rs1335532 — CD58

Intronic CD58 variant that sits inside the miR-548ac stem-loop; the A allele disrupts Drosha cleavage, simultaneously lowering CD58 mRNA and raising miR-548ac levels — the functional mechanism underlying the CD58 locus MS association

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CD58 rs1335532 — The miR-548ac Mechanism at the Heart of the MS Locus

CD58 (LFA-3) is a cell-surface adhesion glycoprotein that anchors T-cell co-stimulation and regulatory T-cell (Treg) induction by binding CD2 on T cells. The CD58 intronic locus on chromosome 1q23 has been genome-wide significantly associated with multiple sclerosis (MS) since 2009, and four intronic variants — rs2300747, rs12044852, rs1016140, and rs1335532 — form a block of strong linkage disequilibrium that collectively shape CD58 expression. Of these, rs1335532 holds a mechanistically privileged position: it sits within the stem-loop of hsa-miR-548ac11 hsa-miR-548ac
A primate-specific microRNA that evolved from a Made1 mariner-class transposable element; hosted in the first intron of CD58 and co-expressed from the same primary transcript, the microRNA whose biogenesis is directly perturbed by the MS risk allele.

Unlike rs2300747 — which tags the overall CD58 eQTL — rs1335532 (in r²=0.93 LD with the causal candidate rs1414273) is the variant whose alleles physically alter the RNA secondary structure of the miRNA precursor, providing the most parsimonious molecular explanation for why risk-allele carriers have lower CD58 mRNA and higher miR-548ac simultaneously. A second independent mechanism — Wnt/ASCL2 transcription factor binding — operates specifically through the G allele of rs1335532, adding a second layer of protection beyond the miRNA pathway.

The Mechanism

miR-548ac stem-loop disruption: rs1335532 introduces either an A or G nucleotide at a position near the base of the hsa-miR-548ac stem-loop, in near-complete LD with the causal SNP rs1414273 which sits exactly at the stem base. The A allele creates a Watson-Crick A-U base pair22 Watson-Crick A-U base pair
A canonical base-pair with full hydrogen bonding; the Drosha-DGCR8 complex recognises the junction between the flanking ssRNA and the dsRNA stem; canonical pairs at this position may alter the geometry of Drosha recognition at the stem base, while the G allele creates a wobble G-U pair. The A allele configuration enhances Drosha cleavage efficiency, producing more pre-miRNA and therefore more mature miR-548ac — but at the cost of reducing the primary transcript available for CD58 mRNA production. The net result is an eQTL paradox: the same A allele that increases MS risk simultaneously raises miR-548ac levels and lowers CD58 mRNA levels in peripheral blood.

ASCL2/Wnt transcription factor axis: Independently of the miRNA mechanism, Afanasyeva et al. 201833 Afanasyeva et al. 2018 demonstrated that the G allele of rs1335532 creates a functional binding site for ASCL2 (Achaete-Scute Family BHLH Transcription Factor 2), a downstream effector of the Wnt signalling pathway. In B-lymphoblastoid cell lines, primary B cells, and monocytic cells, activation of Wnt signalling increased CD58 promoter activity specifically in G-allele carriers; ASCL2 knockdown abolished this effect. This mechanism operates on the transcriptional rather than the post-transcriptional level, reinforcing G-allele protection through an entirely different molecular route.

The Evidence

The miRNA mechanism was established by Hecker et al. 2019 in PLoS Genetics44 Hecker et al. 2019 in PLoS Genetics
Blood-derived cells from ~1,000 subjects; eQTL analysis in three independent datasets (KORA, GTEx whole blood, brain); rs1335532 used as a proxy for rs1414273 at r²=0.93. Risk-allele carriers showed significantly reduced CD58 mRNA and significantly elevated hsa-miR-548ac levels across all three datasets. The concordance across independent cohorts and tissue types substantially strengthens the mechanistic inference.

The MS odds ratio associated with the risk allele at this locus ranged from 1.30 to 2.63 across cohorts in the Hecker study, with higher ORs in familial and northern European samples. The De Jager et al. 2009 PNAS study55 De Jager et al. 2009 PNAS study
2,624 cases and 7,220 controls; genome-wide significant P = 4×10⁻⁹ for the CD58 locus; CD58 mRNA levels in MS patients positively correlated with G-allele dosage established the broader CD58 locus association, with rs1335532 one of the four variants forming the risk haplotype.

The ASCL2/Wnt mechanism reported by Afanasyeva et al. 2018 adds functional resolution to the transcriptional arm of CD58 regulation. The study used both cell line and primary cell models and confirmed the allele-specificity of ASCL2 binding by knockdown experiments, meeting standard functional validation criteria.

Population genetics mirror the MS epidemiology closely: in European populations, where MS prevalence is highest, the risk A allele is the major allele (~86%), while in East Asian populations, where MS is considerably less common, the protective G allele is the major allele (~60%). This population-frequency inversion parallels the pattern at rs2300747 and is consistent with the two variants tagging the same protective haplotype.

Practical Actions

For individuals carrying the AA genotype — the most common configuration in Europeans — the principal modifiable lever remains vitamin D optimisation. Vitamin D drives FoxP3 expression in regulatory T cells through a parallel pathway to CD58-mediated co-stimulation, and vitamin D deficiency is an established environmental modifier of MS risk. No supplement directly compensates for reduced CD58 mRNA or elevated miR-548ac, but maintaining immune regulatory capacity through vitamin D and general inflammatory-load reduction is the most evidence-supported strategy.

For AG heterozygotes, the single protective G allele provides a partial ASCL2/Wnt boost to CD58 expression and partially normalises the miRNA balance; monitoring and vitamin D sufficiency are appropriate.

Interactions

rs1335532 is in near-complete LD (r²=0.93) with rs2300747 and in strong LD with rs12044852 (r²=0.929 for the latter pair). These three variants almost certainly tag the same functional haplotype, with rs1335532/rs1414273 being the best candidate for the causally active position by virtue of its location within the miR-548ac stem-loop. The fourth CD58 intronic variant rs1016140 has a partially independent signal (associated with NMO and autoimmune thyroid disease through distinct allelic directions), suggesting it may not be fully explained by the miRNA haplotype.

The CD58 co-stimulatory axis converges with rs6897932 (IL7R)66 rs6897932 (IL7R)
IL7R regulates T-cell homeostasis and Treg survival, a pathway that overlaps with CD58-mediated Treg co-stimulation and rs2476601 (PTPN22), which lowers the TCR activation threshold. Individuals carrying high-risk alleles at multiple T-cell regulatory loci face compounding impairments of immune self-tolerance.

Genotype Interpretations

What each possible genotype means for this variant.

GG Full ASCL2/Wnt Protection Beneficial

Two protective G alleles — highest CD58 expression through both the ASCL2/Wnt transcriptional pathway and normalised miR-548ac biogenesis

You carry two copies of the G allele at rs1335532, the configuration associated with the highest CD58 mRNA levels and the most effective regulatory T cell co-stimulation at this locus. Both mechanisms operate at full capacity: the ASCL2/Wnt transcription factor binding site is doubly activated, and miR-548ac biogenesis is minimised relative to primary CD58 transcript production. This genotype is the major configuration in East Asian populations (~36%), where MS prevalence is substantially lower than in Europe, and is rare in Europeans (~2%). This locus contributes protection against MS susceptibility; overall disease risk depends on many other genetic and environmental factors.

AG One Protective Allele Intermediate

One protective G allele partially restores CD58 expression through both the ASCL2/Wnt and miRNA pathways

The heterozygous AG genotype generates both the risk and protective configurations in the relevant RNA structures. ASCL2 binding studies showed that the protective effect operates in a dose-dependent manner: one G allele provides partial rescue of CD58 expression through Wnt activation, and two G alleles provide full rescue. The eQTL studies by Hecker et al. confirmed additive effects of the G allele on CD58 mRNA levels, consistent with this dose-response.

The MS odds ratio for heterozygous carriers is intermediate — estimated in the range of OR 0.85 (heterozygous model in Liu 2016 meta-analysis at the LD-correlated rs2300747), representing a modest but real reduction in MS susceptibility compared to AA homozygotes.

AA Reduced CD58 / Elevated miR-548ac High Risk

Two copies of the risk allele — lowest CD58 expression, highest miR-548ac levels, and highest MS susceptibility at this locus

The AA genotype places you at the far end of the CD58 expression spectrum at this locus. Hecker et al. 2019 confirmed across three independent eQTL datasets that the risk allele (A) significantly lowers CD58 mRNA while simultaneously raising hsa-miR-548ac — an apparent paradox explained by the SNP's location near the Drosha cleavage site of the miRNA precursor. Enhanced Drosha processing of the primary transcript diverts more RNA into the miRNA pathway and less into the CD58 mRNA pool.

The ASCL2/Wnt mechanism identified by Afanasyeva et al. 2018 compounds this effect at the transcriptional level: without the G allele's ASCL2 binding site, Wnt pathway activation cannot boost CD58 promoter activity, leaving CD58 expression dependent solely on basal transcriptional mechanisms that are themselves already reduced by the miRNA pathway.

In practice, most AA individuals never develop MS — MS is a complex polygenic disease with strong environmental contributions (vitamin D status, Epstein-Barr virus, latitude, smoking). This genotype represents one genetic component of risk, not a deterministic outcome. The overlap of this locus with rs2300747 (in near-complete LD) means that the practical implications are very similar to what is described for the rs2300747 AA genotype: the cumulative evidence points to monitoring, vitamin D optimisation, and awareness of early MS symptoms.