Hanwen Zhang

Most causal variants for neuropsychiatric disorders (NPD) remain unknown. A major hurdle is that disease variants may act in specific contexts, such as during neuronal activation, which is difficult to study in vivo at the population level. We profiled single-nucleus neuron-activation multiomics in human induced pluripotent stem cell–derived neurons from 100 donors, revealing the NPD-relevant transcriptomic and epigenomic landscape of neuronal activation. We identified abundant genetic variants associated with activity-dependent gene expression and chromatin accessibility, the latter explaining larger proportions of NPD heritability. Integrating multiomics data with genome-wide association studies further revealed NPD risk variants and genes with effects detected only upon stimulation, such as activity-dependent cholesterol metabolism. Our work highlights the power of cell stimulation to reveal context-specific “hidden” genetic effects.

On the Greenland Ice Sheet, drainage of supraglacial lakes via hydrofracture can transport substantial volumes of meltwater into the subglacial drainage system within hours, generating subglacial “blisters” that transiently accelerate adjacent ice flow. The blisters subsequently dissipate, with their thickness diminishing as water spreads laterally, propagates, and leaks into adjacent components of the subglacial drainage system. Although field observations reveal surface-elevation and velocity anomalies associated with blisters, existing subglacial hydrology models—typically comprised of linked cavities and channels—do not include the physics of elastic ice uplift, and therefore cannot reproduce the observed flood propagation or ice-flow anomalies.We present a modelling framework that integrates elastic ice uplift with an established subglacial hydrology model of linked cavities and channels to model subglacial blisters and their interactions with the surrounding hydrological network. We further couple this framework to a depth-integrated ice-flow model, and simulate the resulting, transient surface-uplift and velocity anomalies following lake drainages. This unified model provides a new tool for interpreting remote-sensing and in situ observations of drainage events on short timescales, and for assessing how lake-drainage processes influence ice dynamics and the long-term mass balance of the Greenland Ice Sheet.

SUMMARY: Human induced pluripotent stem cells (hiPSC) and iPSC-differentiated neural cells, in combination with CRISPR editing, are commonly used for studying neurodevelopmental and other brain disorders. Female iPSCs undergo random X-chromosome inactivation (XCI) via epigenetic silencing by noncoding X inactive specific transcript ( XIST ). It is known that female iPSCs may lose XIST expression, leading to XCI erosion that affects both X-linked and autosomal gene expression. However, the effects of CRSIPR editing and neural differentiation on XCI erosion in iPSC-derived neurons and how this may confound a real-world transcriptomic analysis of differentially expressed genes (DEGs) are poorly understood. Here, leveraging bulk RNA-seq of hundreds of CRISPR-edited female iPSC lines from four donor lines for 66 genes and single-cell RNA-seq of iPSC-derived neurons of a subset of 42 edited genes, we investigated the effects of XCI erosion during CRISPR editing and in iPSC-derived neurons. We found that XCI erosion was variable in CRISPR-edited female iPSCs and largely preserved in iPSC-derived neurons. Like in iPSCs, XIST in neurons predominately influenced the expression of X-linked genes; however, its effect on autosomal genes was more pronounced in single neurons. Mechanistically, XIST epigenetically causes allelic imbalance of both X-linked and autosomal genes, with the former showing stronger allele-specific expression (ASE) bias. Notably, XIST- induced ASE bias exhibited a conserved positional pattern at loci affecting neurodevelopmental genes across different female lines and cell types. Finally, we demonstrated a confounding effect of XCI erosion on DEG analyses in iPSC-derived neurons. These results have significant implications in hiPSC modeling of neurodevelopmental and other brain disorders.

Schizophrenia (SCZ) is a complex neuropsychiatric disorder associated with both common risk variants of small effect sizes and rare risk variants of high penetrance. Rare premature open reading frame (ORF) termination variants in SETD1A (SET Domain Containing 1A) show a strong association with SCZ; however, it remains largely unclear how rare premature ORF termination variants in SETD1A contribute to the pathophysiology of SCZ. To understand the impact of SETD1A rare premature ORF termination variants in human neurons, we CRISPR/Cas9-engineered five isogenic pairs of human induced pluripotent stem cells (iPSCs), with a recurrent heterozygous patient-specific premature ORF termination mutation c.4582-2delAG in two donor lines and a heterozygous frameshift mutation c.4596_4597insG (p. Leu1533fs) in three donor lines. These two mutations are predicted to cause a premature stop codon in exon 16 of SETD1A , leading to SETD1A haploinsufficiency. We found that these presumably loss-of-function (LoF) mutations caused the SETD1A mRNAs to be degraded by nonsense-mediated decay (NMD), accompanied by a reduction of full-length SETD1A protein level in iPSCs. We then characterized the morphological, electrophysiological, and transcriptomic impacts of SETD1A ^+/− LoF mutations in iPSC-derived human excitatory neurons induced by NGN2. We found that the SETD1A ^+/− exon-16 LoF mutations altered dendrite complexity, dysregulated synaptic transmission, and synaptic plasticity, likely by dysregulating genes involved in synaptic function. These results provide mechanistic insights into how SETD1A ^+/− exon-16 patient-specific LoF mutations affect neuron phenotypes that may be relevant to the pathophysiology of SCZ.

Despite genome-wide association studies (GWAS) of late-onset Alzheimer’s disease (LOAD) having identified many genetic risk loci^1,2,3, the underlying disease mechanisms remain largely unclear. Determining causal disease variants and their LOAD-relevant cellular phenotypes has been a challenge. Here, using our approach for identifying functional GWAS risk variants showing allele-specific open chromatin, we systematically identified putative causal LOAD-risk variants in human induced pluripotent stem (iPS)-cell-derived neurons, astrocytes and microglia, and linked a PICALM LOAD-risk allele to a microglial-specific role of PICALM in lipid droplet (LD) accumulation. Allele-specific open-chromatin mapping revealed functional risk variants for 26 LOAD-risk loci, mostly specific to microglia. At the microglial-specific PICALM locus, the LOAD-risk allele of the single-nucleotide polymorphism rs10792832 reduced transcription factor (PU.1) binding and PICALM expression, impairing the uptake of amyloid beta (Aβ) and myelin debris. Notably, microglia carrying the PICALM risk allele showed transcriptional enrichment of pathways for cholesterol synthesis and LD formation. Genetic and pharmacological perturbations of microglia further established a causal link between reduced PICALM expression, LD accumulation and phagocytosis deficits. Our work elucidates the selective LOAD vulnerability in microglia at the PICALM locus through detrimental LD accumulation, providing a neurobiological basis that can be exploited for developing clinical interventions.

Drainage of supraglacial lakes to the ice-sheet bed can occur when a hydrofracture propagates downward, driven by the weight of the water in the lake. For supraglacial lakes in the grounding zones of Antarctic glaciers, drainage mechanics are complicated by the glaciers' proximity to the grounding line. Recently, a series of supraglacial lake drainage events through hydrofractures were observed in the Amery Ice Shelf grounding zone, East Antarctica. The lake depth at drainage varied considerably between events, raising questions about the mechanisms that induce hydrofractures even at low lake depth. Here, we use a modelling approach to investigate the contribution of tidally driven flexure to hydrofracture propagation in the grounding zone. We model the viscoelastic response of a laterally unconfined marine ice sheet to tides, the tidally induced stress, and the contribution of this stress to hydrofracture propagation. A sensitivity analysis is used to explore the dependence of viscoelastic grounding-line dynamics on the material properties of ice and local bedrock bathymetry. We propose a model-based criterion that predicts hydrofracture and supraglacial lake drainage as a function of daily maximum tidal amplitude and pre-drainage lake depth in laterally unconfined grounding zones. Although lateral confinement may contribute to the dynamics of lake drainage at Amery, our model predictions are consistent with observations of hydrofracture events from this grounding zone.

Despite hundreds of genetic risk loci identified for neuropsychiatric disorders (NPD), most causal variants/genes remain unknown. A major hurdle is that disease risk variants may act in specific biological contexts, e.g., during neuronal activation, which is difficult to study in vivo at the population level. Here, we conducted a single-cell multiomics study of neuronal activation (stimulation) in human iPSC-induced excitatory and inhibitory neurons from 100 donors, and uncovered abundant neuronal stimulation-specific causal variants/genes for NPD. We surveyed NPD-relevant transcriptomic and epigenomic landscape of neuronal activation and identified thousands of genetic variants associated with activity-dependent gene expression (i.e., eQTL) and chromatin accessibility (i.e., caQTL). These caQTL explained considerably larger proportions of NPD heritability than the eQTL. Integrating the multiomic data with GWAS further revealed NPD risk variants/genes whose effects were only detected upon stimulation. Interestingly, multiple lines of evidence support a role of activity-dependent cholesterol metabolism in NPD. Our work highlights the power of cell stimulation to reveal context-dependent “hidden” genetic effects.

Drainage of supraglacial lakes to the ice-sheet bed can occur when a hydrofracture propagates downward, driven by the weight of the water in the lake. For supraglacial lakes in the grounding zones of Antarctic glaciers, the mechanics of drainage is complicated by their proximity to the grounding line. Recently, a series of supraglacial lake-drainage events through hydrofractures was observed in the Amery Ice Shelf grounding zone, East Antarctica. The lake depth at drainage varied considerably between events, raising questions about the mechanisms that induce hydrofracture, even at low lake depths. Here we use a modelling approach to investigate the contribution of tidally driven flexure to hydrofracture propagation. We model the viscoelastic response of a marine ice sheet to tides, the stresses that are induced, and the contribution of tidal stresses to hydrofracture propagation. Our results show that ocean tides and lake-water pressure together control supraglacial lake drainage through hydrofractures in the grounding zone. We give a model-based criterion that predicts supraglacial lake drainage as a function of daily maximum tidal amplitude and lake depth. Our model-based criterion agrees with remotely sensed data, indicating the importance of tidal flexure to processes associated with hydrofracturing such as supraglacial lake drainage, rifting and calving.

Drainage of supraglacial lakes to the ice-sheet bed can occur when a hydrofracture propagates downward, driven by the weight of the water in the lake. For supraglacial lakes in the grounding zones of Antarctic glaciers, the mechanics of drainage is complicated by their proximity to the grounding line. Recently, a series of supraglacial lake-drainage events through hydrofractures was observed in the Amery Ice Shelf grounding zone, East Antarctica. The lake depth at drainage varied considerably between events, raising questions about the mechanisms that induce hydrofracture, even at low lake depths. Here we use a modelling approach to investigate the contribution of tidally driven flexure to hydrofracture propagation. We model the viscoelastic response of a marine ice sheet to tides, the stresses that are induced, and the contribution of tidal stresses to hydrofracture propagation. Our results show that ocean tides and lake-water pressure together control supraglacial lake drainage through hydrofractures in the grounding zone. We give a model-based criterion that predicts supraglacial lake drainage as a function of daily maximum tidal amplitude and lake depth. Our model-based criterion agrees with remotely sensed data, indicating the importance of tidal flexure to processes associated with hydrofracturing such as supraglacial lake drainage, rifting and calving.

Drainage of supraglacial lakes to the ice-sheet bed can occur when a hydrofracture propagates downward, driven by the weight of the water in the lake. For supraglacial lakes in the grounding zones of Antarctic glaciers, the mechanics of drainage is complicated by their proximity to the grounding line. Recently, a series of supraglacial lake-drainage events through hydrofractures was observed in the Amery Ice Shelf grounding zone, East Antarctica. The lake depth at drainage varied considerably between events, raising questions about the mechanisms that induce hydrofracture, even at low lake depths. Here we use a modelling approach to investigate the contribution of tidally driven flexure to hydrofracture propagation. We model the viscoelastic response of a marine ice sheet to tides, the stresses that are induced, and the contribution of tidal stresses to hydrofracture propagation. Our results show that ocean tides and lake-water pressure together control supraglacial lake drainage through hydrofractures in the grounding zone. We give a model-based criterion that predicts supraglacial lake drainage as a function of daily maximum tidal amplitude and lake depth. Our model-based criterion agrees with remotely sensed data, indicating the importance of tidal flexure to processes associated with hydrofracturing such as supraglacial lake drainage, rifting and calving.