Objectives mosaic chromosomal alterations (mCAs) increase with age and are associated with age-related diseases. The association between mCAs and rheumatoid arthritis (RA), particularly late-onset rheumatoid arthritis (LORA), has not been explored.

Methods mCAs were detected in peripheral blood samples from two independent Japanese datasets (Set 1:2,107 RA cases and 86,998 controls; Set 2:2,359 RA cases and 86,998 controls). The associations between mCAs and RA were evaluated in each dataset using logistic regression models and meta-analysis. In each dataset, we evaluated the effect sizes of mosaic loss of Y (mLOY) and polygenic risk score (PRS) of RA in males and subsequently performed a meta-analysis. The interaction between mLOY and PRS was assessed. These models were applied separately to RA, LORA, and young-onset RA (YORA).

Results mLOY increased significantly in LORA (OR=1.43, P=0.0070). We observed a negative association between mLOY and YORA (OR=0.66, P=0.0034). On the other hand, we found consistently negative associations of autosomal mCAs or mosaic loss of X (mLOX) with RA, LORA, and YORA. The effect sizes of PRS were lower for LORA than for YORA. mLOY with a high cell fraction strengthened the association between PRS and LORA (P=0.0036), whereas the association with YORA was independent of mLOY.

Conclusion LORA was characterised by the presence of a high burden of mLOY. The observed interaction between mLOY and PRS in LORA, but not in YORA, supports different gene-environment interactions between the subsets. These data suggest that distinct pathophysiological mechanisms underlie the development of LORA and YORA.

What is already known about this subject?

□ The prevalence of late-onset rheumatoid arthritis (LORA) in aging societies is increasing worldwide.

□ LORA has unique clinical characteristics, including higher prevalence in males, acute onset of the disease, and lower proportion of seropositivity compared with young-onset RA (YORA), suggesting distinct genetic and environmental components between the RA subsets.

□ Mosaic chromosomal alterations (mCAs) accumulate with age and are associated with age-related disorders. mCAs occur in both autosomes and sex chromosomes and would reflect the clonal expansion of dysregulated immune cells.

What does this study add?

□ Mosaic loss of Y (mLOY) is increased in male patients with LORA.

□ While mLOY is positively associated with LORA, mLOY is negatively associated with YORA.

□ The association of the RA-polygenic risk score (PRS) with LORA was more apparent in the presence of mLOY, while the association with YORA was independent of mLOY.

How might this impact clinical practice or future developments?

□ mLOY plays an acquired risk for RA in males by modifying the contribution of the genetic risk to RA development depending on age at onset.

□ Further investigation of the different effects of mLOY on LORA and YORA would lead to a better understanding of the pathological basis of RA influenced by aging and sex.

S.U., Y.I., K.I., S.H., K.H., E.T., and C.T. have no conflicts of interest. Y.K. has research grants from Takeda Pharmaceuticals. T.G. received speaking fees from Asahi Kasei Pharma, Astellas, Boehringer-Ingelheim, Bristol-Myers Squibb, Chugai, Eisai, Eli Lily, Gilead Sciences, Ono Pharmaceuticals, Pfizer, and Tanabe Mitsubishi. G.G. declared competing interests, and patent application PCT/WO2019/079493 has been filed for the mosaic chromosomal alteration detection method used in this study. M.K. has received consulting fees, speaking fees, and/or research grants from Argenx, Asahi Kasei Parma, AstraZeneca, Boehringer Ingelheim, Chugai, GSK, Janssen, Kissei, MBL, Mochida, MSD, Novartis, Ono Pharmaceuticals, and Tanabe Mitsubishi.

This work was supported by the Japan Agency for Medical Research and Development (AMED) grants 21ek0109555, 21tm0424220, 21ck0106642, 23ek0410114, and 23tm0424225; the Japan Society for the Promotion of Science (JSPS) KAKENHI grant JP20H00462; and Takeda Hosho Grants for Research in Medicine. The cartoons shown in Fig. 1 were created using Bio-Render. com. We thank the staff of BBJ for collecting and managing the samples and clinical information.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

the ethics committees of RIKEN Center for Integrative Medical Sciences gave ethical approval for this work.

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Statistical codes are available from Chikashi Terao (ORCID 0000-0002-6452-4095) at any time, only on reasonable request. The Mosaic Chromosomal Alterations (MoChA) pipelines used for mosaic calling (mocha.wdl) are available at (https://github.com/freeseek/mochawdl).