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Relapsing polychondritis (RP) is a multisystem disorder of cartilaginous tissues. Previously, we found that patients with respiratory involvement and patients with auricular involvement were mutually exclusive in the RP cohort, which suggests a strong inverse relationship between respiratory and auricular involvement. Here, we examined the clinical manifestation patterns in a subgroup of patients with respiratory involvement (R subgroup) and a subgroup of patients with auricular involvement (A subgroup) and investigated the clinical and laboratory characteristics of each subgroup.There were 47 patients (19.7%) and 118 patients (49.4%) allocated to the R and A subgroups, respectively. Saddle nose deformity and a progressive disease course were observed frequently in the R subgroup. Arthritis, conjunctivitis, and CNS involvement were observed frequently in the A subgroup.The remaining RP patients formed a third subgroup of patients that had both respiratory involvement and auricular involvement. We designated this subgroup as the O (overlap) subgroup, and 75 patients (31.4%) were allocated to the O subgroup. Disease duration in the O subgroup (5.70 ± 0.64 years) was significantly longer than that in the A subgroup (4.12 ± 0.45 years) and relatively longer than that in the R subgroup (4.80 ± 0.63 years).We found that cardiovascular involvement was more predominant in the O subgroup than in the R and A subgroups. Higher concentrations of serum matrix metalloproteinase (MMP)3 were observed in the O subgroup than in the R and A subgroups.We measured serum MMP3 concentrations in another patient cohort including 22 newly recruited RP patients. MMP3 concentrations were significantly higher in the O subgroup (n = 10) than those in the R subgroup (n = 6) and A subgroup (n = 10).RP patients in the R and A subgroups had different characteristics from each other, and the overlap of respiratory and auricular involvement was an important prognostic factor in patients with RP. Cardiovascular involvement was not observed in the R subgroup in RP patients. The current study may provide insights into the classification and treatment of RP.