Definition: An experiment that measures the impact or outcome of the disease.

Assays are how scientists study how a potential treatment affects a disease. - a crucial step in diagnoses. These tests or experiments are designed to address a specific component of a disease, such as how much calcium enters neurons. Assays can be used during any stage of the therapeutic development process.

Scientists in the CACNA1A research network use assays in their labs to learn about how variants impact channel function or structure. The data from those studies can be used to test drugs or medications in the presence of variants and see if they make the channel better or worse in cell and/or animal models. Oftentimes, biomarkers are used as a readout of the assays.

Definition: Impairment of muscle control and coordination of voluntary movements.

One of the most common phenotypes exhibited by those living with CACNA1A-related disorders is ataxia. This is due to loss of motor learning in the cerebellum, the part of the brain that is responsible for motor movements and coordination. Disruption of the electrical circuits in the cerebellum can prevent the brain from learning how to move muscles correctly. Ataxia often results in poor balance, an uneven or unsteady gait, impairment of fine motor skills and speech, and abnormal eye movements.

CACNA1A variants are linked to congenital ataxia and Episodic Ataxia Type 2 (EA2). Congenital ataxia is present from birth. It often manifests as hypotonia or delayed developmental milestones in babies and toddlers. As they grow older, the ataxia will become more apparent in their gait, speech, and fine motor skills. EA2 is characterized by sudden and sporadic episodes of severe impairment of balance and coordination. These are often accompanied by vertigo, dizziness, vomiting, and enhancement of abnormal eye movement such as nystagmus. This can last anywhere from 30 minutes to days. EA2 often manifests in early adolescence although some cases have been reported to occur earlier during childhood.

While some congenital ataxia can be mild, it can also be severe enough that some in the CACNA1A community require assistance to move about safely. Furthermore, EA2 can be very debilitating when the attacks occur. Unfortunately, there are limited treatments available for both types of ataxia. That’s why the CACNA1A Foundation is working with our CACNA1A Research Network to develop therapeutics that restore normal CACNA1A function and decrease the impairments exhibited by those living with ataxia.

Definition: A characteristic of the body that can be measured or quantified.

A big part of finding the right therapeutic treatments for those living with a CACNA1A-related disorder is finding the right biomarkers. These are crucial for understanding how a potential treatment impacts a disease. This is a priority for the CACNA1A Foundation and our research collaborators.

Biomarkers can be as simple as blood pressure or body temperature! While other biomarkers can be more in-depth such as MRIs to look at changes in brain structure, EEGs to look at changes in brain activity or even measuring eye movement abnormalities.

When we compare biomarkers in populations undergoing a potential treatment versus those with a placebo, we can start to identify what could work to improve the quality of life for our CACNA1A Champions

Definition: A voltage-gated calcium ion channel expressed in the brain, especially in the cerebellum.

Ion channels play essential roles in our bodies, especially in signaling (communication) between cells. Voltage-gated ion channels allow ions, or charged molecules, to pass through cell membranes in response to changes in the membrane potential.

The CACNA1A gene encodes for a protein called Alpha1A, which is the pore-forming subunit of CaV2.1. The primary role of CaV2.1 is to allow calcium ions into neurons when the membrane potential changes. Cav2.1 is a large protein made up of four repeated regions. Each region has six membrane-spanning subunits (S1-S6). The S1-S4 subunits have the job of detecting when the membrane potential changes. The S5 and S6 subunits help form the channel, or pore, in the membrane through which calcium moves. The four repeated regions fold into a 3D structure that places all S5 and S6 subunits in the middle to form the channel, with the remaining S1-S4 subunits surrounding them.

Definition: A research study done in people to evaluate the effectiveness and safety of a new medical treatment.

Before any new drug or medical treatment can be approved by the FDA for a patient population, it must undergo rigorous testing in a clinical trial to make sure it is helpful and it is safe. There are several phases to a clinical trial, starting with a small number of people to test dosages and efficacy.

Scientists and clinicians work together to determine the best metrics that will be used to evaluate the new treatment in any given clinical trial. This is based on scientific research data, but they also heavily rely on data collected directly from patients and caregivers. Without that valuable patient data, researchers won't know which symptoms to target and which treatments are needed.

Definition: A temporary wave of neuronal activation across the brain followed by a wave of neuronal deactivation. This usually precedes a migraine with aura.

Cortical spreading depression is a neurological change that is associated with hemiplegic migraine with aura in those living with CACNA1A variants. Normally, neurons fire at their own rates depending on which type they are, which circuit they are in, and what type of information they are sending. However, a phenomenon that occurs right before the aura phase of a hemiplegic migraine, involves a slow, synchronized wave of membrane depolarization, which activates all neurons in its path across the surface of the brain. This is known as cortical spreading depression. It is usually quickly followed by a wave of membrane repolarization, which deactivates the neurons for a longer period of time.

This wave of neuronal activation and deactivation disrupts the normal timing of neurotransmission. First, neurons are firing when they shouldn’t, causing an overload of information throughout the brain. Then, the prolonged period of deactivation leads to a sudden loss of information when neurotransmission stops. This polarizing event causes changes in vision (blindspots or flashing lights), speech, and even tingling or numbness in the body.

To date, researchers are still unclear as to how cortical depression spreading is initiated. Furthermore, it can occur in people with variants in genes other than CACNA1A. The mechanism of this debilitating phenomenon is a question that many researchers are trying to answer, including scientists within the CACNA1A research network. Understanding how cortical spreading depression starts, as well as how it can be stopped, is key to finding the most effective treatments for those in our CACNA1A community who are impacted.

Definition: A systemic collection and curation of survey data from patients, caregivers, and clinicians, to learn about the burden and the impacts on the quality of life from a disease.

In 2012, the FDA established the Patient Focused Drug Development (PFDD) Initiative to learn more about specific diseases and gaps in available treatments, directly from patients. Since then, many patient advocacy groups, especially those representing rare diseases, have completed a disease concept model study that can be presented to the FDA during PFDD meetings as a pre-clinical assessment of their disease.

A disease concept model uses a qualitative approach to provide a snapshot of how a disease impacts the lives of patients and their caregivers. The survey data is coded and analyzed to uncover the symptoms that create the most burden. It can also bring underreported symptoms to the forefront.

This is especially important when identifying the types of treatments that are needed for the community. The data can also be used to generate the right outcome measures or endpoints for clinical trials, to ensure that the most accurate assessments are utilized to determine whether or not a treatment is effective. Having this data can also increase the chances of getting a treatment approved by the FDA.

Definition: A neurological condition characterized by recurrent seizures.

Seizures are sudden bursts of electrical activity in the brain. There are different types of seizures that are categorized based on factors such as triggers, whether they affect motor or non-motor functions, or whether they affect the entire brain or just certain regions.

People can have multiple seizures in a lifetime, but that doesn’t necessarily mean they have epilepsy. Someone with epilepsy not only has multiple seizures but is also at a higher risk of having recurrent seizures. This risk can sometimes be attributed to an underlying genetic condition, such as having a variant on the CACNA1A gene.

About 55% of those with CACNA1A variants reported having epilepsy, according to our CACNA1A Natural History Study. The spectrum of seizures included tonic-clonic, absence, and status epilepticus. Each type can lead to debilitating effects that can significantly decrease quality of life. In fact, some forms of epilepsy are so severe that they can impair development in children. This is known as Developmental and Epileptic Encephalopathy or DEE. Furthermore, many of these epileptic seizures are also refractory, meaning they are not responsive to currently available anti-epileptic medications.

Definition: A variant where one or more nucleotides are deleted or inserted into the DNA sequence of a gene.

When proteins are being made or translated, the ribosome carefully reads each codon in the mRNA. This ensures that the correct amino acid is added in the right order. When there is a mistake in the codon, this can lead to the incorrect protein synthesized or no protein made at all. Frameshift variants are an example of a change that can result in either consequence.

When a nucleotide is taken out or added into a gene’s coding sequence, this changes every codon following that deletion or insertion. Imagine reading a sentence and discovering there are words missing or words added. The rest of the sentence doesn’t make any sense. This is what can happen with frameshift variants. Unfortunately, the ribosome continues to read every group of three nucleotides as a codon, even if they are incorrect, leading to a new protein being synthesized. However, since this protein has the wrong amino acids, it cannot fold into the correct shape and carry out its normal function. Frameshifts can also lead to a nonsense variant if the shift in the coding sequence creates a stop codon prior to the naturally occurring one. In this case, the mRNA is usually degraded before protein translation even occurs. Either scenario is detrimental to the cell.

Definition: A change in the DNA sequence of a gene that results in a new function.

There are several different ways that a gene’s function can be disrupted. Variants such as nonsense, frameshifts, and deletions tend to lead to a gene losing its ability to carry out its normal tasks. Missense variants can also be Loss-of-Function variants. However, they can sometimes result in a gene doing more than it should. This can be just as disruptive to the cell. We call those missense variants Gain-of-Function (GoF) variants.

GoF variants can sometimes enhance the function of a gene. CACNA1A encodes for Cav2.1, a calcium ion channel required for neurotransmission. Cav2.1 is embedded in the cell membrane in the pre-synaptic space of neurons. It opens up to let calcium ions inside when a signal or information must be transmitted to neighboring neurons. A GoF variant might allow the channel to open for too long. Why is this a problem? Too much calcium entering the neuron means too much information being transmitted. This uncontrolled increase in firing, or neurotransmission, causes neurons to be overactive and leads to symptoms such as hemiplegic migraine and severe seizures or epilepsies. Many anti-seizure medications work by preventing or dampening this increased firing. However, they do not target Cav2.1 specifically, which can lead to the unwanted side effects that are seen.

Definition: Every single thing that happens in our bodies relies on instructions that come from our DNA. All of our DNA together forms our genome. Within that genome are smaller sections of information called genes. Humans have over 23,000 genes! Each one contains instructions on how to make tools like RNA or proteins that are used to physically do work. Each gene has a specific purpose or function in a cell. If there is a mistake in the gene, such as a mutation or variant, this can lead to disruptions of important cellular tasks that can result in disease.

The average size of a gene in the human body is about 8,000 nucleotides long. The CACNA1A gene however, is a big gene with over 300,000 nucleotides! It has instructions to make the pore-forming subunit of a voltage-gated calcium ion channel called Cav2.1. This channel allows calcium to enter neurons and signal for the release of neurotransmitters (chemical messengers) to the next neuron, and so on. This is what allows information from the brain to be transmitted to the rest of the body.

When there is a change in the CACNA1A gene, the signals in the brain are disrupted. This leads to the neurodevelopmental symptoms that we see in the CACNA1A patient community. Understanding what a gene does is important for learning how to treat diseases linked to that gene.

Definition: The process of turning on a gene.

When scientists talk about a gene and its function, they often talk about where a gene is expressed. That's because where and when a gene is turned on, meaning that the gene's DNA sequence is being transcribed or rewritten into RNA, usually indicates where and when that gene is going to get work done. Sometimes having too little or too much of a gene expressed leads to problems in the cell.

Successfully treating a disease requires a good understanding about gene expression. Looking at gene expression levels in a variant background can help identify what could be causing symptoms that a patient is exhibiting.

For example, if the expression level is too high, a potential therapeutic treatment could focus on decreasing gene expression. On the other hand, if a gene is being expressed at significantly lower levels, a potential treatment could be designed to increase gene expression. The tricky part is figuring out what that ideal gene expression level is to ease or get rid of the symptoms. This could differ between patients, even if they have the same variant.

Definition: A migraine associated with aura and temporary weakness or paralysis of one side of the body.

Hemiplegic migraine (HM) is one of the least understood disorders in the CACNA1A community, but one that can be very debilitating and life-threatening if not treated correctly. HM is characterized by cortical spreading depression. This leads to aura, which can manifest as temporary neurological symptoms including increased light sensitivity, changes in speech, and tingling or numbness in the limbs. The aura also leads to a period of hemiplegia or weakness or paralysis of one side of the body. While the symptoms can come on quickly, the recovery period of HM can often range from hours to days and sometimes even weeks. The exact mechanism of how cortical spreading depression starts is still unclear. However, HM can be triggered by various reasons such as an illness, injury to the head, lack of sleep, or hormonal changes.

Familial Hemiplegic Migraine Type 1 (FHM1) is specifically linked to variants in the CACNA1A gene. These variants have been passed on to subsequent generations and tend to be manageable with the right treatment. Sporadic HM is due to de novo variants (new variants that are not inherited) and is reported to be more severe. Some of these HMs can result in severe seizures and sometimes even swelling in the brain, in addition to hemiplegia. These types of HMs require immediate attention and often trips to the ER. Furthermore, HM can often be misdiagnosed as a stroke, which means the correct medications are not given, and symptoms can worsen.

Definition: Having low or decreased muscle tone.

Have you ever been accidentally bumped but were able to catch yourself before you fell over? Most people are able to do so because of something called muscle tone. Muscle tone is defined as the tension in your muscles when you are resting. Or, think of it as the passive resistance your body has when someone or something pushes against you. Someone who has hypotonia has low muscle tone. That means that they don’t have that same amount of resistance or tension when their muscles are relaxed. If they were to get bumped, they might move erratically or even fall over because they aren’t able to resist the force they have encountered.

Many of our CACNA1A warriors have some level of hypotonia. This is because muscle tone is controlled by electrical signals from the brain. When the signals reach muscle cells, they tell the entire muscle to contract and provide more resistance or tone. When Cav2.1 activity is disrupted by variants in the CACNA1A gene, those electrical signals are interrupted, leading to a loss of muscle contraction and thus hypotonia. Hypotonia affects all muscles in your body and can make it hard to use them in a coordinated fashion. This is why we see ataxia or loss of balance/coordination of movements in those living with CACNA1A-related disorders.

Definition: A regulatory group required by the FDA to review and monitor any research involving human subjects.

Any time a scientific study is done that requires human participation, there are strict rules and regulations put in place. This ensures that the rights to safety and privacy of those participating are established and protected. An IRB usually has 5 members who represent different perspectives in the area of human research. Some have interest in scientific areas, some are focused on the non-scientific regulations. Most represent different professions, and one must represent the research participant perspective. The diversity of the members also ensures that there is a fair and comprehensive review of the research study at hand.

Definition: A change in the DNA sequence of a gene that lessens or takes away its normal function.

When a variant leads to the channel losing its ability to carry out a normal function, it’s known as a Loss-of-Function (LoF) variant. This type of variant might prevent the channel from opening at the right time or for the correct duration of time. It could also prevent the normal channel protein from trafficking, or getting to the cell surface, where it is needed.

All of these consequences would interrupt communication from the brain to the rest of the CNS. Missense variants can be LoF if they have any of the above-mentioned impacts on the protein. Nonsense, frameshift, and insertion/deletion variants are all considered LoF. They normally result in half the normal amount of protein in a cell, meaning that the cell only has the ability to carry out 50% of the protein-dependent tasks.

LoF make up most of the CACNA1A variants reported to date. The differences in the effects of LoF CACNA1A variants on protein function highlight why it is important to investigate the molecular mechanisms of variants beyond the LoF label. Variants that interrupt protein trafficking most likely require a new molecule or a chaperone to help the protein get to the surface. Variants that decrease protein levels would benefit from an ASO that could increase gene expression.

Definition: The electrical charge across a cell membrane

The cell membrane is the boundary of a cell. Its main job is to protect the cell and control what moves in and out to keep our bodies working properly. It also has special properties to carry out some of these functions, especially in neurons. Charged molecules called ions are present inside and outside of the cell and are important in helping transmit electrical signals (information) through the brain.

Think of the membrane like a battery, with one node inside the cell and the other outside the cell. The distribution, or separation, of positively and negatively charged ions across the nodes (or membrane) creates an electric field or membrane potential.

Why do we care about a membrane potential? Because it controls when CaV2.1, our calcium ion channel, opens in order to pass information on to the next neuron. When the membrane becomes more positively charged, CaV2.1 opens to let calcium in, and neurons can communicate. When the membrane becomes more negative again, CaV2.1 closes to stop the calcium flow and the neuron communication stops.

So not only is it important for calcium ion channels to open and close, it's also important to make sure the membrane potential changes at the right time for correct transmission of information throughout the brain.

Definition: A single nucleotide change in the DNA sequence of a gene that leads to an amino acid change.

The human genome contains over 20,000 genes. Each gene contains specific instructions, in the form of a DNA sequence, on how to make a protein. The instructions determine the order of amino acids that are strung together to form a final protein product. However, the DNA sequence of a gene isn’t necessarily identical from person to person.

Each of our genomes contains millions of changes at single nucleotide positions. Not every change has a detrimental effect, fortunately. However, sometimes a single change is enough to have a negative impact.

A mutation, or a variant, is a permanent change in a DNA sequence. A DNA sequence can be altered in a number of ways. When the variant is due to a single nucleotide change, or a point mutation, that alters the amino acid sequence, it is called a missense variant. If the amino acid change alters the protein’s normal function, this can lead to disease .

There are over 1,000 CACNA1A missense variants reported in ClinVar. While only a fraction are classified as likely pathogenic/pathogenic (disease-causing), it is still unclear how each of those missense variants contributes to a CACNA1A-related disorder. This is an important gap in knowledge to fill in order to determine the correct therapeutic treatments to develop.

Definition: A study that collects health information over time from those living with a disease or medical condition.

One of the most important factors necessary for developing treatments for a rare disease is availability of patient data. One of the ways that patient data can be collected is through a natural history study. This allows researchers to learn how a disease progresses over a lifetime, directly from a patient or a caregiver.

Examples of the data collected include the variant a patient has, symptoms a patient is exhibiting and when they began, any medications used and how symptoms have changed. It’s also important to have as many participants as possible enrolled in a natural history study to get an accurate representation of the patient population.

Definition: A single nucleotide change in the DNA sequence of a gene that creates a premature STOP codon.

The coding sequence of every gene contains a natural STOP codon. This signals to the ribosome, the cellular machinery that makes proteins, to stop protein synthesis because all of the correct amino acids have been added. Even one extra or one less amino acid can disrupt the protein’s final 3D structure and interfere with its correct function. This is why nonsense variants can often have a severe effect.

When a new stop codon is created prior to the natural codon, this is called a premature stop codon. This usually leads to the mRNA being destroyed by a process called nonsense-mediated decay, which is the cell’s surveillance system to prevent short, dysfunctional proteins from being made. However, this also means that someone with a nonsense variant only has about 50% of normal protein present in their cells (from the one good copy of the gene remaining).

Definition: The variable or trait being used to determine whether a treatment works or not.

Outcome measures are crucial when it comes to designing a clinical trial for a medical intervention. In order to accurately determine if a new treatment works, scientists must choose the right thing to measure. This might sound easy to do, but disease phenotypes or symptoms can often have multiple outcome measures.

If a drug for ataxia is being tested, potential outcome measures could be gait analysis, reduction in falls, or increased distance in mobility. Which do you choose? Clinical trials have failed because the wrong outcome was used. While you can have more than one outcome measure, too many can make it hard to determine if the treatment truly worked if there are positive impacts on one but negative impacts on another.

So how do we make sure the right outcome measures are chosen? We look at patient data. It can tell us which symptoms are the most prominent or detrimental. Then we can see which of those can be measured and which assays should be used.

Definition: A meeting that informs the FDA about the impact of a specific disease.

In the rare disease space, emphasis is placed on patient data because it provides first-hand accounts of what it is like to live with the disease. This is important for therapeutic development since we need to understand the impacts and the mechanisms of disease to find the right treatments.

Most of the time, patient data is sought out by scientists who are working on or interested in the disease. However, in 2012, the FDA also realized a need to learn about diseases directly from those living with them. It established the Patient-Focused Drug Development (PFDD) Initiative to understand the disease burden placed on patients and caregivers and identify gaps in available treatments.

PFDD meetings bring together different stakeholders that include the FDA, patients, advocates, researchers, clinicians, and representatives from drug development companies. Patients and caregivers are given the powerful opportunity to speak honestly and provide a unique look into how the disease impacts their lives every day.

Definition: An assay or experiment that is used to see if a treatment works.

Before a treatment can be considered for clinical trials, it must have evidence that it works in a disease model system. Proof-of-concept studies are used to generate that type of data and also show that the gene or disease is treatable.

This is important to the FDA when considering Investigational New Drug (IND) applications for new treatments and ultimately deciding which ones move forward to clinical trials.

Proof-of-concept studies are often carried out in patient-derived cells or whole animal models such as mice. They can also be done on patients. These studies provide information such as which disease symptoms can be treated, the effective dose(s), the right outcome measures and endpoints, and initial safety data.

This can also help improve the design of clinical trials to best assess the treatment in a larger number of patients.

Definition: A large molecule that performs various tasks in cells, including cellular organization, building tissues and organs, and regulating cellular processes.

Proteins are what physically do the work in cells. They are fairly large molecules made up of long chains of amino acids that fold into intricate 3-D structures. The structure of a protein is very important because it determines the function or the type of work the protein does. For example, the CACNA1A gene provides instructions for making the alpha-1A subunit of a calcium ion channel in the brain called CaV2.1.

This protein subunit forms the hole (pore) in the cell membrane through which calcium ions enter. CaV2.1 channels play an essential role in communication between neurons in the brain. When calcium enters a neuron through the channel, it signals the release of neurotransmitters, which are chemical messengers, to the next neuron.

CaV2.1 channels are also thought to be involved in the growth and survival of neurons. Variants in the CACNA1A gene disrupt the function of Cav2.1, leading to the neurodevelopmental symptoms we see in individuals affected by CACNA1A disorders.

Definition: The process of converting data from basic or foundational research into methods or results that directly benefit humans.

The CACNA1A Foundation’s research grant program is focused on funding translational research that will ultimately find specific treatments and a cure for our CACNA1A Champions. Our research grant program provides seed grants to scientists for translational research, clinical studies, and infrastructure to support the development of potential new treatments for individuals with a CACNA1A variant.