Biology subjects

Novina, C. D.

Publications and source records attributed to Novina, C. D..

3 recordsLinked to original sources

bioRxiv2021

Genome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution

3 untranslated region (3UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the Massively Parallel Reporter Assay for 3UTRs (MPRAu) to sensitively assay 12,173 3UTR variants. We applied MPRAu to six human cell lines, focusing on genetic variants associated with genome-wide association studies (GWAS) and human evolutionary adaptation. MPRAu expands our understanding of 3UTR function, suggesting that low-complexity sequences predominately explain 3UTR regulatory activity. We adapt MPRAu to uncover diverse molecular mechanisms at base-pair resolution, including an AU-rich element of LEPR linked to potential metabolic evolutionary adaptations in East Asians. We nominate hundreds of 3UTR causal variants with genetically fine-mapped phenotype associations. Using endogenous allelic replacements, we characterize one variant that disrupts a miRNA site regulating the viral defense gene TRIM14, and one that alters PILRB abundance, nominating a causal variant underlying transcriptional changes in age-related macular degeneration.

genetics↗

bioRxiv2019

Lfc/Arhgef2 regulates mitotic spindle orientation in hematopoietic stem and progenitor cells and is essential for productive hematopoiesis

How hematopoietic stem cells (HSCs) coordinate their divisional axis relative to supportive niche cells and whether or not their divisional orientation is important for stem cell-driven hematopoiesis is poorly understood. Single cell RNA sequencing data from patients with the inherited bone marrow failure Shwachman-Diamond syndrome (SDS) show that ARHGEF2, a RhoA-specific guanine nucleotide exchange factor (GEF) and determinant of mitotic spindle orientation, is one of a restricted group of genes specifically downregulated in SDS HSCs and multipotent progenitors. Here, we describe Lfc/Arhgef2 as an important regulator of hematopoiesis in vivo. Transplanted Lfc/Arhgef2-/- bone marrow shows impaired hematopoietic recovery and a production deficit of long-term HSCs. These phenotypes cannot be explained by differences in numbers of transplanted HSCs, their cell cycle status, level of apoptosis, progenitor output or homing ability. Using live imaging of dividing hematopoietic stem and progenitor cells (HSPCs), we show an increased frequency of misoriented divisions in the absence of Lfc/Arhgef2. Functional ARHGEF2 knockdown in human HSCs also impairs their ability to regenerate hematopoiesis, culminating in significantly smaller hematopoietic xenografts. Together, these data provide evidence demonstrating a conserved role for Lfc/Arhgef2 in orienting HSPC division and suggest that HSCs divide in certain orientations to establish hematopoiesis, the loss of which leads to their exhaustion in a mechanism that may underlie certain bone marrow failure syndromes.

cell biology↗

bioRxiv2018

Human bone marrow disorders recapitulated in vitro using organ chip technology

Understanding human bone marrow (BM) pathophysiology in the context of myelotoxic stress induced by drugs, radiation, or genetic mutations is of critical importance in clinical medicine. However, study of these dynamic cellular responses is hampered by the inaccessibility of living BM in vivo. Here, we describe a vascularized human Bone Marrow-on-a-Chip (BM Chip) microfluidic culture device for modeling bone marrow function and disease states. The BM Chip is comprised of a fluidic channel filled with a fibrin gel in which patient-derived CD34+ cells and bone marrow-derived stromal cells (BMSCs) are co-cultured, which is separated by a porous membrane from a parallel fluidic channel lined by human vascular endothelium. When perfused with culture medium through the vascular channel, the BM Chip maintains human CD34+ cells and supports differentiation and maturation of multiple blood cell lineages over 1 month in culture. Moreover, it recapitulates human myeloerythroid injury responses to drugs and gamma radiation exposure, as well as key hematopoietic abnormalities found in patients with the genetic disorder, Shwachman-Diamond Syndrome (SDS). These data establish the BM Chip as a new human in vitro model with broad potential utility for studies of BM dysfunction.

bioengineering↗