Transcriptomic signatures of Shwachman-Diamond Syndrome at single cell resolution

Dana-Farber Cancer Inst, Boston MA

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Abstract

DESCRIPTION (provided by applicant): Ribosomopathies are a class of rare human syndromes that are associated with genetic defects in ribosome biogenesis and function. Although ribosomopathies are genetically and phenotypically heterogeneous, they nearly always encompass hematological deficiencies, congenital defects and cancer predisposition. Shwachman-Diamond Syndrome (SDS) is an autosomal recessive ribosomopathy caused by hypomorphic mutations in the SBDS gene. Patients often present in infancy with severe neutropenia and later develop multi-lineage bone marrow aplasias. Currently, the only curative treatment for bone marrow failure in SDS patients is transplantation. Thus, there is an imminent need for targeted molecular therapies. The constellation of symptoms in SDS is seemingly paradoxical given what is known about the molecular function of SBDS. SBDS is a ubiquitously expressed protein co-factor for 60S subunit joining. However, mutations in SBDS selectively affect certain blood lineages while sparing other cell types and tissues. Additionally, SBDS mutations are expected to decrease translation rates. Yet, up to one-third of SDS patients progress from bone marrow failure to myelodysplastic syndrome or acute myeloid leukemia in young adulthood. This is unusual because cancer is usually accompanied by increased metabolic demands that require increased rates of protein synthesis. Our lab may have uncovered a novel mechanism of disease pathogenesis that could explain these conundrums. We recently perfomed a screen for regulators and effectors of microRNA activity and demonstrated that knockdown of ribosomal pathway components decreases microRNA function. Given that microRNAs target many genes involved in hematopoiesis and oncogenesis, reduced microRNA activity could underlie SDS symptoms. Systematic molecular analyses of bone marrow failure in SDS have been hindered by the rarity and heterogeneity of bone marrow progenitors in patients. These obstacles can now be overcome by recent developments in RNA sequencing technology that enable single cell analysis. I have developed a pipeline for single cell transcriptional profiling of SDS bone marrow progenitors that converts fresh cells to stable cDNA intermediates within six hours. Thus, I propose the first systematic transcriptomic analysis of SDS hematopoietic progenitors, along with carefully tailored bioinformatic and experimental analyses that will 1) define the affected cell type(s) in SDS bone marrow, 2) characterize SDS-specific transcriptional networks in affected cells and 3) interrogate the role of microRNAs in SDS pathogenesis. Overall, these analyses will illuminate the molecular consequences of reduced ribosome function and identify new therapeutic targets for SDS.