Abstract 4219: Breast cancer distribution and survival among Buddhist and Muslim women in southern Thailand

Objective: Thailand is undergoing a period of rapid economic growth, which has led to an epidemiologic transition from infectious to chronic diseases such as cancer. Preliminary research shows a difference in rates of breast cancer incidence and mortality between Buddhist and Muslim women in southern Thailand. This study examines differences in breast cancer and potential explanations for this disparity. Methods: Demographic, diagnostic, and outcome data from breast cancer patients diagnosed from 2001-2015 were collected from a population-based cancer registry in southern Thailand and matched with formalin-fixed paraffin-embedded blocks from Songklanagarind Hospital. This region was selected due to the relatively high proportion of Muslim women. Of 424 cases selected, 369 were Buddhist and 55 were Muslim. Formalin-fixed paraffin-embedded blocks were sent to Michigan Medicine and histological and subtype analyses were performed by two pathologists. Statistical analysis was performed in RStudio using chi-square tests of independence, logistic regression, and Cox proportional hazards models. Results: Muslim women were generally diagnosed at a younger age than Buddhist women (Muslim mean: 46.6 years, Buddhist mean: 52.7 years) and with later stage cancers (Muslim: 36% stage 3 and 14% stage 4, Buddhist: 20% stage 3 and 8% stage 4). Buddhist and Muslim women had similar distributions of Luminal A and B subtypes, but Muslim women were more likely to be diagnosed with Triple Negative breast cancer (Muslim: 30%, Buddhist: 18%), the histological subtype with the worst prognosis. Invasive ductal carcinoma was most common in both groups, but Buddhists had more heterogeneity in subtypes. There were no significant differences in tumor histology or subtype by religion. Conclusions: These analyses show differences in the distribution of breast cancer between Buddhist and Muslim women. Muslim women are diagnosed younger with later stage breast cancers, and with histological differences, which generally lead to lower survival rates. Lack of statistical significance may be due to small sample size, necessitating further studies.

Citation Format: Kali Defever, Katie M. Rentschler, Ana Khazan, Elizabeth Pinkerton, Shama Virani, Hutcha Sriplung, Judy Pang, Celina G. Kleer, Carlos F. Mendes de Leon, Justin A. Colacino, Laura S. Rozek. Breast cancer distribution and survival among Buddhist and Muslim women in southern Thailand [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 4219.

Vitamin D intake and survival and recurrence in head and neck cancer patients

OBJECTIVES/HYPOTHESIS

With an unacceptably low 5-year survival rate and few identified modifiable factors that affect head and neck cancer (HNC) outcomes, HNC survival remains an important public health problem. Vitamin D has been shown to be associated with immune reactivity and improved outcomes for some cancer sites, but findings are mixed, and few studies have examined vitamin D in relation to HNC. This study aimed to assess the association between vitamin D intake and survival outcomes in HNC patients.

STUDY DESIGN

Prospective cohort study.

METHODS

This study utilized data on 434 HNC patients with valid pretreatment food frequency questionnaire data who participated in the University of Michigan Head and Neck Specialized Program of Research Excellence epidemiology project. Cox proportional hazard models were used to estimate the associations between total, dietary, and supplemental vitamin D intake and HNC outcomes, while adjusting for other known prognostic factors.

RESULTS

After multivariable adjustment, we found a statistically significant inverse trend between total vitamin D intake and recurrence (Q4 vs. Q1 hazard ratio: 0.47, 95% confidence interval: 0.20-1.10, P trend = .048). We observed no association with dietary or supplemental intake separately, and no association was observed with all-cause or HNC-specific mortality.

CONCLUSIONS

These findings suggest that HNC patients with lower levels of vitamin D intake are at higher risk of recurrence. If borne out in future studies, our results suggest that increased vitamin D intake through dietary intervention or the use of supplements may be a feasible intervention for prevention of recurrence in HNC patients.

LEVEL OF EVIDENCE

2b. Laryngoscope, E371-E376, 2018.

Ethnic disparity in breast cancer survival in southern Thai women

BACKGROUND

Breast cancer has the highest incidence in women of all cancers and its burden is expected to continue to increase worldwide, especially in middle-income countries such as Thailand. The southern region of Thailand is unique in that it is comprised of 30% Muslims, whereas the rest of Thailand is 95% Buddhist. Breast cancer incidence and survival differ between these religious groups, but the association between clinical subtype of breast cancer and survival has not yet been assessed.

METHODS

Here we characterized differences in breast cancer survival with consideration to clinical subtype by religious group (Muslim Thai and Buddhist Thai women). We compared distributions of age, stage and clinical subtype and assessed overall survival by religion.

RESULTS

Our findings show that Muslim Thai women with breast cancer are diagnosed at a younger age, at later stages and have shorter overall survival times compared to Buddhist Thai women with breast cancer. We also observe a higher proportion of triple negative tumors characterized in Muslim Thai women.

CONCLUSIONS

Our findings confirm previous studies that have shown lower survival rates in Muslim Thai women compared to Buddhist women with breast cancer and offer novel information on subtype distribution. To date, this is the first study assessing clinical subtypes in southern Thailand by religious status.

IMPACT

Our findings are critical in providing information on the role of clinical subtype in cancer disparities and provide evidence from the Southeast Asian region for global studies on breast cancer survival.

Abstract 1511: Mutational signatures from RNA-seq data distinguish HPV(+) and HPV(-) HNSCC

IntroductionHead and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide, and an increasing percentage of HNSCC cases are associated with human papillomavirus (HPV) which have improved prognosis compared to HPV(-) HNSCC. Identifying distinctions between HPV(+) and HPV(-) HNSCC may lead to improved prognosis or new treatments, such as determining mutagen(s) that are driving accumulation of genetic variants in each tumor. A recent approach uses the fact that different mutagens cause different types of mutations, referred to as a mutagen's signature. By comparing the mutations in a tumor sample with the mutagen signatures, the mutagens responsible for most of the mutations in the tumor can be identified. We hypothesized that mutational signatures could distinguish HPV(+) from HPV(-) HNSCC tumors.

Materials and Methods

We performed RNA-sequencing on 18 HPV(+) and 18 HPV(-) tumor samples collected from HNSCC patients by the University of Michigan Head and Neck SPORE. Variant calling was performed on each sample using a GATK best practices for RNA-seq pipeline. These variants were then filtered to include only variants that were both rare (<5%) and predicted to have a functional effect. The bases 5’ and 3’ of each variant were extracted to identify its sequence context. The observed mutations in each sample were then approximated by a non-negative linear combination of previously reported mutagen signatures. Certain signatures are associated with dysregulation of particular pathways; this dysregulation was validated with expression and mutation analysis of the RNA data.

Results

In the studied HNSCC tumors, signatures related to aging and impaired DNA repair were responsible for the largest proportion of the mutations found. The signatures that were significantly different between HPV(+) and HPV(-) tumors were associated with APOBEC editing and defective DNA mismatch repair. Expression and mutational analysis validated that APOBEC is more active in HPV(+) than HPV(-) tumors. Interestingly, signatures associated with smoking were not among the most relevant.

Conclusion

The evaluation of mutational signatures in HNSCC tumors identified the main sources of mutations for HNSCC. The differences in mutational signatures between HPV(+) and HPV(-) identify distinct methods of carcinogenesis for these two subtypes of HNSCC.

Citation Format: Pelle Hall, Shama Virani, Charles Warden, Yanxiao Zhang, Lada Koneva, Katie M. Rentschler, Alisha Virani, Laura S. Rozek, Maureen A. Sartor, The UM Head and Neck SPORE Investigators. Mutational signatures from RNA-seq data distinguish HPV(+) and HPV(-) HNSCC. [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 1511.

DNA methylation is differentially associated with environmental cadmium exposure based on sex and smoking status

The adverse health effects of cadmium (Cd) are well known in human populations; however, much of what is known about biological mechanisms of Cd comes from in vitro and animal studies. The adverse health outcomes due to high levels of Cd exposure in the population of Mae Sot, Thailand have been extensively characterized. Here, for the first time, this population is being studied in an epigenetic context. The objective of this study was to characterize the association between DNA methylation markers and Cd exposure, taking into account sex and smoking differences, in an adult population at an increased risk of experiencing adverse health outcomes from high body burden of Cd. One hundred and sixty-nine residents from known exposure areas of Mae Sot, Thailand and one hundred residents from non-exposed areas nearby were surveyed in 2012. Urine and blood samples were collected for measurement of urinary Cd (UCd) and DNA methylation of Cd-related markers (DNMT3B, MGMT, LINE-1, MT2A). UCd levels were 7 times higher in the exposed compared to the unexposed populations (exposed median: 7.4 μg/L, unexposed median: 1.0 μg/L, p < 0.001). MGMT hypomethylation was associated with increasing levels of UCd in the total population. Sex-specific associations included MT2A and DNMT3B hypomethylation in women and LINE-1 hypermethylation in men with increasing UCd. Upon subanalysis, these associations separated by smoking status. In summary, environmental Cd exposure is associated with gene-specific DNA methylation in a sex and smoking dependent manner.

Abstract 2184: Gene expression analysis of human papillomavirus positive head and neck cancer primary tumor samples reveals two distinct subgroups

Introduction:

Human Papillomavirus (HPV) infection is recognized as a major cause for an increasing percent of oropharyngeal squamous cell carcinomas (OPSCC). Patients with HPV-induced OPSCC have a better prognosis than those who are HPV-negative, which implies distinct molecular mechanisms. However, predicting prognosis with the HPV-positive population remains elusive. In this study, we aimed to characterize molecular aspects of HPV expression, HPV integration, and host gene expression to later correlate with survival and recurrence as those data become available for our study population.

Materials and methods:

Thirty-six primary head and neck SCC (HNSCC) tumor samples were collected between 2011-2013 at University of Michigan hospital, of which 18 were determined to be HPV+ (type16, 18 or 35). Paired-end RNA-Seq libraries were generated using Illumina HiSeq for all samples. The sequences were aligned to both the human and HPV genome. Gene expression levels were quantified for both human and HPV genes using TopHat2 and HTSeq, and HPV integration events were determined using Virus-seq.

Results:

Hierarchical clustering of the gene expression levels showed three distinct clusters among the samples. The HPV- samples were first separated from the HPV+ samples, and then there were two robust subgroups within the HPV+ samples. Subsequent analysis revealed one subgroup had significantly higher HPV expression levels than the other (p-value: 0.03; Wilcoxon test). The subgroups were also highly correlated with HPV-integration status (8 of the 16 tumors had at least one identified HPV integration event). Differentially expressed genes between HPV-integration positive and negative samples were found to be enriched for interesting pathways, including “keratinocyte differentiation”, “cell adhesion” and “growth factor binding”, suggesting possible differences in carcinogenesis We also examined the HPV integration sites and found the majority of them were transcription factors. These also include several cancer-related genes, such as “BIRC3”, “CD274” and “PBX1”. One gene, KLF12, contained an integration event in one of our tumors and in one of the 36 HPV+ tumors from The Cancer Genome Atlas (TCGA). Network analysis of the genes harboring an integration event in our population or the TCGA HNSCC population (38 total genes) revealed interactions around p63 and ETS.

Conclusion:

Our data is an important addition to TCGA HNSCC cohort data, because as opposed to TCGA, we did not enforce selection bias towards large tumor size. With our data, we identified two distinct HPV+ subgroups characterized by RNA-Seq expression levels and strongly correlated with HPV viral expression levels and integration status. A significant portion of the HPV+ tumors (50%) had integrated HPV genome, implying important oncogenic potentials for integration events.

Citation Format: Yanxiao Zhang, Lada A. Koneva, Shama Virani, Alisha Virani, Katie M. Rentschler, Thomas E. Carey, Laura S. Rozek, Maureen A. Sartor, the University of Michigan Head and Neck SPORE. Gene expression analysis of human papillomavirus positive head and neck cancer primary tumor samples reveals two distinct subgroups. [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 2184. doi:10.1158/1538-7445.AM2015-2184

Abstract 4808: Identification of genes with variants in HPV-associated head and neck squamous cell carcinoma

Introduction:

Human papilloma virus (HPV)-associated head and neck squamous cell carcinomas have a distinct etiologic mechanism of carcinogenesis compared to non-HPV associated HNSCCs. These tumors are also generally thought to harbor less mutations compared to non-HPV associated HNSCCs. However, recent research suggests that not only do HPV-associated HNSCCs contain mutations, they are distinct from mutations found in non-HPV associated HNSCCs. Identification of these genetic variants is necessary to determine potential prognostic markers or novel insight into the mechanism of HPV-induced carcinogenesis. In this study, we identified genes with variants that are more common in HPV-associated HNSCCs compared to non-HPV associated HNSCCs.

Materials and methods:

Thirty-six primary head and neck SCC (HNSCC) tumor samples were collected between 2011-2013 at University of Michigan hospital, of which 18 were determined to be HPV+ (type16, 18 or 35). Paired-end RNA-Seq libraries were generated using Illumina HiSeq for all samples and aligned to both the human and HPV genome. Variant calling was employed using an established pipeline to identify single nucleotide polymorphisms (SNPs) from RNA-Seq data. Briefly, data was aligned using STAR, followed by indel realignment and base recalibration. Variants were called using HaplotypeCaller and filtered by Fisher Strand values (FS &gt; 30.0) and Qual By Depth values (QD &lt; 2.0). Variants were annotated and filtered by SnpEff and SnpSift to determine genes with nonsynonymous variants by HPV status.

Results:

Out of all samples, nine genes showed nonsynonymous variants in HPV-associated tumors greater than 60% of the time compared to non-HPV associated tumors. These are PTCH1 (associated with eosophageal squamous cell carcinoma), ATRX (involved in chromatin binding), ERCC2 (associated with skin cancers), FOXA1 (transcription factor), CCDC6 (associated with thyroid papillary carcinoma), FNBP1 (involved in lipid binding), and POU5F1 (transcription factor). Seventy-five percent of the samples with nonsynonymous variants in TMPRSS2, a gene shown to be associated with prostate cancer, were HPV-associated tumors. Eighty-two percent of all samples with nonsynonymous variants in FANCD2, a gene involved in maintenance of chromosomal stability, were HPV-associated tumors.

Conclusion:

Although HPV-associated HNSCCs generally harbor fewer mutations than non-HPV associated HNSCCs, our data suggests they do contain variants in cancer-related genes. This is important as these genes may play a role in the mechanism of HPV-induced tumorigenesis subsequent to viral initiation.

Citation Format: Shama Virani, Pelle B. Hall, Yanxiao Zhang, Lada A. Koneva, Alisha Virani, Katie M. Rentschler, Thomas E. Carey, Laura S. Rozek, Maureen A. Sartor. Identification of genes with variants in HPV-associated head and neck squamous cell carcinoma. [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 4808. doi:10.1158/1538-7445.AM2015-4808