Trying To Solve The Puzzle Of ALS By Going From Mutations To Protein Networks

Amyotrophic Lateral Sclerosis (ALS) is one of the most complex neurodegenerative diseases, affecting neurons both in the brain and in the spinal cord, potentially via different mechanisms. This disease represents one of the largest challenges in the medical field. Dr. Ozdinler thinks each patient holds a key, but one key is not sufficient to open the box; all keys need to be used in an orchestrated fashion.

To date, there have been 147 genes identified to be either causative or associated with the disease. When patients have mutations in any of these 147 genes, they either develop a robust ALS pathology or their chances of getting the disease is significantly increased. Diseases are usually characterized by the neurons that die and the circuitries that are affected. Interestingly, in diseases, especially in neurodegenerative diseases, not all neurons display vulnerability to the same level and extent; some show primary vulnerability much earlier than others and undergo progressive degeneration. Therefore, if a single mutation in one gene causes a disease, we know that the function of the protein coded by that gene is very important for the neuron that dies.

Since function is determined by actions, and actions are the results of protein-protein interactions, it makes perfect sense to investigate the binding partners of the proteins, when mutated, cause the disease. Upon careful investigation, 1105 proteins are determined to be direct bindings partners of 3 or more of the proteins whose gene product is mutated in ALS patients. Interestingly, some of these proteins appeared to be more “famous,” binding to more than 20 different ALS-related proteins, and some seem to be playing a regulatory role for the expression and the proper function of others.

Identification of the protein landscape of ALS began to reveal which proteins interact with which, and why this interaction may be important for the motor neurons that die. A pattern of canonical pathways, the cellular events that govern a distinct function, also began to appear. For example, it became obvious that the motor neurons invest in some of the cellular functions more than others, trying to ensure that the key cellular events related to that function are properly performed and that the system is ready for any potential insult or problems.

When analyzed with a wide perspective, the mutated genes cumulatively reveal the crucial protein interaction domains and key canonical pathways important for the health and stability of the motor function. Therefore, the disease develops because mutated proteins cannot maintain their function, resulting in imbalance and perturbations of the system that could not be well tolerated. Thus, not being able to maintain homeostasis is the cause of the disease.

Looking deep into the cellular events that are primarily covered by the ALS proteins, some key events were highlighted. For example, maintaining lipid and protein homeostasis, being ready for a hypoxic insult and DNA damage, making sure cytoskeletal dynamics are in check, and response to growth factors were some of the important cellular events that required utmost attention.  Interestingly, some of the proteins were also determined to be relatively important within pathways and among pathways, and some were responsible for holding the interactome domains together; their elimination disrupted the dynamics and resolved interactome domains. Going back to human, when the expression profiles of these proteins were examined in the motor neurons of the brain in the patients, their expression was either reduced or increased with accumulation in the cytoplasm in distinct aggregates, suggesting their function could be impaired.

Each mutation in the patient holds a secret. When all the secrets cumulatively analyzed, we begin to reveal the mystery behind motor neuron vulnerability and progressive degeneration. What is it that they care about the most, what is their fear, and how do they prepare themselves for the potential insults — how and why they give up becomes clear. The ALS protein landscape informs us of the areas motor neurons need help the most and how we can help them.  This also helps us identify novel targets for drug discovery and new ways to improve their health.  “Being able to see the forest by looking at individual leaves has been rewarding,” said Dr. Ozdinler.

Dr. Hande Ozdinler is an Associate Professor at the Department of Neurology at Northwestern, and her work focuses on understanding the intrinsic and extrinsic mechanisms responsible for selective neuronal vulnerability, with a special focus on upper motor neurons.

These findings are described in the article entitled Protein-protein interactions reveal key canonical pathways, upstream regulators, interactome domains, and novel targets in ALS, recently published in the journal Scientific Reports. This work was conducted by Ina Dervishi, Oge Gozutok, Kevin Murnan, Mukesh Gautam, Daniel Heller, Eileen Bigio, and P. Hande Ozdinler from Northwestern University.