Abstract Previous studies have shown that among populations with a high rate of consanguinity, there is a significant increase in the prevalence of cancer. Single nucleotide polymorphism (SNP) array data (Affymetrix, 50K XbaI) analysis revealed long regions of homozygosity in genomic DNAs taken from tumor and matched normal tissues of colorectal cancer (CRC) patients. The presence of these regions in the genome may indicate levels of consanguinity in the individual's family lineage. We refer to these autozygous regions as identity-by-descent (IBD) segments. In this study, we compared IBD segments in 74 mostly Caucasian CRC patients (mean age of 66 years) to two control data sets: (a) 146 Caucasian individuals (mean age of 80 years) who participated in an age-related macular degeneration (AMD) study and (b) 118 cancer-free Caucasian individuals from the Framingham Heart Study (mean age of 67 years). Our results show that the percentage of CRC patients with IBD segments (≥4 Mb length and 50 SNPs probed) in the genome is at least twice as high as the AMD or Framingham control groups. Also, the average length of these IBD regions in the CRC patients is more than twice the length of the two control data sets. Compared with control groups, IBD segments are found to be more common among individuals of Jewish background. We believe that these IBD segments within CRC patients are likely to harbor important CRC-related genes with low-penetrance SNPs and/or mutations, and, indeed, two recently identified CRC predisposition SNPs in the 8q24 region were confirmed to be homozygous in one particular patient carrying an IBD segment covering the region. [Cancer Res 2008;68(8):2610–21]

AbstractRecently, we identified a novel breast cancer susceptibility locus at 6q22.33 following a genome-wide association study in the Ashkenazi Jewish genetic isolate. To replicate these findings, we did a case-control association analysis on 6q22.33 (rs2180341) in an additional 487 Ashkenazi Jewish breast cancer cases and in an independent non-Jewish, predominantly European American, population of 1,466 breast cancer cases and 1,467 controls. We confirmed the 6q22.33 association with breast cancer risk in the replication cohorts [per-allele odds ratio (OR), 1.18; 95% confidence interval (95% CI), 1.04-1.33; P = 0.0083], with the strongest effect in the aggregate meta-analysis of 3,039 breast cancer cases and 2,616 Ashkenazi Jewish and non-Jewish controls (per-allele OR, 1.24; 95% CI, 1.13-1.36; P = 3.85 × 10-7). We also showed that the association was slightly stronger with estrogen receptor–positive tumors (per-allele OR, 1.35; 95% CI, 1.20-1.51; P = 2.2 × 10-5) compared with estrogen receptor–negative tumors (per-allele OR, 1.19; 95% CI, 0.97-1.47; P = 0.1). Furthermore, this study provides a novel insight into the functional significance of 6q22.33 in breast cancer susceptibility. Due to the stronger association of 6q22.33 with estrogen receptor–positive breast cancer, we examined the effect of candidate genes on estrogen receptor response elements. Upon transfection of overexpressed RNF146 in the MCF-7 breast cancer cell line, we observed diminished expression of an estrogen receptor response element reporter construct. This study confirms the association of 6q22.33 with breast cancer, with slightly stronger effect in estrogen receptor–positive tumors. Further functional studies of candidate genes are in progress, and a large replication analysis is being completed as part of an international consortium. (Cancer Epidemiol Biomarkers Prev 2009;18(9):2468–75)

Supplementary Table 1 from The 6q22.33 Locus and Breast Cancer Susceptibility

Supplementary Figures 1-11. Supplementary Figure 1. Sample and analyses diagram. Supplementary Figure 2. Aggregate mutation spectrum of Guatemalan cervical tumors. Supplementary Figure 3. Highly amplified regions of chromosome (Chr.) 2, 6 and 10 in tumor A4. Supplementary Figure 4. Chromosome breakpoints in cervical tumors. Supplementary Figure 5. PIK3CA mutation and pathology. Supplementary Figure 6. Co-occurring mutations in the PIK3CA and PTEN genes. Supplementary Figure 7. Sanger sequence concordance of mutant read percentage. Supplementary Figure 8. Mutation Fraction of PIK3CA mutations. Supplementary Figure 9. Age range associations with PIK3CA mutation and HPV type. Supplementary Figure 10. PIK3CA and HPV E6 and E7 mRNA expression. Supplementary Figure 11. Model of cervical cancer progression.

Supplementary Tables 1-6. Supplemental Table 1. Primers used in Ion Torrent sequencing of HPV. Supplemental Table 2. Predicted somatic mutations in PIK3CA discovered by targeted sequencing of cervical tumors from Mexico, Venezuela, and Guatemala. Supplementary Table 3. Predicted somatic mutations in 5 candidate genes discovered by targeted sequencing of cervical tumors. Supplementary Table 4. Association of HPV type and PIK3CA mutation. Supplementary Table 5. PIK3CA mutations in histologic subtype in this and other published studies Supplementary Table 6. Fig.3A_B_C raw data

Supplementary Information from The Signatures of Autozygosity among Patients with Colorectal Cancer

Supplementary Table Legend from The 6q22.33 Locus and Breast Cancer Susceptibility

Background: Variants of unknown significance (VUSs) have been identified in BRCA1 and BRCA2 and account for the majority of all identified sequence alterations. Notably, VUSs occur disproportionately in people of African descent hampering breast cancer (BCa) management and prevention efforts in the population. Our study sought to identify and characterize mutations associated with increased risk of BCa at young age.Methods: In our study, the spectrum of mutations in BRCA1 and BRCA2 was enumerated in a cohort of 31 African American women of early age at onset breast cancer, with a family history of breast or cancer in general and/or with triple negative breast cancer. To improve the characterization of the BRCA1 and BRCA2 variants, bioinformatics tools were utilized to predict the potential function of each of the variants.Results: Using next generation sequencing methods and in silico analysis of variants, a total of 197 BRCA1 and 266 BRCA2 variants comprising 77 unique variants were identified in 31 patients. Of the 77 unique variants, one (1.3%) was a pathogenic frameshift mutation (rs80359304; BRCA2 Met591Ile), 13 (16.9%) were possibly pathogenic, 34 (44.2%) were benign, and 29 (37.7%) were VUSs. Genetic epidemiological approaches were used to determine the association with variant, haplotype, and phenotypes, such as age at diagnosis, family history of cancer and family history of breast cancer. There were 5 BRCA1 SNPs associated with age at diagnosis; rs1799966 (P=. 045; Log Additive model), rs16942 (P=. 033; Log Additive model), rs1799949 (P=. 058; Log Additive model), rs373413425 (P=. 040 and.023; Dominant and Log Additive models, respectively) and rs3765640 (P=. 033 Log Additive model). Additionally, a haplotype composed of all 5 SNPs was found to be significantly associated with younger age at diagnosis using linear regression modeling (P=.023). Specifically, the haplotype containing all the variant alleles was associated with older age at diagnosis (OR= 5.03 95% CI=. 91-9.14).Conclusions: Knowing a patient's BRCA mutation status is important for prevention and treatment decision-making. Improving the characterization of mutations will lead to better management, treatment, and BCa prevention efforts in African Americans who are disproportionately affected with aggressive BCa and may inform future precision medicine genomic-based clinical studies.

Our objective has been to establish a pro-angiogenic role for exosomes in endometriosis and to determine whether a differential expression profile of cellular and exosomal microRNAs (miRNAs) exists in endometriosis. We performed an in vitro study of human primary endometrial stromal cells (ESCs) and human umbilical vein endothelial cells (HUVECs). We isolated and characterized exosomes from ESCs from five endometriosis patients and five phase-matched controls. Exosomes were characterized by transmission electron microscopy and NanoSight technology. MiRNA was assessed by deep sequencing and reverse transcription with quantitative polymerase chain reaction. Exosome uptake studies were achieved by means of confocal microscopy. The pro-angiogenic experiments were executed by treating HUVECs with ESC-derived exosomes. We observed differential profiles of exosomal miRNA expression between exosomes derived from endometriosis lesion cells and diseased eutopic stromal cells compared with exosomes derived from control ESCs. We also demonstrated autocrine cellular uptake of exosomes and paracrine functional angiogenic effects of exosomes on HUVECs. The results of this study support the hypothesis that exosomes derived from ESCs play autocrine/paracrine roles in the development of endometriosis, potentially modulating angiogenesis. The broader clinical implications are that Sampson’s theory of retrograde menstruation possibly encompasses the finding that exosomes work as intercellular communication modulators in endometriosis.

Background Genome-wide association studies provide important insights to the genetic component of disease risks. However, an existing challenge is how to incorporate collective effects of interactions beyond the level of independent single nucleotide polymorphism (SNP) tests. While methods considering each SNP pair separately have provided insights, a large portion of expected heritability may reside in higher-order interaction effects. Results We describe an inference approach (discrete discriminant analysis; DDA) designed to probe collective interactions while treating both genotypes and phenotypes as random variables. The genotype distributions in case and control groups are modeled separately based on empirical allele frequency and covariance data, whose differences yield disease risk parameters. We compared pairwise tests and collective inference methods, the latter based both on DDA and logistic regression. Analyses using simulated data demonstrated that significantly higher sensitivity and specificity can be achieved with collective inference in comparison to pairwise tests, and with DDA in comparison to logistic regression. Using age-related macular degeneration (AMD) data, we demonstrated two possible applications of DDA. In the first application, a genome-wide SNP set is reduced into a small number (∼100) of variants via filtering and SNP pairs with significant interactions are identified. We found that interactions between SNPs with highest AMD association were epigenetically active in the liver, adipocytes, and mesenchymal stem cells. In the other application, multiple groups of SNPs were formed from the genome-wide data and their relative strengths of association were compared using cross-validation. This analysis allowed us to discover novel collections of loci for which interactions between SNPs play significant roles in their disease association. In particular, we considered pathway-based groups of SNPs containing up to ∼10, 000 variants in each group. In addition to pathways related to complement activation, our collective inference pointed to pathway groups involved in phospholipid synthesis, oxidative stress, and apoptosis, consistent with the AMD pathogenesis mechanism where the dysfunction of retinal pigment epithelium cells plays central roles. Conclusions The simultaneous inference of collective interaction effects within a set of SNPs has the potential to reveal novel aspects of disease association.

Abstract Purpose: Cervical cancer is one of the most common causes of cancer mortality for women living in poverty, causing more than 28,000 deaths annually in Latin America and 266,000 worldwide. To better understand the molecular basis of the disease, we ascertained blood and tumor samples from Guatemala and Venezuela and performed genomic characterization. Experimental Design: We performed human papillomavirus (HPV) typing and identified somatically mutated genes using exome and ultra-deep targeted sequencing with confirmation in samples from Mexico. Copy number changes were also assessed in the exome sequence. Results: Cervical cancer cases in Guatemala and Venezuela have an average age of diagnosis of 50 years and 5.6 children. Analysis of 675 tumors revealed activation of PIK3CA and other PI3K/AKT pathway genes in 31% of squamous carcinomas and 24% of adeno- and adenosquamous tumors, predominantly at two sites (E542K, E545K) in the helical domain of the PIK3CA gene. This distribution of PIK3CA mutations is distinct from most other cancer types and does not result in the in vitro phosphorylation of AKT. Somatic mutations were more frequent in squamous carcinomas diagnosed after the age of 50 years. Frequent gain of chromosome 3q was found, and low PIK3CA mutation fractions in many tumors suggest that PI3K mutation can be a late event in tumor progression. Conclusions: PI3K pathway mutation is important to cervical carcinogenesis in Latin America. Therapeutic agents that directly target PI3K could play a role in the therapy of this common malignancy. Clin Cancer Res; 21(23); 5360–70. ©2015 AACR.

Diagnosing and screening for tumors through noninvasive means represent an important paradigm shift in precision medicine. In contrast to tissue biopsy, detection of circulating tumor cells (CTCs) and circulating tumor nucleic acids provides a minimally invasive method for predictive and prognostic marker detection. This allows early and serial assessment of metastatic disease, including follow-up during remission, characterization of treatment effects, and clonal evolution. Isolation and characterization of CTCs and circulating tumor DNA (ctDNA) are likely to improve cancer diagnosis, treatment, and minimal residual disease monitoring. However, more trials are required to validate the clinical utility of precise molecular markers for a variety of tumor types. This review focuses on the clinical utility of CTCs and ctDNA testing in patients with solid tumors, including somatic and epigenetic alterations that can be detected. A comparison of methods used to isolate and detect CTCs and some of the intricacies of the characterization of the ctDNA are also provided.

Diagnosing and screening for tumors through noninvasive means represent an important paradigm shift in precision medicine. In contrast to tissue biopsy, detection of circulating tumor cells (CTCs) and circulating tumor nucleic acids provides a minimally invasive method for predictive and prognostic marker detection. This allows early and serial assessment of metastatic disease, including follow-up during remission, characterization of treatment effects, and clonal evolution. Isolation and characterization of CTCs and circulating tumor DNA (ctDNA) are likely to improve cancer diagnosis, treatment, and minimal residual disease monitoring. However, more trials are required to validate the clinical utility of precise molecular markers for a variety of tumor types. This review focuses on the clinical utility of CTCs and ctDNA testing in patients with solid tumors, including somatic and epigenetic alterations that can be detected. A comparison of methods used to isolate and detect CTCs and some of the intricacies of the characterization of the ctDNA are also provided. Diagnosing and screening for tumors through noninvasive means represent an important paradigm shift in precision medicine. In contrast to tissue biopsy, detection of circulating tumor cells (CTCs) and circulating tumor nucleic acids provides a minimally invasive method for predictive and prognostic marker detection. This allows early and serial assessment of metastatic disease, including follow-up during remission, characterization of treatment effects, and clonal evolution. Isolation and characterization of CTCs and circulating tumor DNA (ctDNA) are likely to improve cancer diagnosis, treatment, and minimal residual disease monitoring. However, more trials are required to validate the clinical utility of precise molecular markers for a variety of tumor types. This review focuses on the clinical utility of CTCs and ctDNA testing in patients with solid tumors, including somatic and epigenetic alterations that can be detected. A comparison of methods used to isolate and detect CTCs and some of the intricacies of the characterization of the ctDNA are also provided. A 1-cm carcinoma that has been growing for >10 years contains approximately one billion cells. Such a tumor doubles once every 150 days and weighs just more than half a gram.1Durbin P.W. Jeung N. Williams M.H. Arnold J.S. Construction of a growth curve for mammary tumors of the rat.Cancer Res. 1967; 27: 1341-1347PubMed Google Scholar, 2Friberg S. Mattson S. On the growth rates of human malignant tumors: implications for medical decision making.J Surg Oncol. 1997; 65: 284-297Crossref PubMed Scopus (122) Google Scholar, 3Beerenwinkel N. Antal T. Dingli D. Traulsen A. Kinzler K.W. Velculescu V.E. Vogelstein B. 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Fan A. Tran T. Danila D.C. Keys D. Schwartz M. Ionescu-Zanetti C. Mutational analysis of circulating tumor cells using a novel microfluidic collection device and qPCR assay.Transl Oncol. 2013; 6: 528-538Abstract Full Text PDF PubMed Scopus (12) Google ScholarLymphoprep (Ficoll-Isopaque)Axis-Shield PoC (Oslo, Norway)ProstateEpCAM, PSA, and cytokeratin 7/847Ntouroupi T.G. Ashraf S.Q. McGregor S.B. Turney B.W. Seppo A. Kim Y. Wang X. Kilpatrick M.W. Tsipouras P. Tafas T. Bodmer W.F. Detection of circulating tumour cells in peripheral blood with an automated scanning fluorescence microscope.Br J Cancer. 2008; 99: 789-795Crossref PubMed Scopus (54) Google ScholarMagSweeperStephanie Jeffrey and Ronald W. Davis (Stanford University, Stanford, CA)Breast and prostateEpCAM48Deng G. Krishnakumar S. Powell A.A. Zhang H. Mindrinos M.N. Telli M.L. Davis R.W. Jeffrey S.S. Single cell mutational analysis of PIK3CA in circulating tumor cells and metastases in breast cancer reveals heterogeneity, discordance, and mutation persistence in cultured disseminated tumor cells from bone marrow.BMC Cancer. 2014; 14: 456Crossref PubMed Scopus (1) Google ScholarNanodetectorGilupi (Potsdam, Germany)Breast, lung, and prostateEpCAM49Saucedo-Zeni N. Mewes S. Niestroj R. Gasiorowski L. Murawa D. Nowaczyk P. Tomasi T. Weber E. Dworacki G. Morgenthaler N.G. Jansen H. Propping C. Sterzynska K. Dyszkiewicz W. Zabel M. Kiechle M. Reuning U. Schmitt M. Lucke K. A novel method for the in vivo isolation of circulating tumor cells from peripheral blood of cancer patients using a functionalized and structured medical wire.Int J Oncol. 2012; 41: 1241-1250PubMed Google ScholarNegative enrichment QMSJeffrey Chalmers (Cleveland Clinic, Cleveland, OH)Head and neck and breastCD45 subtraction50Lustberg M. Jatana K.R. Zborowski M. Chalmers J.J. Emerging technologies for CTC detection based on depletion of normal cells.Recent Results Cancer Res. 2012; 195: 97-110Crossref PubMed Scopus (15) Google ScholarOncoQuickGreiner Bio-One (Germany and Monroe, NC)Breast, colorectal, melanoma, and pancreaticDensity (no antibody)51Clawson G.A. Kimchi E. Patrick S.D. Xin P. Harouaka R. Zheng S. Berg A. Schell T. Staveley-O'Carroll K.F. Neves R.I. Mosca P.J. Thiboutot D. Circulating tumor cells in melanoma patients.PLoS One. 2012; 7: e41052Crossref PubMed Scopus (12) Google ScholarRoboSep/EasySepStem Cell Technologies (Vancouver, BC, Canada)MyelomaCD33, CD66, and CD13852Shetty S. Siady M. Mallempati K.C. Wilson A. Poarch J. Chandler B. Gray J. Salama M.E. Utility of a column-free cell sorting system for separation of plasma cells in multiple myeloma FISH testing in clinical laboratories.Int J Hematol. 2012; 95: 274-281Crossref PubMed Scopus (2) Google ScholarScreenCellCytoScreenCell Company (Sarcelles, France)Lung and cell linesSize (no antibody)53Freidin M.B. Tay A. Freydina D.V. Chudasama D. Nicholson A.G. Rice A. Anikin V. Lim E. An assessment of diagnostic performance of a filter-based antibody-independent peripheral blood circulating tumour cell capture paired with cytomorphologic criteria for the diagnosis of cancer.Lung Cancer. 2014; 85: 182-185Abstract Full Text Full Text PDF PubMed Google ScholarThis table is an updated version of Table 2 first published by Parkinson et al.54Parkinson D.R. Dracopoli N. Petty B.G. Compton C. Cristofanilli M. Deisseroth A. Hayes D.F. Kapke G. Kumar P. Lee J. Liu M.C. McCormack R. Mikulski S. Nagahara L. Pantel K. Pearson-White S. Punnoose E.A. Roadcap L.T. Schade A.E. Scher H.I. Sigman C.C. Kelloff G.J. Considerations in the development of circulating tumor cell technology for clinical use.J Transl Med. 2012; 10: 138Crossref PubMed Scopus (81) Google ScholarASCO, American Society of Clinical Oncology; CK, cytokeratin; CTC, circulating tumor cell; EpCAM, epithelial cell adhesion molecule; FDA, Food and Drug Administration; iChip, microfluidic silicon chip; IDE, investigational device exemption; ISET, isolation by size of epithelial tumor cell; MACS, magnetic activated cell sorting; NSCLC, non-small cell lung cancer; PSA, prostate-specific antigen; QMS, quadruple magnetic sorter. Open table in a new tab This table is an updated version of Table 2 first published by Parkinson et al.54Parkinson D.R. Dracopoli N. Petty B.G. Compton C. Cristofanilli M. Deisseroth A. Hayes D.F. Kapke G. Kumar P. Lee J. Liu M.C. McCormack R. Mikulski S. Nagahara L. Pantel K. Pearson-White S. Punnoose E.A. Roadcap L.T. Schade A.E. Scher H.I. Sigman C.C. Kelloff G.J. Considerations in the development of circulating tumor cell technology for clinical use.J Transl Med. 2012; 10: 138Crossref PubMed Scopus (81) Google Scholar ASCO, American Society of Clinical Oncology; CK, cytokeratin; CTC, circulating tumor cell; EpCAM, epithelial cell adhesion molecule; FDA, Food and Drug Administration; iChip, microfluidic silicon chip; IDE, investigational device exemption; ISET, isolation by size of epithelial tumor cell; MACS, magnetic activated cell sorting; NSCLC, non-small cell lung cancer; PSA, prostate-specific antigen; QMS, quadruple magnetic sorter. Because this technology proved sufficient to provide prognostic information,25Allard W.J. Matera J. Miller M.C. Repollet M. Connelly M.C. Rao C. Tibbe A.G. Uhr J.W. Terstappen L.W. Tumor cells circulate in the peripheral blood of all major carcinomas but not in healthy subjects or patients with nonmalignant diseases.Clin Cancer Res. 2004; 10: 6897-6904Crossref PubMed Scopus (746) Google Scholar, 55Cristofanilli M. Budd G.T. Ellis M.J. Stopeck A. Matera J. Miller M.C. Reuben J.M. Doyle G.V. Allard W.J. Terstappen L.W. Hayes D.F. Circulating tumor cells, disease progression, and survival in metastatic breast cancer.N Engl J Med. 2004; 351: 781-791Crossref PubMed Scopus (1548) Google Scholar the US Food and Drug Administration cleared the Veridex CellSearch platform, now owned by Johnson & Johnson (Raritan, NJ), to isolate CTCs. That platform uses EpCAM antibodies attached to magnetic beads to isolate tumor cells in conjunction with proprietary CellSave venipuncture tubes that preserve CTC structure. By using the Veridex device, CTCs can be pulled out of suspension using a magnet.56Riethdorf S. Fritsche H. Muller V. Rau T. Schindlbeck C. Rack B. Janni W. Coith C. 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CTCs have been identified in peripheral blood from patients with metastatic and recurrent disease. As methods for isolating CTCs have matured, several investigators have studied correlations between cell number and patient disease severity. That breast cancer patients with fewer CTCs in their blood lived longer than those with more CTCs was first demonstrated in 2004.55Cristofanilli M. Budd G.T. Ellis M.J. Stopeck A. Matera J. Miller M.C. Reuben J.M. Doyle G.V. Allard W.J. Terstappen L.W. Hayes D.F. Circulating tumor cells, disease progression, and survival in metastatic breast cancer.N Engl J Med. 2004; 351: 781-791Crossref PubMed Scopus (1548) Google Scholar Similar observations were made in other cancer types, including prostate and colorectal cancers.62Doyen J. Alix-Panabieres C. Hofman P. Parks S.K. Chamorey E. Naman H. Hannoun-Levi J.M. 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Leyland-Jones B. Srkalovic G. Tejwani S. Schott A.F. O'Rourke M.A. Lew D.L. Doyle G.V. Gralow J.R. Livingston R.B. Hayes D.F. Circulating tumor cells and response to chemotherapy in metastatic breast cancer: SWOG S0500.J Clin

Introduction Oral Lactococcus lactis engineered to express the immunoregulatory cytokine IL-27 (LL-IL27) is therapeutically active in chronic murine enterocolitis. Here, efficacy in acute colitis was examined. Methods 2 mg 2,4,6-trinitrobenzene sulfonic acid (TNBS) was delivered intra-rectally in 45% ethanol or 45% ethanol alone into 6–8 week old male SJL mice. L. lactis control (LLC) or LL-IL-27 was delivered by oral gavage on 4 occasions, 24 h apart, commencing at colitis induction. Therapeutic effect was assessed clinically and histologically. Potential mechanisms of action were investigated. Results TNBS induced an acute severe distal colitis. LL-IL-27 led to a significant reduction in disease activity index compared to LLC (4.9 vs. 8.7/12 on day 2 (p = 0.001); 3.6 vs. 7.7/12 on day 3 (p = 0.001), improved macroscopic colitis score (p < 0.05), and reduction in serum CRP (p = 0.003, day 2). Histological colitis score was reduced (p = 0.035) with significant improvement in mucosal ulceration (p = 0.008). TNBS increased expression of distal colon Il6, Il1β, Tnf, and Il10, assessed by RT-PCR, with no differential effect seen with LL-IL-27. However, LL-IL-27 led to a significant reduction in IL-6 (p = 0.002), IL-1β (p = 0.001) and TNF (p = 0.014) protein assessed by ELISA. A significant reduction in colonic mucosal myeloperoxidase+ neutrophil infiltrate was seen in the LL-IL-27 group (p = 0.004), along with a significant decrease in the neutrophil chemoattractant CXCL2 (p < 0.001). LPS induced CXCL2 gene and protein expression in macrophages was not inhibited by recombinant IL-27 in vitro , suggesting an indirect mechanism in vivo . Peri-ulceration distal colonic mucosa was isolated by laser capture microdissection and RNA applied to mouse Genome 430 2.0 Affymetrix microarray. Principal component analysis grouped mice by treatment. 285 genes were differentially expressed (>/<1.5 fold change in expression plus p < 0.05) in the LL-IL27 group, including a striking down-regulation of mucosal humoral response genes, (for example, probe sets for IgA heavy chain (-20.6 fold), Igκ chain var1 (-19.0 fold), Igλ chain CR2 (-4.8 fold)). This was not explained by a reduction in CD45R/B220+ B cell infiltrate (p = 0.02). Up-regulated genes include those involved with anti-microbial defense (RegIIIb, Clec7A, ligp1) and innate immune response (cxcl10, cxcl9). Conclusion Intra-luminal IL-27 represents a potential therapy for human inflammatory bowel disease and acute colitis of differing aetiologies. Disclosure of Interest M. McLean: None Declared, M. Hanson: None Declared, B. Gold: None Declared, Y. Golubeva: None Declared, M. Anver: None Declared, X. Wu: None Declared, D. Sun: None Declared, L. Steidler Employee of: ActoGenix, S. Durum: None Declared.

Background Fascin, an actin bundling protein, plays a critical role in cell motility due to formation of actin rich protrusions called filopodia, important in cell migration, invasion and metastatic spread. Fascin overexpression has been associated with epithelial to mesenchymal transition and correlates with progression and unfavourable prognosis in breast carcinoma. Objective To evaluate fascin expression by immunohistochemistry and correlate the expression pattern with clinicopathological parameters in breast cancer in African-American (AA) women, in whom triple negative breast cancer (TNBC), an aggressive subtype, is more prevalent. Methods Tissue microarrays were constructed from formalin-fixed, paraffin-embedded blocks of tumour tissue from primary breast carcinomas in 202 AA women. Immunohistochemical detection of fascin was correlated with four major subtypes of breast carcinoma (luminal A, luminal B, human epidermal growth factor receptor 2 and triple negative (TN)) and other clinicopathological factors, including age, grade, tumour size, stage, regional lymph node status and survival. Results We observed a significant association between fascin expression and TN subtype, oestrogen receptor (ER) negativity, progesterone receptor (PR) negativity, Elston–Nottingham (EN) grade 3 and decreased overall survival. There was also a significant association between expression of CK 5/6, a marker of basal-like phenotype, and fascin expression. Conclusion These results suggest that fascin is a marker for TN subtype having a basal-like phenotype and decreased overall survival. Fascin may represent a target for therapy in TNBC in AA women.

Methods: Colitis was induced in immunodeficient SCID mice by the adoptive transfer of CD4 +

Abstract The retinoblastoma tumor suppressor gene (RB1) is a key regulator of cell cycle control, most notably through E2F transcription factor binding. Deregulation of RB1 is important in many cancers. Survivors of hereditary retinoblastoma, caused by a germline mutation in RB1, experience substantially elevated risks for subsequent neoplasms, particularly bone and soft tissue sarcomas and melanomas. Oncogenic RB1 mutations arise from a range of DNA alterations and occur throughout the gene. No previous study has evaluated how the specific location and functional consequences of these RB1 mutations may differentially confer risk for specific subsequent neoplasms. As part of a biomarker study nested within a long-term follow-up study of the risk of subsequent cancers in retinoblastoma survivors, we identified germline RB1 mutations in 76/80 (95%) survivors of hereditary retinoblastoma who developed at least one subsequent neoplasm and had sufficient DNA for mutation testing (median follow-up time=47 years, range 7-71 years). Survivors were classified into four groups according to whether they ever developed a soft tissue sarcoma (STS, N=47), melanoma (without STS, N=10), bone tumor (without STS, N=5), or another type of subsequent malignant neoplasm (N=14). The identified mutations were distributed throughout RB1, from the promoter through exon 25. Nonsense, frameshift, or splice mutations that resulted in premature termination of the RB1 residue sequence were identified in 51 (67%) survivors, with the remaining classified as having loss of multiple exons (N=6), loss or rearrangement of a single exon (N=5), a splice mutation (N=7), a missense mutation (N=4), or an intronic substitution with unknown consequence (N=3). Preliminary analyses indicated that RB1 mutations resulting in loss of >2 exons were more common in survivors with a subsequent STS (40/47, 85%) than those with a subsequent melanoma (6/10, 60%) or bone tumor (2/5, 40%; Fisher's exact P<0.001). In an analysis of the RB1 regions impacted by the mutation, those that affected E2F binding (including mutations affecting the E2F binding site, Domain B, or Domain C) were more common in survivors with a subsequent STS (46/47, 98%) or melanoma (9/10, 90%) than those with a bone tumor (2/5, 40%; Fisher's exact P=0.020). Further analyses will include 14 additional survivors who developed a subsequent neoplasm for whom mutation testing is ongoing, and comparison of the spectrum of RB1 mutations in these survivors to hereditary retinoblastoma survivors without a subsequent neoplasm. If confirmed, such correlations between specific RB1 mutations and subsequent neoplasm risk may inform long-term surveillance practices for hereditary retinoblastoma survivors and provide insight into the key role of RB1 in oncogenesis. Citation Format: Lindsay M. Morton, Jeannette R. Wong, Brenda L. Gallie, David H. Abramson, Johanna M. Seddon, Michael Dean, Bert Gold, Alisa M. Goldstein, Ruth A. Kleinerman, Margaret A. Tucker. Specific RB1 mutations and risk of subsequent neoplasms among survivors of hereditary retinoblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1333. doi:10.1158/1538-7445.AM2013-1333

Metastatic castration-resistant prostate cancer (mCRPC) is a lethal disease, and molecular markers that differentiate indolent from aggressive subtypes are needed. We sequenced the exomes of five metastatic tumors and healthy kidney tissue from an index case with mCRPC to identify lesions associated with disease progression and metastasis. An Ashkenazi Jewish (AJ) germline founder mutation, del185AG in BRCA1, was observed and AJ ancestry was confirmed. Sixty-two somatic variants altered proteins in tumors, including cancer-associated genes, TMPRSS2-ERG, PBRM1, and TET2. The majority (n = 53) of somatic variants were present in all metastases and only a subset (n = 31) was observed in the primary tumor. Integrating tumor next-generation sequencing and DNA copy number showed somatic loss of BRCA1 and TMPRSS2-ERG. We sequenced 19 genes with deleterious mutations in the index case in additional mCRPC samples and detected a frameshift, two somatic missense alterations, tumor loss of heterozygosity, and combinations of germline missense SNPs in TET2. In summary, genetic analysis of metastases from an index case permitted us to infer a chronology for the clonal spread of disease based on sequential accrual of somatic lesions. The role of TET2 in mCRPC deserves additional analysis and may define a subset of metastatic disease.

Recently, a locus on chromosome 6q22. 33 (rs2180341) was reported to be associated with increased breast cancer risk in the Ashkenazi Jewish (AJ) population, and this association was also observed in populations of non-AJ European ancestry. In the present study, we performed a large replication analysis of rs2180341 using data from 31,428 invasive breast cancer cases and 34,700 controls collected from 25 studies in the Breast Cancer Association Consortium (BCAC). In addition, we evaluated whether rs2180341 modifies breast cancer risk in 3,361 BRCA1 and 2,020 BRCA2 carriers from 11 centers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Based on the BCAC data from women of European ancestry, we found evidence for a weak association with breast cancer risk for rs2180341 (per-allele odds ratio (OR)= 1.03, 95% CI 1.00-1.06, p= 0.023). There was evidence for heterogeneity in the ORs among studies (I (2)= 49.3%; p=