Biology subjects

Zibetti, C.

Publications and source records attributed to Zibetti, C..

4 recordsLinked to original sources

bioRxiv2018

Decomposing cell identity for transfer learning across cellular measurements, platforms, tissues, and species.

New approaches are urgently needed to glean biological insights from the vast amounts of single cell RNA sequencing (scRNA-Seq) data now being generated. To this end, we propose that cell identity should map to a reduced set of factors which will describe both exclusive and shared biology of individual cells, and that the dimensions which contain these factors reflect biologically meaningful relationships across different platforms, tissues and species. To find a robust set of dependent factors in large-scale scRNA- Seq data, we developed a Bayesian non-negative matrix factorization (NMF) algorithm, scCoGAPS. Application of scCoGAPS to scRNA-Seq data obtained over the course of mouse retinal development identified gene expression signatures for factors associated with specific cell types and continuous biological processes. To test whether these signatures are shared across diverse cellular contexts, we developed projectR to map biologically disparate datasets into the factors learned by scCoGAPS. Because projecting these dimensions preserve relative distances between samples, biologically meaningful relationships/factors will stratify new data consistent with their underlying processes, allowing labels or information from one dataset to be used for annotation of the other--a machine learning concept called transfer learning. Using projectR, data from multiple datasets was used to annotate latent spaces and reveal novel parallels between developmental programs in other tissues, species and cellular assays. Using this approach we are able to transfer cell type and state designations across datasets to rapidly annotate cellular features in a new dataset without a priori knowledge of their type, identify a species-specific signature of microglial cells, and identify a previously undescribed subpopulation of neurosecretory cells within the lung. Together, these algorithms define biologically meaningful dimensions of cellular identity, state, and trajectories that persist across technologies, molecular features, and species.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=174 HEIGHT=200 SRC=\"FIGDIR/small/395004_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (81K):\norg.highwire.dtl.DTLVardef@dd1c07org.highwire.dtl.DTLVardef@5b1109org.highwire.dtl.DTLVardef@bb6714org.highwire.dtl.DTLVardef@16c66f0_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2018

A widespread decrease of chromatin accessibility in age-related macular degeneration

Age-related macular degeneration (AMD) is a leading cause of blindness in the elderly. The extent to which epigenetic changes regulate AMD progression is unclear. Here we globally profiled chromatin accessibility in the retina and retinal pigmented epithelium (RPE) from AMD patients and controls. Global decreases in chromatin accessibility occurr in RPE in early AMD, and in the retina with advanced disease, suggesting that dysfunction in RPE cells drives disease progression. Footprints of photoreceptor and RPE-specific transcription factors are enriched in differentially accessible regions (DARs). Genes associated with DARs show altered expression in AMD. Cigarette smoke treatment of RPE cells recapitulates epigenomic changes seen in AMD, providing an epigenetic link between the known risk factors for AMD and AMD pathology. Finally, overexpression of HDAC11 is partially responsible for the reduction in chromatin accessibility, identifying potential new targets for treatment of AMD.

genomics↗

bioRxiv2017

Lhx2 regulates temporal changes in chromatin accessibility and transcription factor binding in retinal progenitor cells.

Retinal progenitor cells (RPCs) pass through multiple stages of developmental competence, where they successively acquire and lose the ability to generate individual cell subtypes. To identify the transcriptional regulatory networks that control these transitions, we conducted epigenomic and transcriptomic profiling of early and late-stage RPCs and observed a developmentally dynamic landscape of chromatin accessibility. Open chromatin regions that showed stage-specificity, as well as those shared by early and late-stage RPCs, were selectively targeted by the homeodomain factor Lhx2, which is expressed throughout retinal neurogenesis but also regulates many stage-specific processes in RPCs. Stage-specific Lhx2 binding sites were frequently associated with target sites for transcription factors that are preferentially expressed in either early or late-stage RPCs, and which were predicted to possess pioneer activity. Lhx2 loss of function in RPCs led to a loss of chromatin accessibility at both direct Lhx2 target sites and more broadly across the genome, as well as a loss of binding by transcription factors associated with stage-specific Lhx2 target sites. These findings demonstrate a central role for Lhx2 in control of chromatin accessibility in RPCs, and identify transcription factors that may guide stage-specific target site selection by Lhx2.\n\nSummaryLhx2 is a central regulator of chromatin accessibility in retinal progenitor cells, and interacts with stage-specific transcription factors to regulate genes that are dynamically expressed during retinal neurogenesis.

neuroscience↗

bioRxiv2017

Ldb1 and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in retina.

Precise control of the relative ratio of retinal neurons and glia generated during development is essential for visual function. We show that Lhx2, which encodes a LIM-homeodomain transcription factor essential for specification and differentiation of retinal Muller glia, also plays a critical role in the development of retinal neurons. Overexpression of Lhx2, and its transcriptional coactivator Ldb1, triggers cell cycle exit and inhibits both Notch signaling and retinal gliogenesis. Lhx2/Ldb1 overexpression also induced the formation of wide-field amacrine cells (wfACs). In contrast Rnf12, which encodes a negative regulator of LDB1, is necessary for the initiation of retinal gliogenesis. We also show that LHX2 protein binds upstream of multiple neurogenic bHLH factors including Ascl1 and Neurog2, which are necessary for suppression of gliogenesis and wfAC formation respectively, and activates their expression. Finally, we demonstrate that the relative level of the LHX2-LDB1 complex in the retina decreases in tandem with the onset of gliogenesis. These findings show that control of Lhx2 function by Ldb1 and Rnf12 acts as a molecular mechanism underpinning the coordinated differentiation of neurons and Muller glia in postnatal retina.\n\nSignificance StatementThe molecular mechanisms that control the ratio neurons and glia that are generated by neuronal progenitors remain unclear. Here we show that Lhx2, a transcription factor essential for retinal gliogenesis, also controls development of retinal neurons. The Lhx2 coactivator Ldb1 promotes Lhx2-dependent neurogenesis, while the Lhx2 corepressor Rnf12 is necessary and sufficient for retinal gliogenesis. Furthermore, Lhx2 directly regulates expression of bHLH factors that promote neural development, which are necessary for Lhx2-dependent neurogenesis. Finally, we show that levels of the LHX2-LDB1 complex, which activates transcription, drop as gliogenesis begins. Dynamic regulation of Lhx2 activity by Ldb1 and Rnf12 thus controls the relative levels of retinal neurogenesis and gliogenesis, and may have similar functions elsewhere in the developing nervous system.

neuroscience↗