Caitlin Loo’s research while affiliated with University of Toronto and other places

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Publications (2)


Figure 1. Pluripotency characterization of induced pluripotent stem cells (iPSCs) from the patient with an ELN variant (ELN1). A, iPSCs stained positive for pluripotency markers OCT (octamer-binding transcription factor)-4, NANOG, and TRA-1-60. Nuclei were stained with 4′,6-diamidino-2-phenylindole (DAPI). B, Endogenous pluripotency genes were upregulated following successful reprogramming of ELN (elastin)-1 iPSCs as detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and comparable to pluripotency gene expression in human embryonic stem cells, H9. C, ELN1 iPSCs differentiated in vitro into all 3 germ layers. Immunocytochemistry showed nestin expression as an example of neuronal ectoderm, SMA (smooth muscle actin) expression for mesoderm, and AFP (α-fetoprotein) expression for endoderm. D, Normal G banding karyotype of ELN1 iPSCs. Results are shown as means and standard deviations from 3 independent replicates for each gene.
Figure 2. Abnormal smooth muscle cell (SMC) differentiation, proliferation and function in elastin insufficiency (EI) induced pluripotent stem cells (iPSC)-SMCs. A, Smooth muscle marker 22α (SM22α) staining (representative images) and (B) quantification by high content imaging revealed the percentage of SM22α positive cells was lower in all patient with Williams syndrome (WS) and in ELN (elastin) patient SMCs compared with control SMCs. C, SMC proliferation measured by cell impedance (representative graph of cell index), and (D) quantification revealed increased proliferation in all 3 WS SMCs and in ELN1 patient SMCs compared to control SMCs. ELN2 patient SMC proliferation was not different from control SMCs. E, Calcium flux in response to endothelin (representative graph from 50 cells from an individual well) and (F) quantification from all replicates of maximum peak of mean fluorescence intensity after background correction (F-F 0 ) showed lower calcium flux in response to endothelin in all patient SMCs compared with control SMCs (n=3 independent biological replicates and 3 technical replicates each for differentiation, proliferation, and calcium assays). G, Biowires generated from iPSC-SMCs from one control (CT1), one WS (WS2), and one ELN mutant patient (ELN1) showed failure of compaction of patient SMCs compared to control SMCs on day 6. H, Graph shows the change in the diameter of SMC-seeded biowires from day 1 to 6. All biowires showed some compaction by day 6, and the biowire diameter on day 6 remained significantly larger in WS2 and ELN1 patients compared to CT1 control. I, Passive tension at baseline was lower in patient SMC biowires compared with control. J, Active tension following treatment with endothelin was lower in patient SMC biowires compared to control (n=3 independent experiments). A-J, Supporting data are included in Table IIIA in the Data Supplement. *P<0.05, patient vs control, łP<0.05, day 6 vs 1.
Figure 3. ELN expression was decreased in elastin insufficiency (EI) induced pluripotent stem cells (iPSC)-smooth muscle cells (SMCs). A, ELN mRNA expression by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was 20%-46% lower in patient iPSCSMCs compared with all control SMCs. B, Parallel reaction monitoring mass spectrometry of the sum of peak area of 4 normalized elastin peptides showed lower elastin formation in all patient iPS-SMCs compared to controls (not statistically significant for ELN2). C, Quantification of 3 elastin peptides upstream of the elastin variants and one elastin peptide downstream of the elastin variants showed lower abundance of both upstream and downstream peptides in all patient cells (n=3 independent experiments). *P<0.05, patient vs control SMCs; †P<0.05, patient vs control SMCs for fourth peptide only. WS indicates Williams syndrome.
Figure 4. Phenotypic rescue by rapamycin. A, Heat map of RNA sequencing data from 5 patient induced pluripotent stem cells (iPSC)-smooth muscle cells (SMCs). Supervised hierarchical clustering showing raw fold difference in gene expression between dimethyl sulfoxide (DMSO) and corresponding rapamycintreated SMCs for genes associated with SMC differentiation, SMC proliferation, and SMC contraction (P<0.05 between rapamycin vs DMSO-treated SMCs). Positive values indicate upregulation and negative values indicate downregulation compared to untreated SMCs. B, Elastin expression measured by mass spectrometry in 3 independent experiments increased in all patient SMCs after treatment with rapamycin. C, Transmission electron microscopy of patient smooth muscle biowires treated with DMSO or rapamycin. SMC maturation was observed after rapamycin treatment with the appearance of myofilaments (arrows and insets) and an elongated cell shape. D, The length to width ratio of the SMCs was higher in rapamycin compared to DMSO-treated biowires. E, Biowires treated with rapamycin showed greater compaction compared to DMSO-treated biowires by day 6. F, Comparison of tissue width from day 1 to 6 showed that both patient biowires showed compaction by day 6, but the compaction was greater in the rapamycin-treated compared to DMSO-treated biowires (*P<0.05, DMSO vs rapamycin-treated biowires, łP<0.05, day 6 vs 1; (n=3 independent experiments). WS indicates Williams syndrome.
Figure 5. Effect of candidate drugs on smooth muscle cell (SMC) differentiation, proliferation, and calcium flux. A-C, mTOR (mammalian target of rapamycin) inhibitors. A, The percentage of smooth muscle marker 22α (SM22α) positive cells measured by high content imaging showed that dimethyl sulfoxide (DMSO)-treated elastin insufficiency (EI) patient SMCs express 50%-70% SM22α (black dots) similar to untreated patient cells (blue) in contrast to 80%-90% expressed in control SMCs (gray). Rapamycin (dark red), everolimus (orange), and temsirolimus (yellow) increased % of SM22α positive cells in all patients when compared to DMSO treatment (black). AZD0857 (brown) only increased SMC differentiation in Williams syndrome (WS) patient SMCs. B, All 4 mTOR inhibitors decreased SMC proliferation in all WS and in ELN (elastin)-1 cells. ELN2 cells were not hyperproliferative and did not show any further change in proliferation with mTOR inhibitors. C, Endothelin-induced calcium flux was increased by everolimus in WS1, WS2, ELN1, and ELN2-SMCs compared with DMSO-treated cells. Rapamycin only improved calcium flux in two patients (WS2, ELN2), temsirolimus in 3 patients (WS1, ELN1, ELN2), and AZD0857 in 1 patient (WS2). WS3 did not respond to any mTOR inhibitor. D-F, Calcium channel blockers. D, Verapamil (dark green) and diltiazem (bright green) increased % of SM22α positive cells only in 3 and 2 WS patients, respectively, but not in elastin mutation patients. E, Verapamil and diltiazem decreased SMC proliferation only in 3 and 2 WS patients, respectively, not in elastin mutation patients. Amlodipine (military green) treatment was associated with cell death (data not shown). F, Verapamil and diltiazem improved endothelin-induced calcium flux only in ELN2 patient SMCs (n=3 independent experiments, using 3 technical replicates for each experiment). A-F, Supporting data are shown in Table IIIB in the Data Supplement. *P<0.05, drug treatment vs DMSO. Downloaded from http://ahajournals.org by on March 26, 2020
Everolimus Rescues the Phenotype of Elastin Insufficiency in Patient Induced Pluripotent Stem Cell–Derived Vascular Smooth Muscle Cells
  • Article
  • Full-text available

March 2020

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320 Reads

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14 Citations

Arteriosclerosis Thrombosis and Vascular Biology

Caroline Kinnear

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Rahul Agrawal

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Caitlin Loo

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[...]

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Objective Elastin gene deletion or mutation leads to arterial stenoses due to vascular smooth muscle cell (SMC) proliferation. Human induced pluripotent stem cells–derived SMCs can model the elastin insufficiency phenotype in vitro but show only partial rescue with rapamycin. Our objective was to identify drug candidates with superior efficacy in rescuing the SMC phenotype in elastin insufficiency patients. Approach and Results SMCs generated from induced pluripotent stem cells from 5 elastin insufficiency patients with severe recurrent vascular stenoses (3 Williams syndrome and 2 elastin mutations) were phenotypically immature, hyperproliferative, poorly responsive to endothelin, and exerted reduced tension in 3-dimensional smooth muscle biowires. Elastin mRNA and protein were reduced in SMCs from patients compared to healthy control SMCs. Fourteen drug candidates were tested on patient SMCs. Of the mammalian target of rapamycin inhibitors studied, everolimus restored differentiation, rescued proliferation, and improved endothelin-induced calcium flux in all patient SMCs except 3 Williams syndrome. Of the calcium channel blockers, verapamil increased SMC differentiation and reduced proliferation in Williams syndrome patient cells but not in elastin mutation patients and had no effect on endothelin response. Combination treatment with everolimus and verapamil was not superior to everolimus alone. Other drug candidates had limited efficacy. Conclusions Everolimus caused the most consistent improvement in SMC differentiation, proliferation and in SMC function in patients with both syndromic and nonsyndromic elastin insufficiency, and offers the best candidate for drug repurposing for treatment of elastin insufficiency associated vasculopathy

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SparCon assays of iPSC-derived SHANK2 ASD neurons compare marked mutant and control neurons seeded on the consistent synaptogenic environment of a lawn of unlabeled control or mutant neurons
a, iPSCs generated from multiple control and affected individuals are differentiated into NPCs. NPCs are differentiated in separate wells for 4 weeks and then differentially fluorescently labeled control (CTRL) and mutant (MUT) cells are sparsely seeded onto a large unlabeled neuronal population (the lawn) and cocultured with astrocytes. b, Timeline of the experiment, starting with seeding of NPCs. Measurements of mutant cells are normalized to control cells in the same well. c, Sparse seeding allows simultaneous analyses of cell morphology and connectivity (total number of SYN1 puncta) of single neurons. Scale bars, 100 μm. d, To compare cell morphology, paired representative traces are shown of control and SHANK2 ASD or engineered SHANK2 KO neurons grown in the same well. e, To compare synaptic function, sEPSCs are recorded from neurons grown in the same well. Confocal images and traces shown in c and d are representative of iPSC-derived neurons imaged in experiments depicted in Fig. 2a–c. sEPSC traces shown in e are representative of patch-clamp recordings of iPSC-derived neurons described in Fig. 3.
Synapse numbers, dendrite length, and neuron complexity are enhanced in SHANK2 mutant neurons, and the length phenotype is exacerbated by treatment with IGF1 and BDNF
a, Total synapse number, normalized within-well by dividing synapse number of individual cells by the geometric mean of the synapse number of control cells in a given well. b, Total dendrite length, normalized within-well by dividing dendrite length of individual cells by the geometric mean of dendrite length of control cells in a given well. c, Sholl analysis, normalized within-well by subtracting the mean of control crossings from the number of crossings made by individual cells at a given radius. Radius step, 10 μm. d, IGF1, BDNF, and TG003 treatments increase dendrite length in R841X compared with isogenic R841X-C control cells. For a–c, SHANK2 mutant cells are compared with cocultured control cells from the same wells: SHANK2 KO (n = 40) versus CTRL (CTRL1, isogenic, n = 46), SHANK2 R841X (n = 89) versus CTRL (CTRL1, CTRL2 (paternal), CTRL3 (maternal), n = 96), and SHANK2 DEL (n = 74) versus CTRL (CTRL1, CTRL2, CTRL3, CTRL4 (paternal), n = 68). For control versus mutant lawn experiments in a–c, SHANK2 R841X cells (n = 22 for control lawn, n = 40 for mutant lawn) are compared with isogenic R841X-C cells (n = 27 for control lawn, n = 33 for mutant lawn) in the same wells. Means + s.e.m. plotted. Total number of neurons = 535 from 5 WT lines from 4 CTRL individuals, 6 SHANK2+/− lines from 2 ASD individuals,1 engineered SHANK2−/− KO line, and 1 engineered isogenic SHANK2 correction line (R841X-C). For d, SHANK2 R841X neurons (total n = 595) were compared with isogenic R841X-C neurons (total n = 651) in all treatment conditions. Total number of neurons = 1,186. See Supplementary Tables 7 and 8 for details of all treatment comparisons and relevant statistics. Means ± s.e.m. plotted; *P < 0.05, **P < 0.01, ***P < 0.005; Anderson–Darling k-samples test for a,b, and d and two-way ANOVA for c.
Excitatory synaptic function is enhanced in SHANK2 mutant neurons on control and mutant lawns
a, Representative sEPSC traces from experiments described in b and c with an averaged sEPSC trace (inset) from single control, ASD, and engineered SHANK2 KO neurons. b,c, sEPSC amplitude (b) and sEPSC frequency (c) normalized within-well by dividing measurements of individual cells by the geometric mean of control cells in the same well. SHANK2 mutants are compared with cocultured control neurons from the same wells: SHANK2 R841X (n = 60, 20 each from lines no. 2, no. 5, and no. 13) versus CTRL (n = 60, 30 each from line no. 2 of CTRL1 and line no. 39 of maternal CTRL3), SHANK2 DEL (n = 60, 20 each from lines no. 1, no. 2, and no. 4) versus CTRL (n = 60, 30 each froms line no. 3 and no. 5 of paternal CTRL4), and SHANK2 KO (n = 60 from line no. H6) versus CTRL (n = 60, 30 from line no. 2 of isogenic CTRL1 and 30 from line no. 4 of CTRL2). SHANK2 R841X+/− (n = 50) and R841X-C+/+ (n = 50) neurons on control and mutant lawns. Total number of neurons = 560 from 5 WT lines from 4 CTRL individuals, 6 SHANK2+/− lines from 2 ASD individuals, and 1 engineered SHANK2−/− KO line. Mean ± s.e.m. plotted; NS, not significant, *P < 0.05, **P < 0.01, ***P < 0.005; Anderson–Darling k-samples test. A detailed statistical summary including exact P values can be found in Supplementary Table 9.
Deeply perturbed transcriptome and defective activity-dependent dendrite extension in R841X neurons
a, Heat maps of cortical identity and synapse gene transcript levels and significant fold changes found by RNA-seq of R841X and isogenic R841X-C controls. See Supplementary Table 10 for all marker gene expression fold change values and relevant statistics. b, Number of differentially expressed genes in pie charts, and enrichment of neurodevelopment, translation, and cell cycle gene sets in R841X neurons. c, Volcano plots and examples of differentially expressed genes in gene sets related to synapse function and neuron projection development. d, Volcano plots and examples of differentially expressed genes in gene sets related to synaptic plasticity and translation. Highlighted points have absolute log2 fold change > 1.25 and Padj < 0.05. e, Starting dendrite length is greater in R841X neurons, which have impaired acute KCl activity-dependent dendrite extension (SHANK2 R841X n = 47 from lines no. 2, no. 5, and no. 13) versus CTRL (n = 44 from CTRL1 line no. 2 and CTRL3 line no. 39), and rescue of R841X dendrite length by chronic DHPG treatment (R841X-C DMSO n = 141, R841X-C + DHPG n = 65, R841X DMSO n = 120, R841X + DHPG n = 76). Mean ± s.e.m. plotted; *P < 0.05; Anderson–Darling k-samples test. f, Enrichment of M16 and M17 ASD gene modules in 9-week and the M3 ASD module in 4-week R841X neurons. For a–d and f, n = 4 independent differentiations for both genotypes at each timepoint. *Padj < 0.05, **Padj < 0.01, ***Padj < 0.005; Wald test with Benjamini–Hochberg correction for multiple testing.
SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons

April 2019

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902 Reads

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135 Citations

Nature Neuroscience

Heterozygous loss-of-function mutations in SHANK2 are associated with autism spectrum disorder (ASD). We generated cortical neurons from induced pluripotent stem cells derived from neurotypic and ASD-affected donors. We developed sparse coculture for connectivity assays where SHANK2 and control neurons were differentially labeled and sparsely seeded together on a lawn of unlabeled control neurons. We observed increases in dendrite length, dendrite complexity, synapse number, and frequency of spontaneous excitatory postsynaptic currents. These findings were phenocopied in gene-edited homozygous SHANK2 knockout cells and rescued by gene correction of an ASD SHANK2 mutation. Dendrite length increases were exacerbated by IGF1, TG003, or BDNF, and suppressed by DHPG treatment. The transcriptome in isogenic SHANK2 neurons was perturbed in synapse, plasticity, and neuronal morphogenesis gene sets and ASD gene modules, and activity-dependent dendrite extension was impaired. Our findings provide evidence for hyperconnectivity and altered transcriptome in SHANK2 neurons derived from ASD subjects. Using a novel assay, Ellis et al. show that stem cell-derived neurons from individuals with autism carrying SHANK2 mutations are hyperconnected, have impaired activity-dependent dendrite extension, and have perturbed transcription of ASD gene modules.

Citations (2)


... For example, the mTOR inhibitor everolimus improves in vitro smooth muscle cell differentiation of stem cells derived from individuals with elastin insufficiency because of ELN mutations. 66 Our results suggest that targeting DD with everolimus is a compelling topic of future research. ...

Reference:

Genome-wide association meta-analysis identifies 126 novel loci for diverticular disease and implicates connective tissue and colonic motility
Everolimus Rescues the Phenotype of Elastin Insufficiency in Patient Induced Pluripotent Stem Cell–Derived Vascular Smooth Muscle Cells

Arteriosclerosis Thrombosis and Vascular Biology

... SHANK2 encodes a synaptic scaffolding protein critical for glutamatergic synapse formation and function. Increased SHANK2 mutation rates highlight the role of synaptic genes in ASD pathology [46], with disruptions potentially leading to synaptic dysfunction, affecting learning, memory, and social behavior-core features of ASD. ...

SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons

Nature Neuroscience