Genome-wide DNA methylation profiling in chronic lymphocytic leukaemia

Background: DNA methylation aberrations are widespread among the malignant B lymphocytes of patients with chronic lymphocytic leukaemia (CLL), suggesting that DNA methylation might contribute to the pathogenesis of CLL. Aim: We aimed to explore the differentially methylated positions (DMPs) associated with CLL and screen the differentially methylated and expressed genes (DMEGs) by combining public databases. We aimed to observe the direction of each DMEG in CLL based on the DMPs in the promoter and the body region respectively to narrow down DMEGs. We also aimed to explore the methylation heterogeneity of CLL subgroups and the effect of B cells maturation on CLL. Methods: In this population-based case control study, we reported a genome-wide DNA methylation association study using the Infinium HumanMethylation450 BeadChip, profiling the DNA methylation of CD19⁺ B Cells from 48 CLL cases and 28 healthy controls. By integrating methylation data and expression data from public databases, gene sets were jointly screened, and then the relationship between methylation sites in promoter and body region and expression of each gene was explored. In addition, support vector machine (SVM) classification algorithm was used to identify subgroups of CLL cases based on methylation pattern, and the effect of B-cell differentiation related methylation sites on CLL-related sites was observed. Results: We identified 34,797 DMPs related to CLL across the genome, most of which were hypomethylated; the majority were located in gene body regions. By combining these DMPs with published DNA methylation and RNA sequencing data, we detected 26,244 replicated DMPs associated with 1,130 genes whose expression were significantly different in CLL cases. Among these DMEGs, nine low expressed DMEGs were selected with hypermethylated in promoter and hypomethylated in body region, and 83 high expressed DMEGs were selected with both hypomethylated in promoter and body region. The 48 CLL cases were divided into 3 subgroups based on methylation site by SVM algorithm. Over 92% of CpGs associated with B cell subtypes were found in CLL-related DMPs. Conclusion: The DNA methylation pattern was altered across the genome in CLL patients. The methylation of ZAP70, FMOD, and ADAMTS17 was significantly different between CLL cases and controls. Further studies are warranted to confirm our findings and identify the underlying mechanisms through which these methylation markers are associated with CLL.

A Mentored Pathway into the Sciences for Underrepresented Populations: A Newly Crafted Educational Modality for Women Exploring Career Opportunities in Science, Technology, Engineering, Mathematics, and Medicine

Purpose: The barriers generally facing women wishing to pursue careers in the disciplines of science, technology, engineering, mathematics, and medicine (STEMM) in the United States have been well described. However, additional layers of cultural beliefs and needs may pose further obstructions to women in certain cultural subgroups who wish to enter STEMM. Recognition of the challenges faced by such subgroups is important and culturally sensitive educational and training approaches may be necessary.

Methods: We therefore created a science mentoring and education program incorporating the specific requirements of our test group, young Orthodox Jewish women. Our goals were to facilitate their knowledge, skills, and attitudes to embark on a scientific career in biomedicine. Interventions were designed to target physical, intellectual, emotional, and spiritual areas of growth with each intervention crafted to the sensitivity of the women's cultural and religious backgrounds.

Results: Over the course of 6 years, we enrolled 59 Orthodox Jewish women, ages 16–20 years. These women spent their summers as part of the larger Summer Internship Program (SIP) at the National Institutes of Health. They participated in cohort sizes ranging from 6 to 26 in dozens of multilevel experiences in the SIP over 6–10 weeks. Participants reported strengthening interest to pursue careers in health care-related fields. Other graduates committed to pursue careers in the general sciences, and other graduate studies.

Conclusion: This unique educational platform shows promise for other intersectional groups approaching educational barriers to careers in STEMM.

Expression of the muscle-associated gene MYF6 in hairy cell leukemia

Hairy cell leukemia (HCL) is a purine analog-responsive B-cell malignancy containing the BRAF V600E mutation, expressing CD22, CD11c, CD103, tartrate resistant acid phosphatase (TRAP) CD25, CD123, and annexin 1A. BRAF V600E and the latter 4 markers are usually absent in the more aggressive and chemoresistant variant HCLv. To evaluate differences between HCL and HCLv, expression microarrays comparing HCL with HCLv were performed for 24694 genes using 47323 probes. Microarray data from 35 HCL and 27 HCLv purified samples showed the greatest HCL-HCLv difference in the muscle-associated gene MYF6, expressed by its 2 probes 18.5- and 10.8-fold higher in HCL than HCLv (p<0.0001). By real-time quantitative PCR (RQ-PCR), 100% of 152 classic HCL samples were MYF6-positive, vs 5 (6%) of 90 blood donors. MYF6-expression was also detected in 18 (35%) of 51 with HCLv, 11 (92%) of 12 with HCL expressing unmutated IGHV4-34, 35 (73%) of 48 with chronic lymphocytic leukemia (CLL), and 1 (8%) of 12 with mantle cell lymphoma. Hypomethylation status of MYF6 supported expression in HCL more than HCLv. Posttreatment blood samples becoming negative by flow cytometry remained MYF6+ by RQ-PCR in 42 (48%) of 87 HCL patients, and MYF6 RQ-PCR could detect 1 HCL in 10⁵ normal cells. MYF6, universally expressed in HCL and in most CLL samples, may be a useful biomarker for these leukemias. Further studies are underway to determine the role of MYF6 in HCL.

Relationship of DNA methylation to mutational changes and transcriptional organization in fusion-positive and fusion-negative rhabdomyosarcoma

Our previous study of DNA methylation in the pediatric soft tissue tumor rhabdomyosarcoma (RMS) demonstrated that fusion-positive (FP) and fusion-negative (FN) RMS tumors exhibit distinct DNA methylation patterns. To further examine the significance of DNA methylation differences in RMS, we investigated genome-wide DNA methylation profiles in discovery and validation cohorts. Unsupervised analysis of DNA methylation data identified novel distinct subsets associated with the specific fusion subtype in FP RMS and with RAS mutation status in FN RMS. Furthermore, the methylation pattern in normal muscle is most similar to the FN subset with wild-type RAS mutation status. Several biologically relevant genes were identified with methylation and expression differences between the two fusion subtypes of FP RMS or between the RAS wild-type and mutant subsets of FN RMS. Genomic localization studies showed that promoter and intergenic regions were hypomethylated and the 3' untranslated regions were hypermethylated in FP compared to FN tumors. There was also a significant difference in the distribution of PAX3-FOXO1 binding sites between genes with and without differential methylation. Moreover, genes with PAX3-FOXO1 binding sites and promoter hypomethylation exhibited the highest frequency of overexpression in FP tumors. Finally, a comparison of RMS model systems revealed that patient-derived xenografts most closely recapitulate the DNA methylation patterns found in human RMS tumors compared to cell lines and cell line-derived xenografts. In conclusion, these findings highlight the interaction of epigenetic changes with mutational alterations and transcriptional organization in RMS tumors, and contribute to improved molecular categorization of these tumors.

Dynamics of Genome Alterations in Crohn's Disease-Associated Colorectal Carcinogenesis

Purpose: Patients with inflammatory bowel diseases, that is, ulcerative colitis and Crohn's disease (CD), face an increased risk of developing colorectal cancer (CRC). Evidence, mainly from ulcerative colitis, suggests that TP53 mutations represent an initial step in the progression from inflamed colonic epithelium to CRC. However, the pathways involved in the evolution of CRC in patients with CD are poorly characterized.Experimental Design: Here, we analyzed 73 tissue samples from 28 patients with CD-CRC, including precursor lesions, by targeted next-generation sequencing of 563 cancer-related genes and array-based comparative genomic hybridization. The results were compared with 24 sporadic CRCs with similar histomorphology (i.e., mucinous adenocarcinomas), and to The Cancer Genome Atlas data (TCGA).Results: CD-CRCs showed somatic copy-number alterations (SCNAs) similar to sporadic CRCs with one notable exception: the gain of 5p was significantly more prevalent in CD-CRCs. CD-CRCs had a distinct mutation signature: TP53 (76% in CD-CRCs vs. 33% in sporadic mucinous CRCs), KRAS (24% vs. 50%), APC (17% vs. 75%), and SMAD3 (3% vs. 29%). TP53 mutations and SCNAs were early and frequent events in CD progression, while APC, KRAS, and SMAD2/4 mutations occurred later. In four patients with CD-CRC, at least one mutation and/or SCNAs were already present in non-dysplastic colonic mucosa, indicating occult tumor evolution.Conclusions: Molecular profiling of CD-CRCs and precursor lesions revealed an inflammation-associated landscape of genome alterations: 5p gains and TP53 mutations occurred early in tumor development. Detection of these aberrations in precursor lesions may help predicting disease progression and distinguishes CD-associated from sporadic colorectal neoplasia. Clin Cancer Res; 24(20); 4997-5011. ©2018 AACR.

Abstract 2633: The effects of aberrant global methylation in hepatocellular carcinoma

A better understanding of the molecular pathology of hepatocellular carcinomas (HCC), particularly in the United States of America (USA), could provide more effective biomarkers for early detection, diagnosis and treatment for this aggressive cancer. From two SEER Residual Tissue Repositories (Hawaii and Iowa), 483 surgical samples were obtained (223 cases of matched tumor/adjacent-normal); 30 were of OCT origin with the remaining FFPE. Purified genomic DNA was tested by the Illumina Infinium HumanMethylation450K BeadChip array according to the manufacturer's recommendations. Data were processed by using Lumi, methylumi, and other relevant R packages and also the Partek Genomics Suite. ANOVA results with FDR&lt;0.01 between tumor and normal samples plus absolute beta value differences greater than 0.2 in FFPE or OCT, respectively, were compared and the overlapping 7279 targets generated the final gene list. In tumor, the genes MYH7 and TPO are hypomethylated, whereas OTX1 and C1orf70 are hypermethylated. Methyl2CGH aggregated patterns (FFPE only), showed that tumor was enriched for large chromosomal losses in Chr 8p and 17p with possible focal losses in Chr 4, 6, 8, 10, 12, 13, 17, 18 and 22. Large aberrations in chromosomal gains were seen in Chr 1q and 8q with possible focal gains seen in most chromosomes (excluding 9, 16, 21, 22). Importantly, 41 tumor suppressor genes are associated with copy number loss; these include RB1, TP53, MAP2K4 and CBFA2T3. However, identification of differentially methylated regions by using a segmentation method (NEXUS) suggested that tumor samples were more likely to be hypermethylated across the genome than hypomethylated (1q only). A possible limitation is that combining OCT and FFPE data is suspect due to at least 40 genes that specifically are hypermethylated in OCT samples but not FFPE. We previously reported that relative telomere length is prognostic for survival in HCC (Yang, et al., 2016). In this study we detected one gene, ZSCAN4, in the telomere maintenance pathway that is hypomethylated in tumor samples; the biological significance of this needs to be explored. In conclusion, for the under-studied USA HCC population, we have established strong preliminary methylation and copy number data indicating that there are specific epigenetic and chromosomal abnormalities that upon verification, could prove useful as biomarkers for improved understanding of the pathogenesis, early detection, and diagnosis of HCC.

Citation Format: Daniel C. Edelman, Fatma Shebl, Yonghong Wang, Holly Stevenson, Lawrence Sternberg, Joshua Sampson, Baiyu Yang, Paul S. Meltzer, Katherine McGlynn. The effects of aberrant global methylation in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2633.

Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients

The clinical course of breast cancer varies from one patient to another. Currently, the choice of therapy relies on clinical parameters and histological and molecular tumor features. Alas, these markers are informative in only a subset of patients. Therefore, additional predictors of disease outcome would be valuable for treatment stratification. Extensive studies showed that the degree of variation of the nuclear DNA content, i.e., aneuploidy, determines prognosis. Our aim was to further elucidate the molecular basis of aneuploidy. We analyzed five diploid and six aneuploid tumors with more than 20 years of follow-up. By performing FISH with a multiplexed panel of 10 probes to enumerate copy numbers in individual cells, and by sequencing 563 cancer-related genes, we analyzed how aneuploidy is linked to intratumor heterogeneity. In our cohort, none of the patients with diploid tumors died of breast cancer during follow-up in contrast to four of six patients with aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however, TP53 mutations were not observed in diploid tumors, but in all aneuploid tumors in our collective. We conclude that quantitative measurements of intratumor heterogeneity by multiplex FISH, detection of MYC amplification and TP53 mutation could augment prognostication in breast cancer patients.

Abstract 4682: Genomic profiles in gene expression and methylation help define the molecular characteristics of hairy cell leukemia subtypes

Hairy cell leukemia (HCL) until recently was characterized as a single blood and bone marrow malignancy, even though clinically at least two pathologies seemed to be at work. This study sought to confirm the clinical observations using genomic evidence. HCL is a chronic mature B-cell malignancy with distinctive immunophenotype, typically expressing CD20, CD22, CD25, CD11c, CD103, CD123, annexin A1 (ANXA1), and tartrate-resistant acid phosphatase (TRAP). Purine analog therapy is highly effective, with most patients achieving durable remissions. HCL- variant (HCLv) was first identified by Cawley et al. (1980) and recently recognized by the World Health Organization as a separate cancer. HCLv lacks CD25, ANXA1, TRAP, and BRAF V600E expression, and patients respond poorly to purine analogs. In order to find detailed biological information involving these two diseases, we studied the genome-wide gene expression and methylation profiles of 75 HCL patient samples; 67 were tested by both methods. Our study results indicate that HCL and HCLv show very distinct gene expression and methylation patterns. Many genes that are differentially expressed are involved in immunological and inflammatory response pathways. Several cancer associated genes such as ANXA1 and FLT3 are down-regulated in HCLv compared to HCL. Correlation patterns between methylation and gene expression for many genes such as ANXA1 suggest that methylation plays an import role in gene expression regulation for these malignancies. This study has begun the process of identifying better biomarkers for disease discrimination between HCL and HCLv and providing potential new targets for strongly needed therapies for HCLv.

Citation Format: Daniel C. Edelman, Holly S. Stevenson, Yonghong Wang, Evgeny Arons, Joshua J. Waterfall, David Petersen, Hong Zhou, Paul S. Meltzer, Robert J. Kreitman. Genomic profiles in gene expression and methylation help define the molecular characteristics of hairy cell leukemia subtypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4682. doi:10.1158/1538-7445.AM2017-4682

Combination of PDL-1 and PARP inhibition in an unselected population with metastatic castrate-resistant prostate cancer (mCRPC)

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Background: About 30% of sporadic mCRPC has defects in DNA repair pathways which may confer sensitivity to PARP inhibition. There is limited data about PDL1 inhibition in mCRPC. We hypothesize increased DNA damage by olaparib (O) will complement anti-tumor activity of immune checkpoint blocking antibody, durvalumab (D), in mCRPC:NCT02484404. Methods: Single arm pilot study with accrual of 25 patients (pts) with mCRPC and biopsiable disease. Prior treatment with enzalutamide and/or abiraterone is required. D is given at 1500 mg iv q28 days + O 300 mg po q12 h. Primary endpoint is PFS. Pretreatment and on-study core biopsies undergo mutational analysis. Results: 10 pts have enrolled (median age 65 yr [range 51-79], median baseline PSA: 85.78 [22.17-809.9 ng/mL]). 7 pts have GS ≥ 8. Grade 3/4 adverse events include anemia 2/7 (29%), thrombocytopenia, lymphopenia, neutropenia, nausea, fatigue, UTI, and lung infection [1/7 each, (14%)]. 5/7 pts (71%) on-study >2 months (mos) have PSA declines > 50%. Median PFS is 7.8 mos (95% CI: 1.8 mos-undefined). Conclusions: Preliminary data shows D+O is well tolerated with activity in an unselected population. Accrual is ongoing with biomarker analysis. Clinical trial information: NCT02484404. [Table: see text]

A phase II study of the anti-programmed death ligand-1 antibody durvalumab (D; MEDI4736) in combination with PARP inhibitor, olaparib (O), in metastatic castration-resistant prostate cancer (mCRPC)

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Background: Recent data suggests 25-30% of sporadic mCRPC has defects in DNA repair pathways which may confer sensitivity to PARP inhibition. Immune checkpoint blockade is a promising avenue in mCRPC treatment. We hypothesize that increased DNA damage by O will complement anti-tumor activity of immune checkpoint inhibitor, D, in mCRPC (NCT02484404). Methods: Eligible pts have mCRPC with adequate end organ function and biopsiable disease (bone or soft tissue). Prior treatment with enzalutamide and/or abiraterone is required. D is administered at 1500 mg iv q28 days with O at 300 mg po q12 h. Primary endpoint is PFS. Secondary endpoints include PSA responses, safety and ORR. Single arm pilot study with a total accrual of 25 pts. On-study core biopsies undergo mutational analysis. Results: 6 pts have enrolled (median age 67 yr [range 60-79], median ECOG PS 1 [1-2]). Median baseline PSA: 258.1 (54.1-809.9 ng/mL). 4 pts have Gleason score (GS) > 8 and 2 pts have GS of 7. Grade 3/4 adverse events include anemia 2/6 (33%), thrombocytopenia, lymphopenia, nausea, febrile neutropenia, aspiration pneumonia [1 each, (17%)]. Conclusions: Exploiting synergy of D+O is a treatment option for heavily pre-treated pts. Preliminary data shows D+O is tolerable and active in mCRPC pts without germline BRCA mutation. Paired tumor biopsies and blood samples including ctDNA are being collected. Accrual is ongoing. Clinical trial information: NCT02484404. [Table: see text]

Telomere Length and Survival of Patients with Hepatocellular Carcinoma in the United States

BACKGROUND

Telomere shortening is an important molecular event in hepatocellular carcinoma (HCC) initiation; however, its role in HCC progression and prognosis is less clear. Our study aimed to examine the association of telomere length with survival of patients with HCC.

METHODS

We measured telomere length in tumor and adjacent non-tumor tissues from 126 persons with HCC in the United States (U.S.) who were followed for mortality outcomes. Relative telomere length (RTL) was measured by a monochrome multiplex quantitative polymerase chain reaction assay. Multivariable Cox proportional hazards modeling was used to calculate hazard ratios (HRs) and 95% CIs for the association between telomere length and all-cause mortality. We also examined associations between telomere length and patient characteristics using multiple linear regression.

RESULTS

During a mean follow-up of 6.0 years, 79 deaths occurred among 114 individuals for whom survival data were available. The ratio of RTL in tumor relative to non-tumor tissue was greater for individuals with regional or distant stage tumors (0.97) than localized stage tumors (0.77), and for individuals with grade III or IV tumors (0.95) than grade II (0.88) or grade I (0.67) tumors. An RTL ratio ≥1 was not associated with survival (HR 0.92, 95% CI 0.55, 1.55) compared to a ratio <1, after adjusting for age at diagnosis, sex, tumor stage and tumor size. Similarly, RTL in the tumor and non-tumor tissue, respectively, were not associated with survival.

CONCLUSIONS

This U.S. based study found that telomeres may be longer in more aggressive HCCs. There was no evidence, however, that telomere length was associated with survival of patients with HCC. Future investigations are warranted to clarify the role of telomere length in HCC prognosis.

Abstract 2434: DNA methylation characterization of fusion-positive and fusion-negative rhabdomyosarcoma primary tumors and cell lines

BACKGROUND: Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood and comprises two major subtypes: fusion-positive (FP, most commonly PAX3-FOXO1 or PAX7-FOXO1) and fusion-negative (FN). Our previous study demonstrated that FP and FN RMS tumors exhibit distinct DNA methylation profiles. The current study will explore these issues in a larger, separate cohort of RMS tumors and compare DNA methylation in RMS cell lines and primary tumors.

METHODS: DNA methylation was examined in 48 RMS tumors (21 FP and 27 FN) as well as 10 RMS cell lines (5 FP and 5 FN) on the Illumina HumanMethylation450 BeadChip platform.

RESULTS: Unsupervised clustering analysis using the most variable probes (top 1%) in the 48 RMS tumors revealed that patterns of DNA methylation segregated these tumors into two distinct subgroups; one subgroup contains all 21 FP cases along with 2 FN cases and a second subgroup contains 25 of the 27 FN cases. A principal component analysis confirmed this close association of methylation pattern and fusion status, and showed that the two “discordant” FN cases map in a region between the FP and FN clusters. The FP tumors showed substantially lower overall levels of methylation compared to FN tumors. Application of an 11-gene methylation signature developed in our earlier study classified these 48 cases into FP and FN categories with &gt;95% accuracy. In contrast to our previous findings, there was a significant difference in the distribution of PAX3-FOXO1 binding sites between genes with and without differential methylation. Though unsupervised clustering analysis indicated that FP tumors and cell lines cluster as do the FN tumors and cell lines, a principal component analysis clarified these relationships by showing that the two groups of cell lines are located at a considerable distance from the two tumor subtypes. Analysis of the most varied probes in the tumors indicated that the vast majority of these probes are hypermethylated in all RMS cell lines. In a complementary analysis with the most variable probes (top 1%) in the cell lines, most of these probes are hypomethylated in all RMS tumors, though two smaller groups of probes show differential methylation between both groups of FP and FN samples.

CONCLUSIONS: This study provides an independent validation that FP and FN RMS tumors possess distinct and characteristic methylation profiles. The enrichment of PAX3-FOXO1 binding sites in genes that are differentially methylated between these FP and FN tumors suggests that the PAX3-FOXO1 fusion protein may contribute to this methylation pattern. These analyses also indicate that RMS cell lines do not faithfully recapitulate the DNA methylation patterns that characterize primary tumors.

Citation Format: Wenyue Sun, Bishwanath Chatterjee, John F. Shern, Yonghong Wang, Holly S. Stevenson, Daniel C. Edelman, Paul S. Meltzer, Javed Khan, Frederic G. Barr. DNA methylation characterization of fusion-positive and fusion-negative rhabdomyosarcoma primary tumors and cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2434.

Abstract 818: Shortened telomere length in hepatocellular carcinoma in the United States

Background: Telomeres play an important role in the maintenance of chromosomal stability. It has been previously reported that telomere length is shortened in hepatocellular carcinoma (HCC) compared to paired non-tumor tissue. However, most studies have been conducted in high-risk regions such as Asia. To date, no prior study has examined telomere length and HCC in the United States, a low risk region where HCC etiology may differ from that of high risk regions.

Methods: We measured telomere length in 127 paired tumor and non-tumor tissue samples from persons with HCC in Iowa, Hawaii and Connecticut. Formalin-fixed, paraffin-embedded tissues were collected at the time of diagnosis. Relative telomere length was measured by a monochrome multiplex quantitative PCR assay. The Wilcoxon signed-rank test was used to compare telomere length between tumor and paired non-tumor tissues. Cox proportional hazards modeling was used to estimate the association between telomere length and mortality, adjusting for age at diagnosis, sex, and tumor stage and size at diagnosis.

Results: Of the 127 pairs of samples, telomere length was shorter in the tumor in 88 pairs (69%), longer in the tumor in 33 pairs (26%) and the same length in the tumor and non-tumor tissue in 6 pairs (5%). Overall, the HCC tissues had statistically significantly shorter telomere length than their matched non-tumor tissues (p &lt; 0.01). The proportion of pairs in which the tumor telomere was shorter than non-tumor was higher among those with localized stage tumors (81%) compared to those with regional or distant stage tumors (50%) (p &lt; 0.01 after adjusting for age at diagnosis, sex, and source of the case). In addition, we observed a 119% higher risk of mortality (adjusted relative risk 2.19) among persons whose tumors had shorter telomeres than their non-tumor tissue, compared to persons whose tumors had longer telomeres; however, the confidence interval was relatively wide (0.94-5.12).

Conclusion: Using tissue samples from persons with HCC in the United States, we found that telomere length was shorter in tumor tissue compared to paired non-tumor tissue, especially among localized stage tumors. In addition, there was a suggestion that tumor telomere shortening might be associated with higher risk of mortality. Together, these results may provide insight into the role of biological mechanisms associated with telomere shortening and into the prognosis of HCC in lower risk populations.

Citation Format: Baiyu Yang, Fatma M. Shebl, Lawrence R. Sternberg, Andrew C. Warner, David E. Kleiner, Daniel C. Edelman, Allison Gomez, Casey L. Dagnall, Belynda D. Hicks, Sean F. Altekruse, Brenda Y. Hernandez, Charles F. Lynch, Paul S. Meltzer, Katherine A. McGlynn. Shortened telomere length in hepatocellular carcinoma in the United States. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 818.

COXEN prediction of antineoplastic drug sensitivity in bladder cancer patients

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Background: COXEN (Co-eXpression ExtrapolatioN) uses molecular profiles as a “rosetta stone” for translating drug sensitivities of one set of cancers into predictions for another completely independent set of cell lines or human tumors. The ability of COXEN to predict drug effectiveness in pts using tumor samples from in vitro assays is unique. Methods: We tested the predictive value of COXEN for standard chemotherapies in a cohort of bladder cancer pts. Total RNA was extracted from formalin fixed paraffin embedded (FFPE) tissue and converted to cDNA, amplified with Ovation FFPE WTA, and hybridized to a GeneChip Human Genome U133 Plus 2.0 array. Using gene expression data from 278 independent bladder tumors, COXEN scores were generated using bioinformatics models originally built using the NCI-60 cell line panel and a model building algorithm (MiPP). Gene expression data was processed to score 76 FDA approved antineoplastic drugs. Results: A total of 24 samples were tested (15 tumors with 1 sample and 9 tumors with 2 biological replicas (2 samples from the same tumor)) from 15 pts who received chemotherapy (median age 64 (41-74); 73% male; with muscle invasive bladder cancer (MIBC) (12/15, 80%) or metastatic bladder cancer (mBC) (3/15, 20%)). Response to therapy was confirmed by pathologic response in MIBC pts and radiologic response in mBC pts. Chemotherapies evaluated included: methotrexate/vinblastine/doxorubicin/cisplatin; gemcitabine/cisplatin; gemcitabine/carboplatin; and cisplatin/etoposide. COXEN accurately predicted antineoplastic drug sensitivity in 11/15 (73%) pts (75% MIBC and 67% mBC), of which 7/11 pts had 2 biological samples. However, only 3/7 (43%) biological replicas confirmed COXEN prediction. COXEN accurately predicted drug sensitivity in 9/10 (90%) pts with response and 2/5 (40%) pts with resistance to therapy. Conclusions: COXEN did well in predicting antineoplastic drug response for the majority of bladder cancer pts in this cohort. However, predictions from 2 samples within the same tumor were not always consistent, likely due to the expected tumor heterogeneity found in bladder cancer tumors. A prospective clinical trial in patients with mBC using COXEN to select next best therapy is in development.

Impact of telomere length on survival in classic and variant hairy cell leukemia

Telomeres, which protect the ends of chromosomes, are shortened in several hematologic malignancies, often with adverse prognostic implications, but their effect on prognosis of classic and variant hairy cell leukemia (HCL and HCLv) has not been reported. HCL/HCLv genomic DNA from 46 patients was studied by PCR to determine the ratio of telomere to single copy gene number (T/S). T/S was unrelated to diagnosis of HCL or HCLv (p=0.27), but shorter T/S was associated with unmutated immunoglobulin rearrangements (p=0.033) and age above the median at diagnosis (p=0.017). Low T/S was associated with shorter overall survival from diagnosis (OS), particularly T/S <0.655 (p=0.0064, adjusted p=0.019). Shorter OS was also associated with presence of unmutated (p<0.0001) or IGHV4-34+ (p<0.0001) rearrangements, or increasing age (p=0.0002). Multivariable analysis with Cox modeling showed that short T/S along with either unmutated or IGHV4-34+ rearrangements remained associated with reduced OS (p=0.0071, p=0.0024, respectively) after age adjustment. While T/S is relatively long in HCL and the disease usually indolent with excellent survival, shortened telomeres in HCL/HCLv are associated with decreased survival. Shortened T/S could represent a risk factor needing further investigation/intervention to determine if non-chemotherapy treatment options, in addition to or instead of chemotherapy, might be particularly useful.

Distinct methylation profiles characterize fusion-positive and fusion-negative rhabdomyosarcoma

Rhabdomyosarcoma comprises two major subtypes, fusion positive (PAX3-FOXO1 or PAX7-FOXO1) and fusion negative. To investigate the significance of DNA methylation in these subtypes, we analyzed methylation profiles of 37 rhabdomyosarcoma tumors and 10 rhabdomyosarcoma cell lines, as well as 8 normal tissues. Unsupervised clustering of DNA methylation clearly distinguished the fusion-positive and fusion-negative subsets. The fusion-positive tumors showed substantially lower overall levels of methylation compared with fusion-negative tumors. Comparison with the methylation pattern of normal skeletal muscle and bone marrow indicates that fusion-negative rhabdomyosarcoma is more similar to these normal tissues compared with fusion-positive rhabdomyosarcoma, and suggests that many of the methylation differences between these subtypes arise from 'aberrant' hyper- and hypomethylation events in fusion-positive rhabdomyosarcoma. Integrative methylation and gene expression analysis revealed that methylation differences between fusion-positive and fusion-negative tumors could either be positively or negatively associated with mRNA expression. There was no significant difference in the distribution of PAX3-FOXO1-binding sites between genes with and without differential methylation. However, the finding that PAX3-FOXO1-binding sites were enriched among genes that were both differentially methylated and differentially expressed suggests that the fusion protein interacts with DNA methylation to regulate target gene expression. An 11-gene DNA methylation signature, classifying the rhabdomyosarcoma tumors into fusion-positive and fusion-negative subsets, was established and validated by pyrosequencing assays. Notably, EMILIN1 (part of the 11-gene signature) showed higher methylation and lower mRNA expression in fusion-positive compared with fusion-negative tumors, and demonstrated demethylation and re-expression in multiple fusion-positive cell lines after treatment with 5-aza-2'-deoxycytidine. In conclusion, our study demonstrates that fusion-positive and fusion-negative rhabdomyosarcoma tumors possess characteristic methylation profiles that contribute to the expression differences between these fusion subtypes. These findings indicate an important relationship between fusion status and epigenetic changes in rhabdomyosarcoma, present a novel approach for ascertaining fusion status, and may identify new therapeutic targets in rhabdomyosarcoma.

Abstract 3278: Distinct methylation profiles characterize fusion-positive and fusion-negative rhabdomyosarcoma

BACKGROUND: Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood. Based on the presence or absence of a characteristic fusion gene (either PAX3-FOXO1 or PAX7-FOXO1), RMS comprises two major subtypes: fusion-positive (FP) and fusion-negative (FN). The goal of this study is to analyze DNA methylation differences between FP and FN tumors and to determine how these methylation differences contribute to biological differences between FP and FN RMS.

METHODS: DNA methylation profiles of 37 RMS tumors (20 FP and 17 FN) and 10 RMS cell lines (5 FP and 5 FN) as well as 8 normal tissues (4 muscles and 4 bone marrows) were assessed using DNA methylation arrays. Expression array analysis was performed on 58 RMS tumors (33 FP and 25 FN, including 16 with matched methylation data). Bioinformatic methods including classification, differential methylation, differential expression, methylation-expression correlation and gene set analysis were carried out.

RESULTS: Unsupervised clustering clearly distinguished the FP and FN subsets in 37 RMS primary tumors and in 10 RMS cell lines. The FP tumors showed substantially lower overall levels of methylation compared to FN tumors. Integrative methylation and gene expression analysis revealed that methylation differences between FP and FN tumors could either be positively or negatively associated with mRNA expression. Though there was no significant difference in the distribution of PAX3-FOXO1 binding sites between genes with and without differential methylation, PAX3-FOXO1 binding sites were enriched among genes that were both differentially methylated and differentially expressed. An 11-gene DNA methylation signature, classifying the RMS tumors into FP and FN subsets, was established in 37 RMS primary tumors and validated in 10 RMS cell lines. Pyrosequencing studies of 6 of the methylation signature genes independently confirmed differential methylation between FP and FN cases for the CpG site queried on the methylation array as well as other nearby CpG sites. To further investigate the relationship between DNA methylation and expression, we focused on the EMILIN1 gene, which shows higher methylation and lower mRNA expression in FP tumors compared to FN tumors. After treating RMS cell lines with 5-Aza-2′-deoxycytidine, the EMILIN1 gene demonstrated decreased DNA methylation and increased mRNA expression in multiple FP cell lines.

CONCLUSION: FP and FN RMS tumors possess characteristic methylation profiles that contribute to the expression differences between these fusion subtypes. These findings indicate an important role of epigenetics in RMS tumorigenesis, suggest novel approaches for identifying fusion status, and may find new therapeutic targets in RMS.

Citation Format: Wenyue Sun, Bishwanath Chatterjee, Yonghong Wang, Holly S. Stevenson, Daniel C. Edelman, Paul S. Meltzer, Frederic G. Barr. Distinct methylation profiles characterize fusion-positive and fusion-negative rhabdomyosarcoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3278. doi:10.1158/1538-7445.AM2015-3278

Abstract 5307: Analysis of telomere length in classic and variant hairy cell leukemia

Telomeres are ribonucleoprotein structures which protect the ends of chromosomes from aberrant recombination events and have been reported to be relatively short in several hematologic malignancies; adverse prognosis has been documented in chronic lymphocytic leukemia and several non-B-cell malignancies. However, their association with prognosis of classic and variant hairy cell leukemia (HCL and HCLv) has not been described. To study telomeres in HCL and HCLv, DNA from leukemic cells of patients was measured by monochrome multiplex quantitative PCR (MMQPCR) to determine relative telomere length (RTL). Of 46 patients in the cohort, 5 of 27 HCL (19%) vs. 12 of 19 HCLv (63%) patients had unmutated (&gt;98% homology to germline sequence) immunoglobulin rearrangements (p = 0.0045). IGHV4-34+ rearrangements were present in 12 of the 17 (70%) unmutated cases, including five HCL and seven HCLv. RTL was shown to be shorter in unmutated HCL (p = 0.03) and in patients who had died of their disease (p = 0.03). RTL negatively correlated with IGHV homology to germline sequence (r = -0.331; p = 0.025), and age (r = -0.315; p = 0.035). Shorter RTL was associated with death from disease in either HCL (p = 0.0063) or HCLv (p = 0.0034), in patients with mutated IGHV rearrangements (p = 0.005), or in all patients combined (p = 0.0008). Median survival from diagnosis was less in time in patients with shorter RTL (p = 0.016) and this significant difference persisted when examining just the 19 patients with HCLv (p = 0.029). Gene expression profiling identified several genes related to telomere maintenance with significantly different expression levels between mutated and unmutated cases. This first of kind study in HCL/HCLv suggests that telomeres play a role in the relative pathology of HCL and HCLv and RTL could be used as a prognostic biomarker in gauging the indolent course of these cancers.

Citation Format: Daniel C. Edelman, Evgeny Arons, Holly Stevenson, Allison Gomez, David Petersen, Hong Zhou, Yonghong Wang, Joshua J. Waterfall, Paul S. Meltzer, Robert Kreitman. Analysis of telomere length in classic and variant hairy cell leukemia. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5307. doi:10.1158/1538-7445.AM2015-5307

Long-term stability of total RNA in RNAstable® as evaluated by expression microarray

Storage of labile RNA in laboratories is accomplished through ultra-low freezing of the nucleic acids. This however requires expensive freezers, convenient storage, reliable electrical power, and increased shipping costs, thereby making it a less viable option. Biomatrica (San Diego, CA) has created RNAstable(®), a stabilization reagent that is used to store RNA in a dehydrated state at room temperature (RT) and protects the RNA from degradation. Our objective was to investigate the sequence integrity and suitability of RNA when stored in RNAstable at extended time periods and at varying temperatures through use of Illumina and Agilent RNA expression microarrays. We observed in Bioanalyzer electropherograms that total RNA extracted from 293 cells stored at RT in RNAstable for 4.5 and 11.5 months is similar in quality to RNA stored at -80°C. Illumina mRNA expression array QC metrics and gene expression patterns from RNAstable-protected RNA, in contrast to RNA stored without RNAstable, correlated well with those of freezer controls. Significantly, when RNA was stored in RNAstable at 45°C for 4.5 months, equivalent to 22 months RT storage, RNA quality, microarray probe signal intensities, probe detection rates, and expression profiles remained similar between RNAstable-protected RNA at RT and the -80°C controls. At 10.5 months, miRNA levels were compared among the storage conditions using miRNA expression arrays. Here too we found strong concordance between miRNA expression patterns when total RNA was stored in RNAstable or at -80°C. Further, Bioanalyzer electrophoresis of RNAstable-protected samples stored at RT for a relative total of 33 months or 50.5 months showed comparable integrity scores to those of -80°C controls. We conclude that use of RNAstable holds promise as an effective stabilization reagent for total RNA and should be useful in situations where shipping and storage options are limited resources.

Genetic and epigenetic analysis of monozygotic twins discordant for testicular cancer

Despite the notion that monozygotic (identical) twins share 100% identical genetic information, genetic differences among monozygotic twin pairs do occur and can be explained by mechanisms occurring during post-zygotic events. Despite such twins being fundamentally "identical", these post-zygotic genetic changes may give rise to phenotypic differences and genetic diseases. Consequently, studies of monozygotic twin pairs discordant for specific genetic diseases represent an important tool for the identification of disease genes. We used array comparative genomic hybridization (aCGH) and methylation arrays to search for genetic and epigenetic differences in blood drawn from four monozygotic twin pairs discordant for testicular germ cell tumors. No consistent differences were identified. A larger twin study would be required to achieve confident discovery of very subtle differences between monozygotic twins discordant for testicular germ cell tumors.

Abstract 3019: Aberrant NF-κB and Notch pathways promote CD133+ cancer stem cells in human primary cutaneous squamous cell carcinoma

The cancer stem cell (CSC) subpopulation has been implicated in inducing tumorigenesis and drug resistance, however, the unique gene program and regulatory signaling that contribute to the CSC phenotypes in human cutaneous squamous cell carcinoma (hcSCC) have not been defined. In this study, a newly improved cell sorting method was developed using a panel of multiple cell surface markers to isolate the small percentage of CD133+ cell population enriched for CSC in primary hcSCC specimens. These cells exhibited CSC features including enhanced spheroid formation in vitro and tumor formation in vivo. Distinct gene expression signatures of the CD133+ subset were profiled by comparing CD133+ CSC with CD133- cancer cells using microarray, which revealed that CD133+ cells expressed enriched stem cell and cancer-related gene programs. In the CD133+ subset, 80 differentially expressed stem cell genes were identified, with an additional set of 69 altered genes enriched in key regulatory pathways, including Notch, NF-κB, Wnt, EMT, and STAT signaling, using Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA). The expression patterns of combined signature genes of CSC and the key regulatory pathways were validated with Nanostring gene expression assay in independent tumor samples. Notch and NF-κB signaling emerged as important pathways. Inhibitors or siRNA knockdown of Notch1/2 and IKKα inhibited NF-κB activity and altered CSC phenotypes, including percentage of CD133+ cells, colony and spheroid formation. Elevated NF-κB signaling was observed in CSCs in the tumor tissues, where immunofluorescent staining showed co-localization of CD133+ and molecules of NF-κB pathway in SCC tumor specimens. Our data support the importance of aberrant NF-κB and Notch signaling in promoting CSC gene program and biologic functions, which could represent predictive diagnostic and prognostic parameters and potential targets for skin cancer prevention and treatment.

Supported by NIDCD intramural projects ZIA-DC-000016, 73 and 74.

Citation Format: Xinxin Quan, Nga Voong, Weiping Chen, Jamie Coupar, Steven Lee, David W. Petersen, Daniel C. Edelman, Paul S. Meltzer, Andrew Montemarano, Martin Braun, Jonathan Vogel, Carter Van Waes, Zhong Chen. Aberrant NF-κB and Notch pathways promote CD133+ cancer stem cells in human primary cutaneous squamous cell carcinoma. [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 3019. doi:10.1158/1538-7445.AM2014-3019

Abstract 5100: Development of a direct-measurement molecular assay to determine telomere length in human samples

Telomere length (TL) is a recognized biomarker in cancer. Epidemiology studies suggest that blood and/or buccal cell TL is associated with certain cancers; however, TL measurement is still an under-utilized biomarker in clinical trials. The molecular testing platforms currently used for TL determination are not optimal due to inherent technical limitations. While qPCR based assays have high throughput and are inexpensive, they are difficult to develop and are very sensitive to subtle permutations in reaction components. We evaluated a strategy that relies on direct hybridization and detection of the telomere target utilizing the NanoString nCounter System (NS). The NS is a semi-quantitative assay that compares the number of reporter probe hybridization events of telomere-specific versus chromosomal invariant regions in DNA samples. Performed without nucleic acid amplification, it has potential to more accurately quantify telomeric sequences than any other assay currently in use. NS uses moderate DNA quantities per test (600ng), and has a throughput that can be expanded in multiples of 12. In each sample, the Ratio of Telomere Length (RTL) is obtained by normalizing the signal produced by the telomere specific code set probes to the signal produced by multiple control probes as compared to commercial normal human DNA.

NS was validated in a three stage process using commercial DNA (n=3), cell lines (n=11) and human clinical samples (n=43) that had previously been tested by other TL tests. A blinded panel of six research samples previously tested in-house by multiplex monochrome quantitative PCR (qPCR) was sent to NanoString for in-house testing. NS exactly reproduced the panel's previous RTL ranking. The telomere code sets were subsequently tested at NCI on a panel of 11 established cell lines. Good correlation was observed compared with our in-house qPCR assay (R2 = 0.89). For the third stage of the validation, we evaluated the assay's utility on human clinical samples for which 43 whole blood leukocyte DNA samples were tested (18 dyskeratosis congenita (DC) patients with very short TL, 25 mutation-free (normal) DC relatives) and compared against leukocyte flow cytometry with in situ hybridization (flow-FISH, FF) TL measurement; FF is the gold standard in clinical testing for DC. The correlation between NS and FF lymphocyte TL was high, R2 = 0.72. Notably, the two sample t test showed that the NS assay could discriminate RTL between normals and DC patients (p = 4.6x10-8); normal relatives have longer telomeres. These data suggest that the NS RTL assay has the ability to be specific and sensitive to differences in TL between individuals with DC and healthy individuals. To determine the assay's exact clinical parameters a greater number of samples will need to be tested. The NS assay is less costly than the FF test by at least one half and if shown to be reproducible would be a viable alternative to FF and qPCR, especially in a diagnostic setting.

Citation Format: Daniel C. Edelman, David Petersen, Allison Gomez, Shahinaz Gadalla, Philippa Webster, Lucas Dennis, Mike Krouse, Sharon Savage, Paul S. Meltzer. Development of a direct-measurement molecular assay to determine telomere length in human samples. [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 5100. doi:10.1158/1538-7445.AM2014-5100

Genome-wide methylation patterns in papillary thyroid cancer are distinct based on histological subtype and tumor genotype

CONTEXT

Aberrant DNA methylation is known to be a major factor in oncogenesis and cancer progression, but effects of methylation in papillary thyroid cancer (PTC) are not well defined.

OBJECTIVE

The objective of the study was to identify altered methylation patterns, which may be associated with PTC disease behavior.

DESIGN

This study was a genome-wide methylation analysis of PTC.

SETTING

The study was conducted at the National Institutes of Health Clinical Center.

PATIENTS

PTC tissue from 51 patients were analyzed and compared with normal thyroid tissue from seven patients.

INTERVENTIONS

CpG methylation status was assessed using advanced genome-wide methylation bead chips.

OUTCOME MEASURES

Altered methylation patterns in PTC were analyzed by stage, recurrence, histological subtype of tumor, and tumor genotype.

RESULTS

PTC is globally hypomethylated compared with normal thyroid with 2837 differentially methylated CpG sites. The follicular variant of PTC demonstrated less differential methylation with only 569 differentially methylated CpG sites. Tumors with mutations in BRAF, RET/PTC, and RAS demonstrated a 3.6-fold increase in the number of differentially methylated sites compared with wild-type tumors. The differentially methylated genes were associated with oncological pathways including cellular movement, growth, and proliferation.

CONCLUSION

PTC is epigenetically distinct from the follicular variant of PTC and by gene mutation status (BRAF, RET/PTC, and RAS).

MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis

Metabolic profiling of cancer cells has recently been established as a promising tool for the development of therapies and identification of cancer biomarkers. Here we characterized the metabolomic profile of human breast tumors and uncovered intrinsic metabolite signatures in these tumors using an untargeted discovery approach and validation of key metabolites. The oncometabolite 2-hydroxyglutarate (2HG) accumulated at high levels in a subset of tumors and human breast cancer cell lines. We discovered an association between increased 2HG levels and MYC pathway activation in breast cancer, and further corroborated this relationship using MYC overexpression and knockdown in human mammary epithelial and breast cancer cells. Further analyses revealed globally increased DNA methylation in 2HG-high tumors and identified a tumor subtype with high tissue 2HG and a distinct DNA methylation pattern that was associated with poor prognosis and occurred with higher frequency in African-American patients. Tumors of this subtype had a stem cell-like transcriptional signature and tended to overexpress glutaminase, suggestive of a functional relationship between glutamine and 2HG metabolism in breast cancer. Accordingly, 13C-labeled glutamine was incorporated into 2HG in cells with aberrant 2HG accumulation, whereas pharmacologic and siRNA-mediated glutaminase inhibition reduced 2HG levels. Our findings implicate 2HG as a candidate breast cancer oncometabolite associated with MYC activation and poor prognosis.

Abstract 3508: Measurement of telomere repeats in human cancer cell lines and tissues using a monochrome multiplex quantitative PCR assay

Telomeres are repetitive DNA sequences located at the ends of chromosomes that serve as cap-like protective mechanisms that allow complete DNA replication and help keep the chromosome structure intact. With each cell division, a normal chromosome's overall telomere length (TL) continually shortens. Once telomeres become too short, the cell undergoes senescence or apoptosis. In order to avoid this biological fate in cancer, a tumor cell can activate telomerase, an enzyme that prevents further telomere shortening by adding the telomeric hexa-nucleotide repeat sequence (5′-TTAGGG) to the ends of the chromosomes. A smaller fraction of tumor cells can elongate their TL by initiating the alternative lengthening of telomeres (ALT) pathway.

Previously investigated as a biomarker for aging and general disease, TL has recently shown promise as a possible biomarker in cancer. A TL pattern between cancers might then provide valuable diagnostic or prognostic information to create a better understanding of the molecular or pathogenic characteristics of specific cancer types.

To measure TLs or more accurately telomere repeats, we based our assay on a Monochrome Multiplex Quantitative PCR (Cawthon 2009). This approach measures the signal generated from the telomere repeats against the signal from a single copy gene in the same DNA sample. The method is unique in that it measures both fluorescent signals using one DNA-intercalating dye within the same reaction tube. We compared the TLs of various cancer cell line DNAs (n=27) derived from organ specific tumors to explore a cancer-specific pattern. Seven transformed cell lines or normal DNA samples were used as controls.

Preliminary data show that pancreatic (n=9) and prostate cancers (n=3) produce cell lines with much shorter TLs than those derived from breast cancer (n=4) and osteosarcoma (n=8). Between the shortest and longest TLs, a 4-fold TL range was observed with pancreatic, a 6-fold range difference between breast cancer, and as much as a 9-fold difference within the osteosarcoma group. The osteosarcoma cell lines divided into two sub-classes of very short and very long TLs. The long TLs could possibly a product of the activation of the ALT pathway as indicated by prior C-circle test results. Control lymphoblastoid cell lines (n=3) in general presented longer TLs than cancerous cell lines, except for the proposed ALT-pathway osteosarcoma lines (n= 5 of 8). Only 6/29 cancer cell lines had TLs greater than the normal female Promega DNA control (#G1528). We plan to further investigate additional cell lines and to validate the utility of the assay on matched tumor/normal pairs derived from FFPE specimens.

Citation Format: Daniel C. Edelman, David Petersen, Allison Gomez, Gabriela Canales, Holly Stevenson, Paul S. Meltzer. Measurement of telomere repeats in human cancer cell lines and tissues using a monochrome multiplex quantitative PCR assay. [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 3508. doi:10.1158/1538-7445.AM2013-3508

Translational predictive biomarker analysis of the phase 1b sorafenib and bevacizumab study expansion cohort

Predictive biomarkers are needed to triage patients to the best therapy. We prospectively planned examination of sequential blood, biopsy, and functional imaging with which to confirm the mechanism and to identify potential predictive biomarkers in a phase Ib clinical trial expansion of patients with solid tumors receiving sorafenib/bevacizumab. The maximally tolerated doses of sorafenib at 200 mg twice daily with bevacizumab at 5 mg/kg every other week were given to biopsiable patients. Patients were randomized to receive either sorafenib or bevacizumab monotherapy for the first 28-day cycle with the second drug added with cycle 2. Biopsies, dynamic contrast-enhanced MRI, and fluorodeoxyglucose-proton emission tomography were done pre-therapy and at 2 and 6 weeks (2 weeks into combination therapy). Tumor and serum proteomics, Ras/Raf mutational analysis, and functional imaging results were examined individually and across the dataset to identify potential changes predictive of response to therapy and those that confirm the biochemical drug mechanism(s). Therapy with sorafenib/bevacizumab resulted in clinical benefit in 45% of this mixed solid tumor group. ERK activation and microvessel density were decreased with monotherapy treatment with sorafenib or bevacizumab, respectively; whereas a decreased signal over the group of total AKT, phospho(p)-VEGF receptor2, p-endothelial nitric-oxide synthase, b-RAF, and cleaved poly(ADP-ribose) polymerase was associated with earlier progression of disease. Tumor metabolic activity decreased in those patients with clinical benefits lasting longer than 4 months, and activity increased with progression of disease. Cleavage of caspase 3 and poly(ADP-ribose) polymerase was increased, and Ki67 expression decreased in patients with prolonged clinical benefits, consistent with decreased proliferation and increased apoptosis. The conglomerate analysis, incorporating pharmacodynamic and tumor biochemistry, demonstrated sorafenib/bevacizumab-targeted vascular activity in the tumor. Results suggest potential biomarkers for which changes, as a group, during early therapeutic exposure may predict clinical benefit.

DNA methylation profiling identifies global methylation differences and markers of adrenocortical tumors

CONTEXT

It is not known whether there are any DNA methylation alterations in adrenocortical tumors.

OBJECTIVE

The objective of the study was to determine the methylation profile of normal adrenal cortex and benign and malignant adrenocortical tumors.

METHODS

Genome-wide methylation status of CpG regions were determined in normal (n = 19), benign (n = 48), primary malignant (n = 8), and metastatic malignant (n = 12) adrenocortical tissue samples. An integrated analysis of genome-wide methylation and mRNA expression in benign vs. malignant adrenocortical tissue samples was also performed.

RESULTS

Methylation profiling revealed the following: 1) that methylation patterns were distinctly different and could distinguish normal, benign, primary malignant, and metastatic tissue samples; 2) that malignant samples have global hypomethylation; and 3) that the methylation of CpG regions are different in benign adrenocortical tumors by functional status. Normal compared with benign samples had the least amount of methylation differences, whereas normal compared with primary and metastatic adrenocortical carcinoma samples had the greatest variability in methylation (adjusted P ≤ 0.01). Of 215 down-regulated genes (≥2-fold, adjusted P ≤ 0.05) in malignant primary adrenocortical tumor samples, 52 of these genes were also hypermethylated.

CONCLUSIONS

Malignant adrenocortical tumors are globally hypomethylated as compared with normal and benign tumors. Methylation profile differences may accurately distinguish between primary benign and malignant adrenocortical tumors. Several differentially methylated sites are associated with genes known to be dysregulated in malignant adrenocortical tumors.

Inhibition of Polo-like kinase 1 prevents the growth of metastatic breast cancer cells in the brain

Few therapeutic strategies exist for the treatment of metastatic tumor cells in the brain because the blood-brain barrier (BBB) limits drug access. Thus the identification of molecular targets and accompanying BBB permeable drugs will significantly benefit brain metastasis patients. Polo-like kinase 1 (Plk1) is an attractive molecular target because it is only expressed in dividing cells and its expression is upregulated in many tumors. Analysis of a publicly available database of human breast cancer metastases revealed Plk1 mRNA expression was significantly increased in brain metastases compared to systemic metastases (P = 0.0018). The selective Plk1 inhibitor, GSK461364A, showed substantial uptake in normal rodent brain. Using a breast cancer brain metastatic xenograft model (231-BR), we tested the efficacy of GSK461364A to prevent brain metastatic colonization. When treatment was started 3 days post-injection, GSK461364A at 50 mg/kg inhibited the development of large brain metastases 62% (P = 0.0001) and prolonged survival by 17%. GSK461364A sensitized tumor cells to radiation induced cell death in vitro. Previously, it was reported that mutations in p53 might render tumor cells more sensitive to Plk1 inhibition; however, p53 mutations are uncommon in breast cancer. In a cohort of 41 primary breast tumors and matched brain metastases, p53 immunostaining was increased in 61% of metastases; 44% of which were associated with primary tumors with low p53. The data suggest that p53 overexpression occurs frequently in brain metastases and may facilitate sensitivity to Plk1 inhibition. These data indicate Plk1 may be a new druggable target for the prevention of breast cancer brain metastases.

Abstract 4862: Whole genome amplification allows for testing of valuable specimens by array comparative genomic hybridization

Many cancer clinical specimens are obtained in minute quantities and in varying states of degradation; for example, when they are formalin or ethanol fixed. In addition, many investigators seek tests on multiple genomic analytes and frequently insufficient DNA remains for all inquiries after the initial priority testing. To accommodate all clinical scientific inquiries, the Sigma GenomePlex whole genome amplification (WGA) protocol has been evaluated as a means to produce sufficient genomic material for array comparative genomic hybridization (aCGH) downstream testing. However previous studies, including our own, have shown that testing degraded samples with WGA coupled to oligo CGH arrays resulted in decreased data quality. We contend this could be due to unequal genomic representation in the WGA product. Our objective was to assess the importance and efficacy of using correctly matched reference DNA and to compensate for the WGA amplification bias, potentially improving aCGH results.

We obtained DNA from ethanol-fixed prostate tissues in which both tumor and normal tissue compartments were separately isolated by laser capture microdissection or by directed needle-core sampling from formalin-fixed paraffin embedded blocks. We sought to optimize the Sigma WGA protocol by testing the following parameters: source of reference DNA (commercial versus matched normal), WGA cycle number, and the use of size-exclusion columns post-WGA. Quality control measures for the purified WGA product included electrophoresis (gel and Agilent Bioanalyzer), and a multiplex PCR to determine the extent of DNA genomic representation across the WGA product. ChromaSpin columns were used to reduce the number of smaller WGA amplicons prior to aCGH. WGA products were assayed with Agilent 8×60K CGH microarrays and chromosomal aberrations and data quality were assessed using BioDiscovery Nexus software.

Data will be presented comparing the effectiveness of using sheared reference DNA as opposed to matched normal DNA, the use of QC methods prior to hybridization, any benefit in removing small WGA DNA products, and varying the WGA cycle number. We continue to evaluate how these modifications can bring improvement to WGA when coupled to aCGH, because there is promise that this method could expand the genomic testing opportunities for valuable and rare clinical specimens.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4862. doi:10.1158/1538-7445.AM2011-4862

Abstract C27: Evaluation of the telomere QPCR assay for use in gauging the effect of storage conditions on telomere length

Telomere length has been reported as potentially biomarker and prognostic indicator in cancer. Our goal was to evaluate whether DNA storage/handling or sample source would result in fragmented telomere DNA using an established QPCR-based telomere assay that quantifies the length of telomeres (Cawthon 2002) Because the effect of storage conditions on telomere length has not been thoroughly evaluated, we were concerned that the QPCR could misclassify telomere length and lead to misleading epidemiological results.

Genomic DNA samples for this preliminary study were gathered from either The Nurses Health Study, healthy volunteers, the MDA-MB-231 cell line (human breast cancer), and a commercial source (Promega). To create a model system of degraded DNA, the DNA were either subjected to multiple freeze thaws (FT, &lt;20), Covaris S2 sonication (&lt;6 Cycles; intensity 5/8, 200/500 bursts), or DNase I treatment (&lt;1 U/ 1 ug). The QPCR assay modified the reactants, parameters, and the thermocycler. By examining the distribution of telomeric PCR amplicons on the Agilent Bioanalyzer 2100 based upon their relative quantity and size, we sought to analyze the effects of damaging measures. Ct measurements provided data as to the relative number of telomeric targets present in the respective samples and melt peak analyses (MPA) identified the unique amplicon Tm compositions.

Due to the repetitive nature of the telomeric sequence, we expected to see discrete amplicon sizes starting at 76 Bp reaching over hundreds of Bps. Bioanalyzer electropherograms indicated that eight to twelve major products of ∼8 Bp iterations are commonly produced up to 150 Bp with some minor products &lt;200 Bp. A primer generated amplicon at ∼84 Bp, although not always present, confounded the analyses. Interestingly, MPA showed a single melt peak at ∼79C for all telomeric amplicons; the aberrant peak had a lesser Tm of ∼78C. Ct data do suggest that although the telomeres are sensitive to enzymatic assault (two–three log reduction), as many as 20 FTs and extensive sonication seem not to degrade the telomere (no Ct change). Ct values indicated that differences in telomere length exist between persons (range: 16–19); the MDA-MB-231 cell line had the shortest telomere length (Ct 22). However, neither individual samples nor samples subjected to DNase I digestion were significantly differentiated via end-point analysis on the Bioanalyzer.

In summary, under the current experimental conditions, the QPCR assay does not generate sufficient variable length amplicons as to present a measurable metric using the Bioanalyzer. Elevated Ct values do seem to correlate with the presence of degraded DNA, and therefore suggest under the conditions used multiple FTs and sonication do not damage the telomeric sequences. However this assay design cannot currently determine the relative contribution of full length vs. degraded telomeric sequence to the Ct value. Further investigation is warranted before this assay becomes clinically diagnostic or prognostic.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C27.

Human herpesvirus 8--a novel human pathogen

In 1994, Chang and Moore reported on the latest of the gammaherpesviruses to infect humans, human herpesvirus 8 (HHV-8) [1]. This novel herpesvirus has and continues to present challenges to define its scope of involvement in human disease. In this review, aspects of HHV-8 infection are discussed, such as, the human immune response, viral pathogenesis and transmission, viral disease entities, and the virus's epidemiology with an emphasis on HHV-8 diagnostics.

Detection of ultra-low levels of pathologic prion protein in scrapie infected hamster brain homogenates using real-time immuno-PCR

Pathologic prion protein (PrP(Sc)), implicated in transmissible spongiform encephalopathies, is detected by antibody-based tests or bioassays to confirm the diagnosis of prion diseases. Presently, the Western blot or an ELISA is officially used to screen the brain stem in cattle for the presence of PrP(Sc). The immuno-polymerase chain reaction (IPCR), a technique whereby the exponential amplification ability of PCR is coupled to the detection of proteins by antibodies in an ELISA format, was applied in a modified real-time IPCR method to detect ultra-low levels of prion protein. Using IPCR, recombinant hamster PrP(C) was consistently detected at 1 fg/mL and proteinase K (PK)-digested scrapie infected hamster brain homogenates diluted to 10(-8) (approximately 10-100 infectious units) was detected with a semi-quantitative dose response. This level of detection is 1 million-fold more sensitive than the levels detected by Western blot or ELISA and poises IPCR as a method capable of detecting PrP(Sc) in the pre-clinical phase of infection. Further, the data indicate that unless complete PK digestion of PrP(C) in biological materials is verified, ultrasensitive assays such as IPCR may inaccurately classify a sample as positive.

Lowering the detection limits of HIV-1 viral load using real-time immuno-PCR for HIV-1 p24 antigen

Presently, the assay that attains maximal sensitivity and dynamic range of HIV-1 viral copy number (50 copies per milliliter) is nucleic acid amplification of HIV RNA in plasma. Enzyme-linked immunosorbent assay (ELISA) methods for quantification of HIV-1 p24 antigen have been relatively insensitive. In this report, we show data that indicate real-time immuno-polymerase chain reaction (IPCR), a combination of the ELISA and PCR techniques, is more sensitive for HIV-1 p24 antigen detection than other currently reported methods. When derived from an IPCR standard curve, a dose response was observed from patient samples with known viral loads diluted within a 3-log range (1.68-6,514 viral RNA copies per milliliter). IPCR detected 42% (22/52) of patient samples that had fewer than 50 viral RNA copies per milliliter by reverse transcriptase-PCR. IPCR shows the potential to become the most analytically sensitive test available for determination of HIV-1 viral load by the detection of HIV-1 p24 antigen.

Real-time PCR provides improved detection and titer determination of bacteriophage

The plaque assay is the traditional method for the quantification of bacteriophage, particularly for lambda cloning vectors. Unfortunately, this technique is fraught with procedural difficulties, and the quality of the data obtained from this "gold standard" assay may be inaccurate due to the subjective interpretation of the results. The application of quantitative real-time PCR (QPCR) technology can address these issues and be a more accurate platform to evaluate phage growth conditions and quantify viral titers in phage preparations. QPCR, with an improved primer set specific for lambda phage and coupled with fluorescent dye detection of PCR products, was used to detect and quantify phages in lysates with no prior DNA purification. Phages were detected below one plaque-forming unit, and at least 89 viral copies were detected from a purified DNA sample. When unknown concentrations of various phage preparations were assessed using QPCR, they were attained more efficiently, with greater sensitivity and precision, and the method produced more accurate quantitative data spanning a wider linear range than those obtained by the plaque assay (six logs vs. one log, respectively). Finally, QPCR for the detection of phage has multiple applications, including conventional cloning and in alternative fields of study such as environmental sciences.

Hepatitis C virus transfusion-transmitted infection in Brazilian cardiac surgery patients

In the past two decades, major improvements in blood safety have been achieved, particularly for HIV and hepatitis C virus (HCV). A prospective study was carried out between 1996 and 1999 in Brazil to determine the incidence of post-transfusion infection in surgery patients caused by HCV. One hundred sixty-four patients who received a blood transfusion during cardiac surgery were followed for six months and blood samples collected before and after surgery were assessed to investigate HCV infection. Alanine aminotransferase levels were serially determined, as well as clinical data related to hepatitis. Prior to surgery, HCV infection was detected by anti-HCV ELISA III in 6 patients. Any post-surgical samples which were positive by a third generation ELISA test were confirmed by immunoblot and reverse-transcription polymerase chain reaction (RT-PCR), as were the pre-transfusion samples to exclude pre-transfusion HCV infection not detected by ELISA screening. Results indicated that one patient who was previously considered negative for HCV antibody in the pre-surgical sample was later found to be positive for HCV by RT-PCR in that sample. Seroconversion for HCV antibody after surgery was observed in two patients, one of them with clinical hepatitis; their genotypes were 1a and 1b. The overall prevalence of HCV infection was 4.26% (7/164) and the incidence rate of HCV infection after surgery was 1.27% (2/157). This study shows a high rate of HCV infection acquired post-transfusion in a cohort of surgery patients in Brazil and suggests that better screening methods such as viral RNA assessment may be effective in lowering this rate.

Assessment of the performance of a rapid, lateral flow assay for the detection of antibodies to HIV

Rapid HIV assays have recently been shown to have important applications for various testing situations, including early identification of infected individuals, to allow intervention strategies in a clinically relevant time frame. A rapid, lateral flow, HIV-1/2/O assay was evaluated using 2,000 serum or plasma samples from various risk groups and geographic locations, including HIV-1 and HIV-2 positive sera from five countries. Two U.S. Food and Drug Administration (FDA)-licensed screening assays and a FDA-licensed confirmatory assay were used as reference tests. The rapid assay exhibited a near-perfect sensitivity (99.2%) and an excellent specificity (99.9%). Moreover, its analytical sensitivity was found to be better than most FDA-licensed enzyme-linked immunosorbent assays (ELISAs), detecting infection at the same time as the most sensitive ELISA in two of five seroconversion panels, and at the same time or earlier than four of five ELISAs in all five panels. We conclude that this rapid assay is a suitable test for the detection of HIV infection that could be particularly useful in developing countries where facilities may not support the use of instrumentation.

The incidence of GB virus C / hepatitis G virus infection in Brazilian patients who received blood transfusion during cardiac surgery

The incidence of GBV-C/hepatitis G virus (GBV-C/HGV) infection after blood transfusion is unknown in Brazil. Many studies have so far addressed its relationship with blood transfusion, but its association with liver disease was not confirmed. A prospective study was carried out between 1996 and 1999 in Rio de Janeiro. Ninety three patients who received blood transfusion during cardiac surgery were followed for six months and blood samples were drawn before and after surgery to determine antibodies to GBV-C/hepatitis G virus (anti-HGenv) using a step sandwich immunoassay and GBV-C/HGV-RNA using reverse transcriptase polymerase chain reaction. The alanine aminotransferase (ALT) levels were serially determined as well as clinical data compiled related to hepatitis. Prior to surgery, anti-HGenv was present in 35.5% (33/93) of patients and 4.3%(4/93) were found to be viremic. Seroconversion following transfusion was observed in 9 patients and 4 additional individuals became viremic for a total incidence of 23% (13/56). Six months after blood transfusion, only 4 of those nine patients previously antibody positive still had anti-HGenv detectable in serum. No patients had clinical or laboratory evidence of acute hepatitis and no correlation was found with GBV-C/HGV infection and number of blood units transfused (p = 0.37). This study highlights the importance of using both HGV-RNA PCR and anti-HGenv to accurately estimate the magnitude of GBV-C/HGV infection. The observed high prevalence and incidence rates show that this infection is common in Brazil; however, no clinical or biochemical evidence of liver disease was demonstrated in the period of study and longer longitudinal observation is needed to define any pathogenic effect.

Specifics on the refinement and application of two serological assays for the detection of antibodies to HHV-8

BACKGROUND

Serologic assays for the detection of antibodies to human herpesvirus type 8 (HHV-8) are important for epidemiological studies and to further investigate the proposed pathogenesis of the virus in cancer. Although a variety of assays are available, a lack of optimization and standardization makes their usefulness uncertain, and may be responsible for the controversy concerning the prevalence of infection.

OBJECTIVES

To refine an indirect immunofluorescent assay (IFA) for the detection of latent antibodies and a recombinant ORF 65 ELISA for the detection of lytic antibodies in order to increase their ability to differentiate individuals at higher and lower risk for HHV-8 infection.

STUDY DESIGN

Sera from Kaposi's sarcoma (KS) patients and blood donors (BDs) were used to modify assay parameters in an attempt to better discriminate between the two populations. Modifications included methods of substrate fixation, incubation times, sample dilution, and antigen/conjugate concentrations.

RESULTS

Optimal modifications to the latent IFA included acetone fixation of substrate, and dilution of sera to 1:64 which enhanced detection of HHV-8 antibodies from 68 to 92% in the KS population. Similarly, successful refinement of the ORF 65 ELISA to increase the signal-to-noise ratio included the use of 88 ng of ORF 65 antigen per well and serum dilutions of 1:50. Optical density-to-cut-off ratios directly correlated with titers, thereby introducing a strategy to predict antibody concentrations. The ORF 65 ELISA and the latent IFA were both able to discriminate between the two populations but with different efficiencies.

CONCLUSIONS

Although neither the latent IFA nor the ORF 65 ELISA produced perfect test indices, improvement in their performances was noted following the optimization strategies. The ELISA produced better detection of antibodies to the virus than the IFA and permitted prediction of sample titers, thus improving cost and time effectiveness.

Detection of Kaposi's sarcoma-associated herpesvirus in oral and genital secretions of Zimbabwean women

Kaposi's sarcoma-associated herpesvirus (KSHV) in oral and genital secretions of women may be involved in horizontal and vertical transmission in endemic regions. Nested polymerase chain reaction assays were used to detect KSHV DNA sequences in one-third of oral, vaginal, and cervical specimens and in 42% of peripheral blood mononuclear cell (PBMC) specimens collected from 41 women infected with human immunodeficiency virus type 1 who had Kaposi's sarcoma (KS). KSHV DNA was not detected in specimens from 100 women without KS, 9 of whom were seropositive for KSHV. A positive association was observed between KSHV DNA detection in oral and genital mucosa, neither of which was associated with KSHV DNA detection in PBMC. These data suggest that KSHV replicates in preferred anatomic sites at levels independent of PBMC viremia. Detection of genital-tract KSHV only among relatively immunosuppressed women may provide an explanation for infrequent perinatal transmission of KSHV.

Optimization, assessment, and proposed use of a direct nested reverse transcription-polymerase chain reaction protocol for the detection of hepatitis C virus

OBJECTIVES

To compare the performance of reverse transcription followed by the polymerase chain reaction (RT-PCR), without RNA purification, with the performance of classic protocols.

STUDY DESIGN/METHODS

Direct and classic techniques were used to test three groups of samples: six hepatitis C virus (HCV) seroconversion panels (n = 90), a HCV RNA reference panel (n = 26), and serial dilutions of four HCV-positive sera (n = 24). These methods were then applied sequentially through a clinical diagnostic algorithm to test 268 samples from high-risk patients.

RESULTS

For the three groups of samples, we found a 94% concordance between direct and purified RT-PCR methods. For the detection of HCV RNA in clinical samples, sensitivity was maximized and cost minimized using both protocols according to the proposed algorithm.

CONCLUSIONS

The direct PCR method is reliable, sensitive, and can result in time and cost savings. The suggested testing algorithm can enhance sensitivity and time savings for populations with a high prevalence of infection.

The effect of potential investment expansion and hot strength on the fit of full crown castings made with phosphate-bonded investment

In an earlier investigation, it was shown that when full crowns are cast in gypsum-bonded investments, their relative inaccuracy is affected by both the investment's potential expansion and its hot strength. This study repeated the earlier one, but used a high-melting gold alloy and two phosphate-bonded investments. The investments were used under conditions which gave a range of potential expansions and hot strengths. Casting inaccuracies were determined both diametrally and axially. All castings showed distortion, which varied under the different conditions. All were oversized axially, by amounts varying from + 0.8% to +2.3%. Diametral inaccuracies ranged from -0.2% to +0.7%. Investment expansion had a strong effect on axial inaccuracy, but a negligible effect on diametral inaccuracy. Conversely, hot strength had a strong effect on diametral inaccuracy, but only a very weak effect on axial inaccuracy. With phosphate-bonded investments, both potential expansion and hot strength are important parameters of relative casting inaccuracy. In combination, these properties showed very strong correlations with both diametral and axial inaccuracies. The observed distortions were the result of anisotropic mould expansion and anisotropic alloy shrinkage. The best fit, and least distortion, occurred with an investment setting under dry conditions.

An epidemiological survey of SIDS in the Sydney metropolitan area

Records of 1049 cases of Sudden Infant Death Syndrome (SIDS) (100%) in the Sydney metropolitan area (SMA) from 1980 to 1989 were analysed in relation to ambient temperature, geographical distribution and socio-economic scale. The SIDS rate varied between eastern and western Sydney and between statistical subdivisions; it peaked sharply in July, coinciding with the monthly mean minimum daily temperature (MMMDT; 6.5 and 5.4 degrees C, respectively). The inverse linear relationship between the SIDS rate and the MMMDT for the regions and the subdivisions was highly significant (P < 0.001). The SIDS rate showed a significant inverse linear relationship to two socio-economic scales (allotment and house value) for 82 of the 87 suburbs (94%) of the SMA. Temperature, indicative of cold weather, was the major factor determining SIDS rates, and this, together with socio-economic factors, largely explains the observed geographical distribution of SIDS rates in the SMA.