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Children with Down syndrome (DS) have a 20-fold increased risk of acute lymphoblastic leukemia (ALL) and distinct somatic features, including CRLF2 rearrangement in ∼50% of cases; however, the role of inherited genetic variation in DS-ALL susceptibility is unknown. We report the first genome-wide association study of DS-ALL, comprising a meta-analysis of 4 independent studies, with 542 DS-ALL cases and 1192 DS controls. We identified 4 susceptibility loci at genome-wide significance: rs58923657 near IKZF1 (odds ratio [OR], 2.02; Pmeta = 5.32 × 10-15), rs3731249 in CDKN2A (OR, 3.63; Pmeta = 3.91 × 10-10), rs7090445 in ARID5B (OR, 1.60; Pmeta = 8.44 × 10-9), and rs3781093 in GATA3 (OR, 1.73; Pmeta = 2.89 × 10-8). We performed DS-ALL vs non-DS ALL case-case analyses, comparing risk allele frequencies at these and other established susceptibility loci (BMI1, PIP4K2A, and CEBPE) and found significant association with DS status for CDKN2A (OR, 1.58; Pmeta = 4.1 × 10-4). This association was maintained in separate regression models, both adjusting for and stratifying on CRLF2 overexpression and other molecular subgroups, indicating an increased penetrance of CDKN2A risk alleles in children with DS. Finally, we investigated functional significance of the IKZF1 risk locus, and demonstrated mapping to a B-cell super-enhancer, and risk allele association with decreased enhancer activity and differential protein binding. IKZF1 knockdown resulted in significantly higher proliferation in DS than non-DS lymphoblastoid cell lines. Our findings demonstrate a higher penetrance of the CDKN2A risk locus in DS and serve as a basis for further biological insights into DS-ALL etiology.

While GWAS have uncovered susceptibility loci for B-cell precursor acute lymphoblastic leukemia (BCP-ALL), much of the heritable risk remains undiscovered. Here, the authors perform a meta-analysis of two existing BCP-ALL GWAS together with an unpublished GWAS to identify risk loci at 8q24.21 and 2q22.3.

We previously reported that children in the UKALL XI ALL trial with HLA-DP 1 and -DP 3 supertypes had significantly worse event-free survival (EFS) than children with other DP supertypes. As DP 1 and DP 3 share two of four key antigen-binding amino-acid polymorphisms (aspartic acid84–lysine69), we asked whether Asp84-Lys69 or Asp84 alone were independent prognostic indicators in childhood acute lymphoblastic leukemia (ALL). We analysed EFS in 798 UKALL XI patients, stratified by Asp84-Lys69 vs non-Asp84-Lys69, for a median follow-up of 12.5 years. Asp84-Lys69 was associated with a significantly worse EFS than non-Asp84-Lys69 (5-year EFS: Asp84-Lys69: 58.8% (95% CI (confidence of interval): 52.7–64.9%); non-Asp84-Lys69: 67.3% (63.4–71.2%); 2P=0.007). Post-relapse EFS was 10% less in Asp84-Lys69 than non-Asp84-Lys69 patients. EFS was significantly worse (P=0.03) and post-relapse EFS marginally worse (P=0.06) in patients with Asp84 compared with Gly84. These results suggest that Asp84-Lys69 predicted adverse EFS in the context of UKALL XI because of Asp84, and may have influenced post-relapse EFS. We speculate that this may be due to the recruitment of Asp84-Lys69-restricted regulatory T cells in the context of this regimen, leading to the re-emergence of residual disease. However, functional and molecular studies of the prognostic value of this and other HLA molecular signatures in other childhood ALL trials are needed.

Childhood B-cell precursor acute lymphoblastic leukemia (BCP ALL) is usually initiated in utero and is thought to progress to overt leukemia under the influence of delayed exposure to a common infection. Based on the hypothesis that polymorphic HLA-DP variants can restrict T-cell responses to infection, we previously compared DP supertype frequencies in BCP ALL patients with that of unrelated newborn controls. We reported that the DP2 supertype was associated with susceptibility, whereas DP1 was associated with protection. However, the association of genetic variants in children with early-onset diseases such as ALL may be a proxy for parental effects. Here we examine whether maternal DP1 and DP2 are associated with BCP ALL by fitting log-linear models in a combined series of family triads (both parents and case child) and dyads (1 parent and case child; n = 571) in comparison with similar models in non-BCP leukemia (n = 198). We report no evidence of maternal DP1 or DP2 associations with BCP ALL, but we did identify suggestive evidence of maternal undertransmission of the infrequent supertypes DP11 and DP15. Although these results require confirmation, they suggest that DP11 and DP15 may be protective or that there is transmission ratio distortion of these supertypes in BCP ALL.

Genome-wide association studies (GWAS) have provided strong evidence for inherited predisposition to childhood acute lymphoblastic leukaemia (ALL) identifying a number of risk loci. We have previously shown common SNPs at 9p21.3 influence ALL risk. These SNP associations are generally not themselves candidates for causality, but simply act as markers for functional variants. By means of imputation of GWAS data and subsequent validation SNP genotyping totalling 2,177 ALL cases and 8,240 controls, we have shown that the 9p21.3 association can be ascribed to the rare high-impact CDKN2A p.Ala148Thr variant (rs3731249; Odds ratio = 2.42, P = 3.45 × 10−19). The association between rs3731249 genotype and risk was not specific to particular subtype of B-cell ALL. The rs3731249 variant is associated with predominant nuclear localisation of the CDKN2A transcript suggesting the functional effect of p.Ala148Thr on ALL risk may be through compromised ability to inhibit cyclin D within the cytoplasm.

Craniofacial abnormalities account for about one-third of all human congenital defects, but our understanding of the genetic mechanisms governing craniofacial development is incomplete. We show that GTF2IRD1 is a genetic determinant of mammalian craniofacial and cognitive development, and we implicate another member of the TFII-I transcription factor family, GTF2I , in both aspects. Gtf2ird1 -null mice exhibit phenotypic abnormalities reminiscent of the human microdeletion disorder Williams-Beuren syndrome (WBS); craniofacial imaging reveals abnormalities in both skull and jaws that may arise through misregulation of goosecoid , a downstream target of Gtf2ird1 . In humans, a rare WBS individual with an atypical deletion, including GTF2IRD1 , shows facial dysmorphism and cognitive deficits that differ from those of classic WBS cases. We propose a mechanism of cumulative dosage effects of duplicated and diverged genes applicable to other human chromosomal disorders.

Childhood Acute Lymphoblastic Leukemia (ALL) is a malignant lymphoid disease of which B-cell precursor- (BCP) and T-cell-(T) ALL are subtypes. The role of alleles encoded by major histocompatibility loci (MHC) have been examined in a number of previous studies and results indicating weak, multi-allele associations between the HLA-DPB1 locus and BCP-ALL suggested a role for immunosusceptibility and possibly infection. Two independent SNP association studies of ALL identified loci approximately 37 kb from one another and flanking a strong meiotic recombination hotspot (DNA3), adjacent to HLA-DOA and centromeric of HLA-DPB1. To determine the relationship between this observation and HLA-DPB1 associations, we constructed high density SNP haplotypes of the 316 kb region from HLA-DMB to COL11A2 in childhood ALL and controls using a UK GWAS data subset and the software PHASE. Of four haplotype blocks identified, predicted haplotypes in Block 1 (centromeric of DNA3) differed significantly between BCP-ALL and controls (P = 0.002) and in Block 4 (including HLA-DPB1) between T-ALL and controls (P = 0.049). Of specific common (>5%) haplotypes in Block 1, two were less frequent in BCP-ALL, and in Block 4 a single haplotype was more frequent in T-ALL, compared to controls. Unexpectedly, we also observed apparent differences in ancestral meiotic recombination rates at DNA3, with BCP-ALL showing increased and T-ALL decreased levels compared to controls. In silico analysis using LDsplit sotware indicated that recombination rates at DNA3 are influenced by flanking loci, including SNPs identified in childhood ALL association studies. The observed differences in rates of meiotic recombination at this hotspot, and potentially others, may be a characteristic of childhood leukemia and contribute to disease susceptibility, alternatively they may reflect interactions between ALL-associated haplotypes in this region. © 2014 Thompson et al.

This study was performed to identify the potential role of Alpha-2 Heremans Schmid Glycoprotein (AHSG) in Head and Neck Squamous Cell Carcinoma (HNSCC) tumorigenesis using an HNSCC cell line model. HNSCC cell lines are unique among cancer cell lines, in that they produce endogenous AHSG and do not rely, solely, on AHSG derived from serum. To produce our model, we performed a stable transfection to down-regulate AHSG in the HNSCC cell line SQ20B, resulting in three SQ20B sublines, AH50 with 50% AHSG production, AH20 with 20% AHSG production and EV which is the empty vector control expressing wild-type levels of AHSG. Utilizing these sublines, we examined the effect of AHSG depletion on cellular adhesion, proliferation, migration and invasion in a serum-free environment. We demonstrated that sublines EV and AH50 adhered to plastic and laminin significantly faster than the AH20 cell line, supporting the previously reported role of exogenous AHSG in cell adhesion. As for proliferative potential, EV had the greatest amount of proliferation with AH50 proliferation significantly diminished. AH20 cells did not proliferate at all. Depletion of AHSG also diminished cellular migration and invasion. TGF-β was examined to determine whether levels of the TGF-β binding AHSG influenced the effect of TGF-β on cell signaling and proliferation. Whereas higher levels of AHSG blunted TGF-β influenced SMAD and ERK signaling, it did not clearly affect proliferation, suggesting that AHSG influences on adhesion, proliferation, invasion and migration are primarily due to its role in adhesion and cell spreading. The previously reported role of AHSG in potentiating metastasis via protecting MMP-9 from autolysis was also supported in this cell line based model system of endogenous AHSG production in HNSCC. Together, these data show that endogenously produced AHSG in an HNSCC cell line, promotes in vitro cellular properties identified as having a role in tumorigenesis.

Background The expression of annexin A6 (AnxA6) in AnxA6-deficient non-invasive tumor cells has been shown to terminate epidermal growth factor receptor (EGFR) activation and downstream signaling. However, as a scaffolding protein, AnxA6 may stabilize activated cell-surface receptors to promote cellular processes such as tumor cell motility and invasiveness. In this study, we investigated the contribution of AnxA6 in the activity of EGFR in invasive breast cancer cells and examined whether the expression status of AnxA6 influences the response of these cells to EGFR-targeted tyrosine kinase inhibitors (TKIs) and/or patient survival. Results We demonstrate that in invasive BT-549 breast cancer cells AnxA6 expression is required for sustained membrane localization of activated (phosho-Y1068) EGFR and consequently, persistent activation of MAP kinase ERK1/2 and phosphoinositide 3-kinase/Akt pathways. Depletion of AnxA6 in these cells was accompanied by rapid degradation of activated EGFR, attenuated downstream signaling and as expected enhanced anchorage-independent growth. Besides inhibition of cell motility and invasiveness, AnxA6-depleted cells were also more sensitive to the EGFR-targeted TKIs lapatinib and PD153035. We also provide evidence suggesting that reduced AnxA6 expression is associated with a better relapse-free survival but poorer distant metastasis-free and overall survival of basal-like breast cancer patients. Conclusions Together this demonstrates that the rapid degradation of activated EGFR in AnxA6-depleted invasive tumor cells underlies their sensitivity to EGFR-targeted TKIs and reduced motility. These data also suggest that AnxA6 expression status may be useful for the prediction of the survival and likelihood of basal-like breast cancer patients to respond to EGFR-targeted therapies.

Background AHSG is a calcium-binding glycoprotein synthesized primarily by the liver [1-3] and secreted into serum [1-3]. Primarily known for its role in bone growth and remodeling, it is also reported to be involved in the progression of breast and lung cancer with these cells utilizing the liver synthesized form [1,4,5]. Uniquely, HNSCC cells synthesize their own AHSG, suggesting autocrine signaling fueling cell proliferation and movement. Here we present data showing the presence of AHSG mRNA in HNSCC cell line SQ20B and phenotypic and transcriptomic changes resulting from shRNA knockdown of AHSG protein expression.

The extended major histocompatibility complex (xMHC) is the most gene-dense region of the genome and harbors a disproportionately large number of genes involved in immune function. The postulated role of infection in the causation of childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) suggests that the xMHC may make an important contribution to the risk of this disease. We conducted association mapping across an approximately 4 megabase region of the xMHC using a validated panel of single nucleotide polymorphisms (SNPs) in childhood BCP-ALL cases (n=567) enrolled in the Northern California Childhood Leukemia Study (NCCLS) compared with population controls (n=892). Logistic regression analyses of 1,145 SNPs, adjusted for age, sex, and Hispanic ethnicity indicated potential associations between several SNPs and childhood BCP-ALL. After accounting for multiple comparisons, one of these included a statistically significant increased risk associated with rs9296068 (OR=1.40, 95% CI=1.19-1.66, corrected p=0.036), located in proximity to HLA-DOA. Sliding window haplotype analysis identified an additional locus located in the extended class I region in proximity to TRIM27 tagged by a haplotype comprising rs1237485, rs3118361, and rs2032502 (corrected global p=0.046). Our findings suggest that susceptibility to childhood BCP-ALL is influenced by genetic variation within the xMHC and indicate at least two important regions for future evaluation. © 2013 Urayama et al.

Acute lymphoblastic leukemia (ALL) is the major pediatric cancer diagnosed in economically developed countries with B-cell precursor (BCP)-ALL, accounting for approximately 70% of ALL. Recent genome-wide association studies (GWAS) have provided the first unambiguous evidence for common inherited susceptibility to BCP-ALL, identifying susceptibility loci at 7p12.2, 9p21.3, 10q21.2, and 14q11.2. To identify additional BCP-ALL susceptibility loci, we conducted a GWAS and performed a meta-analysis with a published GWAS totaling 1658 cases and 4723 controls, with validation in 1449 cases and 1488 controls. Combined analysis identified novel loci mapping to 10p12.2 (rs10828317, odds ratio [OR] = 1.23; P = 2.30 x 10(-9)) and 10p14marked by rs3824662(OR = 1.31; P = 8.62 x 10(-12)). The single nucleotide polymorphism rs10828317 is responsible for the N215S polymorphism in exon 7 of PIP4K2A, and rs3824662 localizes to intron 3 of the transcription factor and putative tumor suppressor gene GATA3. The rs10828317 association was shown to be specifically associated with hyperdiploid ALL, whereas the rs3824662-associated risk was confined to nonhyperdiploid non-TEL-AML1 + ALL. The risk allele of rs3824662 was correlated with older age at diagnosis (P < .001) and significantly worse event-free survivorship (P < .0001). These findings provide further insights into the genetic and biological basis of inherited genetic susceptibility to BCP-ALL and the influence of constitutional genotype on disease development.

The present analyses were done to define the role of fetuin-A (Fet) in mammary tumorigenesis using the polyoma middle T antigen (PyMT) transgenic mouse model. We crossed Fet-null mice in the C57BL/6 background with PyMT mice in the same background and after a controlled breeding protocol obtained PyMT/Fet+/+, PyMT/Fet+/−, and PyMT/Fet−/− mice that were placed in control and experimental groups. Whereas the control group (PyMT/Fet+/+) formed mammary tumors 90 days after birth, tumor latency was prolonged in the PyMT/Fet−/− and PyMT/Fet+/− mice. The majority of the PyMT/Fet−/− mice were tumor-free at the end of the study, at approximately 40 weeks. The pathology of the mammary tumors in the Fet-null mice showed extensive fibrosis, necrosis, and squamous metaplasia. The preneoplastic mammary tissues of the PyMT/Fet−/− mice showed intense phopho-Smad2/3 staining relative to control tissues, indicating that transforming growth factor-β signaling is enhanced in these tissues in the absence of Fet. Likewise, p19ARF and p53 were highly expressed in tumor tissues of PyMT/Fet−/− mice relative to the controls in the absence of Fet. The phosphatidylinositol 3-kinase/Akt signaling pathway that we previously showed to be activated by Fet, on the other hand, was unaffected by the absence of Fet. The data indicate that Fet is a powerful modulator of breast tumorigenesis in this model system and has the potential to modulate breast cancer progression in humans.

Background. African-American women (AAW) have more adverse tumor characteristics than non-African American women (non-AAW) and there is a need for a specific predictive marker for AAW recurrence. Tumors with higher grade and proliferative activity are associated with overexpression of the glucose transporter (Glut-1). An examination of Glut-1 expression relative to recurrence and no recurrence was conducted on both groups to determine if it predicts prognosis and could predict a race specific prognosis. Methods. A breast cancer data set containing clinical information including race and biological characteristics was generated between 1991 and 1996. Tissue samples were selected from this group with similar characteristics in both racial groups for a retrospective analysis of Glut-1 expression using tissue microarrays (TMAs). Mean Glut-1 expression for intensity and percent of tumor cells staining was determined using standard immunohistochemistry. Results. Clinical and biological differences were noted in the original data set between AAW and non-AAW. No significant difference between races was noted in mean Glut-1 values using a subset which had similar characteristics. The mean Glut-1 did not predict recurrence but a rounded score did indicate that higher levels of Glut-1 expression was indicative of a lower disease free survival (p = 0.063). The actual average mean for AAW with no recurrence was significantly lower than any other group (p = 0.04). Conclusions. TMA analysis for Glut-1 expression may be useful to predict disease free survival but it does not predict race specific recurrence.

The Alpha-Heremans-Schmid Glycoprotein (AHSG) has tumor promoting properties in animal models of breast cancer and lung cancer (1, 2). These cancer cells do not synthesize AHSG, instead utilizing the liver-generated glycoprotein that is abundant in serum. We have reported that head and neck squamous cell carcinoma (HNSCC) cell lines synthesize AHSG (in press) and have also detected abundant AHSG in primary HNSCC tumors (unpublished). Growth in serum-free medium and in vitro tumorigenic properties, including proliferation, adhesion and migration, are diminished in the HNSCC SQ20B cell line modified with AHSG-specific shRNA to express only twenty percent of the wild-type SQ20B cell line (SQ20B-AH20) compared to SQ20B modified with empty vector alone and expressing the wild-type amount of AHSG (SQ20B-EV) (in press). Here we have used shotgun proteomic analysis to identify additional proteins whose expression may also affect these in vitro properties of tumorigenesis associated with AHSG. The two cell lines were cultured in serum-free medium to avoid the contribution of exogenous AHSG in serum. Cell lysates were obtained, and the proteins were separated in polyacrylamide gels in duplicate. Each full protein lane was cut into 10 pieces, in-gel digested with trypsin and analyzed with tandem liquid chromatography mass spectrometry (LC-MS). MS data were analyzed against a recent human protein database. Proteins differentially expressed were quantified using a spectral counting approach. A total of 1386 distinct protein groups were identified in the two samples. Forty-eight proteins were differentially expressed in these samples (z score > 3, which corresponds to p ≤ 0.001, and Benjamini-Hochberg [statistical] FDR < 0.05). Proteins associated with the cytoskeleton, adhesion and apoptosis were over-represented in the group of differentially expressed proteins. Here we have shown that the human HNSCC cell line SQ20B exhibits changes in the proteome when AHSG expression is diminished. These proteins are critical for the tumorigenic properties of adhesion and migration. These data will help to identify mechanisms of tumorigenesis associated with AHSG in HNSCC. References 1. B. Guillory, A.M. Sakwe, M. Saria, P. Thompson, C. Adhiambo, R. Koumangoye, B. Ballard, A. Binhazim, C. Cone, W. Jahanen-Dechent, J. Ochieng, Lack of fetuin-A (alpha2-HS-glycoprotein) reduces mammary tumor incidence and prolongs tumor latency via the transforming growth factor-beta signaling pathway in a mouse model of breast cancer, The American Journal of Pathology 177 (2010) 2635-2644. 2. M.N. Kundranda, M. Henderson, K.J. Carter, L. Gorden, A. Binhazim, S. Ray, T. Baptiste, M. Shokrani, M.L. Leite-Browning, W. Jahnen-Dechent, L.M. Matrisian, J. Ochieng, The serum glycoprotein fetuin-A promotes Lewis lung carcinoma tumorigenesis via adhesive-dependent and adhesive-independent mechanisms, Cancer Res 65 (2005) 499-506. Citation Format: Dana R. Marshall, Victor Paramov, Siddharth Pratap, Georgina Iyamu, Amos Sakwe, Pamela Thompson, Josiah Ochieng. Shotgun proteomic analysis of human head and neck squamous cell carcinoma cell line SQ20B with diminished AHSG expression. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5306. doi:10.1158/1538-7445.AM2014-5306

Head and neck squamous cell carcinoma (HNSCC) is the eighth most common tumor in the world. Approximately 30,000 new cases of HNSCC are reported each year and 8,000 related deaths, in the United States. HNSCC of the oral cavity is highly metastatic and has a recurrence rate of 20%-50%, with a dismal 5-year survival rate of ∼50%. African-American males have a 5-year survival rate of ∼42% while the survival rate for Caucasian males is 52%. To date, there is no consistent means for early detection or a reliable biomarker for HNSCC, thus perpetuating the lack of improvement in mortality despite advances in delivery of treatment and surgical reconstruction. In a proteomic study seeking possible biomarkers for HNSCC, AHSG was detected at elevated levels in serum. Interestingly, we have found that some HNSCC cell lines synthesize and secrete AHSG. We have also shown in earlier studies, that the lack of AHSG reduces mammary tumor incidence and prolongs tumor latency in a mouse model for breast cancer. Together, this suggests that this hepatocellular glycoprotein that is found in most body fluids including serum could be a potential biomarker for HNSCC. AHSG is a negative acute phase response protein, which makes the findings of elevated levels of AHSG in the proteomic study most intriguing. In order to evaluate the role of AHSG in HNSCC progression (proliferation and metastatic properties) in vitro, we depleted AHSG in the HNSCC cell lineSQ20B. Thus far, we show that depletion of AHSG does not affect the proliferation of SQ20B cells. However, the depletion of AHSG mediates a decrease in migration and invasion of SQ20B cells. We are currently elucidating the molecular mechanisms of AHSG-mediated motility. This work was supported by grants from the NIH-NCI-Score 1 SC1 CA134018-01 (JO); DOD W81XWH-07-1-0254 (J.O); 5 T32 HL007735-15 (SA) and U54 CA091408 (subproject, DM). Citation Format: Pamela D. Thompson, Kurt Watson, Amos Sakwe, Josiah Ochieng, Dana Marshall. Alpha-2 Heremans Schmid glycoprotein (AHSG) promotes migration in head and neck squamous cell carcinoma (HNSCC) cell lines. [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 3788. doi:10.1158/1538-7445.AM2013-3788

Head and neck squamous cell carcinoma (HNSCC) is the eighth most common tumor in the world. In the United States, approximately 30,000 new cases of HNSCC are reported each year and 8,000 related deaths. HNSCC of the oral cavity is highly metastatic and has a recurrence rate of 20%-50%, with a dismal 5-year survival rate of ∼50%. There continues to be no consistent means for early detection or a reliable biomarker for the disease. This has contributed to the lack of improvement in the mortality rates of the disease, despite advances in delivery of treatment and surgical reconstruction. In a proteomic study seeking possible biomarkers for HNSCC, AHSG was detected at elevated serum levels. AHSG is a cell surface glycoprotein that is known to be synthesized by hepatocytes and found in most body fluids including serum. AHSG is also a negative acute phase function protein, which makes the results from the proteomic study, elevated levels of AHSG, intriguing. Our lab has recently shown that the lack of AHSG reduces tumor incidence and prolongs tumor latency. We now show that some HNSCC cell lines synthesize and secrete AHSG at both the message and protein levels. This is important as most cells acquire AHSG through uptake from serum. To our knowledge, this is the first report of AHSG synthesis and expression in HNSCC cell lines. We are currently depleting AHSG expression in these HNSCC cell lines in order to evaluate the effects of AHSG on the growth and metastatic properties (invasiveness and motility) in vitro and in vivo. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-15. doi:1538-7445.AM2012-LB-15

In-frame fusion of two transcription factor genes, TEL (ETV6) on chromosome 12p and AML1 (RUNX1) on chromosome 21q, is thought to be an initiating event in ∼25% of childhood acute lymphoblastic leukemias (ALL). TEL-AML1 fusion leads to the expression of a chimeric oncoprotein which interferes with the function of the normal AML1 protein, leading to arrested B cell development, and enhanced B cell progenitor self-renewal. In vitro studies showed that a TEL-AML1 junctional peptide induced HLA-DP-restricted CD4+ T cell responses. Although expression of TEL-AML1 by pro-leukaemic cells makes it an attractive immunotherapeutic target, information on the number, position, and population distribution of HLA-DR-restricted CD4+ T cell epitopes in TEL-AML1 has not been published. Here, we used the artificial neural network algorithm, NetMHCIIpan (Nielsen et al, PLoS Computational Biology, 2008, 4(7), e1000107) to predict DR-restricted T cell epitopes in TEL-AML1. The 797 residue fusion oncoprotein was screened using NetMHCIIpan to identify 9-mer DR-binding core peptides. 15-mer peptide sequences were submitted in FASTA format to the NetMHCIIpan server (http://www.cbs.dtu.dk/services/NetMHCIIpan/) to facilitate discovery of peptides with strong binding affinity (IC50: Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. 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 2395.

GTF2IRD1 is a member of a family of transcription factors whose defining characteristic is varying numbers of a helix–loop–helix like motif, the I-repeat. Here, we present functional analysis of human GTF2IRD1 in regulation of three genes (HOXC8, GOOSECOID and TROPONIN ISLOW). We define a regulatory motif (GUCE–GTF2IRD1 Upstream Control Element) common to all three genes. GUCE is bound in vitro by domain I-4 of GTF2IRD1 and mediates transcriptional regulation by GTF2IRD1 in vivo. Definition of this site will assist in identification of other downstream targets of GTF2IRD1 and elucidation of its role in the human developmental disorder Williams–Beuren syndrome.