Deep Mouse: An End-to-end Auto-context Refinement Framework for Brain Ventricle and Body Segmentation in Embryonic Mice Ultrasound Volumes

High-frequency ultrasound (HFU) is well suited for imaging embryonic mice due to its noninvasive and real-time characteristics. However, manual segmentation of the brain ventricles (BVs) and body requires substantial time and expertise. This work proposes a novel deep learning based end-to-end auto-context refinement framework, consisting of two stages. The first stage produces a low resolution segmentation of the BV and body simultaneously. The resulting probability map for each object (BV or body) is then used to crop a region of interest (ROI) around the target object in both the original image and the probability map to provide context to the refinement segmentation network. Joint training of the two stages provides significant improvement in Dice Similarity Coefficient (DSC) over using only the first stage (0.818 to 0.906 for the BV, and 0.919 to 0.934 for the body). The proposed method significantly reduces the inference time (102.36 to 0.09 s/volume around 1000x faster) while slightly improves the segmentation accuracy over the previous methods using slide-window approaches.Comment: Full Paper Submission to ISBI 202

High-throughput transgenic mouse phenotyping using microscopic-MRI

With the completion of the human genome sequence in 2003, efforts have shifted towards elucidating gene function. Such phenotypic investigations are aided by advances in techniques for genetic modification of mice, with whom we share ~99% of genes. Mice are key models for both examination of basic gene function and translational study of human conditions. Furthering these efforts, ambitious programmes are underway to produce knockout mice for the ~25,000 mouse genes. In the coming years, methods to rapidly phenotype mouse morphology will be in great demand. This thesis demonstrates the development of non-invasive microscopic magnetic resonance imaging (\muMRI) methods for high-resolution ex-vivo phenotyping of mouse embryo and mouse brain morphology. It then goes on to show the application of computational atlasing techniques to these datasets, enabling automated analysis of phenotype. First, the issue of image quality in high-throughput embryo MRI was addressed. After investigating preparation and imaging parameters, substantial gains in signal- and contrast-to-noise were achieved. This protocol was applied to a study of Chd7+/- mice (a model of CHARGE syndrome), identifying cardiac defects. Combining this protocol with automated segmentation-propagation techniques, phenotypic differences were shown between three groups of mice in a volumetric analysis involving a number of organ systems. Focussing on the mouse brain, the optimal preparation and imaging parameters to maximise image quality and structural contrast were investigated, producing a high-resolution in-skull imaging protocol. Enhanced delineation of hippocampal and cerebellar structures was observed, correlating well to detailed histological comparisons. Subsequently this protocol was applied to a phenotypic investigation of the Tc1 model of Down syndrome. Using both visual inspection and automated, tensor based morphometry, novel phenotypic findings were identified in brain and inner ear structures. It is hoped that a combination of \muMRI with computational analysis techniques, as presented in this work, may help ease the burden of current phenotyping efforts

Automated morphometric analysis and phenotyping of mouse brains from structural µMR images

In light of the utility and increasing ubiquity of mouse models of genetic and neurological disease, I describefully automated pipelines for the investigation of structural microscopic magnetic resonance images of mouse brains – for both high-throughput phenotyping, and monitoring disease. Mouse models offer unparalleled insight into genetic function and brain plasticity, in phenotyping studies; and neurodegenerative disease onset and progression, in therapeutic trials. I developed two cohesive, automatic software tools, for Voxel- and Tensor-Based Morphometry (V/TBM) and the Boundary Shift Integral (BSI), in the mouse brain. V/TBM are advantageous for their ability to highlight morphological differences between groups, without laboriously delineating regions of interest. The BSI is a powerful and sensitive imaging biomarker for the detection of atrophy. The resulting pipelines are described in detail. I show the translation and application of open-source software developed for clinical MRI analysis to mouse brain data: for tissue segmentation into high-quality, subject-specific maps, using contemporary multi-atlas techniques; and for symmetric, inverse-consistent registration. I describe atlases and parameters suitable for the preclinical paradigm, and illustrate and discuss image processing challenges encountered and overcome during development. As proof of principle and to illustrate robustness, I used both pipelines with in and ex vivo mouse brain datasets to identify differences between groups, representing the morphological influence of genes, and subtle, longitudinal changes over time, in particular relation to Down syndrome and Alzheimer’s disease. I also discuss the merits of transitioning preclinical analysis from predominately ex vivo MRI to in vivo, where morphometry is still viable and fewer mice are necessary. This thesis conveys the cross-disciplinary translation of up-to-date image analysis techniques to the preclinical paradigm; the development of novel methods and adaptations to robustly process large cohorts of data; and the sensitive detection of phenotypic differences and neurodegenerative changes in the mouse brai

Magnetic resonance imaging, in situ hybridization, and immunohistochemistry-based analyses of early prenatal ethanol exposure-induced central nervous system abnormalities

Fetal alcohol spectrum disorders (FASD), the collection of defects resulting from prenatal alcohol (ethanol) exposure, has been the subject of basic and clinical investigation for four decades, but remains a major public health problem. At the severe end of the spectrum is fetal alcohol syndrome (FAS), which is characterized by the presence of growth retardation, craniofacial anomalies, and brain deficits. The research described herein was designed to advance our knowledge regarding ethanol's insult to the developing brain, with much of it directed toward testing the hypothesis that the application of magnetic resonance-based imaging to the examination of brain morphology, regional volumes and fiber tracts in ethanol-exposed fetal mice would facilitate new discoveries. As with other teratogens, it is well known that the type and severity of abnormality induced by ethanol is dependent upon the dose, timing, and pattern of maternal exposure. For this study, the CNS dysmorphology resulting from acute gestational day (GD) 7 maternal ethanol administration was examined in fetal mice utilizing state of the art imaging techniques. This time in mouse development is consistent with that in the third week of human gestation. Magnetic resonance microscopy (MRM) allowed for linear, volumetric and 3-dimensional morphologic analyses of ethanol-induced alterations in the fetal CNS and diffusion tensor imaging (DTI) provided for assessment of fiber tract abnormalities. In addition, routine histological techniques were utilized for detailed examination of the ventromedian forebrain in ethanol-exposed embryos and fetuses. Major new findings from these studies include the following regarding the consequences of acute GD7 ethanol exposure in mice 1) cerebral cortical heterotopias are induced; a discovery that was facilitated by MRM-based analyses, 2) fiber tract abnormalities involving the corpus callosum, anterior commissure, and fornix/fimbria occur, as evidenced by DTI, 3) fiber tract abnormalities, as identified in fetal mice, persist into periadolescent stages, 4) ventral forebrain insult preferentially involving the preoptic area and medial ganglionic eminences reduces Olig2 and GABA expression and alters the morphology of somatostatin-expressing cells. Overall, the results of this work promise to aid in clinical recognition, diagnosis, and prevention of FASD

Characterization of Ambra1 heterozygous mice as genetic mouse model of female-specific autism

Autism is known as a heritable neurodevelopmental disorder, diagnosed prior to the age of three years in humans based on three major domains: (1) impairment in social interaction (2) communication deficits (3) restricted interests and repetitive behaviors. Since it is a very heterogeneous disorder with various causes and different combinations of phenotypes, it is also called autism spectrum disorder (ASD). Monogenic heritable forms of ASD enable us to develop genetic mouse models of autism in order to obtain mechanistic insight in this disorder. Ambra1 is a positive regulator of Beclin1, a major player in the formation of autophagosomes during the process of autophagy. While Ambra1 null mutation leads to embryonic lethality, we could show that Ambra1 heterozygous mice (Ambra1+/-) display autism-like behavior only in females. Purpose of this thesis was therefore to characterize this mouse line further. It turned out that communication deficits, measured by ultrasound vocalization, start in the neonatal stage of females, while physical or neurological development is normal in Ambra1+/-. Female Ambra1 mutants had a stronger reduction in Ambra1 expression than male mutants, which gives first hints of the female-specific autism-like behavior in this mouse line. Mild enlargement of whole brain and hippocampus was detected in both Ambra1+/- males and females, with no change of ventricle size. Since β-galactosidase, used as reporter expressed under the Ambra1 promoter, was found only in neuronal cells, I focused on understanding the neural mechanism of its phenotype. Short-term and long-term synaptic plasticity in the hippocampus was normal for males and females of both genotypes. However, the power of gamma oscillations (γ-power), indicative of change in the balance of excitation and inhibition, was age-dependently altered in Ambra1+/- females only. However, this difference was not detected in male. Moreover, increased susceptibility to seizures, a known comorbid condition of ASD was restricted to females, suggesting an association between autism-like behavior, gamma oscillation and seizure propensity in female Ambra1+/- mice. Next, I approached the neuronal substrate of these three phenotypes by morphological analysis of hippocampal pyramidal neurons, such as dendritic arborization and synapse number. A genotype-associated difference of dendritic arborization was detected in neither males nor females. The quantification of spines or synapses and cellular electrophysiology are still on-going. First signals point to an imbalance between excitation and inhibition as a cause of the female autism-like behavior in Ambra1+/- mice

Characterization of Ambra1 heterozygous mice as genetic mouse model of female-specific autism

Autism is known as a heritable neurodevelopmental disorder, diagnosed prior to the age of three years in humans based on three major domains: (1) impairment in social interaction (2) communication deficits (3) restricted interests and repetitive behaviors. Since it is a very heterogeneous disorder with various causes and different combinations of phenotypes, it is also called autism spectrum disorder (ASD). Monogenic heritable forms of ASD enable us to develop genetic mouse models of autism in order to obtain mechanistic insight in this disorder. Ambra1 is a positive regulator of Beclin1, a major player in the formation of autophagosomes during the process of autophagy. While Ambra1 null mutation leads to embryonic lethality, we could show that Ambra1 heterozygous mice (Ambra1+/-) display autism-like behavior only in females. Purpose of this thesis was therefore to characterize this mouse line further. It turned out that communication deficits, measured by ultrasound vocalization, start in the neonatal stage of females, while physical or neurological development is normal in Ambra1+/-. Female Ambra1 mutants had a stronger reduction in Ambra1 expression than male mutants, which gives first hints of the female-specific autism-like behavior in this mouse line. Mild enlargement of whole brain and hippocampus was detected in both Ambra1+/- males and females, with no change of ventricle size. Since β-galactosidase, used as reporter expressed under the Ambra1 promoter, was found only in neuronal cells, I focused on understanding the neural mechanism of its phenotype. Short-term and long-term synaptic plasticity in the hippocampus was normal for males and females of both genotypes. However, the power of gamma oscillations (γ-power), indicative of change in the balance of excitation and inhibition, was age-dependently altered in Ambra1+/- females only. However, this difference was not detected in male. Moreover, increased susceptibility to seizures, a known comorbid condition of ASD was restricted to females, suggesting an association between autism-like behavior, gamma oscillation and seizure propensity in female Ambra1+/- mice. Next, I approached the neuronal substrate of these three phenotypes by morphological analysis of hippocampal pyramidal neurons, such as dendritic arborization and synapse number. A genotype-associated difference of dendritic arborization was detected in neither males nor females. The quantification of spines or synapses and cellular electrophysiology are still on-going. First signals point to an imbalance between excitation and inhibition as a cause of the female autism-like behavior in Ambra1+/- mice

Identifying the Genetic Causes of Congenital Anomalies

Structural organ anomalies (malformations) are common and cause significant mortality and morbidity worldwide. The aim of this study was to identify monogenic causes of malformations to understand their pathogenesis, enhance clinical care and ultimately ease the burden of disease. We used family-based exome (ES) or genome sequencing (GS), cohort-wide analyses, collaborative clinical characterisation, and laboratory validation to identify causative variants in well-known and novel genes. We first studied a cohort of 44 patients with vertebral defects. Via ES, we found the genetic cause in 9/44 individuals from 8/43 families. Two of these families had spondylocostal dysostosis due to pathogenic variants in DLL3 and TBX6. The other six families had multiple congenital anomalies (MCA), with disruptive variants in HAAO, KYNU, SMAD4, STAG2, TBX6, and WBP11. As WBP11, HAAO, and KYNU were not associated with MCA, our laboratory studied their function. We found heterozygous WBP11 variants in two families from our cohort and five additional families via GeneMatcher. Our laboratory produced a Wbp11 mouse model. Our clinical and laboratory findings showed that WBP11 haploinsufficiency in humans and mice leads to MCA with incomplete penetrance and variable expressivity. We next studied patients with cardiac defects. Via GS and GeneMatcher, we identified two additional patients with biallelic HAAO and KYNU variants respectively, who both have hypoplastic left heart and other MCA. HAAO and KYNU encode enzymes in the synthesis of nicotinamide adenine dinucleotide (NAD). Biochemical and animal studies showed that pathogenic biallelic variants in HAAO and KYNU cause NAD deficiency in humans and mice, revealing a novel mechanism that results in MCA. In Haao and Kynu mice, niacin supplementation alleviated NAD deficiency and prevented MCA. Hence, our discovery has revealed a potential preventor of malformations due to genetic and environmental causes of NAD deficiency. Similarly, combining GS with functional assays led us to confirm the pathogenicity of a variant in a gene known to cause MCA, NOTCH1. This highlights the need to establish efficient pipelines to functionally characterise the increasing number of variants identified as ES and GS become more widely used in investigating malformations. We found genetic causes of malformations via family sequencing and functional confirmation, improving the care of families in our study and beyond

Zebrafish Models for Development and Disease 2.0

The special issue (Zebrafish Models for Development and Disease 2.0) is a collection of articles highlighting research using the zebrafish (Danio rerio) experimental organism. Research described in this special issue addresses various developmental biology, genetic, biomedical and neuroscience topics that should be of general interest to the biomedical research community