Entity types

Below I have listed the different categories under which each entity operated on by the web crawler will fall.

  1. Genes
  2. Proteins
  3. Molecules (drugs)
  4. Transmitters (neurotransmitters, inflammatory cytokines etc.)
  5. Receptors
  6. Processes (e.g. apoptosis, glycolysis, oxidative phosphorylation)
  7. Effect (upregulates, downregulates)
  8. ALS type (SOD1 mouse, healthy yeast, limb-onset SALS…)
  9. Laboratory anomalies (homocysteine ceruloplasmin, lipopolysaccharide)

From this initial data, the target is to distill something that can be used to

  1. estimate the relevance of a given molecule as part of an ALS therapeutic cocktail as widely as possible
  2. find pathways through which ALS could be subdivided into categories in order to enable separate therapeutics development for each category


Examples of entities in different categories

ceruloplasmin Appears to be low in PALS’ serum.  Also present as an antioxidant in CNS.
SOD1 superoxide dismutase 1 One of the clumping proteins in ALS. Possible inter-cellular spreading agent.
TDP-43 tar DNA-binding protein 43 Major clumping protein in SALS.
FUS fused in sarcoma Another clumping protein.
MMP-9 matrix metalloproteinase 9 Seems to correlate with cell’s vulnerability in ALS.


Astrocytosis Occurs in ALS patients and presumably contributes to neuron destruction.
Endocytosis Probable route through which SOD1 enters neurons.
Glycolysis Possibly upregulated in ALS
Oxidative phosphorylation Possibly downregulated in ALS.
Mitochondriopathy One characteristic process in ALS
Protein folding Place where something seems to go wrong.
Protein misfolding Characteristic phenomenon in ALS.
Protein aggregation Protein clumping Characteristic phenomenon in ALS.
Axonal transport Another place where things seem to go awry.
Apoptosis Assumed mechanism of neuron destruction.
Neuroinflammation Another potentiall mechanism for neuron destruction.
UPR activation Presumed to occur
Stress granule formation Takes place in affected neurons
ADAR2 downregulation Present at least in some ALS forms
Protein recycling failures Typically present in affected neurones
Dysregulation of cytosolic calcium Typically present in affected neurones
ER stress  Endoplasmic reticulum stress Typically present in affected neurones
Oxidative stress One of the most prominent ALS processes
Hepatic steatosis Apparently present in majority of PALS.
BBB leakage leaking blood brain barrier Occurs early on in disease progression.


Glutamate Assumed source of neurotoxicity
GABA Counters the glutamate-induced excitation.
 Nerve growth factors  NGF  Assumed to be deficient
 C5a  Complement 5a  The “usual suspect” as regards the autoimmunity aspect.
 HIF-1a  hypoxia induced factor 1 alpha


ALCAR Acetyl-L-carnitine Potentially helpful for cell metabolism
Riluzole Counters glutamate toxicity
Baicalin Chinese skullcap Neuroprotective agent
Turmeric Neuroprotective agent
Niacinamide Nicotinamide
Niacinamide riboside Nicotinamide riboside


Laboratory anomalies.

Uric acid Elevated in some ALS forms

Creatine kinase

Free copper Possibly elevated

Homocysteine Elevated in some ALS forms

Neurofilaments  Found in both blood and CSF of PALS.


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