Motile cilia are eukaryotic organelles with essential chemo- and mechano-sensing functions across evolution, from single cell organisms to humans. Motile cilia of the mammalian nervous, respiratory and reproductive systems are characterized by unique motility proteins to generate fluid flow essential for transporting metabolites and removing mucus. The molecular mechanism of motile cilia biogenesis remains unknown. Here, we use mouse genetics, single-molecule motility assays, proteomics, high-resolution imaging, and in situ cryo-tomography to identify mammalian KIF27, a motor protein of the Kinesin-4 family and homologue of the Hedgehog pathway regulator COS2/KIF7, as a key regulator of motile cilia assembly. We show that KIF27 promotes the integrity of the transition zone, a diffusion barrier situated at the cilium base. Loss of KIF27 causes specific and profound defects in axonemal structure and disrupts cilia beating, which collectively lead to organismal phenotypes that recapitulate primary ciliary dyskinesia. We show that the motile properties of KIF27 are dispensable for its function in motile cilia biogenesis. Instead, KIF27 acts as a microtubule scaffold to regulate the transition zone architecture and enable correct ciliary incorporation of motility-generating proteins. Given that KIF27 homologues exist in different evolutionarily lineages, we propose that the ancestral activity of KIF27/KIF7 kinesins was to form a microtubule-associated scaffold for protein-protein interactions pertinent to cilia formation and signaling. The transition-zone associated KIF27 activities may represent a general building principle for motile cilia assembly in diverse species and cell types. ### Competing Interest Statement The authors have declared no competing interest.

The cardiac conduction system (CCS) is a network of specialized cardiomyocytes that coordinates electrical impulse generation and propagation for synchronized heart contractions. Although the components of the CCS, including the sinoatrial node, atrioventricular node, His bundle, bundle branches, and Purkinje fibers, were anatomically discovered more than 100 years ago, their molecular constituents and regulatory mechanisms remain incompletely understood. Here, we demonstrate the transcriptomic landscape of the postnatal mouse CCS at a single-cell resolution with spatial information. Integration of single-cell and spatial transcriptomics uncover region-specific markers and zonation patterns of expression. Network inference shows heterogeneous gene regulatory networks across the CCS. Notably, region-specific gene regulation is recapitulated in vitro using neonatal mouse atrial and ventricular myocytes overexpressing CCS-specific transcription factors, Tbx3 and/or Irx3. This finding is supported by ATAC-seq of different CCS regions, Tbx3 ChIP-seq, and Irx motifs. Overall, this study provides comprehensive molecular profiles of the postnatal CCS and elucidates gene regulatory mechanisms contributing to its heterogeneity. The cardiac conduction system consists of specialized cardiomyocytes that synchronize heart contractions. Here, Oh et al. provide comprehensive molecular profiles of the postnatal cardiac conduction system and elucidate gene regulatory mechanisms contributing to its heterogeneity.

Suppressor of fused (SUFU) is widely regarded as a key negative regulator of the sonic hedgehog (SHH) morphogenic pathway and a known tumor suppressor of medulloblastoma (MB). However, we report here that SUFU expression was markedly increased in 75% of specimens compiled in a tissue array comprising 49 unstratified MBs. The SUFU and GLI1 expression levels in this MB array showed strong positive correlation, which was also identified in a large public data set containing 736 MBs. We further report that increasing Sufu gene dosage in mice caused preaxial polydactyly, which was associated with the expansion of the Gli3 domain in the anterior limb bud and heightened Shh signaling responses during embryonic development. Increasing Sufu gene dosage also led to accelerated cerebellar development and, when combined with ablation of the Shh receptor encoded by Patched1 (Ptch1), promoted MB tumorigenesis. These data reveal multifaceted roles of SUFU in promoting MB tumorigenesis by enhancing SHH signaling. This revelation clarifies potentially counterintuitive clinical observation of high SUFU expression in MBs and may pave way for novel strategies to reduce or reverse MB progression.

A common cause of deafness in humans is dysregulation of the endocochlear potential generated by the stria vascularis (SV). Thus, proper formation of the SV is critical for hearing. Using single-cell transcriptomics and a series of Shh signaling mutants, we discovered that the Shh receptor Patched1 (Ptch1) is essential for marginal cell (MC) differentiation and SV formation. Single-cell RNA sequencing analyses revealed that the cochlear roof epithelium is already specified into discrete domains with distinctive gene expression profiles at embryonic day 14, with Gsc as a marker gene of the MC lineage. Ptch1 deficiency leads to defective specification of MC precursors along the cochlear basal-apical regions. We demonstrated that elevated Gli2 levels impede MC differentiation through sustaining Otx2 expression and maintaining the progenitor state of MC precursors. Our results uncover an early specification of cochlear non-sensory epithelial cells and establish a crucial role of the Ptch1-Gli2 axis in regulating the development of SV.

A gene cadre orchestrates the normal development of sensory and non-sensory cells in the inner ear, segregating the cochlea with a distinct tonotopic sound frequency map, similar brain projection, and five vestibular end-organs. However, the role of genes driving the ear development is largely unknown. Here, we show double deletion of the Iroquois homeobox 3 and 5 transcription factors (Irx3/5 DKO) leads to the fusion of the saccule and the cochlear base. The overlying otoconia and tectorial membranes are absent in the Irx3/5 DKO inner ear, and the primary auditory neurons project fibers to both the saccule and cochlear hair cells. The central neuronal projections from the cochlear apex-base contour are not fully segregated into a dorsal and ventral innervation in the Irx3/5 DKO cochlear nucleus, obliterating the characteristic tonotopic auditory map. Additionally, Irx3/5 deletion reveals a pronounced cochlear-apex-vestibular "vestibular-cochlear" nerve (VCN) bilateral connection that is less noticeable in wild-type control mice. Moreover, the incomplete segregation of apex and base projections that expands fibers to connect with vestibular nuclei. The results suggest the mammalian cochlear apex is a derived lagena reminiscent of sarcopterygians. Thus, Irx3 and 5 are potential evolutionary branch-point genes necessary for balance-sound segregation, which fused into a saccule-cochlea organization.

Iroquois homeobox gene 3 (Irx3) and Irx5 encode transcription factors that play crucial roles in limb development and bone formation. Previous studies using knockout mice have revealed a role of Irx3 and Irx5 in osteogenesis in young adult mice. However, whether these genes are also essential for bone homeostasis in adulthood and contribute to bone diseases remain poorly understood. Osteoporosis is a disease characterized by lower bone mineral density and disrupted bone microarchitecture, typically occurs in postmenopausal women. Here, we demonstrate that Irx3/5dHet mice with a half-reduction of Irx3 and Irx5 dosage serve as a novel model of osteoporosis. By micro-computed tomography, we found that Irx3/5dHet mice exhibited sex-dependent bone loss patterns. While male Irx3/5dHet mice progressively lost trabecular microstructures with aging, female mutants exhibited lower bone mineral density (BMD) and bone volume fraction (BV/TV) at early adulthood (9-15 weeks old) but without further loss later at 1 year of age. Bone marrow adipocytes are known to be elevated at the expenses of lower osteogenesis in osteoporotic bone marrow. Surprisingly, we found sex-dependent changes in adipogenesis at the age of skeletal maturity that bone marrow adipocytes were reduced in female Irx3/5dHet mice along with deteriorated osteogenesis, while male mice exhibited elevated adipogenesis. In summary, we reported a novel genetic model for osteoporosis-like phenotypes, highlighting sex-dependent bone mineral density and bone marrow adipocyte characteristics.

Left ventricular non-compaction cardiomyopathy (LVNC) is a rare heart condition characterized by excessive trabeculae and intertrabecular recesses in the left ventricle of the heart. It is believed to be caused by abnormal trabecular compaction process, which involves trabecular remodelling to form a thick myocardial wall. Embryonic trabeculae consist of bipotent progenitors that differentiate into the ventricular conduction system (VCS) and contractile cardiomyocytes, yet it remains to be further understood how the pathways involved in trabecular cell specifications play a role in the compaction process. Here we present two transcription factors, Iroquois homeobox 3 ( Irx3 ) and Irx4 , playing antagonistic and cooperative roles during trabecular specification and maturation, thereby facilitating proper ventricular compaction. Our single-cell RNA sequencing analysis revealed that the differentiation of trabecular cells into VCS cells was accompanied by increased Irx3 but decreased Irx4 expression. In addition, we found that the loss of Irx4 led to both an increased expression level of Irx3 and an expansion in the number of Irx3 -expressing cells. Conversely, the loss of Irx3 resulted in an upregulation of Irx4 expression within VCS cells. Next, to investigate the functional importance of the antagonistic relationship between Irx3 and Irx4 in trabecular differentiation, we generated Irx3 and Irx4 compound knockout (KO) mice and examined the structure and function of their hearts. Notably, unlike Irx3 KO hearts showing normal ventricular myocardium, Irx4 KO hearts exhibited mild LVNC, and Irx3 and Irx4 double knockouts ( Irx3 /4dKO) hearts displayed severe LVNC. Multiome sequencing of E14.5 ventricles revealed that Irx3 /4dKO ventricles contained an increased number of trabecular cells, expressing higher levels of cell proliferation markers and altered trabecular identity genes, compared to littermate controls. Collectively, our results demonstrate that balanced antagonism between Irx3 and Irx4 is crucial for establishing trabecular identity. This highlights the importance of proper differentiation of trabeculae into the VCS and non-VCS contractile cells during ventricular compaction, thereby preventing noncompaction cardiomyopathy.

Reverse genetics offers precise functional insights into genes through the targeted manipulation of gene expression followed by phenotypic assessment. While these approaches have proven effective in model organisms such as Saccharomyces cerevisiae, large-scale genetic manipulations in human cells were historically unfeasible due to methodological limitations. However, recent advancements in functional genomics, particularly clustered regularly interspaced short palindromic repeats (CRISPR)-based screening technologies and next-generation sequencing platforms, have enabled pooled screening technologies that allow massively parallel, unbiased assessments of biological phenomena in human cells. This review provides a comprehensive overview of cutting-edge functional genomic screening technologies applicable to human cells, ranging from short hairpin RNA screens to modern CRISPR screens. Additionally, we explore the integration of CRISPR platforms with single-cell approaches to monitor gene expression, chromatin accessibility, epigenetic regulation, and chromatin architecture following genetic perturbations at the omics level. By offering an in-depth understanding of these genomic screening methods, this review aims to provide insights into more targeted and effective strategies for genomic research and personalized medicine.

The vagus nerve (VN) is a major component of the parasympathetic nervous system that regulates vital functions, including glucose and energy homeostasis. However, the specific molecular signaling pathways within vagal neurons that regulate metabolism are unclear. Here, we show that enhanced PI3K signaling within the vagal neurons through the deletion of its endogenous negative regulator, phosphatase and tensin homolog (Pten), enhanced VN function along with decreased inflammation within the vagal neurons. This was associated with an anti-inflammatory state in peripheral metabolic tissues such as the adipose, liver and skeletal muscle, with protection against high fat diet (HFD) induced glucose intolerance and insulin resistance. This was driven at least in part by macrophages, such that their depletion led to abolishment of metabolic protection. Single nuclear RNA sequencing analysis of the neuronal clusters within the nodose ganglia of the VN revealed that Pten-deficiency lead to upregulation of genes involved in myelination and neuronal growth, in keeping with large myelinated nerve fibers conducive for improved VN function. Intriguingly, upregulation of genes involved in adrenergic signaling was present in these neurons which correlated with enhanced beiging and lipolysis, increased sympathetic nerve density and increased norepinephrine levels in the adipose tissue. Finally, to assess specific role of insulin signaling given multiple upstream stimuli that can activate PI3K signaling, we generated mice with Insulin receptor deficiency specifically in the vagal neurons. These mice exhibited reduced vagal function and exacerbated HFD-induced metabolic abnormalities and inflammation which was rescued with concomitant Pten deletion. Together, we show that insulin signaling within the vagal neurons plays an essential role in optimizing sympathovagal balance in determining peripheral inflammatory and metabolic homeostasis which can be harnessed as novel therapeutic strategy to combat diabetes and obesity.

The mammalian inner ear houses the vestibular and cochlear sensory organs dedicated to sensing balance and sound, respectively. These distinct sensory organs arise from a common prosensory region, but the mechanisms underlying their divergence remain elusive. Here, we showed that two evolutionarily conserved homeobox genes, Irx3 and Irx5, are required for the patterning and segregation of the saccular and cochlear sensory domains, as well as for the formation of auditory sensory cells. Irx3/5 were highly expressed in the cochlea, their deletion resulted in a significantly shortened cochlea with a loss of the ductus reuniens that bridged the vestibule and cochlea. Remarkably, ectopic vestibular hair cells replaced the cochlear non-sensory structure, the Greater Epithelial Ridge. Moreover, most auditory sensory cells in the cochlea were transformed into hair cells of vestibular identity, with only a residual organ of Corti remaining in the mid-apical region of Irx3/5 double knockout mice. Conditional temporal knockouts further revealed that Irx3/5 are essential for controlling cochlear sensory domain formation before embryonic day 14. Our findings demonstrate that Irx3/5 regulate the patterning of vestibular and cochlear sensory cells, providing insights into the separation of vestibular and cochlear sensory organs during mammalian inner ear development.

Abstract Potassium is the most abundant intracellular cation with crucial functions such as regulating cell proliferation, migration, and differentiation. Potassium flux across cellular membranes is controlled by potassium channels. While the role of cytosolic potassium has been researched for many decades, very little is known about the modulation or significance of potassium in the cell nucleus. Here, we identify potassium channel subunit KCNG1 as a novel regulator of nuclear potassium in medulloblastoma (MB), the most common malignant pediatric brain tumour. Using genetically encoded Förster resonance energy transfer (FRET)-based potassium sensors, we show that KCNG1 regulates nuclear potassium level independently of cytosolic potassium level. KCNG1 knockdown alters the genomic architecture of MB cells by stabilizing G-quadruplex (G4) DNA, inducing DNA damage, and reducing nuclear envelope-associated heterochromatin. Ultimately, KCNG1 deficiency results in nuclear swelling, thereby compromising nuclear envelope integrity and inducing DNA spillage into the cytosol to activate the pro-inflammatory cGAS/STING pathway. Genetic knockdown of KCNG1 mitigates tumour growth and prolongs the survival of mice bearing MB of distinct subgroups. Altogether, our findings reveal that nuclear potassium regulates genomic structure and nuclear envelope integrity and demonstrate that targeting a nuclear potassium channel can be leveraged to activate immunogenic signalling in MB.

Supplementary Figure 2 from Multipotent CD15+ Cancer Stem Cells in Patched-1–Deficient Mouse Medulloblastoma

Supplementary Figures 4-6 from Multipotent CD15+ Cancer Stem Cells in Patched-1–Deficient Mouse Medulloblastoma

Hirschsprung disease is characterized by the absence of enteric neurons caused by the defects of enteric neural crest cells, leading to intestinal obstruction. Here, using induced pluripotent stem cell-based models of Hirschsprung and single-cell transcriptomic analysis, we identify a gene set of 118 genes commonly dysregulated in all patient enteric neural crest cells, and suggest HDAC1 may be a key regulator of these genes. Furthermore, upregulation of RNA splicing mediators and enhanced alternative splicing events are associated with severe form of Hirschsprung. In particular, the higher inclusion rate of exon 9 in PTBP1 and the perturbed expression of a PTBP1-target, PKM, are significantly enriched in these patient cells, and associated with the defective oxidative phosphorylation and impaired neurogenesis. Hedgehog-induced oxidative phosphorylation significantly enhances the survival and differentiation capacity of patient cells. In sum, we define various factors associated with Hirschsprung pathogenesis and demonstrate the implications of oxidative phosphorylation in enteric neural crest development and HSCR pathogenesis.

Introduction and objectiveStress urinary incontinence is of concern in both pediatric and adult population. Double mutant GLI family zinc finger Gli2 +/-/-; Gli3A699/+/- murine model of stress incontinence has been recently developed as a reliable model which does not require surgical manipulation to create incontinence and is shown to survive to adulthood. The aim of this study was to establish the etiology of incontinence in the double mutant Gli2 +/-/-; Gli3A699/+/- mice.Study designWe used 13 cluster of differentiation 1 (CD-1) mice (7-9 weeks) for demonstration of histology of the bladder and urethra. There were 3 Wild Gli2 +/-/- fe-males, 2 Wild Gli2 +/-/-males, 4 Gli2 +/-/-;Gli3A699/+/- females and 4 Gli2 +/-/-;Gli3A699/+/- males. The Wild Gli2 +/-/-mice served as the control group and Gli2 +/-/-;Gli3A699/+/- mice served as the test group. Additionally, eight 16.5 days mice (2 each of Wild Gli2 +/-/-females, Wild Gli2 +/-/-males, double knockout (DKO) Gli2 +/-/-;Gli3A699/+/- females and Gli2 +/-/-;Gli3A699/+/- males) were used to assess the histology of the spinal cord. The gross appearance of bladder and urethra was studied using ink injection assays. Immunohistochemistry was done for smooth muscle actin and cytokeratin.ResultsGross and histologic appearance confirmed the pre-viously reported widening of bladder outlet and hy-poplasia of smooth muscles in female urethra and also established them in the male urethra ofGli2 +/-/-;Gli3A699/+/- mice compared to Gli2 +/-/-mice. The double knockout mice were smaller than the Gli2 mice (5.2 vs 6.1 cm, p Z 0.002). Immunohis-tochemistry demonstrated epithelial hyperplasia and smooth muscle hypoplasia. Additionally, there was prostatic hypoplasia in the Gli2 +/-/-;Gli3A699/+/- male mice. The spinal cord length for body size appeared comparable between the Gli2 +/-/-and Gli2 +/-/-;Gli3A699/+/- mice but histological evaluation revealed abnormal development of the caudal end of the vertebral body with premature termination of the spinal cord (Figure).DiscussionThe histological changes in the bladder neck and urethra were consistent to those previously re-ported. While previous report described the findings in female mice only, we confirmed that these find-ings are also present in males as well as prostatic hypoplasia, a possible additional factor leading to stress incontinence. The most important finding in the present study however, was the detection of premature termination of spinal cord in the DKO Gli2 +/-/-; Gli3A699/+/- mice which has not been re-ported previously and is likely a major contributor to incontinence in this model.ConclusionThe incontinence in male as well as female Gli2 +/-/-; Gli3A699/+/- mice is due to both myogenic and neurogenic involvement. These double knockout mice are a valuable model of stress incontinence related to neurogenic bladder due to low outlet resistance.

Supplementary Figures 1-3 from Multipotent CD15+ Cancer Stem Cells in Patched-1–Deficient Mouse Medulloblastoma

The molecular mechanisms allowing hair follicles to periodically activate their stem cells (HFSCs) are incompletely characterized. Here, we identify the transcription factor IRX5 as a promoter of HFSC activation. Irx5-/- mice have delayed anagen onset, with increased DNA damage and diminished HFSC proliferation. Open chromatin regions form near cell cycle progression and DNA damage repair genes in Irx5-/- HFSCs. DNA damage repair factor BRCA1 is an IRX5 downstream target. Inhibition of FGF kinase signaling partially rescues the anagen delay in Irx5-/- mice, suggesting that the Irx5-/- HFSC quiescent phenotype is partly due to failure to suppress Fgf18 expression. Interfollicular epidermal stem cells also show decreased proliferation and increased DNA damage in Irx5-/-mice. Consistent with a role for IRX5 as a promoter of DNA damage repair, we find that IRX genes are upregulated in many cancer types and that there is a correlation between IRX5 and BRCA1 expression in breast cancer.

Abstract Hirschsprung disease (HSCR) is characterized by the absence of enteric neurons caused by the defects of enteric neural crest cells (ENCCs), leading to intestinal obstruction. Here, using iPSC-based models of HSCR and single-cell transcriptomic analysis, we identified a core gene set of 118 genes commonly dysregulated in all HSCR-ENCCs, with HDAC1 found to be a master regulator of these genes. Furthermore, upregulation of RNA splicing mediators and enhanced alternative splicing events were associated with severe form of HSCR. In particular, the higher inclusion rate of exon 9 in PTBP1 and the perturbed expression of a PTBP1-target, PKM, were significantly enriched in these HSCR-ENCCs, and associated with the defective oxidative-phosphorylation (OXPHOS) and impaired neurogenesis. Hedgehog-induced OXPHOS significantly enhanced the survival and differentiation capacity of HSCR-ENCCs. In sum, we have defined the core factors underpinning HSCR disease and demonstrated the implications of OXPHOS in ENCC development and HSCR pathogenesis.

Objective Obesity, a leading cause of several metabolic abnormalities, is mainly caused by imbalanced energy homeostasis. IRX3 and IRX5 have been suggested as genetic determinants of obesity in connection with the intronic variants of the FTO gene, the strongest genetic risk factor of polygenic obesity in humans. Although the causal effects of Irx3 and its cooperation with Irx5 in obesity and associated metabolic abnormalities have been demonstrated in vivo, the function of Irx5 in energy homeostasis remains unclear. Here we aim to decipher the actions of Irx5 in the regulation of obesity and metabolic abnormalities. Methods We employed a mouse model homozygous for an Irx5 -knockout ( Irx5 KO ) allele and determined its metabolic phenotype in the presence or absence of a high-fat diet challenge. To investigate the function of Irx5 in the regulation of energy homeostasis, adipose thermogenesis and hypothalamic leptin response were assessed, and single-cell RNA sequencing (scRNA-seq) in the hypothalamic arcuate-median eminence (ARC-ME) was conducted. Results Irx5 KO mice were leaner and resistant to diet-induced obesity as well as associated metabolic abnormalities, primarily through loss of adiposity. Assessments of energy expenditure and long-term dietary intake revealed that an increase in basal metabolic rate with adipose thermogenesis and a reduction of food intake with improved hypothalamic leptin response in Irx5 KO mice may contribute to the anti-obesity effects. Utilizing scRNA-seq and marker gene analyses, we demonstrated the number of ARC-ME neurons was elevated in Irx5 KO mice, suggesting a direct role for Irx5 in hypothalamic feeding control. Conclusions Our study demonstrates that Irx5 is a genetic factor determining body mass/composition and obesity and regulates both energy expenditure and intake.