Raquel E. Gur’s research while affiliated with The Children's Hospital of Philadelphia and other places

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Supplementary information: "Tbx1 haploinsufficiency leads to local skull deformity, paraflocculus and flocculus dysplasia, and motor-learning deficit in 22q11.2 deletion syndrome"
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December 2024

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Paraflocculus/flocculus dysplasia in mouse models and human subjects with 22q11DS
a Representative magnetic resonance images (MRIs) of the cerebellum containing the paraflocculus/flocculus (PF/F, arrows) in wild-type (WT) and Df(16)1/+ mice at different ages. b Representative 3D rendering of MRI data from 2-month-old WT and Df(16)1/+ cerebella. Arrows, PF/F. c Representative images of hematoxylin and eosin staining of postnatal day (P) 7 WT and Df(16)1/+ cerebella. d Average PF/F volumes measured by MRI in WT (black, P7: n = 10, P14: n = 14, P28: n = 14, 4-month [M]: n = 10, 8 M: n = 9) and Df(16)1/+ (red, P7: n = 4, P14: n = 6, P28: n = 6, 4 M: n = 11, 8 M: n = 11) mice. Two-way ANOVA (Holm–Sidak’s post hoc): F4,85 = 5.47, **p = 0.0006. e Average regional volumes of the cerebellum manually measured by MRI in 2-month-old WT (n = 3) and Df(16)1/+ (n = 4) mice. Two-way ANOVA (Holm–Sidak’s post hoc): F3,20 = 7.76: **p = 0.0013 (Crus I: p = 0.95; Crus II: p = 0.99; Vermis IV/V: p = 0.99; PF/F: t5 = 5.92, **p = 0.002). f Representative MRIs of a human cerebellum with manual tracings of the regions of interest (ROIs, red, left side; green, right side), i.e., the PF/F in sagittal (top) and axial (bottom) views. g PF/F volume in human subjects with 22q11DS (n = 80) and in typically developing (TD; n = 68) controls. Two-tailed Student’s t-test; t146 = 7.72, **p < 0.0001, 95% CI = –234-138.6. h PF/F volume as a function of the cerebellar (CB) volume in TD (n = 68) and 22q11DS (n = 80); TD: Pearson’s r = 0.50, p < 0.0001, 22q11DS: Pearson’s r = 0.31, p = 0.01). i PF/F volume after adjusting for CB volume in each group. Wald test, t145 = –3.268, **p = 0.001. j, k Probability maps from cerebellar voxel-based morphometry (VBM), projected onto both whole-brain renders (j, left), selected axial and coronal slices (j, right), and a cerebellar flatmap (k). Note that SUIT VBM excludes the cerebrum from the analysis. Data are presented as the mean ± SEM in (d, e) and as violin plots with median values in (g, i). Source data are provided as a Source Data file.
Unbiased screen for the gene(s) responsible for paraflocculus/flocculus dysplasia in 22q11DS mice
a Diagram depicting genes in the 22q11.2 syntenic region of mouse chromosome 16. Rectangles represent individual genes. Horizontal bars represent genomic regions hemizygously deleted in various mouse models of 22q11DS. b Mean PF/F volumes manually measured from MRI data of mice with hemizygous microdeletions of various sizes or hemizygous deletions of individual genes within the 22q11.2 syntenic region. Two-tailed Student’s t-test (Holm–Sidak post hoc): Del(3.0 Mb)/+ (red, 14 mice; 14 WT mice): t26 = 5.47, **p < 0.0001; LgDel/+ (red, 6 mice; 6 WT mice): t14 = 11.47, **p < 0.0001; Df(16)1/+ (red, 11 mice; 10 WT mice): t19 = 12.39, **p < 0.0001; Df(16)2/+ (red, 9 mice; 10 WT mice): t17 = 3.15, *p = 0.006; Df(16)3/+ (red, 7 mice; 5 WT mice): t10 = 3.15, *p = 0.01; Df(16)4/+ (red, 5 mice; 5 WT mice): t8 = 4.17, **p = 0.003; Df(16)5/+ (gray, 18 mice; 17 WT mice): t33 = 0.09, p = 0.93; Znf74l-Ctp/+ (gray, 10 mice; 11 WT mice): t19 = 0.69, p = 0.49; Rtn4r+/– (gray, 4 mice; 6 WT mice): t8 = 0.88, p = 0.4; Dgcr8+/– (gold, 13 mice; 13 WT mice): t24 = 2.49, *p = 0.02; for T10+/– (gray, 8 mice; 8 WT mice): t14 = 0.64, p = 0.53; Arvcf-Txnrd2/+ (gray, 16 mice; 17 WT mice): t31 = 1.38, p = 0.18; Comt+/– (gray, 10 mice; 9 WT mice): t17 = 0.74, p = 0.47; Gnb1l+/– (gray, 11 mice; 11 WT mice): t20 = 0.92, p = 0.37; Tbx1+/– (green, 18 mice; 21 WT mice): t37 = 6.15, **p < 0.0001; Sept5+/– (gray, 10 mice; 10 WT mice): t18 = 0.30, p = 0.77. Data are presented as the mean ± SEM. Source data are provided as a Source Data file.
Compromised vestibulo-ocular reflex–based motor learning and cerebellar-dependent plasticity in 22q11DS mice
a Diagram of the experimental setup for measuring the vestibulo-ocular reflex (VOR) in head-fixed mice on a rotating platform with a visual grating moving in the opposite or same direction, relative to the head¹⁶⁹. b, c The basal level of VOR gain in Df(16)1/+ mice (red, n = 5) and Tbx1+/– mice (green, n = 6) and their respective WT controls (black, b 5 mice, c 7 mice) measured immediately before training. Two-tailed unpaired Student’s t-test: bt8 = 0.46, p = 0.66; ct11 = 0.32, p = 0.76. d, e Average VOR gain after opposite-direction mismatch training (1.5×, 60 min) in WT (d 5 mice, e 7 mice), Df(16)1/+ (n = 5), and Tbx1+/– (n = 6) mice. Two-way ANOVA (Holm–Sidak’s post hoc) after training: dF1,8 = 15.3, **p < 0.0001; eF1,11 = 3.03, *p = 0.04. f, g Average VOR gain after same-direction visual-vestibular mismatches (0×, 60 min) in WT (f 5 mice, g 6 mice), Df(16)1/+ (n = 4), and Tbx1+/– (n = 5) mice. Two-way ANOVA (Holm–Sidak’s post hoc) after training: fF1,7 = 0.56, p = 0.52; gF1,9 = 1.26, p = 0.24. Data are presented as the mean ± SEM. Source data are provided as a Source Data file.
Compromised cerebellar-dependent plasticity in the paraflocculus/flocculus in 22q11DS mice
a Schematic of the recording and stimulation configuration for long-term depression (LTD) induction. Purkinje cells (PCs) were targeted for whole-cell recording while parallel fiber (Pf) and climbing fiber (Cf) inputs were stimulated. b Normalized excitatory postsynaptic potential amplitude (EPSP amp.) shows the LTD time course before and after a 10-min baseline in WT (black) and Df(16)1/+ (red) PCs; LTD was induced by conjunctive Pf and Cf stimulation. Example voltage traces from individual cells (upper) show EPSPs induced by Pf stimulation before (left) and after (right) LTD induction in WT and Df(16)1/+ PCs. The dotted lines show the amplitude of the baseline response. c Average LTD amplitude in WT (n = 7 cells, 4 mice) and Df(16)1/+ (n = 8 cells, 5 mice) PCs. Two-tailed Student’s t-test (Welch’s correction): t8.66 = 2.77, *p = 0.023. d Normalized EPSP amplitude shows the LTD time course, before and after the 10-min baseline in WT (black) and Tbx1+/– (green) PCs. Example voltage traces from individual cells (upper) show EPSPs induced by Pf stimulation before (left) and after (right) LTD induction in WT and Tbx1+/– PCs. The dotted lines show the amplitude of the baseline response. e Average LTD amplitude in WT (n = 8 cells, 5 mice) and Tbx1+/– (n = 9 cells, 6 mice) PCs. Two-tailed Student’s t-test (Welch’s correction): t8.24 = 2.41, *p = 0.042. f Schematic of the recording and stimulation configuration for long-term potentiation (LTP) induction. PCs were targeted for whole-cell recording while Pf inputs were stimulated. g Normalized LTP time course before and after 5-min baseline in WT and Df(16)1/+ PCs, showing LTP induction by tetanic PF stimulation. h Average LTP amplitude in WT (n = 7 cells, 5 mice) and Df1+/– (n = 10 cells, 5 mice) PCs. Two-tailed Student’s t-test (Welch’s correction): t11.33 = 0.04, p = 0.968. i Normalized the LTP time course before and after 5-min baseline in WT and Tbx1+/– PCs, showing LTP induction by tetanic PF stimulation. j Average LTP amplitude in WT (n = 10 cells, 8 mice) and Tbx1+/– (n = 7 cells, 5 mice) PCs. Two-tailed Student’s t-test (Welch’s correction): t9.86 = 0.94, p = 0.37. Data are presented as the mean ± SEM. n.s. not significant. Source data are provided as a Source Data file.
Cerebellar progenitor neurogenesis and migration are normal in the paraflocculus/flocculus of 22q11DS mice
a, d Representative confocal images of Ki67 and PH3 (proliferation markers, red and black, respectively) staining in the external germinal layer (EGL) of P7 WT (black) and Df(16)1/+ (red) mice. b, c, e, f Average normalized numbers of Ki67⁺ cells (b WT: 24 sections, 9 mice; Df(16)1/+: 30 sections, 12 mice; c WT: 23 sections, 9 mice; Df(16)1/+: 30 sections, 12 mice) and PH3⁺ cells (e WT: 22 sections, 9 mice; Df(16)1/+ mice: 23 sections, 12 mice; f WT: 23 sections, 9 mice; Df(16)1/+: 26 sections, 12 mice) in the PF or F of P3–P7 WT and Df(16)1/+ animals. Two-way ANOVA (Holm–Sidak’s post hoc); bF1,50 = 0.42, p = 0.52 (P3: p = 0.89, P5: p = 0.89, P7: p = 0.89); cF1,47 = 0.005, p = 0.95 (P3: p = 0.79; P5: p = 0.6; P7: p = 0.6); eF1,39 = 5.0, p = 0.03 (P3: p = 0.44; P5: p = 0.24; P7: p = 0.44); fF1,43 = 0.009, p = 0.93 (P3: p = 0.93; P5: p = 0.7; P7: p = 0.93). g Representative confocal images of cleaved caspase-3 (c-casp3, apoptosis marker, black) in the PF/F of P7 WT and Df(16)1/+ mice. h, i Average normalized numbers of c-casp3⁺ cells in the PF or F of P3–P14 WT (h, i 48 sections, 16 mice) and Df(16)1/+ (h 68 sections, 20 mice; i 66 sections, 20 mice) animals. Two-way ANOVA (Holm–Sidak’s post hoc); hF1,108 = 3.17, p = 0.08 (P3: p = 0.58; P5: p = 0.39; P7: p = 0.58; P14: p = 0.86); iF1,106 = 0.34, p = 0.56 (P3: p = 0.44; P5: p = 0.44; P7: p = 0.87; P14: p = 0.87). j, k CGN migration in the PF is normal in Df(16)1/+ animals. j Representative confocal images of cerebellar slices showing H2B-mCherry–labeled CGN germinal zone exit and migration. k Cellular distribution analyzed in each binned distance in P7 WT (27 brain sections, 7 mice) and Df(16)1/+ (8 brain sections, 5 mice) animals. Two-way ANOVA (Holm–Sidak’s post hoc); F51,288 = 0.71, p = 0.4 (0–45 µm: p = 0.6; 45–90 µm: p = 0.85; 90–135 µm: p = 0.99; 135–180 µm: p = 0.99; 180–225 µm: p = 0.99; 225–270 µm: p = 0.99). Data are presented as the mean ± SEM, except in (k), where data are presented as a violin plot with median values. Source data are provided as a Source Data file.

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Tbx1 haploinsufficiency leads to local skull deformity, paraflocculus and flocculus dysplasia, and motor-learning deficit in 22q11.2 deletion syndrome

December 2024

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46 Reads

Neurodevelopmental disorders are thought to arise from intrinsic brain abnormalities. Alternatively, they may arise from disrupted crosstalk among tissues. Here we show the local reduction of two vestibulo-cerebellar lobules, the paraflocculus and flocculus, in mouse models and humans with 22q11.2 deletion syndrome (22q11DS). In mice, this paraflocculus/flocculus dysplasia is associated with haploinsufficiency of the Tbx1 gene. Tbx1 haploinsufficiency also leads to impaired cerebellar synaptic plasticity and motor learning. However, neural cell compositions and neurogenesis are not altered in the dysplastic paraflocculus/flocculus. Interestingly, 22q11DS and Tbx1+/– mice have malformations of the subarcuate fossa, a part of the petrous temporal bone, which encapsulates the paraflocculus/flocculus. Single-nuclei RNA sequencing reveals that Tbx1 haploinsufficiency leads to precocious differentiation of chondrocytes to osteoblasts in the petrous temporal bone autonomous to paraflocculus/flocculus cell populations. These findings suggest a previously unrecognized pathogenic structure/function relation in 22q11DS in which local skeletal deformity and cerebellar dysplasia result in behavioral deficiencies.





School’s Out for the Summer: Cognition Varies Across the Calendar Year in Multiple Large-Scale Datasets

November 2024

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47 Reads

“Summer slide” refers to seasonal variation in children’s performance on academic assessments, characterized by decreased performance following an extended school vacation. While this phenomenon has been described by teachers and caregivers and investigated in small-scale studies using linear models of academic performance, no large-scale studies have quantified cyclical, seasonal variation in children’s standardized cognitive assessment scores. Using four large-scale datasets (total n=23,251; Adolescent Brain Cognitive Development Study: n=11,040, 9-11y; Philadelphia Neurodevelopmental Cohort: n=9,416, 8-22y; Growing Up in Singapore Towards healthy Outcomes: n=342, 7y; Oregon ADHD-1000: n=843, 7-21y), we model time-of-year using generalized additive models with cyclic cubic splines. In school-age children but not young adults, we found cognitive performance minima following school vacation (July-September in the U.S.; November-January in Singapore) across cognitive domains. These results demonstrate a generalizable small-magnitude decrease in children’s cognitive performance aligning seasonally with school vacation.


Estimation and Validation of the “c” Factor for Overall Cerebral Functioning in the Philadelphia Neurodevelopmental Cohort

November 2024

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Psychopathology and cognitive ability indicators correlate, within each other, in a way that is well-captured by hierarchical factor models, but integrating both into a single hierarchical framework remains a challenge. Because both aspects of behavior presumably reflect aberrant cerebral function, the highest-order latent variable in such a model would be the “c” (for cerebral) factor. We estimated a tri-factor model of “c” in N=9,494 children and young adults from the Philadelphia Neurodevelopmental Cohort using the Penn Computerized Neurocognitive Battery and the GOASSESS clinical interview. We tested the validity of factor scores resulting from this model by relating them to external criteria, including global functioning, parent education, socioeconomic status, intracranial volume, and longitudinal clinical outcome. Fit of the structural model was acceptable (CFI = 0.98; SRMR = 0.030), and scores correlated with external criteria as expected (functioning = 0.27; parent education = 0.43; socioeconomic status = 0.47; intracranial volume = 0.39; clinical outcome Cohen d = 0.30 and 0.57). For most criteria, the effect for the “c” factor was larger than either the “p” or “g” factors alone. These results provide evidence for the feasibility and potential utility of modeling the “c” factor when cognitive and clinical data are both available.


Sample Demographics by Cohort
Percentage Surface Area Affected Across Models SZ-F vs CON-F SZ-M vs CON-M M vs. F SZ-M vs SZ-F* CON-M vs CON-F
Percentage Surface Area Affected Across Clinical Correlates
Sex differences in deep brain shape and asymmetry persist across schizophrenia and healthy individuals: A meta-analysis from the ENIGMA-Schizophrenia Working Group

October 2024

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111 Reads

Background: Schizophrenia (SCZ) is characterized by a disconnect from reality that manifests as various clinical and cognitive symptoms, and persistent neurobiological abnormalities. Sex-related differences in clinical presentation imply separate brain substrates. The present study characterized deep brain morphology using shape features to understand the independent effects of diagnosis and sex on the brain, and to determine whether the neurobiology of schizophrenia varies as a function of sex. Methods: This study analyzed multi-site archival data from 1,871 male (M) and 955 female (F) participants with SCZ, and 2,158 male and 1,877 female healthy controls (CON) from twenty-three cross-sectional samples from the ENIGMA Schizophrenia Workgroup. Harmonized shape analysis protocols were applied to each site's data for seven deep brain regions obtained from T1-weighted structural MRI scans. Effect sizes were calculated for the following main contrasts: 1) Sex effects; 2) Diagnosis-by-Sex interaction; 3) within sex tests of diagnosis; 4) within diagnosis tests of sex differences. Meta-regression models between brain structure and clinical variables were also computed separately in men and women with schizophrenia. Results: Mass univariate meta-analyses revealed more concave-than-convex shape differences in all regions for women relative to men, across diagnostic groups (d = -0.35 to 0.20, SE = 0.02 to 0.07); there were no significant diagnosis-by-sex interaction effects. Within men and women separately, we identified more-concave-than-convex shape differences for the hippocampus, amygdala, accumbens, and thalamus, with more-convex-than-concave differences in the putamen and pallidum in SCZ (d = -0.30 to 0.30, SE = 0.03 to 0.10). Within CON and SZ separately, we found more-concave-than-convex shape differences in the thalamus, pallidum, putamen, and amygdala among females compared to males, with mixed findings in the hippocampus and caudate (d = -0.30 to 0.20, SE = 0.03 to 0.09). Meta-regression models revealed similarly small, but significant relationships, with medication and positive symptoms in both SCZ-M and SCZ-F. Conclusions: Sex-specific variation is an overriding feature of deep brain shape regardless of disease status, underscoring persistent patterns of sex differences observed both within and across diagnostic categories, and highlighting the importance of including it as a critical variable in studies of neurobiology. Future work should continue to explore these dimensions independently to determine whether these patterns of brain morphology extend to other aspects of neurobiology in schizophrenia, potentially uncovering broader implications for diagnosis and treatment.




Citations (51)


... Drawing inspiration from engineering principles, network control theory (NCT) offers a novel perspective on this problem by conceptualizing the brain as a networked control system in order to explain its dynamics (Gu et al., 2015). In its most basic form, NCT considers brain dynamics as a composite outcome of a region's connectivity profile and the necessary control inputs to guide a neural activity toward a desired state (Gu et al., 2015;Karrer et al., 2020;Parkes et al., 2024; Figure 1A). The former aspect delves into the constant anatomical interactions between various brain regions, while the latter presents an adaptable measure to optimally transition between states within the confines of energy constraints ( Figure 1B). ...

Reference:

The control costs of human brain dynamics
A network control theory pipeline for studying the dynamics of the structural connectome
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Nature Protocols

... A recent large-scale study has supported a difference in left-right brain traits across the lifespan. Genetic factors are one potential mechanism for these differences 47 . Therefore, the ncDNVs prioritized in this analysis could impact both heart and brain development by increasing H3K9me2, consistent with the observation that heart and brain traits have a set of shared genetic influences 48 . ...

Large‐scale analysis of structural brain asymmetries during neurodevelopment: Associations with age and sex in 4265 children and adolescents

... Jirsaraie et al. [83] studied the generalizability of two brain age models across different age samples, discovering that insufficient sample size and diversity can lead to inconsistent performance across different acquisition protocols, impacting prediction accuracy and reliability. Yu et al. [150] systematically evaluated the effects of site harmonization, age range, and sample size on estimating brain age, finding that model accuracy plateaued with sample sizes exceeding 1600 participants. The study noted that insufficient sample sizes limit model generalizability and stability. ...

Brain‐age prediction: Systematic evaluation of site effects, and sample age range and size

... 51,52,53,54,55]. Consistent with prior findings, our modular clustering of the C. elegans anatomical network recapitulates anatomical communities that are each significantly enriched for no more than one of the three C. elegans neuron cell types classes: Sensory, Inter-and Motor neurons[27](Fig. 3 c; Supplementary Fig. 4 a; ...

Network enrichment significance testing in brain–phenotype association studies

... As for the absent rsFC findings in SP, it is plausible that this patient cohort has milder impairment, aligning more with the HC phenotype than PD/AG patients do, leading to differing results when compared to PD/AG. Subtle brain morphologic differences have however recently been described in an ENIGMA metaanalysis in SP [51]. ...

Cortical and Subcortical Brain Alterations in Specific Phobia and Its Animal and Blood-Injection-Injury Subtypes: A Mega-Analysis From the ENIGMA Anxiety Working Group
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American Journal of Psychiatry

... These methods rely solely on the fitness values of individuals to drive the evolutionary process without requiring gradient information. Advances in computational techniques [5] have allowed EAs to provide diverse solutions for highly complex optimization tasks such as neuroevolution [6,7], robotic control [8,9], industrial design [10], and scientific discoveries [11,12]. As the scale and complexity of these tasks increase [1,13], EAs generate a significant amount of valuable knowledge, including historical populations and their fitness data. ...

In vivo whole-cortex marker of excitation-inhibition ratio indexes cortical maturation and cognitive ability in youth
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Proceedings of the National Academy of Sciences

... Functional brain network reorganization during puberty involves increases in centrality (importance of network hub regions), segregation (formation of specialized subnetworks), efficiency (efficiency of network communication), and integration (communication between specialized regions), particularly in attention, task control, and social processing systems (Gracia-Tabuenca et al., 2021). Functional brain network development occurs along a sensorimotor-association axis, with lower-order sensorimotor areas (e.g., motor cortex) maturing earlier and integrating functionally with other regions, while higher-order association areas (e.g., PFC) continue maturing and functionally specializing throughout adolescence Luo et al., 2024;Sydnor et al., 2023). ...

Functional connectivity development along the sensorimotor-association axis enhances the cortical hierarchy

... Participants will be screened in MS clinics and then verified for eligibility using the inclusion and exclusion criteria. During the visit, participants will be asked questions about their demographics, answer mood and anxiety questionnaires, complete the Computerized Neurocognitive Battery (CNB) (27), and the CAT-GOASSESS (28). MS, Multiple Sclerosis. ...

Validation of the Structured Interview Section of the Penn Computerized Adaptive Test for Neurocognitive and Clinical Psychopathology Assessment (CAT GOASSESS)
  • Citing Article
  • March 2024

Psychiatry Research

... This study also indicated that the ED field lags behind in terms of the evidence needed to implement preventive strategies for individuals with sub-threshold ED symptoms, recommending multi-centric cohort studies to identify modifiable risk factors. Of note, a potential example of such a project has been recently implemented in the CHR-P field, with an ongoing large-scale observational cohort study collecting and analyzing multimodal data to improve prognostic precision [79]. If translated to the ED field, an analogous project collecting multimodal data like clinical, environmental, cognitive, and neuroimaging data could increase precision in determining risk factors and prognosis and selecting appropriate preventive treatments for eating pathology. ...

Accelerating Medicines Partnership® Schizophrenia (AMP® SCZ): Rationale and Study Design of the Largest Global Prospective Cohort Study of Clinical High Risk for Psychosis

Schizophrenia Bulletin

... In conclusion, the morpho-structural abnormalities associated with schizophrenia, including increased cerebrospinal fluid volume, widespread gray and white matter reductions, disrupted white matter tracts, and synaptic and dendritic abnormalities, underscore the complex neurobiological basis of the disorder [17]. Understanding these intricate alterations is crucial for developing more targeted interventions that address the clinical symptoms and the underlying structural alterations that drive the disease's progression [18][19][20]. ...

Connectome architecture shapes large-scale cortical alterations in schizophrenia: a worldwide ENIGMA study

Molecular Psychiatry