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Lindsay, K.

Publications and source records attributed to Lindsay, K..

6 recordsLinked to original sources

Snip1-PRC2 governs the intrinsic apoptosis program in the developing brain

Brain development requires the intricate balance between division, death, and differentiation of neural progenitor cells (NPCs). Here, we report the discovery of Snip1 as a key regulator of these NPC phases. The conditional deletion of Snip1 in the mouse embryonic brain causes dysplasia with robust induction of caspase 9-dependent apoptosis. In NPCs, Snip1 suppresses the genetic programs of apoptosis and developmental signaling pathways and promotes the genetic programs of cell cycle, neurogenesis, and cortical development. Mechanistically, Snip1 binds to the Polycomb complex PRC2, co-occupies gene targets with PRC2, and regulates H3K27 marks. Deletion of PRC2 is sufficient to reduce apoptosis and brain dysplasia and partially restore genetic programs and tissue development in the Snip1-depleted brain. Our findings suggest that Snip1 exerts loci-dependent regulation of PRC2 and H3K27me3 to toggle between cell fates in the developing brain.

developmental biology↗

Plankton energy flows using a global size-structured and trait-based model

Plankton community models are critical tools for understanding the processes that shape marine plankton communities, how plankton communities impact biogeochemical cycles, and the feedbacks between community structure and function. Here, using the flexible Marine Biogeochemistry Library (MARBL), we present the Size-based Plankton Ecological TRAits (MARBL-SPECTRA) model, which is designed to represent a diverse plankton community while remaining computationally tractable. MARBL-SPECTRA is composed of nine phytoplankton and six zooplankton size classes represented using allometric scaling relationships for physiological traits and interactions within multiple functional types. MARBL-SPECTRA is embedded within the global ocean component of the Community Earth System Model (CESM) and simulates large-scale, emergent patterns in phytoplankton growth limitation, plankton phenology, plankton generation time, and trophic transfer efficiency. The model qualitatively reproduces observed global patterns of surface nutrients, chlorophyll biomass, net primary production, and the biogeographies of a range of plankton size classes. In addition, the model simulates how predator:prey dynamics and trophic efficiency vary across gradients in total ecosystem productivity. Shorter food chains that export proportionally more carbon from the surface to the ocean interior occur in productive, eutrophic regions, whereas in oligotrophic regions, the food chains are relatively long and export less organic matter from the surface. The union of functional type modeling with size-resolved, trait-based modeling approaches allows MARBL-SPECTRA to capture both large-scale elemental cycles and the structure of planktonic food webs affecting trophic transfer efficiency.

biochemistry↗

An Efficient and Cost-effective Purification Methodology for Cas9 Nuclease

With an ever-increasing demand for laboratory-grade Cas9 proteins by many groups advancing the use of CRISPR technology, a more efficient and scalable process for generating the proteins, coupled with rapid purification methods is in urgent demand. Here, we introduce a modified methodology for rapid purification of active SaCas9 protein within 24 hours. The product has over 90% protein purity. The simplicity and cost-effectiveness of such methodology will enable general labs to produce a sizable amount of Cas9 proteins, further accelerating the advancement of CRISPR/Cas9-based research.

biochemistry↗

Heterozygous Cell Models of STAT1 Gain-of-Function Reveal a Broad Spectrum of Interferon-Signature Gene Transcriptional Responses

Signal Transducer and Activator of Transcription 1 (STAT1) gain-of-function (GOF) is an autosomal dominant immune disorder marked by wide infectious predisposition, autoimmunity, vascular disease and malignancy. Its molecular hallmark, elevated phospho-STAT1 (pSTAT1) following interferon (IFN) stimulation, is seen consistently in all patients and may not fully account for the broad phenotypic spectrum associated with this disorder. While over 100 mutations have been implicated in STAT1 GOF, genotype-phenotype correlation remains limited, and current overexpression models may be of limited use in gene expression studies. We generated heterozygous mutants in diploid HAP1 cells using CRISPR/Cas9 base-editing, targeting the endogenous STAT1 gene. Our models recapitulated the molecular phenotype of elevated pSTAT1, and were used to characterize the expression of five IFN-stimulated genes under a number of conditions. At baseline, transcriptional polarization was evident among mutants compared with wild type, and this was maintained following prolonged serum starvation. This suggests a possible role for unphosphorylated STAT1 in the pathogenesis of STAT1 GOF. Following stimulation with IFN or IFN{gamma}, differential patterns of gene expression emerged among mutants, including both gain and loss of transcriptional function. This work highlights the importance of modelling heterozygous conditions, and in particular transcription factor-related disorders, in a manner which accurately reflects patient genotype and molecular signature. Furthermore, we propose a complex and multifactorial transcriptional profile associated with various STAT1 mutations, adding to global efforts in establishing STAT1 GOF genotype-phenotype correlation and enhancing our understanding of disease pathogenesis.

immunology↗

Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy

BackgroundMicrobes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well adapted microbes, which are able to survive in a narrow pH range. In comparison to other human-associated microbes, vaginal microbes are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. MethodsUsing 16S rRNA and ITS amplicon sequencing, we characterized the cervicovaginal microbiomes of 18 healthy women throughout the three trimesters of pregnancy. Shotgun metagenomic sequencing permitted refinement of the taxonomy established by amplicon sequencing, and identification of functional genes. Additionally, we analyzed saliva and urine metabolomes using GC-TOF and LC-MS/MS lipidomics approaches for samples from mothers and their infants through the first year of life. ResultsAmplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus also have high mannitol levels, which contradicts the basic characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Furthermore, indole-3-lactate (ILA) was also indicative of L. crispatus specifically. ILA has immunomodulatory properties through binding the human aryl hydrocarbon receptor (AhR), which may maintain the especially low diversity of L. crispatus dominated communities. ConclusionsOverall, using a multi- omic approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition.

microbiology↗

A mutation-independent approach via transcriptional upregulation of a disease modifier gene rescues muscular dystrophy in vivo.

Introductory paragraphIdentification of protective and/or pathogenic genetic modifiers provides important insight into the heterogeneity of disease presentations in individuals affected by neuromuscular disorders (NMDs), despite having well-defined pathogenic variants. Targeting modifier genes to improve disease phenotypes could be especially beneficial in cases where the causative genes are large, structurally complex and the mutations are heterogeneous. Here, we report a mutation-independent strategy to upregulate expression of a compensatory disease-modifying gene in Congenital Muscular Dystrophy type 1A (MDC1A) using a CRISPR/dCas9-based transcriptional activation system. MDC1A is caused by nonfunctional Laminin 2, which compromises muscle fibers stability and axon myelination in peripheral nerves 1. Transgenic overexpression of Lama1, encoding a structurally similar protein Laminin 1, ameliorates muscle wasting and paralysis in the MDC1A mouse models, demonstrating its role as a protective disease modifier 2. Yet, upregulation of Lama1 as a postnatal gene therapy is hampered by its large size, which exceeds the current genome packaging capacity of clinically relevant delivery vehicles such as adeno-associated viral vectors (AAVs). In this study, we sought to upregulate Lama1 using CRISPR/dCas9-based transcriptional activation system, comprised of catalytically inactive S. aureus Cas9 (dCas9) fused to VP64 transactivation domains and sgRNAs targeting the Lama1 promoter. We first demonstrated robust upregulation of Lama1 in myoblasts, and following AAV9-mediated intramuscular delivery, in skeletal muscles of dy2j/dy2j mouse model of MDC1A.\n\nWe therefore assessed whether systemic upregulation of Lama1 would yield therapeutic benefits in dy2j/dy2j mice. When the intervention was started early in pre-symptomatic dy2j/dy2j mice, Lama1 upregulation prevented muscle fibrosis and hindlimb paralysis. An important question for future therapeutic approaches for a variety of disorders concerns the therapeutic window and phenotypic reversibility. This is particularly true for muscular dystrophies as it has long been hypothesized that fibrotic changes in skeletal muscle represent an irreversible disease state that would impair any therapeutic intervention at advanced stages of the disease. Here, we demonstrate that dystrophic features and disease progression were significantly improved and partially reversed when the treatment was initiated in symptomatic 3-week old dy2j/dy2j mice with already-apparent hind limb paralysis and significant muscle fibrosis.\n\nCollectively, our data demonstrate the feasibility and therapeutic benefit of CRISPR/dCas9-mediated modulation of a disease modifier gene, which opens up an entirely new and mutation-independent treatment approach for all MDC1A patients. Moreover, this treatment strategy provides evidence that muscle fibrosis can be reversible, thus extending the therapeutic window for this disorder. Our data provide a proof-of-concept strategy that can be applied to a variety of disease modifier genes and a powerful therapeutic approach for various inherited and acquired diseases.

genetics↗