Biology subjects

Shih, B. B.-J.

Publications and source records attributed to Shih, B. B.-J..

4 recordsLinked to original sources

bioRxiv2026

Nanopore sequencing identifies a new Tyr::CreERT2 allele circulating in existing mouse stocks

The Tyr::CreERT2 transgenic mouse lines are essential tools for conditional gene manipulation in melanocytes and are widely used in melanoma research. Two independent lines are in common use: the Bosenberg line and the Larue line. Precise knowledge of transgene integration sites is critical for designing complex genetic crosses, yet the integration sites for these lines have only recently been characterised by whole genome sequencing. Here we report that a Tyr::CreERT2 mouse stock routinely used in BrafCA;Ptenflox melanoma models carries a previously undescribed integration on Chromosome 1, distinct from the previously reported Chromosome 2 integration. Using long-read nanopore sequencing, we mapped the integration to an intergenic locus between Alppl2 and Alpi, revealing a 2,430 bp genomic deletion at the insertion site. We developed position-specific junction PCR and qPCR assays to genotype this allele and confirmed that offspring are born at Mendelian ratios. Given that this stock is associated with elevated spontaneous melanoma penetrance, accurate characterisation of this allele has direct implications for the many laboratories employing this widely distributed melanoma model. SIGNIFICANCEThis study identifies a previously undescribed Tyr::CreERT2 transgene integration on Chromosome 1 in JAX strain 013590, a line widely used across the melanoma research community. Accurate characterisation of this allele has direct practical implications for the many laboratories that rely on this model for studies of melanoma initiation and progression.

genetics↗

bioRxiv2026

CSF1R-dependent macrophages control B cell development and function in the chicken immune system.

Acquired immunity in mammals depends upon capture and presentation of antigens by specialised macrophage populations in splenic marginal zone and lymph node sinuses and follicular dendritic cells (FDC) within germinal centres. Cells referred to as FDC in chickens express CSF1R, the receptor for macrophage colony-stimulating factor (CSF1) and IL34. We utilised single cell RNA-seq on CSF1R+ cells from chicken spleen to identify monocytes and two distinct populations of macrophages. TIMD4/C1Q/MAFB+ macrophages were enriched for expression of genes involved in iron metabolism. A MARCO/VSIG4+ population expressed SPIC, a transcription factor associated with red pulp macrophages in mammals but also expressed receptors (CR2) and trophic factors (TNFSF13, CXCL13) associated with mammalian FDC. SPIC+ cells were located within follicles in spleen, caecal tonsil and bursa. We generated a CSF1R knockout in the chicken germ line. Mutant birds lack macrophages in the embryo. They were indistinguishable from wild type at hatch and behaved and fed normally but from day 5-6 post hatch they failed to thrive. Loss of CSF1R function in hatchlings led to monocytopenia and granulocytosis and the loss of macrophage subpopulations in lymphoid organs. Consistent with their expression of B cell trophic factors, the loss of follicular macrophages in the bursa was associated with involution and severe B cell deficiency in the circulation and spleen. In summary, lymphoid tissues of chickens contain specialised macrophage populations with distinct expression profiles. The details of regulation by CSF1R, specialised functions and underlying transcriptional regulation are quite different between birds and mammals.

immunology↗

bioRxiv2025

Age-associated inflammatory monocytes are increased in menopausal females and reversed by Hormone Replacement Therapy

Biological sex is a crucial, but poorly understood variable in age-related susceptibility to infections and chronic inflammation - inflammageing. Monocytes are important immune cells responsible for initiating and resolving inflammatory responses to infection. While changes in monocyte populations result in increased susceptibility to infection, there is limited research on the impact of age and sex on human monocyte phenotype and function. The aim of this work was to dissect the impact of increasing age and biological sex on human monocyte phenotype and function. Here we show that older females have increased inflammatory intermediate and non-classical monocytes compared to young. These monocyte subsets were the most inflammatory ex vivo and their frequency correlated with markers of systemic inflammation. Proteomic analysis of sorted monocyte populations demonstrated that the three human monocyte subsets have largely distinct phenotypes. Additionally, proteomic analysis identified key age-associated protein pathways, including complement cascade and phagocytosis, downregulated in monocytes from older compared to younger individuals. We confirmed the proteomics findings showing that circulating C3 concentrations were reduced with age in females but not males. This decrease in complement in older females resulted in reduced monocyte phagocytosis. Crucially, we demonstrate that in peri/menopausal females, Hormone Replacement Therapy (HRT) reversed this expansion in intermediate monocytes and decreased circulating CRP as compared to age matched controls. Importantly peri/menopausal females on HRT had increased C3 serum concentrations and significantly improved monocyte phagocytosis. The data presented here indicate the importance of menopause in ageing monocyte phenotype and function. This data highlights the potential use of HRT in restoring monocyte function in females during ageing.

immunology↗

bioRxiv2024

Characterisation of human hair follicle development

Humans have a characteristic distribution of hair across the body. Visible, relatively long and thick terminal hair fibres are present on the scalp and eyebrows in childhood, and are stimulated to grow on other parts of the body, such as the beard and armpits, by hormones during puberty. The short and fine vellus hairs, in contrast, are not readily visible and cover most of the body, including the face. Here we report quantification of the timing and characteristics of hair follicle development in human embryogenesis, from gestational weeks 8 to 19, and compare this to mouse hair follicle development. We find that human hair follicles develop first on the head, where we identify several distinct initiation sites, followed by the torso. Although terminal and vellus hair follicles have clear differences in the adult, both hair types initially develop from placodes and dermal condensates of similar size. Once their development is initiated, we find that human hair follicles grow and mature at the same rate, regardless of anatomical location, but have different density at different body sites. These findings suggest that regional hair differences in human skin, such as the distinction between scalp and forehead, are largely caused by processes acting after the initial hair follicle morphogenesis. Efforts to understand the evolution of human hairlessness should, therefore, focus on genetic and cellular events that take place after hair follicle morphogenesis. Finally, we compared human skin appendages, including eccrine sweat glands, with those in mouse. We found that molecular markers, such as EDA, EDAR, SOX2 and WNT pathway components, are broadly similar in expression between both species, although specific differences do exist. Together with comparison of morphology and gene expression, these results support the use of embryonic mouse primary hair follicles as a model for human hair follicle development.

developmental biology↗