ALS Pathophysiology

Written by Margaret Anne Rockwood | Last updated May 11th, 2026
Medically reviewed by Doreen Ho, MD and Jennifer Morganroth, MD, MBA

ALS has been called a disease of “glutamate excitotoxicity,” “mitochondrial dysfunction,” “proteinopathy,” “neuroinflammation,” “multisystemic proteostatic failure,” “corticospinal network hyperexcitability,” and more. While none would be incorrect, a standalone definition is elusive, since the science is far from settled as to the original triggers of ALS, and sequence of events from initial insult to motor neuron death.

A Heterogeneous Disease with Identifiable Key Mechanisms

ALS appears to arise from the convergence of genetic susceptibility with age-related or environmental factors acting on a vulnerable motor neuron network, where multiple interlocking pathogenic loops progressively overwhelm neuronal resilience and lead to clinical disease.​

Current understanding places TDP-43 proteinopathy and RNA dysregulation—particularly the loss of nuclear TDP-43 and its essential functions_—at the center of most cases. These events are compounded in complexity by glutamatergic excitotoxicity, mitochondrial dysfunction, oxidative stress, axonal transport failure, and neuroinflammation, which together constitute a toxic cellular environment in ALS.

The motor neuron degeneration likely involves both “dying-back” distal axonopathy and “dying-forward” cortical mechanisms, with hyperexcitability and an hypothesized prion-like propagation of misfolded TDP-43 contributing to the characteristic focal onset and regional spread of clinical weakness.

TDP-43 Proteinopathy

A broadly supported hypothesis proposes that disturbances in RNA metabolism and splicing are linked to the dysfunction and mislocation of the protein TAR DNA-binding protein 43 (TDP-43).  TDP-43 (encoded by the TARDBP gene) is involved in RNA and DNA binding, playing a crucial role in gene expression and RNA metabolism.

TDP-43 mislocation may be triggered by an inherited pathogenic gene variant or by aging, stress or environmental factors that cause cellular degradation, including TDP-43 dysregulation. It is important to note that SOD1 and FUS mutant ALS operates through a distinct mechanism (oxidative toxicity from the mutant SOD1 or FUS protein itself) and does not typically involve TDP-43 proteinopathy, though there have been case reports that suggest TDP-43 protein is involved.

The TDP-43 mislocation consists of its leakage from the nucleus into the cytoplasm. Once in the cytoplasm, TDP-43 misfolds and causes clumps of cleaved aggregates that are toxic, phosphorylated and ubiquitinated (marked for degradation or altered function).

When TDP-43 has exited the nucleus, its normal RNA splicing control mechanism is lost, resulting in “cryptic exons” and the consequent failure of downstream proteins. The two best validated splicing casualties are:

• Stathmin-2 (STMN2): a neuronal growth associated protein critical for axonal regeneration, maintenance of the neuromuscular junction, and preservation of axonal caliber and neurofilament organization. . Loss of nuclear TDP-43 leads to cryptic splicing and premature polyadenylation of STMN2 mRNA, producing a truncated, non-functional transcript. In animal models, partial (heterozygous) loss of STMN2 reproduces a slowly progressive, motor-selective neuropathy with neuromuscular junction denervation, closely modeling the motor neuron degeneration seen in ALS.
• UNC13A: The absence of nuclear TDP-43 unmasks a cryptic exon in UNC13A, leading to nonsense-mediated decay.

In the nucleus, TDP-43 normally acts as a splicing “proofreader,” ensuring that non-coding introns are correctly removed and preventing aberrant exon inclusion (cryptic exon repression). It also facilitates the transport of mature mRNA out of the nucleus and down the long axons of motor neurons to sites of protein synthesis. Loss of TDP-43 from the nucleus disrupts all these functions simultaneously.

Motor neurons are among the largest cells in the body, with axons up to 1 meter long. They rely on fast, ATP-dependent microtubule transport systems (dynein and kinesin) to move nutrients to the synapse and waste products back to the soma.

In ALS, evidence suggests that this transport system is undermined as TDP-43 localizes to the mitochondria, where it binds mitochondria-transcribed mRNAs encoding Complex I subunits (ND3 and ND6), impairing their expression and causing Complex I disassembly, the first enzyme in the mitochondrial electron transport chain. The affected mitochondria fail to produce adequate ATP, lose the ability to buffer calcium levels, and release reactive oxygen species (ROS), leaving the motor neuron energy-starved and unable to sustain axonal transport.

Cytoplasmic TDP-43 also impairs the cell’s waste-disposal pathway by inhibiting the ubiquitin-proteasome system (UPS) and disrupting autophagy, preventing the clearance of misfolded proteins. This proteostasis failure leads to the accumulation of damaged proteins and persistent stress granules, compounding cellular stress.

Taken together, these events constitute TDP-43 proteinopathy, which is implicated in approximately 97% of ALS cases, particularly in sporadic ALS, and many familial forms, though not typically in SOD1 or FUS-mutant ALS. In short, TDP-43 proteinopathy exerts a dual impact:  loss of normal nuclear function  (leading to cryptic splicing and RNA dysregulation) and gain of toxic cytoplasmic function (through aggregation, RNA sequestration, and mitochondrial damage).

Impact on the Axon

TDP-43 aggregates extend their obstruction into the axon itself, blocking axonal transport, and preventing nutrients from reaching the synapse. As a result, the axonal telodendria wither and withdraw from the neurons or the muscle tissue they innervate. This cytoskeletal collapse and transport failure produces the characteristic “dying-back” axonopathy of ALS.

This “dying-back” event is not inconsistent with the complementary “dying-forward” hypothesis, which holds that the disease spreads from a focal cortical  upper motor neuron hyperexcitability, driving anterograde degeneration of lower motor neurons via excitotoxic mechanisms. In parallel, TDP-43 aggregates act as toxic seeds that propagate from one neuron to the next via the synapse in a prion-like manner, thought to cause the TDP-43 in healthy cells to also mislocate, misfold and aggregate. This explains why the disease tends to spread contiguously (e.g., starting in the right hand, moving to the right arm, then the left arm).

The Toxic Cellular Environment

TDP-43 proteinopathy does not act in isolation. Several interconnected pathological processes further erode motor neuron resilience:

• Glutamate Excitotoxicity

Glutamate is the primary excitatory neurotransmitter in the central nervous system. In ALS, astrocytic glutamate transporters (EAAT2) fail to clear glutamate from the synaptic cleft. The resulting excessive glutamate causes sustained overstimulation of AMPA and NMDA receptors (ionotropic glutamate receptors), producing a massive influx of calcium (Ca2+) into motor neurons, which are particularly susceptible because they express calcium-permeable AMPA receptors. This calcium overload triggers enzymatic cascades that generate oxidative stress and destroy the neuronal cell membrane and cytoskeleton.

• Hyperexcitability 

Cortical and spinal motor neuron hyperexcitability plays a central role in ALS pathology. This condition can arise from various factors, including:

• • Dysfunction of glutamate transport mechanisms
  • Abnormal activation of glutamate receptors
  • Alterations in inhibitory interneurons and alterations in inhibitory signaling

Part of the “dying forward” hypothesis is the proposition that persistent cortical hyperexcitability produces excessive glutamatergic drive onto spinal motor neurons, producing trans-synaptic excitotoxicity, gliosis, neuroinflammation, neuromuscular junction loss and downstream lower motor neuron degeneration. Degeneration of cortical and spinal motor neurons leads to progressive motor weakness.

• Oxidative Stress

Motor neurons are particularly vulnerable to reactive oxygen species (ROS) because of their length, size and high metabolic demand. Across all ALS subtypes, there is evidence of increased oxidative damage to lipids, proteins and nucleic acids, resulting in the imbalance between free radical production and antioxidant defenses. This oxidative burden contributes to mitochondrial dysfunction and cell death pathways.

• Neuroinflammation (Non-Cell Autonomous Toxicity) and implications for autoimmune association 

In a healthy nervous system, microglia and astrocytes support and protect neurons. In ALS, these glial cells undergo a transition: initially neuroprotective and anti-inflammatory early in disease, they progressively shift toward a pro-inflammatory, neurotoxic phenotype, secreting toxic cytokines (e.g. TNF-alpha, IL-1β, IL-6), chemokines, and other mediators that exacerbate motor neuron injury. This creates a self-sustaining cycle: neuronal damage activates glia, and glial activation in turn accelerates further neuronal loss. The role of this immune dysregulation in disease progression remains an active area of investigation.

Leading Curative Candidates

Current research focuses on shifting from general neuroprotection to mechanism- and mutation-specific interventions, validated in human iPSC models and early clinical trials.

The most realistic near-term “curative” approach is likely to be a layered regimen combining gene- or RNA-targeted therapy for the causal mutation or pathway with small molecules, biologics and immune-modulating treatments to protect and stabilize the motor neuron network over time, though no such combination has yet been validated clinically.

Familial ALS: Curative solutions in familial ALS will likely require combinations of:

• Early gene-targeted therapy (antisense oligonucleotides [ASOs], siRNA, or eventually CRISPR-based editing) to silence or correct the mutation.​ Tofersen, an ASO targeting SOD1, is the first FDA-approved gene-targeted therapy for ALS. ASOs targeting FUS are in clinical trials, though ASOs targeting C9orf72 and ATXN2 have not yet demonstrated clinical benefit.
• Small-molecule and biologic agents that preserve axons and synapses (SARM1 inhibitors, mitochondrial/metabolic drugs, and modulators of complement and excitotoxicity).​ Preclinical evidence supports SARM1 inhibition in TDP-43-mediated neurodegeneration, though results are model-dependent.
• Immune reprogramming to sustain a protective glial and T-cell milieu over the long term. Regulatory T cell (Treg) expansion has shown neuroprotective effects in preclinical models and early-phase human studies, with Treg levels inversely correlating with disease progression rate.

Sporadic ALS: Curative strategies in sporadic ALS are more challenging given its molecular heterogeneity, and are likely to depend more on pathway-targeted combinations including: 

• TDP-43-, STMN2-, and UNC13A-directed genetic therapies such as interventional RNA therapies. ASOs targeting STMN2 cryptic exon inclusion are in development, though restoring STMN2 alone may not be sufficient given that TDP-43 loss of function causes dozens of cryptic mis-splicing events.
• Axon-protective, metabolic support and microglia-modifying agents.
• Robust biomarkers and molecular subtyping technologies, which will be critical for patient stratification, as it remains plausibly unlikely that a single gene target will prove broadly effective.

From the 30,000-foot view, a cure for ALS is likely to require an integrated strategy combining gene-level tools that include pathway-modifying drugs and immune therapies to stabilize a stressed motor neuron network and prevent further degeneration.

References

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