A prespecified IFI27-MCEMP1 transcript score performed well in a newly enrolled group of children evaluated for fever, distinguishing 55 children with Kawasaki disease from 48 febrile controls at the same hospital. Its area under the receiver operating characteristic curve, a measure of how well a test separates two groups, was 0.88, with a 95% confidence interval from 0.80 to 0.95. At the preset cutoff of 2.5, the score identified 81.8% of Kawasaki disease cases and correctly classified 87.5% of controls as negative. Among children with a positive score, 88.2% had Kawasaki disease.
That result was reproduced when the new group was combined with two previously characterized cohorts from the same site, producing an integrated sample of 188 Kawasaki disease cases and 175 febrile controls. The integrated AUC was 0.89, with a 95% confidence interval of 0.86 to 0.93; sensitivity was 85.6% and specificity 84.6%. The score separated Kawasaki disease more strongly from viral controls than from bacterial controls. In the integrated analysis, the corresponding AUCs were 0.96 for viral controls and 0.81 for bacterial controls.
The RNA signal was more tentative
Researchers did not refit the score for these data. They measured IFI27, MCEMP1 and three candidate long noncoding RNAs, CHROMR, MALAT1 and NEAT1, in bulk peripheral blood mononuclear cells, or PBMCs, using technical-duplicate RT-qPCR assays with GAPDH as the reference transcript. They normalized each measurement as a target cycle-threshold value minus the GAPDH cycle-threshold value, then subtracted normalized MCEMP1 from normalized IFI27 to calculate the score. A score of 2.5 or higher was treated as positive. The work was an observational diagnostic-validation and biomarker-association study, not an experiment testing pathway activity, cell-intrinsic regulation or causal mediation.
In the integrated cohort, CHROMR and MALAT1 had higher normalized cycle-threshold values in Kawasaki disease, which indicates lower relative expression. After Holm adjustment for the three RNA comparisons, both differences had P < 0.001. NEAT1 did not differ significantly, with P = 0.081.
CHROMR also had the strongest observed association with IFI27 across all 363 participants, with a Pearson correlation of 0.552. Its association with MCEMP1 was not significant. MALAT1 had only small associations with IFI27 and MCEMP1, with correlations of 0.149 and negative 0.147, respectively, while NEAT1 was not significant for either transcript. A correlation describes how measurements vary together. It does not show that one RNA controls another.
The pattern changed under closer checks
In a smaller complete paired subset of 104 children, the overall score was positively correlated with CHROMR's normalized cycle-threshold value, with a Spearman correlation of 0.617 and an adjusted q value below 0.001. Because higher normalized cycle-threshold values represent lower relative expression, the result corresponded to lower CHROMR expression at higher scores. Score correlations with MALAT1 and NEAT1 were not significant.
When the analysis simultaneously accounted for fever duration and broad PBMC composition, the group differences remained significant in 96 quality-controlled participants: CHROMR was 0.689 standard deviations lower, IFI27 was 1.411 standard deviations lower and MCEMP1 was 0.675 standard deviations higher in Kawasaki disease. MALAT1 was attenuated and no longer statistically significant, with q = 0.077.
A separate exact match by fever day included days 3, 4, 5, 7 and 8; there was no quality-controlled febrile-control sample for day 6. The analysis included 36 Kawasaki disease cases and 14 controls, weighted to 13 per group. The direction of the main differences was unchanged, with CHROMR 0.644 standard deviations lower, IFI27 1.332 lower and MCEMP1 0.826 higher in Kawasaki disease. But the adjusted CHROMR-IFI27 correlation was not significant, with a Spearman correlation of 0.189 and P = 0.312, so the smaller matched analysis did not confirm that association.
Researchers also rechecked the CHROMR assay. Its standard curve showed 96.626% amplification efficiency, and efficiency-corrected analyses still found lower CHROMR abundance in Kawasaki disease and a similar association with IFI27. However, no archived gel or sequencing record confirmed the identity of the amplified CHROMR sequence.
What the study can and cannot answer
The results support same-site diagnostic discrimination and exploratory transcript associations in children evaluated during acute febrile illness. They do not show that CHROMR directly regulates IFI27 or MCEMP1, or that any candidate RNA improves diagnosis beyond the existing score. The bulk-PBMC measurements cannot distinguish cell-composition effects from cell-intrinsic transcription.
Because the study was observational and cross-sectional, it cannot establish cause. The integrated cohort came from one institution rather than an independent external cohort. Kawasaki disease participants were sampled later in fever than controls, with limited temporal overlap, and the exact fever-day analysis used a smaller complete-case sample.
The next steps are independent multicenter replication with standardized fever-day sampling, cell-resolved profiling and a newly generated, sequence-verified CHROMR assay. Longitudinal testing before and after intravenous immunoglobulin, together with prespecified links to coronary outcomes or treatment response, would be needed before the RNA findings could support clinical or mechanistic claims.
Disclosure
The human-participant study had institutional review board approval and written consent from parents or legal guardians. It received NIH funding through grant 1R41TR004351-01 and National Natural Science Foundation of China funding through grant 82070513. Two authors were employees of OncoOmicsDx Clinical Laboratory and two were employees of Nippon Life Insurance Company; the remaining authors declared no relevant commercial or financial relationships.
Paper data and sources
Original title: Long noncoding RNA associations with an IFI27–MCEMP1 transcript pattern in Kawasaki disease
Authors: Liu F, Xue X, Han Z et al.
Journal/Repository: Frontiers in immunology
Status: Peer-reviewed
First online: 2026-10-08
DOI: Not available
Original paper · Full text