Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods.

RNA methylation has emerged recently as an active research domain to study post-transcriptional alteration in gene expression regulation. Various types of RNA methylation, including N6-methyladenosine (m6A), are involved in human disease development. As a newly developed sequencing biotechnology to quantify the m6A level on a transcriptome-wide scale, MeRIP-seq expands RNA epigenetics study in both basic and clinical applications, with an upward trend. One of the fundamental questions in RNA methylation data analysis is to identify the Differentially Methylated Regions (DMRs), by contrasting cases and controls. Multiple statistical approaches have been recently developed for DMR detection, but there is a lack of a comprehensive evaluation for these analytical methods. Here, we thoroughly assess all eight existing methods for DMR calling, using both synthetic and real data. Our simulation adopts a Gamma-Poisson model and logit linear framework, and accommodates various sample sizes and DMR proportions for benchmarking. For all methods, low sensitivities are observed among regions with low input levels, but they can be drastically boosted by an increase in sample size. TRESS and exomePeak2 perform the best using metrics of detection precision, FDR, type I error control and runtime, though hampered by low sensitivity. DRME and exomePeak obtain high sensitivities, at the expense of inflated FDR and type I error. Analyses on three real datasets suggest differential preference on identified DMR length and uniquely discovered regions, between these methods.

Clinical Significance of Haplo-Fever and Cytokine Profiling After Graft Infusion in Allogeneic Stem Cell Transplantation From Haplo-Identical Donors.

Allogeneic stem cell transplantation from haplo-identical donors (haplo-HSCT) has become a well-established therapeutic option for hematological malignancies. The fever of unknown origin (haplo-fever) early after the infusion of T cell repleted graft, which returned to normal right after post-transplantation cyclophosphamide (PTCy), is a unique clinical feature in patients undergoing haplo-HSCT. In the current study, the characteristics of haplo-fever and cytokine profiles during haplo-fever were retrospectively analyzed in a cohort of 37 patients undergoing T cell repleted haplo-HSCT with PTCy as graft versus host disease (GvHD) prophylaxis. In total, 33 patients (89.2%) developed haplo-fever from day 0 to day +7. Patients with high peak temperatures tended to have a lower incidence of chronic GvHD (cGvHD) (p = 0.07), moderate to severe cGvHD (p = 0.08), and superior GvHD and relapse-free survival (GRFS, p = 0.04). During the haplo-fever, there were significant increases in multiple cytokines, such as interferon gamma, interleukin (IL) 6, IL2, IL2 receptor, IL8, IL10, IL17, and tumor necrosis factor (TNF). The increases in IL2 receptor (p = 0.037) and TNF (p < 0.001) on day +4 were correlated with the lower risk of cGvHD. Increased TNF > 1.8055-fold on day +4 was the best predictive threshold for cGvHD, and was correlated with a lower incidence of cGvHD (p < 0.001), moderate to severe cGvHD (p = 0.003), and superior GRFS (p < 0.001). These observations may reflect the early reactivation of donor T cells after haplo graft infusion, which would potentially be eliminated by PTCy. Further studies with larger independent cohorts of patients are warranted, to clarify the clinical significance of haplo-fever, and day +4 TNF as a potential biomarker to predict GvHD and GRFS.