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A novel missense compound heterozygous variant in TLR1 gene is associated with susceptibility to rheumatoid arthritis — structural perspective and functional annotations

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Abstract

Introduction

Besides human leukocyte antigen (HLA-DRB1) locus, more than 100 loci across the genome have been identified and linked with the onset, expression and/or progression of rheumatoid arthritis (RA). However, there are still grey areas in our understanding of the key genetic contributors of the disease, particularly in familial cases.

Methods

In the present study, we have performed the whole exome sequencing (WES) of RA patients from two consanguineous families of Pakistan in a quest to identify novel, high-impact, RA-susceptibility genetic variants.

Results

Through stepwise filtering, around 17,000 variants (common in the affected members) were recognized, out of which 2651 were predicted to be deleterious. Of these, 196 had direct relevance to RA. When selected for homozygous recessive mode of inheritance, two novel pathogenic variants (c.1324T>C, p.Cys442→Arg442; c.2036T>C, p.Ile679→Thr679) in the TLR1 gene displayed the role of compound heterozygosity in modulating the phenotypic expression and penetrance of RA. The structural and functional consequences of the TLR1 missense single nucleotide mutations (Cys442→Arg442; Ile679→Thr679) were evaluated through molecular dynamic simulation (MDS) studies. Analysis showed domain’s rigidification, conferring stability to mutant TLR1-TIR/TIRAP-TIR complex with concomitant increase in molecular interactions with pro-inflammatory cytokines, compared to the wild-type conformation. Gene co-expression network analysis highlighted interlinked partnering genes along with interleukin-6 production of TLR1 (corrected p-value 2.98e-4) and acetylcholine receptor activity of CHRNG (corrected p-value 6.12e-2) as highly enriched associated functions.

Conclusion

The results, validated through case-control study subjects, suggested that the variants identified through WES and confirmed through Sanger sequencing and MDS are the novel disease variants and are likely to confer RA-susceptibility, independently and/or in a family-specific context.

Key Points

• Exploration of population based/ethno-specific big data is imperative to identify novel causal variants of RA.

• Two new deleterious missense mutations in mutational hotspot exon 4 of TLR1 gene have been identified in Pakistani RA patients.

• MD simulation data provides evidence for domain’s rigidification, conferring stability to mutant TLR1-TIR/TIRAP-TIR complex, with concomitant increase in production of pro-inflammatory cytokines, thus adding to the onset/erosive outcome of RA.

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Data availability

The data of TLR1 and CHRNG SNVs has been submitted to ClinVar database and bear the Accession Nos. SCV001441521 (TLR1 mutant NM_003263.3:c.2036T>C), SCV001441522 (TLR1 mutant NM_003263.3:c.1324T>C) and SCV001441520 (CHRNG mutant, NM_005199.4:c.994C>), respectively.

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Acknowledgements

This study was supported by NRPU grant (8488/2017) from the Higher Education Commission (HEC), Government of Pakistan. Authors are especially thankful to the RA patients, volunteers and their families, and the doctors and paramedical staff of Rheumatology Department, Sheikh Zayed Hospital, Lahore, Pakistan for their full cooperation and assistance in collection of blood samples. The authors acknowledge the support and guidance extended by Dr. Xiao Wang and Prof. Haja N. Kadermideen (Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark) in WES data analyses.

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  1. Usman Pasha, Kiran Hanif, and Haseeb Nisar have equal contributions and are joint first authors.

Authors and Affiliations

  1. School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan

    Usman Pasha, Kiran Hanif, Haseeb Nisar, Rizwan Abid & Saima Sadaf

  2. Department of Life Sciences, University of Management and Technology, Lahore, Pakistan

    Haseeb Nisar

  3. Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium

    Muhammad Usman Mirza

  4. Department of Computer Engineering, University of Engineering and Technology, Lahore, Pakistan

    Bilal Wajid

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Pasha, U., Hanif, K., Nisar, H. et al. A novel missense compound heterozygous variant in TLR1 gene is associated with susceptibility to rheumatoid arthritis — structural perspective and functional annotations. Clin Rheumatol 42, 3097–3111 (2023). https://doi.org/10.1007/s10067-023-06702-9

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