Longitudinal blood transcriptome analysis of two patients with cyclic thrombocytopenia

Cyclic thrombocytopenia (CTP) is a rare disease of characterized by periodic platelet count oscillations of uncertain etiology. As part of a study that applied systems biology approaches to investigate two patients with CTP, we performed whole blood transcriptome analyses on semi-weekly collected sequential samples covering two platelet cycles. This blood transcriptome analysis revealed cyclical gene expression changes of platelet-specific genes that are in parallel with, and leading platelet count oscillations in both patients. In addition, erythrocyte-specific genes and neutrophil-specific genes also exhibited cyclic patterns which preceded platelet-specific genes. These findings revealed cyclical trilineage hematopoiesis, most pronounced in megakaryopoiesis in both patients with CTP. Overall design: This study was approved by the Stanford University Institutional Review Board. Two patients with CTP were consented and enrolled in the study. 24 consecutive blood samples from patient 1 (CT1), and 15 samples from patient 2 (CT2) were collected in EDTA blood tubes every 3-4 days covering two platelet cycles. Total RNAs were extracted after red blood cell lysis. 3SEQ (3'-end sequencing for expression quantification) analyses were performed on blood RNA samples. HiSeq 2000 system and NextSeq 500 (Illumina) were used to generate sequencing data for CT1 and CT2, respectively. 3SEQ data were filtered and mapped to human transcriptome hg19, and read counts for each gene were generated. Quantitative analysis of the Significance Analysis of Microarrays-Seq (SAMseq) algorithm was used to obtain genes that are quantitatively associated with platelet count.