Disease-Associated HLA Alleles and Haplotypes in Multiple Sclerosis: Insights from an Albanian Case-Control Study

BackgroundMultiple sclerosis (MS) is a complex autoimmune disease with the HLA region showing the strongest known genetic influence. Although HLA-DRB1*15:01 is a well-known risk allele in European populations, data from Southeastern Europe--and Albania specifically--are still limited. ObjectiveTo assess allele- and haplotype-level associations at HLA class I (A*, B*, C*) and class II (DRB1*, DQB1*) loci with MS risk in Albanians, and to explore their correlations with clinical phenotypes. MethodsWe conducted a case-control study involving 128 consecutive Albanian MS patients diagnosed according to the 2017 revised McDonald criteria and 148 unrelated healthy Albanian controls. Second-field HLA genotyping (PCR-SSP) was performed at A*, B*, C*, DRB1*, and DQB1* loci. Allele frequencies were calculated through direct gene counting, and Hardy-Weinberg equilibrium (HWE) was tested for each locus. Frequencies of five-locus haplotypes (A[~]B[~]C[~]DRB1[~]DQB1) were estimated using maximum likelihood with an expectation-maximization (EM) algorithm. Differences between groups were evaluated with Fishers exact test and odds ratios (OR), along with 95% confidence intervals (CI). Multiple testing corrections were applied using the Bonferroni and Benjamini-Hochberg false discovery rate (FDR) methods. Clinical correlations were compared between DRB1*15:01 carriers and non-carriers across phenotype categories (RR, SP, PP), EDSS scores, relapse rates, and MRI activity. ResultsAll loci in controls conformed to HWE; in patients, class I loci conformed while DRB1* and DQB1* showed deviations. Carrier status for HLA-DRB1*15:01 was significantly higher in patients (40.6%) compared to controls (16.2%) (OR = 3.53; p < 0.0001), remaining significant after Bonferroni and FDR corrections. HLA-DQB1*06:02 also stayed significant after correction, consistent with linkage disequilibrium with DRB115:01. Other significant statistical differences did not persist after multiple testing adjustments. Patients exhibited greater five-locus haplotype diversity than controls (17 vs. 10 haplotypes [&ge;]1%). A patient-enriched haplotype, A*68:01[~]B*18:01[~]C*07:01[~]DRB1*15:01[~]DQB1*06:02, was common among cases and absent in controls, whereas A*02:01[~]B*51:01[~]C*15:02[~]DRB1*16:01[~]DQB1*05:02 was less frequent in cases and remained protective after Bonferroni correction. No significant differences were seen in clinical course (RR/SP/PP), EDSS measures, relapse rate, or MRI activity between DRB115:01 carriers and non-carriers. At the population level, MS prevalence across 22 European countries was positively correlated with DRB115:01 frequency (Spearman {rho} = 0.645; p = 0.0012). ConclusionsIn Albanians, HLA-DRB1*15:01 significantly increases the risk of MS, with DQB1*06:02 reflecting the same signal due to strong linkage. Risk- and protection-associated five-locus haplotypes further clarify the HLA genetic architecture in MS patients; however, DRB1*15:01 carriage does not noticeably influence the clinical phenotype or the severity of disease outcome. The relatively lower frequency of the DRB1*15:01 allele in the Albanian population may help explain the countrys lower MS prevalence compared to Northern Europe. Larger cohorts and inclusion of non-HLA loci are necessary to identify additional factors contributing to MS susceptibility and progression in this population.