Biology subjects

Humphreys, N. E.

Publications and source records attributed to Humphreys, N. E..

8 recordsLinked to original sources

bioRxiv2026

LBR nucleoplasmic domains regulate X-chromosome solubility and nuclear organization

The nuclear lamina plays a central role in genome organization, yet how specific lamina-associated proteins regulate chromosome architecture during development remains unclear. Here, we show that the nucleoplasmic domains of the Lamin B Receptor (LBR) are essential for X-chromosome localization at the nuclear periphery and chromatin architecture during neural differentiation. Using genetic dissection of LBR function, combined with genome-wide chromatin solubility profiling and transcriptional analyses, we demonstrate that loss of LBR N-terminal domains impairs proper cell differentiation and X chromosome inactivation (XCI), selectively disrupting chromatin structure in neural progenitors but not in pluripotent cells. Strikingly, these effects are disproportionately concentrated - but not limited to - on the inactive X chromosome, which undergoes a pronounced shift toward a more soluble chromatin state. Our findings establish the nucleoplasmic function of LBR as a key determinant of X-chromosome functionality and identify chromatin solubility and accessibility as a previously underappreciated layer of genome regulation by the nuclear lamina in XCI. Finally, our work provides definitive genetic evidence that LBRs nuclear architectural functions are molecularly separable from its metabolic sterol reductase activity, which is preserved in our model, and are critically necessary for XCI in differentiating mouse female XX ESCs models.

genetics↗

bioRxiv2026

Depletion and replacement of tissue resident macrophages in mice with germ-line deletion of a conserved enhancer in the Csf1r locus.

Expression of the Csf1r gene in cells of the mononuclear phagocyte lineage is regulated by a conserved enhancer, the fms-intronic regulatory element (FIRE). In mice with a germ-line deletion of FIRE (Fireko) CSF1R expression is undetectable in bone marrow progenitors and classical monocytes. Fireko mice lack subpopulations of macrophages in the brain and periphery but develop normally. Here we show that loss of CSF1R expression in Fireko mice is partly overcome by CSF2 in vitro and inflammatory recruitment in vitro. Analysis of heterozygous mutant mice and deletion of the conserved AP1 motif in FIRE provide evidence that continuous receptor synthesis determines CSF1 responsiveness. The absence of macrophages in kidney and heart of Fireko mice was not associated with detectable loss of physiological function. In a model of renal injury macrophage recruitment and histopathology were similar in WT and Fireko mice. Tissue resident macrophages that were depleted in Fireko mice, including microglia, were replaced by donor-derived cells following intraperitoneal adoptive transfer of wild-type bone marrow at weaning. The Fireko mouse provides a novel platform to dissect the functions of tissue resident macrophages in development, homeostasis and pathology. Summary StatementThis study describes a unique model of selective tissue resident macrophage deficiency arising from dysregulated expression of the mouse Csf1r gene.

immunology↗

bioRxiv2026

Iterative engineering of a compact Cas9 ortholog for in vivo gene editing via single AAV delivery

The development of compact and efficient CRISPR-Cas systems is crucial for biomedical and therapeutic genome editing, particularly in vivo applications based on viral delivery. Here, we performed a comparative functional screen of seven Cas9 orthologs to systematically evaluate their genome editing activity in mammalian cells. Among these, Cme2--a 1008 amino acid nuclease recognizing a 5'-NAGNGC PAM--emerged as a promising candidate based on its compact size and baseline editing activity. To overcome its limited native efficiency, we employed a dual engineering approach combining sgRNA scaffold optimization and rational protein mutagenesis. The resulting variant, enCme2, exhibits markedly improved editing efficiency across multiple loci in both mouse and human cells while maintaining extremely high specificity and minimal off-target activity. Importantly, the small size of enCme2 permits packaging of the complete system into a single rAAV vector, enabling efficient genome editing/HDR in in vivo tissues and mouse embryos, and facile generation of transgenic models. These results establish enCme2 as a compact, precise, and AAV-compatible genome editing platform with broad applicability for in vivo research and therapeutic approaches, especially where high specificity is desirable.

molecular biology↗

bioRxiv2025

The transcription of a single olfactory receptor per neuron is enforced by epigenetic silencing of their enhancers

The ability to discriminate thousands of odors in our environment requires each olfactory neuron to express a single olfactory receptor from hundreds of available genes. The biochemical mechanism enforcing this monogenic expression remains unknown. We show that deletion of the chromatin protein TRIM66 causes individual olfactory neurons to express multiple receptors at a high level, demonstrating that monogenic expression relies on an epigenetic silencing mechanism. Moreover, TRIM66 is specifically recruited to olfactory receptor gene super-enhancers during neuronal progenitor maturation, thereby silencing nearby olfactory receptor genes. Loss of monogenic expression disrupted axonal projections to the olfactory bulb, resulting in an aberrant topographic map and impaired social odor discrimination and reproductive behaviors. These findings uncover the chromatin-based silencing of super-enhancers as the mechanism underlying the organization of the mammalian olfactory system.

molecular biology↗

bioRxiv2025

Generation of a Ym1 Deficient Mouse utilising CRISPR-Cas9 in CB6 Embryos

Chitinase-like proteins (CLPs) are of wide interest due to their significant roles during both biological and pathological processes. Human CLPs such as YKL-40 have been suggested as biomarkers of disease severity in many conditions. Murine CLPs include Brp39, Ym1, and Ym2 and these are similarly upregulated in multiple mouse models of pathology. Investigation of these molecules, particularly Ym1 and Ym2, is plagued by complexity in the genomic locus due to recent gene duplication events in the C57BL/6 strain. Using a novel CRISPR-Cas9 targeting approach involving CB6 mixed background embryos, we generated a Ym1 deficient mouse. Validation using flow cytometry, ELISA, and immunofluorescence confirmed no expression of mature Ym1 protein with no alteration in the expression of related chitinases/CLP genes including Chia and Chil4. This new transgenic mouse line will be key for investigating CLP functions and the genetic approach utilised may provide a useful strategy for other genes which show differences between inbred mouse strains.

genetics↗

bioRxiv2020

LRRC8A regulates hypotonicity-induced NLRP3 inflammasome activation

The NLRP3 inflammasome is a multi-molecular protein complex that converts inactive cytokine precursors into active forms of IL-1{beta} and IL-18. The NLRP3 inflammasome is frequently associated with the damaging inflammation of non-communicable disease states and is considered a therapeutic target. However, there is much regarding the mechanism of NLRP3 activation that remains unknown. Chloride efflux is suggested as an important step in NLRP3 activation, but the identity of which chloride channels are involved is still unknown. We used chemical, biochemical, and genetic approaches to establish the importance of Cl- channels in the regulation of NLRP3 activation. Specifically we identify LRRC8A, an essential component of volume-regulated anion channels (VRAC), as a vital regulator of hypotonicity-induced, but not DAMP-induced, NLRP3 inflammasome activation. Although LRRC8A was dispensable for canonical DAMP-dependent NLRP3 activation, this was still sensitive to Cl- channel inhibitors, suggesting there are additional and specific Cl- sensing and regulating mechanisms controlling NLRP3.

immunology↗

bioRxiv2020

Loss of PKCα increases arterial medial calcification in a uremic mouse model of chronic kidney disease

Arterial medial calcification is an independent risk factor for mortality in chronic kidney disease. We previously reported that knock-down of PKC expression increases high phosphate-induced mineral deposition by vascular smooth muscle cells in vitro. This new study tests the hypothesis that PKC regulates uremia-induced medial calcification in vivo. Female wild-type and PKC-/- mice underwent a two-stage subtotal nephrectomy and were fed a high phosphate diet for 8 weeks. X-ray micro computed tomography demonstrated that uremia-induced medial calcification was increased in the abdominal aorta and aortic arch of PKC-/- mice compared to wild-types. Blood urea nitrogen was also increased in PKC-/- mice compared to wild-types; there was no correlation between blood urea nitrogen and calcification in PKC-/- mice. Phosphorylated SMAD2 immunostaining was detected in calcified aortic arches from uremic PKC-/- mice; the osteogenic marker Runx2 was also detected in these areas. No phosphorylated SMAD2 staining were detected in calcified arches from uremic wild-types. PKC knock-down increased TGF-{beta}1-induced SMAD2 phosphorylation in vascular smooth muscle cells in vitro, whereas the PKC activator prostratin decreased SMAD2 phosphorylation. In conclusion, loss of PKC increases uremia-induced medial calcification. The PKC/TGF-{beta} signaling axis could therefore represent a new therapeutic target for arterial medial calcification in chronic kidney disease.

cell biology↗

bioRxiv2019

Complex deletion and proximal reinsertion of a 150bp regulatory sequence in the mouse Csf1r promoter mediated by CRISPR-Cas9.

This paper describes a deletion/reinsertion event encountered in a genome-editing project using CRISPR-Cas9. The objective was to delete a 150bp enhancer region in the mouse Csf1r locus using a pair of guides and a homology-dependent repair (HDR) template. The editing was successful in generating a founder pup with the anticipated precise deletion. However, the deleted fragment and a duplicated copy of part of the HDR template was reinserted around 50bp downstream. The reinsertion event was recognised because the PCR primer site used in genotyping was duplicated, so that there were three PCR products in a heterozygous animal and two in a homozygote. The event we describe is more subtle and more difficult to detect than large-scale rearrangements reported by others. We suggest that any genomic deletion mediated by CRISPR-Cas9 needs to be confirmed by assessing the copy number in the genome.

molecular biology↗