PLACENTAL DEFECTS ARE HIGHLY PREVALENT IN EMBRYONIC LETHALS

It is widely known that a functional placenta is vital for normal embryonic development, but how much it may contribute to embryonic lethality has never before been systematically studied. Our research, published in Nature, demonstrates for the first time a remarkable co-association between embryonic lethality and placental defects.


A healthy placenta is vital to sustain normal pregnancy, ensuring proper supply of nutrients and oxygen to the baby. Abnormalities in the placenta can therefore have serious repercussions on fetal development, even causing miscarriage. Despite this, remarkably little is known about the identity of genes essential for a normal, functioning placenta and even less about the extent to which placental abnormalities contribute to defects that can arise as the fetus develops.

EXTENT AND IMPACT

We screened more than 100 mouse mutant lines in which affected embryos die before or immediately at birth. Almost 70% showed serious abnormalities in the placenta; in extreme cases this resulted in a placenta incapable of supporting embryo development beyond an early stage (Figure 1), in others, abnormalities in the developing embryo were accompanied by abnormalities in the placenta.

FIGURE 1 – mouse mid-gestation embryos and placentas shown at the same magnification


LEFT: a normal, wild-type (WT) genotype. RIGHT: Nubpl mutation (MUT) shows a growth-retarded and developmentally delayed embryo that will not survive until birth.

The placentas are stained for a marker of the exchange surface (MCT4, in green) across which nutrients are transported from the mother to the embryo. Note the complete absence of this cell type from the MUT placenta. Red staining is for a cell surface protein (CDH1) demarcating the cells underneath the MCT4-positive layer (arrows), which are greatly reduced in number in the MUT placenta.

EMBRYO AND PLACENTA DEFECTS ARE LINKED

Not only do these results identify a large number of genes essential for normal development of the placenta; in addition they show an intriguing link between placental defects and abnormalities affecting the brain , heart and vascular system of the embryo itself. The research, led by Dr Myriam Hemberger and her colleagues at the Babraham Institute demonstrates how common placental abnormalities are when embryos develop abnormally.

RESCUING EMBRYONIC LETHALITY

The team examined in detail three different genes that cause embryonic lethality, and showed that for two of them the loss of the gene affected proper differentiation of placental cell types. For one of these genes they were also able to show that embryo death was a direct result of gene loss in the placenta, by providing the mutant embryo with a genetically normal placenta, which prevented embryo death.

Although the DMDD study uses mice, the results are likely to be just as relevant for studying human pregnancy and the role the placenta may play in pregnancy complications and the origins of birth defects in newborn babies.


REFERENCES

The Advance Online Publication on Nature, ‘Placentation defects are highly prevalent in embryonic lethal mouse mutants is available now .


All image and phenotype data gathered by the DMDD programme is freely available to the scientific community at dmdd.org.uk. The research described in this blog post was funded by the Wellcome Trust with support from the Francis Crick Institute.

LATEST DATA RELEASE HIGHLIGHTS INCLUDING NEW HEART DEFECT ASSOCIATIONS

Our latest data release includes HREM image data for an additional 5 lines, and HREM phenotyping data for 4 lines. Five additional early lethal lines have also been identified, as well as placental phenotype data for more than 100 mutant lines, with associated placenta morphology and yolk sac images.

Throughout the DMDD project we continue to add data for existing lines, and in this release we have added P14 viability for mutant lines, Theiler stage (where assessed), and the voxel size of each HREM image stack.

Initial analysis of the new HREM phenotyping data shows two lines newly associated with heart defects.


Oaz1 ASSOCIATED WITH DORV

Oaz1 is a gene regulating levels of polyamines within the cell and is widely distributed in cells and tissues of the body. Our data now shows that removal of this gene causes a serious abnormality in heart development in which the vessel normally carrying blood from the left ventricle of the heart (the aorta) is in fact attached to the right ventricle (a defect known as “double outlet right ventricle” or DORV). As with many mutant lines, the embryos also show extensive swelling of the body (“edema”).

Left panel: a view of the heart seen from the right side and showing both the pulmonary trunk (red arrow) and the aorta (yellow arrow) drain from the right ventricle. Right panel: a cross section through the body at the level of the heart shows the extent of swelling (arrows) in tissue beneath the skin.

 


Cc2d2a ASSOCIATED WITH VSD AND OSTIUM PRIMUM DEFECT

Cc2d2a encodes a protein that plays a critical role in formation of cell cilia and mutations in this gene are associated with diseases such as Meckel syndrome type 6, which results in a broad range of symptoms such as polydactyly, cleft palate and kidney malformations. Our data reveals that removal of the Cc2d2a gene also has profound effects on heart development. Not only do the embryo hearts fail to complete separation of the left and right ventricular chambers (a “ventricular septal defect”), they also fail to form a proper wall between the left and right atrial chambers (an “ostium primum defect”). In addition, they have lost a swath of tissue at the junction between the atria and ventricles (the “vestibular spine”) that is essential for completing chamber separation.

Shows three views of the embryo heart. The lefthand panel shows the ventricular septal defect; the middle panel shows the osmium primum defect and the right panel shows the absence of vestibular spine tissue which normally enables the atrial and ventricular septal walls to attach to each other.

Many of the genes studied by DMDD do not currently appear to be associated with any disease, however careful analysis of the phenotypes from lines such as these could contribute to the identification of new disease models, and our data is freely available at dmdd.org.uk in order to encourage this. For more information please email contact@dmdd.org.uk.


A FULL LIST OF NEW DATA IN THE LATEST RELEASE

9.5 MILLION EMBRYO IMAGES NOW AVAILABLE

A new set of DMDD embryo and placenta data has been released today, taking our total dataset to 9.5 million images of around 1300 embryos. Phenotypes are available for embryos from 73 different knockout lines, and we have phenotyped the placentas from 124 lines. We have also added data on the sex of each embryo.

Visitors to our website can now compare HREM embryo images with the closest-matching, annotated histological section from the Kaufman Atlas of Mouse Development. This follows a major project by the eMouseAtlas team at the University of Edinburgh to digitise the Kaufman Atlas at high resolution. The annotated Kaufman sections can be viewed alongside DMDD embryo images to help users who are unfamiliar with the detailed morphological features of a mouse embryo as it develops.

All DMDD data can be freely accessed at dmdd.org.uk, or you can continue reading for highlights from the latest lines to be made publicly available.


SEVERE BRAIN PHENOTYPES

Phenotyping of Hmgxb3 knockout embryos revealed severe brain defects, with half of the embryos displaying exencephaly. Embryos from this line also had a range of phenotypes including edema, abnormalities of the optic cup, and defects of the venous system including an abnormal ductus venosus valve and blood in the lymph vessels.

 

Click to view larger image.
An Hmgxb3 homozygous knockout embryo displays exencephaly.

 


 

POTENTIAL MODELS OF HUMAN DISEASE

A number of genes studied by DMDD have already been associated with human diseases. For example, Prmt7 mutations have been associated with Short Stature Brachydactyly Obesity Global Developmental Delay Syndrome, an autosomal recessive disease characterised by developmental delay, learning disabilities, mild mental retardation, delayed speech, and skeletal abnormalities. Strikingly, in the Prmt7 knockout embryos studied, the most common phenotypes included neuroma of the motoric part of the trigeminal nerve (a tumour within the skull, affecting the nerve controlling the jaw movements needed for speaking and chewing) and abnormalities of the hypoglossal nerve (which controls movement of the tongue) and the ribs.

Image data has been added for both Cc2d2a and Xpnpep1 knockouts. Mutations of the Cc2d2a gene are known to cause Meckel and Joubert syndromes, while Xpnpep1 has been associated with billiary atresia.

Many of the genes studied by DMDD do not currently appear to be associated with any disease, for example Hmgxb3 or Cbx6. There is potential that careful analysis of the phenotypes from lines such as these could contribute to the identification of new disease models, and our data is freely available in order to encourage this.


A DETAILED DESCRIPTION OF NORMAL MOUSE EMBRYO DEVELOPMENT

The Atlas of Mouse Development by Professor Matthew Kaufman describes normal mouse embryo anatomy using a series of hundreds of annotated histological sections. Even today, twenty three years after its publication, it is still considered to be the gold standard for describing mouse embryo development. As part of a project to update the book in 2012, the original sections were digitised by the Edinburgh Mouse Atlas Group and made freely available on their eHistology resource.

The images have now been integrated into the DMDD database, and users can directly compare any HREM embryo image with the closest-matching annotated Kaufman section.

 

Click to view larger image.
Each HREM embryo image can now be viewed alongside the closest-matching section from the Kaufman Atlas of Mouse Development.

 

This new feature is intended to help users who are not fully confident of the details of mouse developmental anatomy. It means that mutant mouse data can now be explored alongside a fully-annotated wild-type reference point.


A FULL LIST OF NEW DATA

Embryo phenotype data added for: Hmgxb3 and Prmt7

Embryo image data added for: Cbx6, Cc2d2aHmgxb3, Prmt7 and Xpnpep1

Placenta images and phenotypes added for: Mir96

To explore the data, visit dmdd.org.uk or for more information please email contact@dmdd.org.uk.

HOW MICE ARE KEY TO UNDERSTANDING GENETIC HEART CONDITIONS

Nearly 1 in every 100 babies is born with a heart defect. These are the most common type of birth defect and can range from simple, symptomless cases to life-threatening conditions that require treatment within hours of birth.

Environmental influences such as excessive alcohol consumption or exposure to other toxins are known to cause heart defects. But many are also the result of faulty genes that can be passed on from one generation to the next. Identifying the genes involved is key to understanding when a baby might be at risk, and could also help us develop new ways to treat or prevent these heart defects. But with more than 20,000 genes in the human genome there are a mind-boggling number of possibilities.

A screen of mouse embryos by the DMDD programme (Deciphering the Mechanisms of Developmental Disorders) has identified a huge number of genes related to heart defects and other developmental abnormalities, and is now a potential goldmine of information on the genetic basis of heart conditions. Part of an open data initiative by the Wellcome Trust, the project has made all of its data available online, with a goal to spark further research into heart defects and rare disease.

 

Click to view larger image
Photographs of isolated mouse embryo hearts. On the right is a ‘normal’ heart — this mouse was not missing any genes. On the left, due to a missing gene, the heart has a defect called ‘Double Outlet Right Ventricle’. Here, the heart’s two major arteries (the pulmonary artery and the aorta) both connect to the right ventricle. In a normal heart the aorta connects to the left ventricle.

INACTIVATING GENES TO UNDERSTAND RARE DISEASE

The DMDD team studies mouse embryos that have been bred to have a single one of their 20,000 genes inactivated – a process that’s known as knocking out a gene. As each embryo grows, any abnormalities in the way it develops are likely to be due to the missing gene and this provides powerful information about the sort of birth defects that the gene could be linked to. Although we might look very different, mice and humans are thought to share around 98% of our genes, so the effects of a missing gene on a developing mouse can tell us a lot about what we might expect if the same faulty gene is found in humans.

We concentrate specifically on genes that when knocked out cause a mouse embryo to die before birth.  On the face of it, studying these genes might not seem so important to people living with rare genetic diseases – these people have already survived past birth. But genes like these are a rich source of information about human genetic diseases.

Many rare disease patients have mutations that act as genetic dimmer switches, increasing or decreasing a gene’s activity rather than completely turning it off. A particular gene may only be partially turned on (called a hypomorph mutation) or it may be turned on more than normal (known as a hypermorph mutation). If we are able to understand the effect of fully turning off a gene, we can then begin to infer what might happen to patients who have a hypomorph or hypermorph mutation.

 

Like genetic dimmer switches, gene mutations can increase or decrease the activity of a gene, or knock it out completely.

 

By the end of the project, DMDD will have studied the effects of 250 different gene knockouts – it’s a huge opportunity to learn more about genetic causes of rare diseases in humans. And the biggest surprise in the results so far is the overwhelming prevalence of defects in the developing embryo hearts.


IDENTIFYING HEART DEFECTS

So far the team have analysed more than 200 embryos, each with one of 42 different genes knocked out. But unexpectedly, more than 80% of the gene deletions resulted in heart defects. Using an imaging technique called High Resolution Episcopic Microscopy the embryos were reconstructed in incredible 3D detail and studied down to the level of individual nerves and blood vessels. In the image below, the developing embryo heart is less than 2 mm across – smaller than the thickness of a matchstick – yet even the tiniest abnormality can be picked up.

“Even though we know that heart defects are common, we were really surprised that they were caused by more than 80% of our gene deletions. The data is a potential goldmine of information about the genetic basis of many different types of heart condition.” Dr Tim Mohun, DMDD.

 

Click to view larger image.
A 3D model of a mouse embryo heart using data from High Resolution Episcopic Microscopy.

 

The most common defects were problems with the walls that separate the right and left chambers of the heart. But there were also many defects in the heart valves, the outflow vessels (which carry blood out of the heart to the body or the lungs) and in the structure of the heart itself.

Several of the gene knockouts result in developmental defects that mimic known human genetic disorders. For example knocking out the genes Psph or Psat1 causes a range of developmental defects that appear similar to Neu-Laxova syndrome, a serious condition that leads to miscarriage or neonatal death. Tim Mohun commented “we know that many rare genetic diseases cause problems with the heart as it develops. Having so much new data about heart defects is exciting, because there is the potential for us to learn more about rare disease.”


THE PLACENTA: A NEW WAY TO UNDERSTAND THE HEART?

In the first study of its kind the placentas from a large collection of knockout embryos have also been analysed, and the results show an unexpected link between the placenta and the heart. Around a third of gene knockouts that cause placental abnormalities also cause a heart defect in the developing embryo. A more detailed statistical study of the data (publication in progress) has shown that this is a genuine link. Myriam Hemberger of the Babraham Institute, who performed the work as part of the DMDD programme, said “it could be that the restricted nutrient supply or blood circulation defects caused by an abnormal placenta adversely affect heart development. It does suggest there is more we could learn about some rare heart conditions by studying the placenta.

 [The results] suggest there is more we could learn about some rare heart conditions by studying the placenta. Myriam Hemberger, DMDD.


Initial analysis of the DMDD embryo and placenta data has shown it to be a rich resource for those studying rare disease and developmental disorders. But, unexpectedly, it may shed particular light onto the genetic basis of heart disease.

All data from the DMDD programme is freely available at dmdd.org.uk. For further information please email contact@dmdd.org.uk.

 

NEW DATA REVEALS HOW GENE KNOCKOUTS AFFECT WHOLE EMBRYO GENE EXPRESSION

New DMDD data released on Expression Atlas today reveals the effect of single gene knockouts on the expression of all other genes in the mouse genome. The gene expression profiles of 11 knockout lines have been derived from whole embryos harvested at E9.5, and the results can be compared with wild-type controls using an interactive online tool. Users can investigate which genes are differentially expressed as a result of a gene knockout, with the potential to uncover genes with similar roles or compensatory effects when a related gene is knocked out.

Data for additional lines will be released throughout 2017. The ultimate goal is to bring these molecular phenotypes together with the morphological phenotypes that have already been derived by the DMDD programme, to offer new insights about the effects of gene knockout on embryo development.


THE GENOMIC EFFECTS OF Ssr2 KNOCKOUT

The knockout of Ssr2 in the mouse was found to affect the expression level of 325 genes in total, and this is one of the 11 new datasets that can be explored in Expression Atlas.

The differential expression of each gene is described using the log2 fold change – a measure that describes the ratio of gene expression in the knockout to the level of gene expression in a wild-type control. A negative fold change (shown in blue in the image below) means that the gene was expressed at a lower level in the mutant. A positive fold change (shown in red in the image below) means that the gene was expressed at a higher level in the mutant.

 

A visualisation of the level of differential expression of 8 genes affected by the knockout of Ssr2.
Eight genes that are differentially expressed due to a knockout of the gene Ssr2 (above a cut off log2 fold change of 0.4). Six genes are expressed at a higher level, while Mfap2 and Ssr2 are expressed at a lower level.

 

The interactive tool in Expression Atlas allows different cut-offs to be applied to the fold change, so the genes displayed can be restricted to those with a large differential expression. The image above shows the 8 genes with a fold change greater than 0.4 as a result of knocking out the gene Ssr2.

The tool can also be used to visualise the data in graphical form. The plot below shows the fold change for each gene, allowing the user to quickly ascertain the extent to which a gene knockout caused differential expression of other genes. All 325 genes considered to have a significant change in the level of gene expression are plotted in red, with the rest shown in grey.

 

Graphical visualisation of the fold change for each gene in the mouse genome, following knockout of the Ssr2 gene.
A graphical visualisation of the fold change for each gene. The outlier with a fold change of -3.5 is the gene Ssr2, which has a much-reduced expression level in an Ssr2 knockout embryo.

 


The full list of lines with data currently available is: 1700007K13Rik, 4933434E20Rik, Adamts3, Anks6, Camsap3, Cnot4, Cyp11a1, Mir96, Otud7b, Pdzk1 and Ssr2.

The full dataset for any line can be downloaded for further analysis, while the individual line pages on Expression Atlas integrate the DMDD data with other pre-existing data, in cases where a gene has already been shown to alter expression.

MEET THE DMDD TEAM – DAVID ADAMS

Dr David Adams.In a series of interviews we’re hearing from members of the DMDD programme. Who are they? What inspires them? And what do they hope that DMDD will achieve? This month we hear from David Adams, who oversees the production of embryonic lethal knockout mouse strains for the project.


What has been your main area of research in your career so far?

I lead the Mouse Programme (MGP) at the Wellcome Trust Sanger Institute, which generates around 200 genetically modified mouse strains each year. The MGP explores the role of genes in a range of biological processes including in development, immunology and infection, and in metabolism and cancer. I am primarily a cancer geneticist interested in how the immune system controls tumour growth and the genetic wiring of cancer cells. Remarkably this had led me to explore aspects of developmental biology as we try and understand what these genes do.

 

What inspired you to devote your career to developing animal models of human disease

In all areas of medicine and biology, animal models have contributed significantly to our understanding of disease processes. For example, our understanding of the fundamentals of how the immune system recognises pathogens and cancer result from experiments in mice. The development of induced pluripotent stem cells, which appear to have huge potential in regenerative medicine, was also pioneered in mice. If that’s not enough, the role of literally thousands of mammalian genes in development has been elucidated in mouse model systems. The contribution has been huge. Further, virtually every drug approved for treating patients was tested in rodent models.

 

What do you think is the most exciting recent development in your field?

This has to be CRISPR. The ability to rapidly alter the genome with unprecedented precision makes generating new animal models significantly easier. In particular, we are able to introduce point mutations found in patients to essentially humanise the mouse genome.

 

What is the biggest outstanding problem in your field that you wish could be solved?

There are still many many genes where we don’t have even the most basic understanding of their role in development or disease. Cell culture systems will undoubtedly contribute to further understanding, as will the analysis of human tissues, but to really understand what a gene does you need to manipulate it in the context of the whole organism and see what happens. We call this the post-genomics era but in fact we are still very much living in a time where we don’t know how the genome works and how individual genes function. I think there are many surprises and delights still to be found.

 

Why did you decide to become involved with the DMDD programme?

My role is to represent the Sanger Institute as a member of the DMDD programme. The DMDD is a group of world-leading investigators using cutting edge technology to explore processes involved in development and embryonic lethality. I find the idea of contributing to such a large-scale co-operative endeavour very compelling. It is also wonderful that the data is released to the research community to facilitate further discovery.

 

What do you hope the DMDD programme will achieve?

So far there have been some big surprises. In particular, the significance of the placenta in development and the high frequency of cardiac malformations in developmental disorders have been a surprise to me. Large-scale programmes such as the DMDD that make no assumptions about how genes work or what they do have the potential to challenge dogma, and that’s what I think the DMDD is achieving.

 

If you could have been a fly on the wall during any scientific discovery, which would you choose?

I have a particular interest in how the immune system regulates the growth of cancers. In the last few years there have been substantial advances in understanding how T-cells control tumour growth. I would love to have been involved in, or seen first-hand, the development of T-cell checkpoint therapies because these are truly changing people’s lives and a proportion of patients with advanced disease are being cured.

 

What are you most proud of achieving outside of science?

I have two delightful children, which is a surprise given my genetic contribution. I am also a keen runner like other members of the DMDD (Tim Mohun and Jim Smith) and routinely run 20 km a week. I am currently training for the Cambridge Half Marathon.

 

Tell us a surprising fact about yourself

I used to breed, raise, and show chickens as a child. I guess this was probably the basis for my interest in genetics. Like everything I do I was extremely competitive.

 

David Adams is a Senior Group Leader at the Wellcome Trust Sanger Institute, and a joint grant holder for the DMDD programme.

NEW EMBRYO PHENOTYPE DATA AVAILABLE

New image and phenotype data for embryos and placentas from embryonic lethal knockout mouse lines has been made available on the DMDD website today. The knockout data includes the ciliary gene Rpgrip1l as well as Atg16l1, a gene encoding a protein that forms part of a larger complex needed for autophagy. In total we have added HREM image data for 10 new lines, embryo phenotypes for 11 lines and placenta image and phenotype data for 6 lines.

The new data was released at the same time as enhancements to our website, which have been described in a separate blog post. Keep reading to see some highlights from the phenotype data.


DETAILED EMBRYO PHENOTYPES REVEALED

The comprehensive and detailed nature of DMDD embryo phenotyping means that we are able to identify a wide range of abnormalities. In the data released today, a total of 423 phenotypes were scored across 78 embryos. These included gross morphological defects such as exencephaly and edema, but also abormalities on a much smaller scale such as an unusually small dorsal root ganglion, absent hypoglossal nerve and narrowing of the semicircular ear canal.

In the image below, a Trim45 embryo at E14.5, was found to have abnormal optic cup morphology and aphakia (a missing lens).

Click to view larger image.
HREM imaging of a Trim45 knockout embryo reveals abnormal optic cup morphology and aphakia on the left side.

3D modelling of the exterior of an Rpgrip1l knockout embryo at E14.5 revealed a cleft upper lip, as well as polydactyly.

Click to view larger image.
A 3D HREM model of an Rpgrip1l embryo shows a cleft upper lip.

All phenotypes are searchable on the DMDD website, highlighted on relevant images, and the full-resolution image data is available to explore online.


SYSTEMATIC PLACENTAL ANALYSIS

DMDD also carries out systematic phenotyping of the placentas from knockout lines. The image below shows a Cfap53 knockout placenta at E14.5, which was found to have an aberrant fibrotic lesion. The density of fetal blood vessels was also considerably reduced, the overall effect being to reduce the nutrient flow from mother to embryo.

Click to view larger image.
Placental histology for the line Cfap53 shows a fibrotic lesion (large arrow) and several regions of reduced blood vessel density (small arrows).

 


GENE EXPRESSION PROFILES

Work is underway to measure the gene expression profiles for embryos from embryonic lethal knockout lines, a study that complements the morphological phenotype data we are gathering. One of our ultimate goals is to allow data users to explore correlations between gene, morphological phenotype and gene expression profile. The first part of this dataset was released recently – a temporal baseline gene expression profile for wild type embryos.

Click to view larger image
Example expression profiles of Nacad and Pdzk1 with increasing somite number. The data shows that, at this depth of sequencing, Nacad is switched on during somitogenesis and Pdzk1 is switched off.

 

The expression data is now accessible via a dedicated wild type gene expression profiling page on the DMDD website, which also gives background information about the analysis. Mutant expression data will follow in the new year.


LINKS BETWEEN DMDD GENES AND HUMAN DISEASE

Many of the genes studied by the DMDD programme are known to have links to human disease, including several new lines that have been made available in this release.

Rpgripl1: in humans, mutations in RPGRIPL1 are known to cause Joubert Syndrome (type 7) and Meckel Syndrome (type 5), a rare disorder affecting the cerebellum.

Cfap53: the human ortholog of this gene is known to be associated with visceral heterotaxy-6, in which organs have an abnormal placement and/or orientation.

Arhgef7: in humans the ortholog is associated with Borjeson-Forssman-Lehmann Syndrome.

Arid1b: in humans, mutations in ARID1B are associated with Coffin-Siris Syndrome.

Embryonic lethal lines with no known links to human disease may also be novel candidate genes for undiagnosed genetic disorders. Visit the DMDD website to explore the phenotype data.


A FULL LIST OF NEW DATA

HREM embryo image data has been added for Actn4, Arid1b, Cfap53, Crim1, Cyp11a1, Dmxl2, Fut8, Gas2l2, Mfsd7c, Rala.

Embryo phenotype data has been added for Atg16l1, Capza2, Coro1c, Crim1, Cyfip2Gas2l2, Gm5544Rala, Rpgrip1l, Syt1, Trim45.

Placenta image and phenotype data has been added for Arhgef7, Arid1b, Fam21, Fut8, Med23, Timmdc1.

If you have questions about the DMDD programme or our data, please email contact@dmdd.org.uk.

3 NEW RESULTS FROM KNOCKOUT MOUSE SCREENS

Around a third of mammalian genes are essential for life, and the recent Nature paper from the IMPC  ‘High-throughput discovery of novel developmental phenotypes‘ [1] describes some achievements from sytematic study of these genes in knockout mice.

Screens like those of the IMPC and DMDD are vital to understand gene function on a genome-wide scale and, based on the results recently published in Nature, here are some reasons why.


FURTHER EVIDENCE THAT MOUSE DATA IS RELEVANT TO CLINICAL STUDIES

Lethal genes in the mouse are known to be enriched for human disease genes [2,3]. When additional data from the IMPC was included on the genes essential for survival of the embryo, this enrichment was increased even further. More than half of the human disease genes considered were essential for mouse embryo survival. The study also found a remarkable correlation between the core essential genes in humans and mice.

Systematic knockout mouse screens provide data that could not be derived from human patients. These new results further underline the importance of mouse models in the study of human disease, and their relevance in a clinical setting.


INCOMPLETE PHENOTYPE PENETRANCE

A suprising observation from knockout mouse screens is the incomplete penetrance of phenotypes for many lines.

One example of this is the sub-viability of lines. The IMPC has found that in around 11% of knockout lines some homozygous pups were observed, but fewer than the 1 in 4 pups predicted by Mendelian genetics. Some pups were able to survive with the homozygous gene knockout, but some weren’t.

Incomplete penetrance is a result also echoed in DMDD data. For example, in the seven Adamts3 knockout embryos studied, all display subcutaneous edema and absent lymph sac, while only two display a bifid ureter.

Click to view larger image.
Subcutaneous edema and bifid ureter (left side) observed in an Adamts3 mutant embryo. The red arrows highlight a single ureter on the right side, but two branches on the left side.

Data from systematic screens of knockout mice is showing, on an unprecedented scale, that even for a complete gene knockout, the observed phenotypes can vary from embryo to embryo. Given the standardised background and allele construction, this is a suprising result and could suggest an underlying stochastic process.


CANDIDATES GENES FOR UNDIAGNOSED HUMAN DISEASE

As part of its systematic screen, the IMPC has identified 22 essential mouse genes with human orthologs that are not known to be associated with any human disease. These are potential candidates for undiagnosed diseases and could shine new light on the causes of genetic disorders.

Efforts are continuing to study knockouts of every gene in the mouse genome. As these datasets grow in size, so too does the potential for them to help us understand gene expression and the genetic basis of human disease.

The DMDD database of embryonic-lethal mouse knockouts can be found at dmdd.org.uk.

The IMPC database of knockout mice can be found at www.mousephenotype.org.


REFERENCES

[1] The IMPC Collaboration (2016)
High-throughput discovery of novel developmental phenotypes
Nature  doi:10.1038/nature19356

[2] B. Georgi1, B. F. Voight1, M. Bućan1 (2013)
From mouse to human: evolutionary genomics analysis of human orthologs of essential genes
PLoS Genet 9(5): e1003484. doi: 10.1371/journal.pgen.1003484

1 Department of Genetics, Perelman School of Medicine, University of Pennsylvania, USA

[3] J. E. Dickerson 1, A. Zhu1, D. L. Robertson1 K. E. Hentges1 (2011)
Defining the role of essential genes in human disease
PLoS ONE, 6(11), e27368. http://doi.org/10.1371/journal.pone.0027368

1 Faculty of Life Sciences, University of Manchester, UK