Fig. 2: Identification of inflammatory genes within HAM-characteristic open chromatin regions.

A The scatter plot shows differences in ATAC-seq peak values in promoter regions (x axis) and differences in gene expression levels from RNA-seq data (y-axis) in HTLV-1–infected cells from HAM patients compared with acute ATL cells. Red and purple dots represent 190 and 270 genes strongly expressed in HTLV-1–infected cells from HAM patients (groups a and b) and aATL cells (groups d and e), respectively. Spearman’s correlation coefficient was calculated using a two-sided test (R = 0.41, P < 0.001). B Similar scatter plot comparing HTLV-1–infected cells from HAM patients and ACs. Red and ocher dots represent 434 and 213 genes significantly upregulated in HAM and AC samples, respectively (fold change > 1.5, adjusted P < 0.05). Spearman’s correlation coefficient was calculated using a two-sided test (R = 0.52, P < 0.001). C Venn diagram showing the overlap of OCRs detected in HTLV-1–infected T cells from patients with HAM versus those from ACs (red), normal CD4⁺ T cells (green), and CD4⁺ T cells stimulated with anti-CD3/CD28 antibodies (blue). D Heatmap (left) depicting Pearson correlation coefficients between transcripts levels (TPM) of eight selected genes and the CSF concentrations of CXCL10 (pg/mL) or neopterin (pmol/mL). Scatter plots (middle and right) show the correlation between MAP3K8 expression and CSF levels of CXCL10 or neopterin (R = 0.823 and 0.753, respectively). E Boxplot showing normalized MAP3K8 expression levels in AC_P (n = 10), AC_D (n = 8), and AC_N (n = 9) in asymptomatic individuals; HAM _D (n = 13) in patients with HAM; iATL_D (n = 5) and iATL_N (n = 9) in patients with indolent ATL; and aATL_N (N = 13) in patients with acute ATL, based on RNA-seq data. Each data point represents an individual patient sample. Boxes indicate the interquartile rage (IQR), with the line representing the median. Whiskers extend to 1.5 * IQR, and outliers beyond this range are shown as individual points. Statistical significance was assessed using one-way ANOVA. Exact P value are as follows: AC_P vs HAM_D, P = 0.000078, AC_D vs HAM_D, P = 0.0196, HAM_D vs iATL_D, P = 0.0128, HAM_D vs AC_N, P = 0.00005, HAM_D vs iATL_N, P = 0.0000096, HAM_D vs aATL_N, P = 0.0000067. Asterisks indicate statistical significance (* P < 0.05, ** P < 0.01, *** P < 0.001). (F) Representative histogram images of MAP3K8 from ATAC-seq and RNA-seq in normal CD4⁺ T cells, AC_D, HAM_D, and aATL_N. The highlighted region shows HAM-characteristic OCR.