Study Uncovers 198 Genes Associated With Brain Morphogenesis in Mice

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By IMPC

Published 4th October 2019

With a contribution from the IMPC, recent research, published in Nature Communications, has identified 198 genes associated with brain morphogenesis in mice – 83% of these constitute genes newly implicated in brain architecture.

Brain development and morphogenesis is critical to higher-order cognition, but our knowledge of its biological basis is at best incomplete, and at worst, severely lacking. Previous studies have demonstrated that there is a significant genetic influence on brain morphology. However knowledge of which genes influence brain morphology is limited, and this presents an important problem in developmental biology. By identifying 198 genes that are associated with mouse brain morphogenesis the study provides a complementary resource to human genetic studies and predicts that many more genes could be involved in mammalian brain morphogenesis.

Binnaz Yalcin, corresponding author of the study says “This study aims at understanding the genetics of brain anatomy in the mouse. It provides a wealth of novel knowledge about which genes control the size and the shape of the brain, and a foundation on which neurobiologists can build to further study how exactly these genes control the brain anatomy”.

“I have no doubt that this resource will help medical geneticists working on ultra-rare human neurodevelopmental disorders

The researchers obtained brain samples of 1566 mutant mouse lines from the Sanger Institute Mouse Genetics Project, a partner of the IMPC. Using a histological pipeline, 118 brain morphological parameters were analysed, covering brain size, commissures, ventricles, cortex, subcortex and cerebellum. To detect neuroanatomical phenotypes (NAPs), the researchers used PhenStat, a statistical method developed by the IMPC for the identification of abnormal phenotypes. 198 genes associated with neuroanatomical phenotypes (NAP genes) were subsequently identified. The vast majority of these genes (94%) have never previously been associated with brain anatomy in mice.

Interestingly, unique human orthologs were identified for 173 of the identified mouse NAP genes. Whilst 17% of human unique orthologs of mouse NAP genes are known loci for cognitive dysfunction, 83% constitute a vast number of genes that are newly implicated in brain architecture. This dataset may therefore help in improving clinical interpretation.

Yalcin states “I have no doubt that this resource will help medical geneticists working on ultra-rare human neurodevelopmental disorders who sometimes struggle to determine the genetic mutation responsible for the underlying disease, when for example there is only one patient world-wide. So when a mutation is found in a patient’s genome and that patient exhibits the same phenotype than the mouse, a molecular diagnosis can finally be made.”

This study would not have been possible without the IMPC

The identified NAP genes converge into a small number of groups of functionally similar genes participating in shared cellular pathways. Disruption of genes within the same module can yield a similar pattern of neuroanatomical abnormalities, revealing interesting neurodevelopmental pathway/phenotype relationships. For example, the study indicates that mechanisms confined to sub-cellular compartments as subtle as dendritic spines can translate into major anatomical features.

The study represents the largest atlas of the link between genetic mutation and its associated neuroanatomical features yet, and contributes a wealth of new knowledge on the genetics of brain morphogenesis. The authors were keen to note the contribution of the IMPC towards their work, with Yalcin commenting that “This study would not have been possible without the IMPC and is a tribute to the remarkable work of the people involved in this consortium.”

The IMPC is aiming to design and produce a genome-wide mouse strain resource of human disease-associated coding variants associated with rare disease that can be used for validation of putative functional variants and insight into disease mechanism(s). To find out more, click here.


Original publication: Large-scale neuroanatomical study uncovers 198 gene associations in mouse brain morphogenesis

Members of the IMPC Consortium at CNR-Monterotondo (Italy) have used embryonic stem (ES) cells produced as part of the IMPC project, to engineer a Ccdc151 ‘knockout’ mouse model that is valuable for the study of human ciliopathies, gaining significant insight into this set of rare conditions.

Primary ciliary dyskinesia (PCD) is a rare, genetic disorder that results in chronic respiratory tract infections, abnormally orientated internal organs and infertility. The root cause of these symptoms are dysfunctional cilia and flagella, which if functioning correctly, are finger-like projections on the surface of cells that act to clear mucus and debris by coordinated beating. In addition, normal function of cilia is required for migration of egg and sperm cells.

Ccdc151 is a gene that is known to be associated with PCD, and here, researchers have engineered a mouse model, using embryonic stem cells from the IMPC, in which the gene is deleted. Common features of PCD in human patients such as left-right body asymmetry and dysfunctional spermatogenesis were detected in these Ccdc151-knockout mice. “The Ccdc151-knockout mouse model faithfully recapitulates several features of human PCD disease” remark Francesco Chiani and Tiziana Orsini, co-first authors of the paper. “The availability of this animal model will allow researchers to further dissect the mechanisms by which pathological conditions develop in different organs”.

This animal model will be useful for studying mechanisms underlying hydrocephalus, a condition whose treatment has not changed for decades.

The researchers also observed that Ccdc151-knockouts develop severe hydrocephalus – a condition in which cerebrospinal fluid accumulates in the brain, causing increased pressure inside the skull and potentially leading to brain damage and other complications. This is the first example of hydrocephalus caused by loss of function in the Ccdc151 gene. Although hydrocephalus is rarely seen in human patients with PCD, having a mouse model that exhibits all of the features of hydrocephalus could be useful for researchers. “This animal model will be useful for studying mechanisms underlying hydrocephalus, a condition whose treatment has not changed for decades”, said the lead authors. It is hoped that further studies may help to uncover other genes that interact with Ccdc151 that lead to the development of hydrocephalus.

this micro-CT imaging methodology could be applied to facilitate studies on gene expression directly in the intact brain

The researchers made extensive use of X-ray micro-CT 3D imaging to study the hydrocephalic brains of Ccdc151 knockout mice – a technique that uses X-rays to create a virtual 3D model of a target object. Additionally, a novel micro-CT method was used to study expression of the Ccdc151 gene in the brain. This novel method is based on the generation of a molecular signal within the mouse brain. The authors remarked that “this micro-CT imaging methodology could be applied to facilitate studies on gene expression directly in the intact brain carrying the lacZ reporter gene, which is widely used as a reporter gene in mouse models.”

The link between Ccdc151 and ciliary function is now clear, but the mechanism by which the Ccdc151 protein contributes is less so. “The precise mechanism by which Ccdc151 protein accomplishes its function is unknown and will be addressed in future research”, says Chiani. The Ccdc151-knockout mouse model, generated via IMPC resources, could be “instrumental to dissect the role of the motile cilia in diverse physiological processes during development, adult life and aging”.

In addition to providing biological resources that can contribute to research such as this, the IMPC is curating a catalogue of mammalian gene function, with phenotyping data for knockout mouse models such as Ccdc151.

Research paper: Functional loss of Ccdc151 leads to hydrocephalus in a mouse model of primary ciliary dyskinesia

Quotes taken from interview with Disease Models & Mechanism: First person – Francesco Chiani and Tiziana Orsini

CLOVES syndrome is a rare condition that is characterised by tissue overgrowth and vascular abnormalities, caused by mosaic gain-of-function mutations in the PIK3CA gene. The way in which CLOVES syndrome manifests itself is highly variable but common features include fatty overgrowths, vascular anomalies, kidney problems and spinal-related symptoms. The condition has no specific treatment and a low survival rate. It is one of a number of conditions that can be grouped under the umbrella of PIK3CA-related overgrowth syndromes (PROS).

By initially undertaking research on a mouse model, and subsequently with human patients, it has been shown by Dr Guillaume Canaud and his team at the Necker-Enfants Malades Hospital in Paris, that BYL719 (an inhibitor of PIK3CA, currently undergoing clinical trials for treating PIK3CA dependent tumours) can prevent and improve organ dysfunction and can improve disease symptoms in patients suffering from CLOVES syndrome.

A mouse model of CLOVES syndrome

The researchers generated mice that express a PIK3CA transgene upon the administration of tamoxifen, mimicking the activity of human CLOVES syndrome. These mice showed similar symptoms to human sufferers of CLOVES, with MRI revealing scoliosis, kidney cysts and muscle abnormalities. Subsequent histological examination revealed further organ abnormalities including additional kidney problems, and abnormalities in the liver and spleen. Furthermore, a high level of cell proliferation was observed in all of the affected organs.

Rapamycin or BYL719?

Rapamycin has previously shown evidence of improving vascular malformations, and when tested on the mouse model of CLOVES syndrome it improved survival rate. However, it did not improve organ abnormalities and did not significantly reduce tumour growth. In contrast, mice treated with BYL719 were found to have preserved tissues and normal vessels. Importantly, BYL719 administration strongly reduced cell proliferation in all affected organs. Withdrawal of BYL719 led to the recurrence of tumours within four weeks, suggesting that continuous administration of BYL719 could relieve the symptoms of CLOVES syndrome.

BYL719 leads to huge improvements in patients with CLOVES syndrome

BYL719 was initially administered to two patients suffering with CLOVES syndrome, who both, after being treated with BYL719, showed dramatic and rapid improvement in their condition. There was a major reduction of vascular tumour abnormalities and overgrowths in addition to improved renal function and a significantly increased quality of life in both patients. The only observed side-effect was hyperglycaemia, which was able to be controlled by a controlled diet.

On the basis of these initial results, Canaud and his team were given permission to treat 17 additional patients with CLOVES syndrome by administering BYL719. The 14 children and 3 adults all showed substantial clinical improvement. A reduction in size of vascular tumours was observed in all of the patients, as well as a drastic reduction in metabolic activity of affected areas. In addition to an improvement to skin capillary abnormalities and scoliosis, all patients reported decreased tiredness. The growth of the children was not affected during the 6 months of treatment and the only side-effects seen were discrete mouth ulcerations in 3 patients (that ultimately disappeared spontaneously) and the aforementioned hyperglycaemia.

The IMPC is aiming to design and produce a genome-wide mouse strain resource of human disease-associated coding variants associated with rare disease that can be used for validation of putative functional variants and insight into disease mechanism(s). To find out more, click here


Research paper: Targeted therapy in patients with PIK3CA-related overgrowth syndrome

Research published in Nature identifies SET domain protein 3 (SETD3) as a physiological actin methyltransferase, and uncovers SETD3’s crucial role in the regulation of smooth muscle contractility and its link to primary dystocia in mammals.

For many years it has been known that actin, essential for a large number of cellular processes such as cell motility and the regulation of DNA transcription, is methylated at the amino acid histidine 73 (His73). His73 methylation is found in several model organisms, but its function for many years had remained unclear. After identifying SETD3 as the methylator of actin His73, researchers sought to discover the purpose of actin His73 methylation, and with the help of some mice, they were successful.

Identifying the function of SETD3

To identify the enzymatic function of SETD3, the researchers performed in vitro methylation assays, which showed that the only potential substrate methylated by SETD3 was β-actin. The researchers were then able to identify the exact location of methylation on actin by SETD3 using tandem mass spectrometry. This turned out to be His73. In order to analyse the catalytic specificity of SETD3, the scientists compared methylation events in human cells both with and without the presence of SETD3. Of the 180 histidine methylated peptides, actin-His73 methylation was the only modification that was altered in the absence of SETD3 – identifying actin-His73 methylation as the primary physiological function of SETD3.

Studying SETD3 deficient mice

To confirm the physiological function of SETD3 in vivo, the researchers obtained mice with one copy of their Setd3 gene knocked out (Setd3+/-) from the Canadian Mouse Mutant Repository. The mouse strain was made at the Toronto Centre for Phenogenomics, an IMPC member institution, using embryonic stem cells. From this strain, it was possible to generate Setd3 null homozygote mice (Setd3-/-) i.e. mice with both of their copies of Setd3 knocked out. The methylation of actin wasn’t detected in any tissues obtained from SETD3-deficient mice, however, in tissues that expressed SETD3, the majority of actin was methylated – confirming the role of SETD3 as the actin His73 methyltransferase.

Actin methylation regulates actin polymerisation

Previous studies suggest that the methylation of His73 influences actin polymerization dynamics, and here the researchers observed that methylation promoted actin polymerization kinetics in vitro. To explore this idea further, they obtained mouse embryonic fibroblasts that were positive for actin-His73me and compared them with fibroblasts from Setd3-/- mice that lacked methylation. Cells containing methylated actin were more efficient at migrating than cells without methylated actin – consistent with the idea that methylation of actin by SETD3 positively regulates the polymerisation of actin.

Uterine cell contraction and primary dystocia

Mice without functioning SETD3 protein are able to survive, despite the cell migration defect observed in their embryonic fibroblasts. The researchers were able to infer therefore, that actin-His73me must have a specialised role that isn’t a necessity for survival. IMPC data for Setd3 identifies several phenotypes associated with Setd3 knockout mice including short tibia, decreased body length and decreased lean body mass. In addition to this, the researchers noticed that litter sizes in female Setd3-/- mice were significantly smaller than expected. After mating Setd3-/- females with wild type males, dystocia, normally a rare phenotype, was noted in 8 out of 9 Setd3-/- mice. The lack of obvious pelvic abnormalities in the Setd3-/- females mean that the cause of dystocia is most likely genetic. Unlike with wild type mice, early labour could not be induced in Setd3-/- mice with oxytocin, suggesting a specific requirement for SETD3 in the contraction of the uterus during labour, a process which relies upon correctly functioning actin. This led to the proposal that actin-His73me is linked to uterine cell contraction in the primary dystocia of SETD3 deficient mice.


More IMPC related research: Research Reveals Novel Genetic Influences On Osteoporosis


Research paper covered in this article: SETD3 is an actin histidine methyltransferase that prevents primary dystocia

Recent research, published in nature genetics, identifies novel genetic influences on osteoporosis, with the potential to empower future research on osteoporosis and potentially lead to new drug targets.

Osteoporosis is a condition that develops slowly over several years and leads to increased bone fragility. Fragile bones are more prone to fracture, with hip, wrist and spine bones being particularly vulnerable to breakage. Whilst there are many factors that affect the chances of an individual developing osteoporosis such as low body weight, certain medical conditions and age, the disease is highly heritable – you are much more likely to develop osteoporosis if your family has a history of the condition. By assessing the genetic determinants of bone mineral density (BMD), the most clinically relevant factor for diagnosis, the researchers were able to create an atlas of genetic influences on osteoporosis.

GWAS identifies gene loci linked to bone mineral density and fracture risk

Using UK Biobank data, the researchers carried out a genome-wide association study (GWAS), with the aim of identifying the common genetic variants associated with estimated bone mineral density (eBMD). The study found 518 genome-wide significant loci, with 301 of these being novel. Additionally, they undertook a GWAS aimed at identifying genetic loci linked with fracture risk. The results revealed 13 loci associated with risk of fracture. As might be expected, genetic variation associated with risk of fracture was also found to be associated with BMD i.e. alleles associated with low eBMD increased fracture risk.

Causal genes linked to genetic loci

Genetic associations in humans, however, rarely result in improved clinical care, usually due to a lack of identification of causal genes at the associated loci. With this in mind, the researchers tested the DNA locations associated with BMD and fracture risk, to see which features of the DNA linked to genes that are known to influence bone biology in humans. This resulted in a set of ‘Target Genes’ that are known to have an effect on bone density and strength in humans – prioritising genes at associated loci for functional testing.

Using mouse models for in-depth analysis

The study initially used mouse models to successfully test the validity of the identified Target Genes, with outlier phenotypes more frequent in mice with disruptions to 126 Target Genes compared with 526 unselected knockout lines. The in vivo and in vitro data produced thus far in the study converged to identify DAAM2 as a highly credible and novel osteoporosis gene.

After discovering that inducing a double strand break in the DAAM2 gene severely impairs mineralization in human bone cells, the researchers used mice obtained from the Wellcome Trust/Sanger Institute (generated as part of the IMPC, using ES cells) for in-depth characterisation of DAAM2. Mice with both versions of their DAAM2 gene disrupted (Daam2tm1a/tm1a) exhibited reduced vertebral bone mineral content accompanied by a small reduction in femur length.  Perhaps most significantly, the mutant mice also had markedly reduced bone strength. The increased cortical porosity observed in both male and female Daam2tm1a/tm1a mutants, along with the abnormal bone composition and structure exhibited, allowed the researchers to conclude that this decreased bone strength in Daam2tm1a/tm1a mice was not simply a result of abnormal bone turnover. If DAAM2 proves to be a viable drug target – it could result in a complementary therapeutic strategy for the prevention and treatment of osteoporosis.

The goal of the IMPC is to knock out and phenotype all 20,000 or so genes in the mouse genome, potentially providing major insights into unexplored areas of the mammalian genome. To order IMPC mice, click on the shopping cart on the top part of the gene page of interest or scroll down to “Order Mouse and ES Cells”.

IMPC Data

Details on more phenotype associations for DAAM2 can be found on the IMPC Daam2 gene page. Various phenotype association data can be found such as that shown below.


Research Paper: An atlas of genetic influences on osteoporosis in humans and mice

The inhibition of alkaptonuria by the chemical nitisinone in a mouse model led to a full-scale clinical trial funded by the European Commission – the results of which are expected to produce medicine for a condition for which there was previously no treatment available.

 

Alkaptonuria (AKU) is caused by a deficiency of homogentisate 1,2 dioxygenase, an enzyme that is required for breaking down the two amino acids tyrosine and phenylalanine. The lack of a functional copy of this enzyme results in a vast increase in circulating concentration of homogentisic acid (HGA), leading to a darkening of the urine upon exposure to air.

High levels of homogentisic acid within the human body eventually leads to ochronosis – a progressive pigmentation of connective tissues and eventually severe joint disease, which can become fatal later in life.

Whilst AKU is a serious condition, for many years it was not seen as prevalent enough among the population to be lucrative for drug developers. However, physicians had long suspected that nitisinone, a chemical that was first developed for use as a weed-killer, could be used to treat AKU – nitisinone was being used effectively to treat tyrosinemia (a condition that results from disruption to the same metabolic pathway as AKU).

There was a small-scale clinical trial run in the US between 2005 and 2008, but too few patients were recruited and the clinical endpoint (the success of the treatment) was defined very narrowly. No positive results were obtained.

In order for a clinical trial to succeed, a more reliable endpoint would have to be suggested, and this required more knowledge of how the disease developed. With this in mind, funding obtained from Britain’s Big Lottery Fund went to a research team at the University of Liverpool to develop a mouse model of AKU.

A colony of Hgd-/- (the genetic equivalent of human AKU) mice were bred by the research team in Liverpool and the mice were established as a model of the plasma biochemistry of AKU and its associated arthropathy. The concentration of plasma HGA was found to be 0.149 ± 0.019 mM, whilst HGA levels in WT mice were below the level of UV detection. The researchers were also able to determine that pigmentation of connective tissue increased linearly with increasing age. Perhaps most importantly though, a significant difference was found between HGA concentrations before and after treatment with nitisinone. Levels of plasma HGA dropped by 88% – a figure that was maintained over the mouse lifetime, with joint tissue from nitisinone-treated AKU mice showing no pigmented tissue.

The results of this mouse model study led to a full-scale clinical trial, funded by the European Commission, with use of nitisinone as a treatment for AKU expected to be approved across Europe once the trial comes to an end.

The aim of the IMPC is to generate similar knock out lines – on a much broader scale, with the goal of producing knock out mutations in embryonic stem cells for 20,000 known and predicted mouse genes, and determining the function of each of these genes. The mouse’s genetic similarity to humans (95% at the gene level) means that data generated by the IMPC could be a powerful tool as we seek to understand the genetic basis of human disease. As our knowledge of rare genetic diseases increases in line with rapid technological advancement, the desire for treatments targeted to small groups of sufferers with these diseases will also likely increase – the case involving alkaptonuria is likely to be just one instance of a mouse model proving to be a driver behind new treatments.


Research article: Ochronotic osteoarthropathy in a mouse model of alkaptonuria, and its inhibition by nitisinone

 

By Kathryn Hentges and Andrew Doig

Essential genes are those that are required for an organism to survive. We have been interested in studying genes that are essential during development, which could be viewed as the genetic basis for building an organism. Developmentally essential genes thus produce lethal phenotypes in knockout experiments. In some organisms with small genomes and experimental accessibility, essential genes have been identified through direct testing. Although the IMPC is in the process of determining gene function for all protein coding genes in the mouse genome, at present thousands of genes have not yet been tested. To identify essential genes on a genome-wide scale, and also determine the properties that distinguish essential genes from non-essential genes, we utilized machine learning to predict the essentiality status of all mouse protein coding genes that lack experimental data at present.

To generate a machine learning classifier for mouse gene essentiality, we compiled a list of approximately 1300 known essential mouse genes and approximately 3400 known non-essential mouse genes, previously studied in knockout experiments.  A set of features, which included genomic, proteomic, and expression data, were obtained for each gene in the genome. We then used machine learning to find features that were likely to be associated with essential genes and those that were not likely to be associated with essential genes. We found that features associated with intracellular functions, such as transcriptional regulation, were highly likely to be associated with essential genes, and those associated with cellular interactions, such as extra cellular signaling, were likely to be found in non-essential genes. Using these features, our classifier was used to predict the essentiality status of all protein coding genes in the mouse genome.  We confirmed that our classification predictions were accurate by checking our predictions against experimental results that were generated by the IMPC during the course of our study and hence not included in our initial gene sets.  This comparison showed that our machine learning classifier was correct for approximately 80% of genes. Our results can be found at http://essentiality.ls.manchester.ac.uk.

Additionally, we compared our findings on mouse essential genes to studies of human essential genes.  Orthologous genes in both species tended to have the same essentiality status. Overall, features enriched in essential and non-essential mouse genes were enriched in human genes of the same essentiality status.  Due to this conservation in function, our predictions may be useful for identification of human gene essentiality and understanding the functions required for mammalian development.  Our predictions can also aid investigators planning mouse knockout experiments by giving an indication of whether a lethal phenotype is likely to result from creating a null allele of the gene of interest.


Original Publication: Tian D, Wenlock S, Kabir M, Tzotzos G, Doig AJ, Hentges KE. Identifying mouse developmental essential genes using machine learning. Dis Model Mech. 2018 Dec 13;11(12). pii: dmm034546. doi: 10.1242/dmm.034546. PMID:30563825

For the first time scientists have identified how to halt kidney disease in a life-limiting genetic condition, which may pave the way for personalised treatment in the future. Researchers at Newcastle University, UK, have shown in a cell model and in a mouse model that gene editing could be used for Joubert syndrome to stop kidney damage in patients who have the CEP290 faulty gene.

Joubert syndrome is a brain disorder, causing varying degrees of physical, mental and sometimes visual impairments. The condition affects approximately one in 80,000 newborns, and one third also get kidney failure. Not all patients with Joubert syndrome carry the CEP290 gene, but those who do will develop kidney disease during their lifetime and may require a transplant or dialysis.

The study, which was funded by Kidney Research UK, has found it is possible to use a strand of engineered DNA to trick the cells’ own editing machinery to bypass the CEP290 mutation that causes kidney damage – a technique known as ‘exon-skipping’.

Professor John Sayer, from the Institute of Genetic Medicine, Newcastle University, led the research that is published in the Proceedings of the National Academy of Sciences (PNAS). He said: “This is the first time that gene editing within the kidney has been performed, even in a mouse model, as the design and delivery of the gene editing to the kidney has previously been thought to be too difficult.

“Our research is a major step forwards as we now know how we may be able to offer a therapy that corrects the gene mistake within kidney cells and prevent the development of genetic kidney disease.

“This work paves the way towards personalised genetic therapies in patients with the inherited kidney disease.”

The European study used kidney cells from patients with Joubert syndrome and a mouse model to progress the research. Experts used urine samples to grow kidney cells in the laboratory to see how the cells responded to gene editing. They also performed gene editing to halt kidney disease in a mouse that had Joubert syndrome and rodents suffering from kidney cysts and kidney failure.

Scientists are now looking to work with a drug manufacturing company to bring the exon-skipping technology into patients’ clinics.

Research article: Targeted exon skipping of a CEP290 mutation rescues Joubert syndrome phenotypes in vitro and in a murine model

ASHG 2018 Annual Meeting – research using mouse models

Guest post by Bum-Jun Kim (ASHG talk: Wednesday, 4:30pm – 4:45pm in Room 6D)

1p36 deletion syndrome is a genetic disorder caused by deletion of specific regions in p arm of chromosome 1 (1p36). Deletion of chromosome 1p36 is one of the most common terminal deletions in humans and found in children with incidence of 1 in 5,000 newborns. People carrying terminal or interstitial deletions have problems in the heart, the brain, growth, vision, and intelligence. A few genes are suggested as a causative gene for defects seen in 1p36 deletion syndrome due to wide range of deletion length. We have unveiled that RERE is one of the causative genes for symptoms seen in these individuals by using the mouse models (RERE-deficient mice) in which function of RERE is limited. RERE-deficient mice show similar defects developed in 1p36 deletion syndrome. We also described that individuals with single mutations in RERE gene present many of defects seen in 1p36 deletion syndrome.

Congenital heart defect is seen in approximately 70% of individuals with 1p36 deletions, with 23% having ventricular septal defects (VSDs), and 28% having atrial septal defects (ASDs). We have described that RERE-deficient mice also show VSDs with other congenital heart defects. In order to understand how RERE deficiency develops VSDs, we investigated RERE-deficient mice and heart specific RERE-deficient mice in which Rere is ablated from the heart by Tie2 Cre. In wild type mice, the atrioventricular cushions (AVCs) are filled with mesenchymal cells produced by epithelial-to-mesenchymal transition (EMT) and contribute to complete development of ventricular septum. However, RERE-deficient mice show decreased number of mesenchymal cells and abnormal EMT in the AVCs, which leads VSDs. Heart specific RERE deficiency also results in same defects seen in the heart of RERE-deficient mice. A gene called, Gata4 is known to be important for development of the heart and ablation of GATA4 in the heart causes similar phenotypes developed in the heart of RERE-deficient mice. Expression of Gata4 is reduced in the heart of RERE-deficient mice. In addition, we demonstrated that RERE regulates transcriptional activity of Gata4 promoter in vitro systems. The main finding of this study is that RERE-deficiency leads to decrease of GATA4 expression and development of VSDs with abnormal EMT.

Our research is currently published in Disease Models & Mechanisms 2018

ASHG 2018 Annual Meeting – research using mouse models

Guest post by John Morris (ASHG talk: Wed Oct 17, 9:00am – 9:15am in Room 6D)

Osteoporosis is a common, aging-related disease characterized by decreased bone strength and, consequently, increased fracture risk. Bone mineral density (BMD), a non-invasive measurement, is the most clinically relevant risk factor for diagnosing osteoporosis and is highly heritable (i.e. determined by genetics). To understand the genetic determinants of osteoporosis, we performed a genome-wide association study (GWAS) in 426,824 UK Biobank participants to identify regions of the genome associated with BMD estimated from quantitative heel ultrasound (eBMD). This approach is unbiased in that it systematically tests millions of single nucleotide polymorphisms (SNPs) in the human genome—sites of common, uncommon, or rare genetic variation in the general population—for association with eBMD measurements. BMD-associated SNPs can then be used to identify novel bone genes, but such genes would require further study in human cells or animal models to understand their function. Therefore, we collaborated with the Origins of Bone and Cartilage Disease (OBCD, www.boneandcartilage.com) to examine genes in knockout mice. Such genes, when validated by knockout mouse skeletal phenotyping, represent strong candidates for developing new therapies to prevent and treat osteoporosis.

Our eBMD GWAS identified 518 significant regions of the genome, 301 of which were novel findings. Next, to identify target genes, we performed statistical fine-mapping and integrative bone cell functional genomics data analyses. First, by leveraging SNP association summary statistics and SNP-by-SNP correlations, we can identify a subset of plausibly causal SNPs. Then, by intersecting this list of plausibly causal SNPs with genomic characteristics that indicate function (e.g. coding SNPs, osteoblast open chromatin, osteoblast 3D contacts with gene promoters), we can identify a list of target genes likely to be functional in bone cells. These orthogonal approaches resulted in a list of 515 target genes, identified by plausibly causal and putatively functional SNPs, that we found were strongly enriched for known bone genes and osteoporosis drug targets. We sought to examine the effects of as many of these genes as possible in knockout mice and found the OBCD had skeletal phenotyping data on 126. Importantly, the OBCD receives all knockout mouse lines for skeletal phenotyping at random from the International Mouse Phenotyping Consortium (IMPC), therefore it is not known beforehand if a given knockout mouse has a skeletal phenotype. These 126 genes were found to be enriched for outlier skeletal phenotypes, providing strong evidence that our target genes are disease-relevant, and we focused on one such gene in further detail: disheveled-associated activator of morphogenesis 2 (DAAM2).

Mice with hypomorphic Daam2 alleles were found to have increased cortical porosity and markedly reduced bone strength, even though all other cortical bone parameters, including BMD, were normal. We performed further analyses on DAAM2, such as CRISPR-Cas9 mediated knockouts in human osteoblast cell lines, revealing a decreased ability of this crucial bone-forming cell to mineralize. We concluded that DAAM2 is a novel risk gene for osteoporosis meriting further study and highlighted five other strong candidates for follow-up: CBX1, WAC, DSCC1, RGCC, and YWHAE. In summary, we have generated an atlas of genetic influences on osteoporosis in humans and mice, more fully describing its genetic architecture. Human and mouse genetics identified DAAM2 and other genes previously unknown to function in bone biology. We expect the genes identified here to include new drug targets for the treatment of osteoporosis, where novel therapeutic options are a health priority.

Our work is currently available on bioRxiv at www.biorxiv.org/content/early/2018/07/27/338863

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By IMPC

Published 11th October 2018

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