Genome-wide association studies (GWASs) have identified many sources of genetic variation associated with bone mineral density (BMD), a clinical predictor of fracture risk and osteoporosis. Aside from the identification of causal genes, other difficult challenges to informing GWAS include characterizing the roles of predicted causal genes in disease and providing additional functional context, such as the cell-type predictions or biological pathways in which causal genes operate. Leveraging single-cell transcriptomics (scRNA-seq) can assist in informing BMD GWAS by linking disease-associated variants to genes and providing a cell-type context for which these causal genes drive disease. Here, we use large-scale scRNA-seq data from bone marrow-derived stromal cells cultured under osteogenic conditions (BMSC-OBs) from Diversity Outbred (DO) mice to generate cell type-specific networks and contextualize BMD GWAS-implicated genes. Using trajectories inferred from the scRNA-seq data that map cell state transitions, we identify networks enriched with genes that exhibit the most dynamic changes in expression across trajectories. We discover 21 network driver genes, which are likely to be causal for human BMD GWAS associations that colocalize with expression/splicing quantitative trait loci (eQTLs/sQTLs). These driver genes, including Fgfrl1 and Tpx2, along with their associated networks, are predicted to be novel regulators of BMD via their roles in the differentiation of mesenchymal lineage cells. In this work, we showcase the use of single-cell transcriptomics from mouse bone-relevant cells to inform human BMD GWAS and prioritize genetic targets with potential causal roles in the development of osteoporosis.

Osteoporosis is characterized by low bone mineral density (BMD) and elevated fracture risk. Most BMD-associated GWAS variants lie in noncoding regions, complicating efforts to identify causal genes and mechanisms. To overcome this variant-to-function challenge, we previously developed STING-seq, a framework integrating biobank-scale GWAS with single-cell CRISPR inhibition (CRISPRi) screening to directly connect noncoding cis -regulatory elements (CREs) to their target genes. Applied to human fetal osteoblast (hFOB) cells across osteogenic differentiation, STING-seq linked 76 CREs to 75 target genes at BMD loci. Arrayed CRISPRi and activation validated key CRE-gene relationships, including long-range enhancers regulating CXCL12 (over 500 kb apart). We further uncovered trans -regulatory networks and characterized the DAP3 - YY1AP1 bidirectional promoter, demonstrating a role for DAP3 in mineralization via mitochondrial pathways. Together, these findings provide mechanistic insight into how noncoding GWAS variants shape osteoblast activity and highlight the genes and pathways that mediate genetic effects on BMD.

SCN8A encodes the voltage-gated sodium channel Nav1.6, which plays a key role in facilitating neuronal excitability. Mutations in SCN8A, particularly gain-of-function variants, cause SCN8A developmental and epileptic encephalopathy (DEE), a severe epilepsy syndrome characterized by seizures, cognitive dysfunction, movement disorders, and sudden unexpected death in epilepsy (SUDEP). The recurrent SCN8A variant R1872W impairs channel inactivation, causing neuronal hyperexcitability and seizures. Current treatments, including antiseizure medications, are often ineffective for patients with SCN8A DEE, highlighting the need for targeted therapies. We employed base editing to correct the R1872W SCN8A variant. An adenine base editor and guide RNA (SCN8A-ABE) were packaged within dual PhP.eB-adeno-associated viruses (AAVs) and administered to R1872W mice at P2. SCN8A-ABE significantly increased survival of mice expressing R1872W and either reduced seizure incidence and severity or eliminated seizure occurrence. Electrophysiological recordings revealed a rescue of seizure-associated neuronal hyperexcitability and suppression of the pathogenic persistent sodium current (INaP) in treated mice. Comorbidities, including diminished mobility and anxiety-like behaviors, were improved by SCN8A-ABE. These effects were achieved by a 32% absolute reduction in mutant transcripts, accompanied by conversion to SCN8A WT transcripts. Our findings demonstrate base editing as an effective targeted therapeutic approach for SCN8A DEEs by addressing the underlying genetic cause.

A 26-year-old man was evaluated for an elevated serum bone-specific alkaline phosphatase (BSAP). His medical history was significant for a neurodevelopmental disorder with generalized epilepsy. Symptoms included chronic pain in the ankles, hands, and right ribs, and a progressive decline in physical activity. Vitamin D deficiency was discovered, but the elevated BSAP persisted despite vitamin D replacement. Imaging studies reported diffusely increased scintigraphic uptake in the axial and appendicular skeleton, and low bone mineral density, but no radiographic sclerotic or lytic lesions. Genetic screening revealed a heterozygous pathogenic variant in the sodium voltage-gated channel α subunit 8 gene (SCN8A) (c.2924 T>A; p.L975*). Loss-of-function mutations in SCN8A are responsible for neurologic disease and bone loss. Expression analysis revealed that SCN8A was present in human osteoblasts and osteocytes, but not in osteoclasts, suggesting that the voltage-gated sodium channel, Nav1.6, encoded by SCN8A, may have direct actions in bone. The patient was subsequently prescribed alendronate, resulting in a lower alkaline phosphatase and symptomatic improvement in bone pain.

SCN8A encodes the voltage-gated sodium channel Nav1.6 which plays a key role in facilitating neuronal excitability. Mutations in SCN8A , particularly gain-of-function missense variants, are associated with SCN8A developmental and epileptic encephalopathy (DEE), a severe epilepsy syndrome characterized by spontaneous seizures, movement disorders, cognitive dysfunction, and sudden unexpected death in epilepsy (SUDEP). The recurrent SCN8A variant R1872W destabilizes inactivation of the sodium channel, resulting in neuronal hyperexcitability and onset of seizures. Current treatments, including anti-seizure medications (ASMs) that broadly target sodium channels, are often ineffective in SCN8A DEE patients and are associated with significant side effects, highlighting the need for targeted therapies. In this study, we utilized base editing as a therapeutic strategy to correct the patient derived R1872W SCN8A variant. Using two engineered mammalian cell line screens, we identified several targeting constructs that successfully reverted the R1872W variant to the reference allele. Our most effective construct, a modified adenine base editor, along with a paired successful guide RNA, was selected and packaged within a dual PhP.eB-adeno-associated virus (AAV) delivery system. This dual AAV therapy, referred to as SCN8A -ABE, was administered to mice expressing the R1872W variant at P2. Treatment with SCN8A -ABE significantly increased survival of mice expressing R1872W and either significantly reduced or completely inhibited seizure occurrence. Assessment of editing efficiencies revealed approximately 30% conversion of the mutant tryptophan to wildtype arginine observable in RNA transcripts from hippocampal and cortex tissue. Electrophysiological recordings revealed a rescue of seizure-associated neuronal hyperexcitability and a suppression of the pathogenic sodium channel behavior in treated mice. Associated comorbidities, including movement disorders and anxiety-like behaviors, were also improved in treated mice. These findings demonstrate the profound potential of base editing as a targeted and effective therapeutic approach for SCN8A DEE, addressing the underlying genetic mutation driving the disease. ### Competing Interest Statement The authors have declared no competing interest.

During disuse, mechanical unloading causes extensive bone loss, decreasing bone volume and strength. Variations in bone mass and risk of osteoporosis are influenced by genetics; however, it remains unclear how genetic variation affects the skeletal response to unloading. We previously found that genetic variation affects the musculoskeletal response to 3 weeks of immobilization in the 8 Jackson Laboratory J:DO founder strains: C57Bl/6J, A/J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ. Hindlimb unloading (HLU) is the best model for simulating local and systemic contributors of disuse and therefore may have a greater impact on bones than immobilization. We hypothesized that genetic variation would affect the response to HLU across the eight founder strains. Mice of each founder strain were placed in HLU for 3 weeks, and the femurs and tibias were analyzed. There were significant HLU and mouse strain interactions on body weight, femur trabecular BV/TV, and femur ultimate force. This indicates that unloading only caused significant catabolic effects in some mouse strains. C57BL/6 J mice were most affected by unloading while other strains were more protected. There were significant HLU and mouse strain interactions on gene expression of genes encoding bone metabolism genes in the tibia. This indicates that unloading only caused significant effects on bone metabolism genes in some mouse strains. Different mouse strains respond to HLU differently, and this can be explained by genetic differences. These results suggest the outbred J:DO mice will be a powerful model for examining the effects of genetics on the skeletal response to HLU.

A major fraction of loci identified by genome-wide association studies (GWASs) mediate alternative splicing, but mechanistic interpretation is hindered by the technical limitations of short-read RNA sequencing (RNA-seq), which cannot directly link splicing events to full-length protein isoforms. Long-read RNA-seq represents a powerful tool to characterize transcript isoforms, and recently, infer protein isoform existence. Here, we present an approach that integrates information from GWASs, splicing quantitative trait loci (sQTLs), and PacBio long-read RNA-seq in a disease-relevant model to infer the effects of sQTLs on the ultimate protein isoform products they encode. We demonstrate the utility of our approach using bone mineral density (BMD) GWAS data. We identified 1,863 sQTLs from the Genotype-Tissue Expression (GTEx) project in 732 protein-coding genes that colocalized with BMD associations (H4PP ≥ 0.75). We generated PacBio Iso-Seq data (N = ∼22 million full-length reads) on human osteoblasts, identifying 68,326 protein-coding isoforms, of which 17,375 (25%) were unannotated. By casting the sQTLs onto protein isoforms, we connected 809 sQTLs to 2,029 protein isoforms from 441 genes expressed in osteoblasts. Overall, we found that 74 sQTLs influenced isoforms likely impacted by nonsense-mediated decay and 190 that potentially resulted in the expression of unannotated protein isoforms. Finally, we functionally validated colocalizing sQTLs in TPM2, in which siRNA-mediated knockdown in osteoblasts showed two TPM2 isoforms with opposing effects on mineralization but exhibited no effect upon knockdown of the entire gene. Our approach should be to generalize across diverse clinical traits and to provide insights into protein isoform activities modulated by GWAS loci.

Introduction: Despite higher selectivity of the second-generation Bruton tyrosine kinase inhibitor (BTKi) acalabrutinib compared with the first-generation BTKi ibrutinib, 15%-23% of patients treated with acalabrutinib discontinued treatment due to adverse events (AEs) in clinical trials. The next-generation BTKi zanubrutinib was designed to maximize efficacy with increased potency as well as bioavailability and tolerability by minimizing off-target binding. Previous results from this ongoing phase 2 study (BGB-3111-215; NCT04116437) showed that zanubrutinib was well tolerated in patients intolerant of ibrutinib and/or acalabrutinib. Here, we report the updated results of the tolerability and efficacy of zanubrutinib in patients intolerant of acalabrutinib (cohort 2). Methods: Eligible patients with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), Waldenström macroglobulinemia (WM), mantle cell lymphoma (MCL), or marginal zone lymphoma (MZL) who met protocol-defined criteria for intolerance of acalabrutinib received zanubrutinib 160 mg twice daily or 320 mg once daily. Patients whose disease progressed with prior BTKi therapy were excluded. Safety and efficacy, including recurrence of acalabrutinib-intolerance events, were evaluated by investigators. Results: As of May 1, 2024, 35 patients intolerant of prior acalabrutinib received zanubrutinib (CLL/SLL, n=27; WM, n=4; MCL, n=2; MZL, n=2). Median age was 71 y (range, 51-87 y); median zanubrutinib treatment duration was 14.8 mo (range, 0.1-43.8 mo), with median follow-up of 18.9 mo (range, 0.1-43.8 mo). Median number of prior therapies was 2 (range, 1-6); 14 patients (40%) also received prior ibrutinib. Median cumulative exposure to acalabrutinib was 5.7 mo (range, 0.2-68.6 mo). Eleven patients discontinued zanubrutinib (AE, n=5; physician decision, n=3; progressive disease, n=2; withdrawal, n=1), and 24 patients remained on treatment. A total of 48 acalabrutinib-intolerance events were reported in 35 patients, most commonly arthralgia (n=7 events); myalgia (n=6); headache (n=5); rash (n=4); and diarrhea, fatigue, and hemorrhage (n=3 each). Thirty-three acalabrutinib-intolerance events (69%) did not recur with zanubrutinib, corresponding to 23 patients (66%) not experiencing any recurrence of acalabrutinib-intolerance events. Fifteen events (31%) recurred (8 at a lower grade, 7 at the same grade, 0 at a higher grade), and 3 patients discontinued due to recurrence (myalgia, rash, and diarrhea; all recurred at the same grade). Of 4 patients who experienced the same intolerance event with prior ibrutinib and acalabrutinib, 2 patients (one experiencing atrial fibrillation and the other hemorrhage) did not have a recurrence of these events with zanubrutinib, and 2 patients (one experiencing diarrhea of grade 3 with ibrutinib and grade 2 with acalabrutinib and the other experiencing pain in extremity of grade 2 with both ibrutinib and acalabrutinib) had a recurrence with zanubrutinib at a lower grade (all grade 1). In the 32 efficacy-evaluable patients, the disease control rate was 93.8%: 13 patients (40.6%) had a best response of stable disease and 17 patients (53.1%) had better response. Conclusions: Patients with prior intolerance to acalabrutinib are able to safely and effectively switch to treatment with zanubrutinib based on our data. Despite longer median drug exposure duration on zanubrutinib than prior acalabrutinib (14.8 vs 5.7 mo, respectively), the majority of patients (66%) did not experience any recurrence of prior acalabrutinib-intolerance events. Treatment switch to zanubrutinib maintained or improved efficacy in 94% of efficacy-evaluable patients treated with zanubrutinib. These results suggest that switching to zanubrutinib in patients who are intolerant of acalabrutinib is an effective treatment option in such patients. Enrollment and follow-up are ongoing.

Understanding the genetic basis of cortical bone traits can allow for the discovery of novel genes or biological pathways regulating bone health. Mice are the most widely used mammalian model for skeletal biology and allow for the quantification of traits that cannot easily be evaluated in humans, such as osteocyte lacunar morphology. The goal of our study was to investigate the effect of genetic diversity on multi-scale cortical bone traits of 3 long bones in skeletally-mature mice. We measured bone morphology, mechanical properties, material properties, lacunar morphology, and mineral composition of mouse bones from 2 populations of genetic diversity. Additionally, we compared how intrabone relationships varied in the 2 populations. Our first population of genetic diversity included 72 females and 72 males from the 8 inbred founder strains used to create the Diversity Outbred (DO) population. These 8 strains together span almost 90% of the genetic diversity found in mice (Mus musculus). Our second population of genetic diversity included 25 genetically unique, outbred females and 25 males from the DO population. We show that multi-scale cortical bone traits vary significantly with genetic background; heritability values range from 21% to 99% indicating genetic control of bone traits across length scales. We show for the first time that lacunar shape and number are highly heritable. Comparing the 2 populations of genetic diversity, we show that each DO mouse does not resemble a single inbred founder, but instead the outbred mice display hybrid phenotypes with the elimination of extreme values. Additionally, intrabone relationships (eg, ultimate force vs. cortical area) were mainly conserved in our 2 populations. Overall, this work supports future use of these genetically diverse populations to discover novel genes contributing to cortical bone traits, especially at the lacunar length scale.

Gene expression is known to be affected by interactions between local genetic variation and DNA accessibility, with the latter organized into three-dimensional chromatin structures. Analyses of these interactions has previously been limited, obscuring their regulatory context, and the extent to which they occur throughout the genome. Here we undertake a genome-scale analysis of these interactions in a genetically diverse population to systematically identify global genetic-epigenetic interaction, and reveal constraints imposed by chromatin structure. We establish the extent and structure of genotype-by-epigenotype interaction using embryonic stem cells derived from Diversity Outbred mice. This mouse population segregates millions of variants from eight inbred founders, enabling precision genetic mapping with extensive genotypic and phenotypic diversity. With 176 samples profiled for genotype, gene expression, and open chromatin, we used regression modeling to infer genetic-epigenetic interactions on a genome-wide scale. Our results demonstrate that statistical interactions between genetic variants and chromatin accessibility are common throughout the genome. We found that these interactions occur within the local area of the affected gene, and that this locality corresponds to topologically associated domains (TADs). The likelihood of interaction was most strongly defined by the three-dimensional (3D) domain structure rather than linear DNA sequence. We show that stable 3D genome structure is an effective tool to guide searches for regulatory elements and, conversely, that regulatory elements in genetically diverse populations provide a means to infer 3D genome structure. We confirmed this finding with CTCF ChIP-seq that revealed strain-specific binding in the inbred founder mice. In stem cells, open chromatin participating in the most significant regression models demonstrated an enrichment for developmental genes and the TAD-forming CTCF binding complex, providing an opportunity for statistical inference of shifting TAD boundaries operating during early development. These findings provide evidence that genetic and epigenetic factors operate within the context of three-dimensional chromatin structure.

Objective: To determine whether deoxyribonucleic acid (DNA) methylation alterations exist in the first-trimester human placenta between conceptions using fertility treatments and those that do not and, if so, whether they are the result of underlying infertility or fertility treatments. We also assessed whether significant alterations led to changes in gene expression. Design: We compared DNA methylation of the first-trimester placenta from singleton pregnancies that resulted in live births from unassisted, in vitro fertilization (IVF), and non-IVF fertility treatment (NIFT) conceptions using the Infinium MethylationEPIC BeadChip array. Significant CpG sites were compared with corresponding ribonucleic acid sequencing analysis in similar cohorts to determine whether methylation alterations lead to differences in gene expression. Setting: Academic medical center. Patient(s): A total of 138 singleton pregnancies undergoing chorionic villus sampling resulting in a live birth were recruited for methylation analysis (56 unassisted, 38 NIFT, and 44 IVF conceptions). Ribonucleic acid-sequencing data consisted of 141 subjects (74 unassisted, 33 NIFT, and 34 IVF conceptions) of which 116 overlapped with the methylation cohort. Intervention(s): In vitro fertilization-conceived pregnancy or pregnancy conceived via NIFT, such as ovulation induction and intrauterine insemination. Main Outcome Measure(s): Significant methylation changes at CpG sites after adjustment for multiple comparisons. The secondary Result(s): Of the 741,145 probes analyzed in the placenta, few were significant at Bonferroni <0.05: 185 CpG sites (0.025%) significant in pregnancies conceived with the fertility treatments (NIFT thorn IVF) vs. unassisted conceptions; 28 in NIFT vs. unassisted; 195 in IVF vs. unassisted; and only 13 (0.0018%) in IVF vs. NIFT conceptions. Of all significant CpG sites combined, 10% (35) were located in genes with suggestive gene expression changes, but none were significant after adjustment for multiple comparisons (ribonucleic acid sequencing false discovery rate <0.05). None of the 13 differentially methylated probes in the IVF vs. NIFT placenta were located in genes with suggestive IVF vs. NIFT gene expression differences. Conclusion(s): Underlying infertility is the most significant contributor to the minimal differences in first-trimester placental methylation, and not the specific fertility treatment used, such as IVF. (Fertil Sterile 2023;119:301-12. (c) 2022 by American Society for Reproductive Medicine.)

ABSTRACT Genome‐wide association studies (GWASs) have advanced our understanding of the genetics of osteoporosis; however, the challenge has been converting associations to causal genes. Studies have utilized transcriptomics data to link disease‐associated variants to genes, but few population transcriptomics data sets have been generated on bone at the single‐cell level. To address this challenge, we profiled the transcriptomes of bone marrow–derived stromal cells (BMSCs) cultured under osteogenic conditions from five diversity outbred (DO) mice using single‐cell RNA‐seq (scRNA‐seq). The goal of the study was to determine if BMSCs could serve as a model to generate cell type–specific transcriptomic profiles of mesenchymal lineage cells from large populations of mice to inform genetic studies. By enriching for mesenchymal lineage cells in vitro, coupled with pooling of multiple samples and downstream genotype deconvolution, we demonstrate the scalability of this model for population‐level studies. We demonstrate that dissociation of BMSCs from a heavily mineralized matrix had little effect on viability or their transcriptomic signatures. Furthermore, we show that BMSCs cultured under osteogenic conditions are diverse and consist of cells with characteristics of mesenchymal progenitors, marrow adipogenic lineage precursors (MALPs), osteoblasts, osteocyte‐like cells, and immune cells. Importantly, all cells were similar from a transcriptomic perspective to cells isolated in vivo. We employed scRNA‐seq analytical tools to confirm the biological identity of profiled cell types. SCENIC was used to reconstruct gene regulatory networks (GRNs), and we observed that cell types show GRNs expected of osteogenic and pre‐adipogenic lineage cells. Further, CELLECT analysis showed that osteoblasts, osteocyte‐like cells, and MALPs captured a significant component of bone mineral density (BMD) heritability. Together, these data suggest that BMSCs cultured under osteogenic conditions coupled with scRNA‐seq can be used as a scalable and biologically informative model to generate cell type–specific transcriptomic profiles of mesenchymal lineage cells in large populations. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).