehensive characterization of gene exp
A human glomerular SAGE transcriptome database
Jenny Nystr?m, Wolfgang Fierlbeck, Anna Granqvist, Stephen C Kulak, Barbara J Ballermann
BMC Nephrology , 2009, DOI: 10.1186/1471-2369-10-13
Abstract: The database contains 22,907 unique SAGE tag sequences, with a total tag count of 48,905. For each SAGE tag, the ratio of its frequency in glomeruli relative to that in 115 non-glomerular tissues or cells, a measure of transcript enrichment in glomeruli, was calculated. A total of 133 SAGE tags representing well-characterized transcripts were enriched 10-fold or more in glomeruli compared to other tissues. Comparison of data from this study with a previous human glomerular Sau3A-anchored SAGE library reveals that 47 of the highly enriched transcripts are common to both libraries. Among these are the SAGE tags representing many podocyte-predominant transcripts like WT-1, podocin and synaptopodin. Enrichment of podocyte transcript tags SAGE library indicates that other SAGE tags observed at much higher frequencies in this glomerular compared to non-glomerular SAGE libraries are likely to be glomerulus-predominant. A higher level of mRNA expression for 19 transcripts represented by glomerulus-enriched SAGE tags was verified by RT-PCR comparing glomeruli to lung, liver and spleen.The database can be retrieved from, or interrogated online at http://cgap.nci.nih.gov/SAGE webcite. The annotated database is also provided as an additional file with gene identification for 9,022, and matches to the human genome or transcript homologs in other species for 1,433 tags. It should be a useful tool for in silico mining of glomerular gene expression.Renal glomeruli are highly specialized capillary tufts that produce a nearly protein-free ultrafiltrate of plasma at a rate of about 30 plasma volumes daily. Several hereditary, immune-mediated and metabolic disorders cause glomerular injury, proteinuria, and can lead to renal failure. The three intrinsic glomerular cell types, podocytes, mesangial cells, and glomerular endothelial cells (EC) are highly specialized. Podocytes extend an elaborate array of actin-rich foot processes around the exterior of the glomerular capillary loops, for
A Case Report: Lobular Carcinoma In Situ in a Male Patient with Subsequent Invasive Ductal Carcinoma Identified on Screening Breast MRI  [cached]
Linda Kao, Yekaterina Bulkin, Susan Fineberg, Leslie Montgomery, Tova Koenigsberg
Journal of Cancer , 2012,
Abstract: Lobular carcinoma in situ is a form of in situ neoplasia that develops within the terminal lobules of the breast. It is an extremely rare finding in males due to the lack of lobular development in the male breast. The authors herein report an unusual case of incidentally discovered lobular carcinoma in situ in a male patient with recurrent bilateral gynecomastia who was subsequently diagnosed with invasive ductal carcinoma of the left breast. The pathology of lobular carcinoma in situ in a male as well as screening MRI surveillance of male patients at high risk for breast cancer are discussed, emphasizing the importance of screening and imaging follow up in men who are at high risk for breast cancer.
Protein expression of c-erbB-2 and p53 in normal ducts, ductal carcinoma in situ and invasive carcinoma of the same breast
Menezes, Marcus Vinicius Martins de;Cestari, Anna Letícia Oliveira;Almeida, Orlando;Alvarenga, Marcelo;Pinto, Glauce Aparecida;Gurgel, Maria Salete Costa;Souza, Gustavo Ant?nio de;Zeferino, Luiz Carlos;
Sao Paulo Medical Journal , 2006, DOI: 10.1590/S1516-31802006000300002
Abstract: context and objective: breast cancer is thought to derive from progressively aberrant, non-invasive breast lesions, but it is not known exactly how invasive breast cancer develops from these lesions. the aim of this study was to verify the changes in c-erbb-2 and p53 protein expression between non-neoplastic ducts, ductal carcinoma in situ and invasive ductal carcinoma found in the same breast. design and setting: this was a cross-sectional study at centro de aten??o integral à saúde da mulher, campinas, brazil. methods: fifty-six women with invasive ductal carcinoma and ductal carcinoma in situ in the same breast were included. the expression of c-erbb-2 and p53 proteins was assessed in non-neoplastic and neoplastic cells using immunohistochemical techniques. results: the c-erbb-2 protein was absent in non-neoplastic ducts but was present in 46% and 36% of in situ and invasive carcinoma components, respectively. only 2% of non-neoplastic ducts, and 18% and 16% of ductal carcinoma in situ and invasive carcinoma components, respectively, were positive for p53 protein. no significant difference in c-erbb-2 and p53 protein expression was observed between in situ and invasive components. the nuclear grade agreement between in situ and invasive carcinoma was very good. conclusions: the invasiveness of ductal carcinoma in situ seems to be independent of the her-2/neu and tp53 genes. the general features of an occurrence of breast carcinoma are formulated at the outset of carcinogenesis, and the her-2/neu and tp53 genes are involved.
A Comparison of Tumor Biology in Primary Ductal Carcinoma In Situ Recurring as Invasive Carcinoma versus a New In Situ  [PDF]
Wenjing Zhou,Christine Johansson,Karin Jirstr?m,Anita Ringberg,Carl Blomqvist,Rose-Marie Amini,Marie-Louise Fjallskog,Fredrik W?rnberg
International Journal of Breast Cancer , 2013, DOI: 10.1155/2013/582134
Abstract: Introduction. About half of all new ipsilateral events after a primary ductal carcinoma in situ (DCIS) are invasive carcinoma. We studied tumor markers in the primary DCIS in relation to type of event (invasive versus in situ). Methods. Two hundred and sixty-six women with a primary DCIS from two source populations, all with a known ipsilateral event, were included. All new events were regarded as recurrences. Patient and primary tumor characteristics (estrogen receptor (ER), progesterone receptor (PR), HER2, EGFR, and Ki67) were evaluated. Logistic regression was used to calculate odd ratios and 95% confidence intervals in univariate and multivariate analyses. Results. One hundred and thirty-six of the recurrences were invasive carcinoma and 130 were in situ. The recurrence was more often invasive if the primary DCIS was ER+ (OR 2.5, 95% CI 1.2–5.1). Primary DCIS being HER2+ (OR 0.5, 95% CI 0.3–0.9), EGFR+ (OR 0.4, 95% CI 0.2–0.9), and ER95?/HER2+ (OR 0.2, 95% CI 0.1–0.6) had a lower risk of a recurrence being invasive. Conclusions. In this study, comparing type of recurrence after a DCIS showed that the ER?/HER2+ tumors were related to a recurrence being a new DCIS. And surprisingly, tumors being ER+, HER2?, and EGFR? were related to a recurrence being invasive cancer. 1. Introduction Ductal carcinoma in situ (DCIS) of the breast is a clinically and molecularly heterogeneous disease with different malignant potentials [1, 2]. The risk of local recurrence after breast-conserving surgery only (BCS) is rather high and even higher than after surgery for invasive breast cancer [3, 4]. In DCIS, adding radiotherapy after BCS lowered the relative risk with approximately 50%, from 28.1% to 12.9% after ten years in a meta-analyses including four randomized studies [5, 6]. About half of the women with a local recurrence develop a new DCIS and the other half an invasive carcinoma [7–10]. Although women with a primary DCIS have a very good prognosis [6], those with a subsequent invasive carcinoma have an increased risk of dying from breast cancer. In a recently published study the 15-year breast cancer specific survival was just over 60% among those with an invasive recurrence after a primary DCIS [11, 12]. One of the major goals of the treatment of DCIS is to prevent invasive disease. There are surgical and biological risk factors for local recurrence, for example, young age, mode of detection (clinically detected as compared to screening detected), margins, and grade [13, 14]. Also, a recently published study using the Oncotype DX DCIS score showed that
FGFR1 is amplified during the progression of in situ to invasive breast carcinoma
Min Jang, Eun Kim, Yoomi Choi, Hee Lee, Yu Kim, Jee Kim, Eunyoung Kang, Sung-Won Kim, In Kim, So Park
Breast Cancer Research , 2012, DOI: 10.1186/bcr3239
Abstract: We performed fluorescence in situ hybridization of the selected genes on tissue microarrays composed of 179 pure DCIS and 438 invasive carcinomas. Two hundred and sixteen of the latter had DCIS components, and in those cases we compared gene amplification in the intraductal and invasive components of each carcinoma.The rate of amplification of FGFR1 was higher in invasive carcinomas than in the pure DCIS, but the opposite was true for HER2 amplification. These findings applied consistently to high-grade tumors, but not to low/intermediate-grade tumors. The amplification status of HER2, C-MYC, CCND1 and FGFR1 was generally similar in the matched invasive and DCIS components of the same tumors. However, FGFR1 amplification was more common in the invasive components than in the DCIS components. In survival analyses, FGFR1 amplification was found to be an independent prognostic factor for poor disease-free survival for all patients with invasive carcinoma and for the hormone receptor-positive subgroup.Amplification of HER2, C-MYC and CCND1 seems to play a role in the early development of breast cancer, but not in its progression. However, the increased frequency of FGFR1 amplification in invasive carcinomas compared with pure DCIS and in the invasive components of individual tumors, and its association with decreased disease-free survival, suggests a role for FGFR1 amplification in the progression of breast cancer including in situ-to-invasive transition, as well as initiation.Development of breast cancer depends on the accumulation of a variety of genetic alterations, including activation or amplification of oncogenes [1]. In breast cancer, the most prominent and frequent amplicons have been located at chromosomal positions 1q, 8p12, 8q24, 11q13, 12p13, 16p13, 7q12-21 and 20q13, and several target oncogenes have been identified [2-5]. The best characterized oncogene is HER2, located at 17q12-21, which is amplified in 15 to 20% of breast cancers [6,7]. Other oncogenes t
A quantitative view of the transcriptome of Schistosoma mansoni adult-worms using SAGE
Elida PB Ojopi, Paulo SL Oliveira, Diana N Nunes, Apu? Paquola, Ricardo DeMarco, Sheila P Gregório, Karina A Aires, Carlos FM Menck, Luciana CC Leite, Sergio Verjovski-Almeida, Emmanuel Dias-Neto
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-186
Abstract: After extracting mRNA from pooled male and female adult-worms, a SAGE library was constructed and sequenced, generating 68,238 tags that covered more than 6,000 genes expressed in this developmental stage. An analysis of the ordered tag-list shows the genes of F10 eggshell protein, pol-polyprotein, HSP86, 14-3-3 and a transcript yet to be identified to be the five top most abundant genes in pooled adult worms. Whereas only 8% of the 100 most abundant tags found in adult worms of S. mansoni could not be assigned to transcripts of this parasite, 46.9% of the total ditags could not be mapped, demonstrating that the 3 sequence of most of the rarest transcripts are still to be identified. Mapping of our SAGE tags to S. mansoni genes suggested the occurrence of alternative-polyadenylation in at least 13 gene transcripts. Most of these events seem to shorten the 3 UTR of the mRNAs, which may have consequences over their stability and regulation.SAGE revealed the frequency of expression of the majority of the S. mansoni genes. Transcriptome data suggests that alternative polyadenylation is likely to be used in the control of mRNA stability in this organism. When transcriptome was compared with the proteomic data available, we observed a correlation of about 50%, suggesting that both transcriptional and post-transcriptional regulation are important for determining protein abundance in S. mansoni. The generation of SAGE tags from other life-cycle stages should contribute to reveal the dynamics of gene expression in this important parasite.Quantitative and qualitative transcriptome analyses reveal some of the most important biological aspects of an organism. Transcriptome examination is crucial for the understanding of significant biological processes, allowing the study of transcription/translation relationships, the dynamics of gene expression and, an important feature in parasites, a quantitative evaluation of the expression of genes that are potential targets for drugs or
Transcriptome of pig muscle assessed by erial analysis of gene expression (SAGE)
S. Dal Monego,A. Pallavicini,G. Graziosi,B. Stefanon
Italian Journal of Animal Science , 2010, DOI: 10.4081/ijas.2005.2s.88
Abstract: Serial analysis of gene expression (SAGE) is a molecular biology technique applied to measure the global gene expression levels, characterise transcriptomes, compare the transcript levels between tissues and uncover new molecules within defined signal transduction pathways (Tutela and Tuteja, 2004).
Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature
Stephen J Robinson, Isobel AP Parkin
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-434
Abstract: Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4°C). Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Interpretation of these data was facilitated by representing the SAGE data by gene identifier, allowing more robust statistical analysis, cross-platform comparisons and the identification of genes sharing common expression profiles. Simultaneous statistical calculations across all five libraries identified 920 low temperature responsive genes, only 24% of which overlapped with previous global expression analysis performed using microarrays, although similar functional categories were affected. Clustering of the differentially regulated genes facilitated the identification of novel loci correlated with the development of freezing tolerance. Analysis of their promoter sequences revealed subsets of genes that were independent of CBF and ABA regulation and could provide a mechanism for elucidating complementary signalling pathways. The SAGE data emphasised the complexity of the plant response, with alternate pre-mRNA processing events increasing at low temperatures and antisense transcription being repressed.Alternate transcript processing appears to play an important role in enhancing the plasticity of the stress induced transcriptome. Novel genes and cis-acting sequences have been identified as compelling targets to allow manipulation of the plant's ability to protect against low temperature stress. The analyses performed provide a contextual framework for the interpretation of quantitative sequence tag based transcriptome analysis which will prevail with the application of next generation sequencing technology.Abiotic stresses, including temperature, are a major constrain
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