1. LYMPHOID MALIGNANCIES AND HLA COMPLEX ASSOCIATIONS
Kylie Alvarez1, Sandeep K Singh2, Amy E Kennedy2, Mehmet T Dorak2
1TERRA Environmental Research Institute, 2Florida International University, Robert Stempel College of Public Health and Social Work,
Department of Environmental and Occupational Health, Miami, FL

2. HLA is the most gene-dense region in the genome.
It contains classical HLA genes related to immune response
Besides, it also contains more than 200 genes with diverse functions (next slide)
Shiina et al, 2004 (www)

3. Non-HLA Genes of the HLA Complex Involved in Fundamental Cellular Processes
Non-HLA genes of the HLA region are involved in a variety of non-immunologic phenomena including those relevant to cancer development (apoptosis, cell cycle regulators, DNA repair, angiogenesis). There are even two proto-oncogenes within the HLA complex (NOTCH4 and PBX2).

4. Many different HLA antigens have shown associations with increased or decreased risk for various cancers. The very first such association was with lymphoma, a tumor derived from lymphoid cells.

5. Lymphoid Malignancies & HLA Region Associations
In following studies, childhood acute lymphoblastic leukemia (ALL) and adult lymphomas showed associations with serologically determined HLA antigens, HLA alleles determined by DNA analysis or single nucleotide polymorphisms (SNPs) from the HLA region in recent genome-wide association studies (GWAS).

6. Genome-wide Association Study
Candidate Gene Study
HLA Association
Our Aim. The HLA associations found in previous studies and SNP associations found in current studies should have some correlations but most studies do not examine those.
Genome-wide Association Study
SNP Association

7. In this study, we examined correlations between HLA types and SNPs associated with childhood ALL and adult follicular lymphoma (FL). In my experiment, I used 102 HLA-typed homozygous reference cell lines (IHWG panel) and TaqMan allelic discrimination assays on the Bio-Rad CFX96 real-time PCR instrument.
- IHWG (International Histocompatibility Working Group)

8. TaqMan Allelic Discrimination Plot
Homozygotes for common allele
Heterozygotes
Homozygotes for rare allele
TaqMan allelic discrimination plot. Because we were using 102 HLA-typed homozygous reference cell lines, there should barely be any heterozygotes.
NTC

9. Genome-wide Association Study Genome-wide Association Study
Candidate Gene Study
HLA Association
Childhood Leukemia
HLA-DRB4 Association
Here, I investigated the SNP counterpart of the HLA-DRB4 association in childhood leukemia.
Genome-wide Association Study
SNP Association
Genome-wide Association Study
SNP Association ?

10. The Data on the IHWG Panel
This is how the data look like.

11. The DRB region SNP rs2395185 shows an absolute correlation with DRB4/DR53 haplotypes
After going through several SNPs, we found that the SNP, rs , shows an absolute correlation with the HLA-DRB4 association in childhood ALL.
DRB4 codes for DR53

12. The DRB region SNP rs2395185 shows an absolute correlation with DRB4/DR53 haplotypes

13. Follicular Lymphoma Risk and Protection Markers
Protection - OR = 0.7
Risk - OR = 1.6
This is now the second part of my experiment where we go backwards and find the HLA association that correlates with a SNP found in lymphoma. In this graph, you can see how these two SNPs have the strongest association with follicular lymphoma. The risk marker increases the chances of developing the lymphoid malignancy, while the protection marker decreases the chances.

14. Genome-wide Association Study Genome-wide Association Study
Candidate Gene Study
HLA Association
Follicular Lymphoma
HLA Association ?
Here, I investigated the HLA counterpart of the SNP associations in follicular lymphoma.
Genome-wide Association Study
SNP Association
Genome-wide Association Study
SNP Association

15. rs10484561 ~ DRB1*01/10 rs2647012 ~ DRB3 rs2395185 ~ DRB4
The SNP associated with childhood ALL is found in the DRB4 lineage. The risk marker that is associated with lymphoma is found within the DRB1-10 lineages, and the protection marker is found within the DRB3 lineages. rs
~ DRB4
Klein, 1990 (www)

16. Lymphoid Malignancies & HLA Region Associations
The Authors of the lymphoma GWAS paper also ran a phylogenetics analysis and identified that the two risk and protection associated SNPs belog to two different lineages. In this study, I identified the evolutionary lineages of HLA families reprsented by these two SNPs.

17. Conclusions
The SNPs associated with these two lymphoid malignancies are proxy markers for evolutionary lineages rather than individual allele or haplotypes
Classical HLA association studies would not be able to show these associations, but SNPs that group HLA alleles into lineages unraveled strong associations