Expression profiling of snoRNAs in normal hematopoiesis and AML

Abstract

Key Points• A subset of snoRNAs is expressed in a developmental-and lineage-specific manner during human hematopoiesis.• Neither host gene expression nor alternative splicing accounted for the observed differential expression of snoRNAs in a subset of AML.Small nucleolar RNAs (snoRNAs) are noncoding RNAs that contribute to ribosome biogenesis and RNA splicing by modifying ribosomal RNA and spliceosome RNAs, respectively. We optimized a next-generation sequencing approach and a custom analysis pipeline to identify and quantify expression of snoRNAs in acute myeloid leukemia (AML) and normal hematopoietic cell populations. We show that snoRNAs are expressed in a lineage-and development-specific fashion during hematopoiesis. The most striking examples involve snoRNAs located in 2 imprinted loci, which are highly expressed in hematopoietic progenitors and downregulated during myeloid differentiation. Although most snoRNAs are expressed at similar levels in AML cells compared with CD34 1 , a subset of snoRNAs showed consistent differential expression, with the great majority of these being decreased in the AML samples. Analysis of host gene expression, splicing patterns, and whole-genome sequence data for mutational events did not identify transcriptional patterns or genetic alterations that account for these expression differences. These data provide a comprehensive analysis of the snoRNA transcriptome in normal and leukemic cells and should be helpful in the design of studies to define the contribution of snoRNAs to normal and malignant hematopoiesis.

Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies

“…NGS-based analysis of snoRNAs is more tricky as their size, ranging from 60 to 250 nucleotides [187], overlaps with a gap between conventional small RNA sequencing and RNA-seq, devoted to mRNAs and other RNA molecules longer than 200 nt. Developing their own sequencing approach, Warner et al [188] showed that snoRNAs, e.g., orphan snoRNAs contained in the imprinted DLK-DIO3 and SNURF/SNRPN loci, are expressed in a lineage- and developmentally restricted manner in human hematopoiesis. Moreover, 120 snoRNAs, including SNORA21 , SNORA36C and SCARNA15 , displayed consistent differential expression in AML, and, what is even more interesting, all of them were decreased in AML samples compared to normal CD34+ cells.…”

“…No somatic mutations were detected in the snoRNA genes, either. By the way, the authors found a few novel snoRNAs and proved standard transcriptome sequencing cannot reliably distinguish unspliced primary host gene RNA from correctly processed snoRNA [188].…”

Are spliced ncRNA host genes distinct classes of lncRNAs?

“…In fact, our data suggest that the sequence flanking miRNAs and snoRNAs indeed contribute to payload processing. Other, more dynamical effects, such as a potential contribution of host gene abundance to the regulation of payload (Baskerville and Bartel 2005;Warner et al 2018), on the other hand, cannot be assessed at sequence level alone and thus have to remain a topic for future research. Similarly, indirect links between miRNAs and sdRNAs (snoRNA-derived sRNAs) on factors that regulate hostgene transcription as well as direct interactions of the payload with the hostgene, known, e.g., in the case of let-7 (Jiao and Slack 2012;Minchington et al 2020) are beyond the scope of this contribution.…”

Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications

“…In addition, snoRNAs and their host genes have attracted renewed attention and have been recognized as new players in cancers (Williams and Farzaneh, 2012; McMahon et al, 2015). Several recent studies reported the general downregulation of a number of snoRNAs in normal hematopoiesis and leukemia (Valleron et al, 2012; Ronchetti et al, 2013; Warner et al, 2018). However, AML1–ETO, AML1–ETO9a, and MLL–AF9 enhanced snoRNA expression, and similar results were obtained in t(8;21) patient samples compared with purified CD34 + progenitor cells or normal bone marrow (Zhou et al, 2017).…”

“…Overexpression of the 14q32 snoRNA transcripts located at the DLK1-DIO3 locus is believed to be related to fusion transcripts harboring the RARA gene (Cohen et al, 2012). Neither host gene expression nor alternative splicing and mutations accounted for the aberrant expression of snoRNAs (Valleron et al, 2012; Warner et al, 2018). Further analyses of the underlying mechanisms are needed.…”