Biology subjects

Naqvi, S.

Publications and source records attributed to Naqvi, S..

16 recordsLinked to original sources

bioRxiv2026

dubTAGs enable on-demand stabilization for tunable and reversible control of endogenous protein levels

Precise and rapid control over cellular protein levels is essential to dissect complex biological systems. Chemical genetic approaches such as dTAG, in which a target is fused to a degron tag (FKBP12F36V) and degraded upon small molecule-mediated recruitment of E3 ligases, have enabled rapid and tunable control over protein abundance. However, no analogous tool exists to precisely increase protein levels and actively reverse dTAG-mediated degradation. Here, we developed heterobifunctional small molecules (dubTAGs) that stabilize FKBP12F36V-tagged proteins by recruiting endogenous deubiquitinases. Utilizing stem cell-derived cranial neural crest cells (CNCCs) in which the transcription factors SOX9 or TWIST1 are endogenously tagged with FKBP12F36V, we identified OTUB1- or USP7-recruiting heterobifunctional molecules that demonstrated effective target stabilization and ternary complex formation. We demonstrate that dubTAG-mediated protein stabilization is dependent on deubiquitinase recruitment, target-specific, and can tunably and rapidly reverse dTAG-mediated degradation. We applied dubTAGs to assess how stabilizing endogenous SOX9 impacts chromatin accessibility in CNCCs, finding both monotonic and non-monotonic regulatory element responses that are driven by distinct sequence features. dubTAGs are readily applicable tools for investigating the effects of elevated protein levels and tunably reversing targeted degradation, enabling new approaches to study protein dosage effects in development, disease, and therapeutic discovery.

molecular biology↗

bioRxiv2025

The craniofacial shape of modern humans embodies genomic signatures of evolution, diversity, and clinical conditions

Human craniofacial morphology is a hallmark of our species diversity and evolutionary history, shaped by adaptation, introgression, and global dispersal. Cranial globularization and chin emergence are well-documented morphological transformations whose genetic basis remains poorly understood, whereas Neandertal introgression is primarily documented through genomic evidence. How these evolutionary phenomena relate to craniofacial variation in present-day humans remains largely unresolved. Here, we leverage 3D craniofacial data from over 50,000 UK Biobank participants and employ a multivariate, multiscale genome-wide association approach to define axes of variation aligned with inter-population allele frequency shifts, evolutionary processes, and clinical conditions. We identify continuous craniofacial trends within our cohort that mirror global patterns of genetic diversity, indicating that facial differences between human populations arise at the phenotypic axes already present within a single population. We further demonstrate that modern human-derived alleles underlie the origins of the human chin by reducing midfacial projection relative to other hominins and reveal the persistent effects of Neandertal introgression on craniofacial diversity today. We also model genetically informed endophenotypes for orofacial clefts, obstructive sleep apnoea, and myopia. These findings provide insights into our species evolutionary history and endophenotypes of clinical conditions and establish a framework for contextualizing craniofacial diversity into biologically meaningful axes of variation relevant to diverse scientific disciplines.

genetics↗

bioRxiv2025

High-dose oral pyrophosphate inhibits connective tissue calcification in Abcc6 null mice but affects bone structure

Pseudoxanthoma elasticum is a rare inherited disorder marked by abnormal calcium phosphate deposition in soft connective tissues, particularly the skin, arteries, and eyes. It is caused by inactivating mutations in the ABCC6 gene, which encodes a hepatic efflux transporter. Loss of ABCC6 function leads to reduced plasma levels of pyrophosphate, a key inhibitor of calcification, thereby promoting ectopic mineralization. Oral pyrophosphate therapy has emerged as a potential treatment, but its effectiveness is uncertain. Most ingested pyrophosphate is hydrolyzed in the gut to inorganic phosphate, which may worsen calcification. Moreover, its impact on mineralized tissues remains largely unexplored. Abcc6-/- mice closely mimic human pseudoxanthoma elasticum and are widely used in preclinical studies. Although patients are most concerned about ocular complications, eye calcification is rarely assessed in translational studies using Abcc6-/- mice. Using microcomputed tomography we found that ectopic calcification at the ciliary margin is a reliable marker of ocular disease progression in these mice. Administering pyrophosphate in drinking water at concentrations up to 90 mM did not increase calcification in skin or eyes. However, only very high doses effectively prevented ectopic calcification - doses that would equate to an impractical 2.5 g/kg/day of disodium pyrophosphate in humans. These high doses also led to pyrophosphate accumulation in bone and negatively affected bone structure and strength. In summary, only supraphysiological doses of orally administered pyrophosphate inhibited ectopic calcification in Abcc6-/- mice, but these doses are not feasible for human use and may compromise bone function. These data are especially important considering the currently ongoing clinical trial evaluating the safety and efficacy of oral pyrophosphate administration as a treatment for pseudoxanthoma elasticum. LAY SUMMARYPseudoxanthoma elasticum (PXE) is a rare inherited mineralization disorder caused by the absence of functional ABCC6, a liver-expressed protein. This deficiency leads to reduced plasma levels of pyrophosphate, a key inhibitor of mineralization, resulting in abnormal calcium phosphate deposition in the skin, eyes, and blood vessels. Oral pyrophosphate has been proposed as a therapeutic strategy for PXE, and a clinical trial evaluating its efficacy recently began in France. In a PXE mouse model, we show that only very high oral doses of pyrophosphate are effective, but these doses impair bone quality and are not suitable for human use.

pathology↗

bioRxiv2024

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

Deep learning approaches have made significant advances in predicting cell type-specific chromatin patterns from the identity and arrangement of transcription factor (TF) binding motifs. However, most models have been applied in unperturbed contexts, precluding a predictive understanding of how chromatin state responds to TF perturbation. Here, we used transfer learning to train and interpret deep learning models that use DNA sequence to predict, with accuracy approaching experimental reproducibility, how the concentration of two dosage-sensitive TFs (TWIST1, SOX9) affects regulatory element (RE) chromatin accessibility in facial progenitor cells. High-affinity motifs that allow for heterotypic TF co-binding and are concentrated at the center of REs buffer against quantitative changes in TF dosage and strongly predict unperturbed accessibility. In contrast, motifs with low-affinity or homotypic binding distributed throughout REs lead to sensitive responses with minimal contributions to unperturbed accessibility. Both buffering and sensitizing features show signatures of purifying selection. We validated these predictive sequence features using reporter assays and showed that a biophysical model of TF-nucleosome competition can explain the sensitizing effect of low-affinity motifs. Our approach of combining transfer learning and quantitative measurements of the chromatin response to TF dosage therefore represents a powerful method to reveal additional layers of the cis-regulatory code.

genomics↗

bioRxiv2023

DNA-guided transcription factor cooperativity shapes face and limb mesenchyme

Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how Coordinator, a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.

genomics↗

bioRxiv2022

Joint Multi-Ancestry and Admixed GWAS Reveals the Complex Genetics behind Human Cranial Vault Shape

The cranial vault - the portion of the skull surrounding the brain and cerebellum - is highly variable, clinically relevant, and heritable, yet its genetic architecture remains poorly understood. Here, we conducted a joint multi-ancestry and admixed multivariate GWAS on 3D cranial vault shape extracted from magnetic resonance images of 6,772 children from the ABCD study cohort, identifying 30 genome-wide significant genetic loci and replicating 20 of these signals in 16,947 additional individuals of the UK Biobank. This joint multi-ancestry GWAS was enriched for genetic components of cranial vault shape shared across ancestral groups and yielded a greater discovery than a European-only GWAS. We present supporting evidence for parietal versus frontal bone localization for several of the identified genes based on expression patterns in E15.5 mice. Collectively, our GWAS loci were enriched for processes related to skeletal development and showed elevated activity in cranial neural crest cells, suggesting a role during early craniofacial development. Among the identified genes, were RUNX2 and several of its upstream and downstream actors, highlighting the prominent role of intramembranous ossification - which takes place at the cranial sutures - in influencing cranial vault shape. We found that mutations in many genes associated with craniosynostosis exert their pathogenicity by modulating the same pathways involved in normal cranial vault development. This was further demonstrated in a non-syndromic sagittal craniosynostosis case-parent trio dataset of 63 probands (n = 189), where our GWAS signals near BMP2, BBS9, and ZIC2 contributed significantly to disease risk. Moreover, we found strong evidence of overlap with genes influencing the morphology of the face and the brain, suggesting a common genetic architecture connecting these developmentally adjacent structures. Overall, our study provides a comprehensive overview of the genetics underlying normal cranial vault shape and its relevance for understanding modern human craniofacial diversity and the etiology of congenital malformations.

genetics↗

bioRxiv2022

Precise modulation of transcription factor levels reveals drivers of dosage sensitivity

Transcriptional regulation displays extensive robustness, but human genetics indicate sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, which are lacking to date. TFs play central roles in both normal-range and disease-associated variation in facial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitors and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin Sequence, PRS). We found that most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses predict gene expression responses. Sensitive REs and genes underlie the vulnerability of chondrogenesis and PRS-like craniofacial shape variation to SOX9 dosage perturbation. We propose that such REs and genes drive the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.

genetics↗

bioRxiv2022

Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery

Most signals in genome-wide association studies (GWAS) of complex traits point to noncoding genetic variants with putative gene regulatory effects. However, currently identified expression quantitative trait loci (eQTLs) explain only a small fraction of GWAS signals. By analyzing GWAS hits for complex traits in the UK Biobank, and cis-eQTLs from the GTEx consortium, we show that these assays systematically discover different types of genes and variants: eQTLs cluster strongly near transcription start sites, while GWAS hits do not. Genes near GWAS hits are enriched in numerous functional annotations, are under strong selective constraint and have a complex regulatory landscape across different tissue/cell types, while genes near eQTLs are depleted of most functional annotations, show relaxed constraint, and have simpler regulatory landscapes. We describe a model to understand these observations, including how natural selection on complex traits hinders discovery of functionally-relevant eQTLs. Our results imply that GWAS and eQTL studies are systematically biased toward different types of variants, and support the use of complementary functional approaches alongside the next generation of eQTL studies.

genomics↗

bioRxiv2021

A genome-wide genetic screen uncovers novel determinants of human pigmentation

The skin color is one of the most diverse human traits and is determined by the quantity, type and distribution of melanin. Here, we leverage light scattering properties of melanin to conduct a genome-wide CRISPR-Cas9 screen for novel regulators of melanogenesis. We identify functionally diverse genes converging on melanosome biogenesis, endosomal transport and transcriptional/posttranscriptional gene regulation, most of which represent novel associations with pigmentation. A survey of transcriptomes from diversely pigmented individuals reveals that the majority of genes discovered in our screen are upregulated in dark skin melanocytes, in agreement with their melanin-promoting function and potential contribution to skin color variation. This association is further buttressed by the significant skin color heritability enrichment in the vicinity of these genes. Taken together, our study presents a novel approach to assay pigmentation and uncovers a plethora of melanogenesis regulators, with broad implications for human variation, cell biology and medicine. One Sentence SummaryGenetic screen uncovers genes involved in human melanogenesis, many of which are differentially expressed in individuals of diverse skin color.

cell biology↗

bioRxiv2021

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map connections between regulatory genes and their downstream targets. However, we lack comprehensive knowledge of the upstream regulators of most genes. Here we developed an approach for systematic discovery of upstream regulators of critical immune factors - IL2RA, IL-2, and CTLA4 - in primary human T cells. Then, we mapped the network of these regulators target genes and enhancers using CRISPR perturbations, RNA-Seq, and ATAC-Seq. These regulators form densely interconnected networks with extensive feedback loops. Furthermore, this network is highly enriched for immune-associated disease variants and genes. These results provide insight into how immune-associated disease genes are regulated in T cells and broader principles about the structure of human gene regulatory networks. HighlightsO_LIA systematic approach to identify upstream regulators of key immune genes in primary human cells C_LIO_LIComprehensive RNA-Seq and ATAC-Seq perturbation maps after KO of individual discovered regulators C_LIO_LIAnalysis uncovers a highly interconnected regulatory network of enhancers and genes in T cells C_LIO_LIThis network is highly enriched for immune disease variants and genes shedding light on the trans-regulatory connections among key immune genes in health and disease C_LI

genomics↗

bioRxiv2020

Shared heritability of face and brain shape distinct from cognitive traits

Evidence from both model organisms and clinical genetics suggests close coordination between the developing brain and face1-8, but it remains unknown whether this developmental link extends to genetic variation that drives normal-range diversity of face and brain shape. Here, we performed a multivariate genome-wide association study of cortical surface morphology in 19,644 European-ancestry individuals and identified 472 genomic loci influencing brain shape at multiple levels. We discovered a substantial overlap of these brain shape association signals with those linked to facial shape variation, with 76 common to both. These shared loci include transcription factors with cell-intrinsic roles in craniofacial development, as well as members of signaling pathways involved in brain-face crosstalk. Brain shape heritability is equivalently enriched near regulatory regions active in either brain organoids or in facial progenitor cells. However, brain shape association signals shared with face shape are distinct from those shared with behavioral-cognitive traits or neuropsychiatric disorder risk. Together, we uncover common genetic variants and candidate molecular players underlying brain-face interactions. We propose that early in embryogenesis, the face and the brain mutually shape each other through a combination of structural effects and paracrine signaling, but this interplay may have little impact on later brain development associated with cognitive function.

genetics↗

bioRxiv2020

IL-23 production is regulated via an MSK1/2 - CREB dependent signaling pathway downstream of Toll like receptors.

IL-23 is an IL-12 family cytokine that is important in promoting Th17 responses and has been strongly linked to autoimmunity and psoriasis. It is a heterodimeric cytokine made up of a p19 subunit unique to IL-23 and a p40 subunit that is shared with IL-12. We show here that in response to LPS, the induction of IL-23p19 mRNA is regulated by a MSK1/2 - CREB dependent pathway downstream of ERK1/2 and p38 MAPK. Knockout of MSK1/2 resulted in a decrease in both IL-23p19 mRNA transcription and IL-23 secretion in GM-CSF differentiated bone marrow cells. Similar effects were seen when the MSK1/2 phosphorylation site in CREB was mutated to alanine. Stimulation with PGE2 promotes the nuclear localisation of CRTC3, a co-activator for CREB. In combination with LPS, PGE2 promoted IL-23p19 mRNA transcription and this was blocked by knockdown of CRTC3. Imiquimod induced skin inflammation in mice has been used as a model for psoriasis and is dependent on IL-23. While MSK1/2 knockout reduced the induction of IL-23 in vivo following i.p. injection of LPS, the knockout mice were not protected from Imiquimod induced skin inflammation. MSK1/2 knockout did not reduce the induction of IL-17 producing {gamma}{delta}T cells following Imiquimod treatment, although MSK1/2 knockout did reduce the levels of these cells in mice receiving a control cream. The lack of protection in the Imiquimod model may be due to the known anti-inflammatory roles or MSKs, such as its contribution to the induction of IL-10.

immunology↗

bioRxiv2020

Insights into the genetic architecture of the human face

The human face is complex and multipartite, and characterization of its genetic architecture remains intriguingly challenging. Applying GWAS to multivariate shape phenotypes, we identified 203 genomic regions associated with normal-range facial variation, 117 of which are novel. The associated regions are enriched for both genes relevant to craniofacial and limb morphogenesis and enhancer activity in cranial neural crest cells and craniofacial tissues. Genetic variants grouped by their contribution to similar aspects of facial variation show high within-group correlation of enhancer activity, and four SNP pairs display evidence of epistasis, indicating potentially coordinated actions of variants within the same cell types or tissues. In sum, our analyses provide new insights for understanding how complex morphological traits are shaped by both individual and coordinated genetic actions.

genetics↗

bioRxiv2020

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background

Genome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety of complex diseases and other traits. We describe UK Biobank GWAS results for three molecular traits--urate, IGF-1, and testosterone--with better-understood biology than most other complex traits. We find that many of the most significant hits are readily and surprisingly interpretable. We observe huge enrichment of associations near genes involved in the relevant biosynthesis, transport, or signaling pathways. We show how GWAS data illuminate the biology of each trait, including differences in testosterone regulation between females and males. At the same time, even these molecular traits are highly polygenic, with many thousands of variants spread across the genome contributing to trait variance. In summary, for these three molecular traits we identify strong enrichment of signal in putative core gene sets, even while most of the SNP-based heritability is driven by a massively polygenic background.

genetics↗

bioRxiv2017

Preexisting heterogeneities in gene dosage sensitivity shaped sex chromosome evolution in mammals and birds

Mammalian X and Y chromosomes evolved from an ordinary autosomal pair; genetic decay decimated the Y, which in turn necessitated X chromosome inactivation (XCI). Genes of the ancestral autosomes are often assumed to have undertaken these transitions on uniform terms, but we hypothesized that they varied in their dosage constraints. We inferred such constraints from conservation of microRNA (miRNA)-mediated repression, validated by analysis of experimental data. X-linked genes with a surviving Y homolog have the most conserved miRNA target sites, followed by genes with no Y homolog and subject to XCI, and then genes with no Y homolog but escaping XCI; this heterogeneity existed on the ancestral autosomes. Similar results for avian Z-linked genes, with or without a W homolog, lead to a model of XY/ZW evolution incorporating preexisting dosage sensitivities of individual genes in determining their evolutionary fates, and ultimately shaping the mammalian and avian sex chromosomes.

genetics↗

bioRxiv2017

Preexisting heterogeneities in gene dosage sensitivity shaped sex chromosome evolution in mammals and birds

Mammalian X and Y chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals. Preexisting heterogeneities in dosage sensitivity, manifesting as differences in the extent of miRNA-mediated repression, predicted either the retention of a Y homolog or the acquisition of XCI following Y gene decay. Analogous heterogeneities among avian Z-linked genes predicted either the retention of a W homolog or gene-specific dosage compensation following W gene decay. Genome-wide analyses of human copy number variation indicate that these heterogeneities consisted of sensitivity to both increases and decreases in dosage. We propose a model of XY/ZW evolution incorporating such preexisting dosage sensitivities in determining the evolutionary fates of individual genes. Our findings thus provide a more complete view of the role of dosage sensitivity in shaping the mammalian and avian sex chromosomes, and reveal an important role for post-transcriptional regulatory sequences (miRNA target sites) in sex chromosome evolution.

genetics↗