Mutations disrupting neurogenesis genes confer risk for cerebral palsy

Jin, S. C., Lewis, S. A., Bakhtiari, S., Zeng, X., Sierant, M. C., Shetty, S., Nordlie, S. M., Elie, A., Corbett, M. A., Norton, B. Y., van Eyk, C. L., Haider, S., Guida, B. S., Magee, H., Liu, J., Pastore, S., Vincent, J. B., Brunstrom-Hernandez, J., Papavasileiou, A., Fahey, M. C., … Kruer, M. C. (2020). Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nature genetics, 52(10), 1046–1056. https://doi.org/10.1038/s41588-020-0695-1

Journal club, teaching others about science and new innovations are some of the things I love. However, most of the peer-reviewed articles are very dense and many times even a small bit of help understanding them can go a long way. This week we will be taking a look at an important paper on Cerebral Palsy. Often, I re-read these papers with others and try to formulate a method to help everyone understand them. I am not the original author of this paper, and I hope I have given proper credit to the authors. Research takes time, and every time you read a paper like this one please understand, it may represent years of research. Hopefully, the link to the original paper works, if not, copy-paste the title.

1) How would you summarize the article in 1 sentence? Approx. 40% of individuals that have CP is inherited, however, the discovery of the RHOB and FBXO31 is a new finding. Loss of function mutations, RHOB, and FBXO31 is enough to cause CP. Damaging single-nucleotide variants represent an independent risk factor.

2) What genes are discussed in detail and what is known about them?

RHOB, FBXO31, DHX32, ALK, TUBA1A, CTNNB1, ATL1, CTNNB1, SPAST and TUBA1A have previously been associated with human CP pheno- types.

RHOB and FBXO31 when mutated, each alone are sufficient to cause cerebral palsy.

TUBA1A gene has been previously been associated with human CP phenotypes, heterozygous mutations, associated with a spectrum of cortical malfunctions.

CTNNB1 gene previously associated with CP encodes beta-catenin harbors 3 LoF DNMs.

3) What is cerebral palsy and how does it manifest?

Movement disorder, 2 years of age, 2% inheritance autosomal recessive, preterm birth, low birth weight 28 weeks, hypoxia, being a twin, conceived in vitro, mom had an infection during pregnancy, untreated newborn jaundice, complications at birth, having brain infections, more boys than girls. What are the roles of gender, age, pattern of inheritance? Rare, damaging single-nucleotide variants represent an independent risk factor for CP. 75 genes that contribute to CP through a de novo mechanism.

CP is the most common motor disability in childhood. About 1 in 323 children has been identified with CP according to estimates from CDC’s

4) What clinical applications does this study provide to researchers, clinicians, etc.? CP can be considered a spectrum disease. Parents are not to blame for an unknown genetic problem. More research on the new discoveries RHOB and FBXO31.

RHOB and FBXO31 when mutated, each alone are sufficient to cause cerebral palsy.

Largest study. 14% possibility linked to genes. 8 genes found 4 in this study. 12% of CP pts in the study the genetic mutations were from chance and were NOT inherited by either parent. 2% of pts in study mutations inherited from both parents (who did not have cp) the remaining 86% of cases could have an environmental cause.

CP is the most common motor disability in childhood. 4 common types

Spastic CP 80%. Increased muscle tone = stiffness

Dyskinetic CP problems controlling movement

Ataxic CP problems with balance and coordination

Mixed CP more than one type

Brain damage that leads to CP can happen before birth (congenital CP) during birth, within a month of birth, or during the first year’s, the brain is still developing (acquired CP).

LOF: Loss of Function

Overall, the data indicate that genomic variants should be considered alongside environmental insults when assessing the etiology of an individual with Cerebral palsy. Damaging single-nucleotide variants represent an independent risk factor.

TUBA1A gene has been previously been associated with human CP phenotypes, heterozygous mutations, associated with a spectrum of cortical malfunctions.

CTNNB1 gene previously associated with CP encodes beta-catenin harbors 3 LoF DNMs.

Cerebral Palsy could be classified as a “spectrum disease”

28% had an intellectual disability, 11% epilepsy, and 6.3% autism spectrum disorder.

Involves how the brain is wired in development. Several “key” genetic pathways discovered. Rare genetic mutations. Damaging de novo mutations DNMs

“de novo” could be the sperm or egg or after conception, possibly 11.9% representing 62.8% of cases in the study.

DAVID, PANTHER, AND MSigDB are bioinformatics tools Disease-gene network tool DisGeNET, ClinVar, ClinGen, UniProt

Figure 1. GTP binding is enhanced

Figure 2. show decreased cyclin D expression the whisker plots indicate the 10th and the 90th percentiles

Figure 3. Venn diagram CP and Alzheimer’s.

Figure 4. Loss of function in locomotor phenotype Whisker plots

Using whole-genome sequencing

Using Zebrafish and Drosophila (fruit fly) mutations in 70% causing motor problems, balance. Cyclin D in Drosophila is 477 amino acids in length. Drosophila and many other organisms only have one cyclin D protein.

These findings indicate an over-representation of genes involved in ECM biology, cell-matrix interactions (focal adhesions), cytoskeletal dynamics, and Rho GTPase function. Rho family of GTPases are signaling G proteins (guanine nucleotide-binding proteins) the Ras superfamily regulate many aspects of intercellular actin dynamics switches. Organelle development, cytoskeletal, cell movement, and other common cellular functions. Monogenic etiologies, FBXO31, RHOB. RHOB mutation enhances the active state Rho effector binding.

FBXO31mutation diminished cyclin levels.

Cyclin D is a member of the cyclin family that is involved in regulating cell cycle progression. The synthesis of cyclin D is imitated during G1 and drives the G1/S phase translation. Cyclins are eukaryotic proteins that form holoenzymes with cyclin-dependent protein kinases (Cdk) which they activate.

In general, all stages of the cell cycle are chronologically separated in humans and are triggered by cyclin-Cdk complexes which are periodically expressed and partially redundant in function. In mice and humans, two more cyclin D proteins have been identified. The three homologs, called cyclin D1, cyclin D2, and cyclin D3 are expressed in most proliferating cells and the relative amounts expressed differ in various cell types

Homolog

In genetics, the term “homolog” is used both to refer to a homologous protein and to the gene (DNA sequence) encoding it. As with anatomical structures, homology between protein or DNA sequences is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a speciation event (orthologs) or a duplication event (paralogs). Homology among proteins or DNA is often incorrectly concluded on the basis of sequence similarity. The terms “percent homology” and “sequence similarity” are often used interchangeably. As with anatomical structures, high sequence similarity might occur because of convergent evolution, or, as with shorter sequences, because of chance. Such sequences are similar, but not homologous. Sequence regions that are homologous are also called conserved.

• A homologous gene (or homolog) is a gene inherited in two species by a common ancestor. While homologous genes can be similar in sequence, similar sequences are not necessarily homologous.
• Orthologous are homologous genes where a gene diverges after a speciation event, but the gene and its main function are conserved.
• If a gene is duplicated in a species, the resulting duplicated genes are paralogs of each other, even though over time they might become different in sequence composition and function.
• conserved: In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences (such as RNA and DNA sequences), protein sequences, protein structures.
• selective pressure: Any cause that reduces reproductive success in a proportion of a population, potentially exerts evolutionary pressure or selection pressure.

What are single nucleotide polymorphisms (SNPs)?

Single nucleotide polymorphisms, frequently called SNPs (pronounced “snips”), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine © with the nucleotide thymine (T) in a certain stretch of DNA.

SNPs occur normally throughout a person’s DNA. They occur almost once in every 1,000 nucleotides on average, which means there are roughly 4 to 5 million SNPs in a person’s genome. These variations may be unique or occur in many individuals; scientists have found more than 100 million SNPs in populations around the world. Most commonly, these variations are found in the DNA between genes. They can act as biological markers, helping scientists locate genes that are associated with disease. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene’s function.

Most SNPs have no effect on health or development. Some of these genetic differences, however, have proven to be very important in the study of human health. Researchers have found SNPs that may help predict an individual’s response to certain drugs, susceptibility to environmental factors such as toxins, and risk of developing particular diseases. SNPs can also be used to track the inheritance of disease genes within families. Future studies will work to identify SNPs associated with complex diseases such as heart disease, diabetes, and cancer.

PLEIOTROPIC = Pleiotropic: Producing or having multiple effects from a single gene. For example, the Marfan gene is pleiotropic, potentially causing such diverse effects as long fingers and toes (arachnodactyly), dislocation of the lens of the eye, and dissecting aneurysm of the aorta, mitral valve prolapse.

Using whole-genome sequencing

Whole-genome sequencing has largely been used as a research tool but was being introduced to clinics in 2014. In the future of personalized medicine, whole-genome sequence data may be an important tool to guide therapeutic intervention. The tool of gene sequencing at SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response.

DNA sequencing is the process of determining the nucleic acid sequence — the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.

A single-nucleotide polymorphism (SNP; /snɪp/; plural /snɪps/) is a substitution of a single nucleotide at a specific position in the genome, that is present in a sufficiently large fraction of the population (e.g. 1% or more).[1]

For example, at a specific base position in the human genome, the C nucleotide may appear in most individuals, but in a minority of individuals, the position is occupied by an A. This means that there is a SNP at this specific position, and the two possible nucleotide variations — C or A — are said to be the alleles for this specific position.

SNPs pinpoint differences in our susceptibility to a wide range of diseases (e.g. sickle-cell anemia, β-thalassemia, and cystic fibrosis result from SNPs. The severity of illness and the way the body responds to treatments are also manifestations of genetic variations. For example, a single-base mutation in the APOE (apolipoprotein E) gene is associated with a lower risk for Alzheimer’s disease.