Neuroinflammation Biomarker Panel for Early AD Detection¶
Notebook ID: nb-SDA-NEUROINFLAM-BIOMARKERPANEL-0b9129bc Analysis: SDA-NEUROINFLAM-BIOMARKERPANEL-0b9129bc Generated: 2026-04-21T18:49:54
Research question¶
What is the optimal blood-based biomarker panel combining established markers (GFAP, p-tau217, NfL) and novel inflammatory markers for preclinical Alzheimer's disease (AD) staging?
This notebook was regenerated from live SciDEX PostgreSQL data. The analysis has scored hypotheses but no parseable target genes, so this artifact emphasizes hypothesis scoring, debate provenance, PubMed literature context, and KG edges instead of gene/pathway tools.
1. Hypothesis table from PostgreSQL¶
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
hyp_rows = [{'id': 'h-b9c26a65', 'title': 'TREM2 Agonism with CX3CR1 Antagonism for Microglial Homeostasis', 'type': '', 'disease': 'neurodegeneration', 'composite_score': 0.105, 'confidence_score': 0.5, 'evidence_for': "{'pmid': '24250719', 'claim': 'TREM2 R47H variant increases AD risk and impairs microglial amyloid clearance'}; {'pmid': '25686174', 'claim': 'CX3CR1 deficiency reduces tau pathology in P301S mice'}; {'pmid': '31043486',", 'evidence_against': "{'pmid': '29328995', 'claim': 'TREM2 agonism worsens cerebral amyloid angiopathy (CAA) in aged APP/PS1 mice'}; {'claim': 'Dose-limiting liver enzyme elevations observed in AL002 Phase I', 'source': 'Clinical trial monito"}, {'id': 'h-dacf4657', 'title': 'NLRP3 Inflammasome Suppression via Selective Caspase-1 Inhibition', 'type': '', 'disease': 'neurodegeneration', 'composite_score': 0.105, 'confidence_score': 0.5, 'evidence_for': "{'pmid': '23974753', 'claim': 'NLRP3 inflammasome activation is documented in AD brains and correlates with cognitive decline'}; {'pmid': '23164578', 'claim': 'Caspase-1 deletion reduces amyloid pathology and improves co", 'evidence_against': "{'pmid': '31289364', 'claim': 'MCC950 and dapansutrile failed in gout and cardiovascular Phase II trials'}; {'pmid': 'GWAS catalog', 'claim': 'NLRP3 genetic variants show inconsistent associations with AD risk in GWAS'};"}, {'id': 'h-1ed9eec4', 'title': 'CD300f Immunoglobulin Receptor as Neuroinflammatory Brake', 'type': '', 'disease': 'neurodegeneration', 'composite_score': 0.105, 'confidence_score': 0.5, 'evidence_for': "{'pmid': '26928465', 'claim': 'CD300f negatively regulates neuroinflammation in mouse models of CNS injury'}; {'pmid': '31395389', 'claim': 'CD300f deficiency leads to increased microglial activation and neuronal damage'", 'evidence_against': "{'pmid': 'none', 'claim': 'No physiological ligand has been definitively identified—agonistic antibody development premature'}; {'pmid': 'GWAS catalog', 'claim': 'CD300f is not a GWAS-implicated AD risk gene'}; {'pmid': "}, {'id': 'h-f886036d', 'title': 'P2RX7-PANX1 Channel Blockade for Neuroinflammatory Cascade Interruption', 'type': '', 'disease': 'neurodegeneration', 'composite_score': 0.105, 'confidence_score': 0.5, 'evidence_for': "{'pmid': '26887441', 'year': '2015', 'claim': 'P2X7 receptor activation induces NLRP3 inflammasome and IL-1β release in cultured microglia', 'source': 'J Neuroinflammation'}; {'pmid': '30542063', 'year': '2018', 'claim':", 'evidence_against': "{'pmid': 'none', 'claim': 'CE-224,535 (Pfizer) showed no efficacy in rheumatoid arthritis Phase II'}; {'pmid': 'none', 'claim': 'GSK-1482160 terminated due to pharmacokinetic issues'}; {'pmid': 'none', 'claim': 'AZD9056 "}, {'id': 'h-5e0c4ddf', 'title': 'IL-33/ST2 Axis Augmentation for Synaptic Protection', 'type': '', 'disease': 'neurodegeneration', 'composite_score': 0.105, 'confidence_score': 0.5, 'evidence_for': "{'pmid': '25240225', 'year': '2014', 'claim': 'IL-33 administration reduces amyloid burden and improves cognitive performance in APP/PS1 mice', 'source': 'Brain'}; {'pmid': '29499312', 'year': '2018', 'claim': 'IL-33/ST2", 'evidence_against': "{'pmid': '31296952', 'claim': 'IL-33 administration delayed recovery and increased inflammation in spinal cord injury'}; {'pmid': 'none', 'claim': 'IL-33 promotes tumor growth in cancer models through ST2+ immune cell re"}, {'id': 'h-9e51501a', 'title': 'TYROBP Causal Network Inhibition for Microglial Repolarization', 'type': '', 'disease': 'neurodegeneration', 'composite_score': 0.105, 'confidence_score': 0.5, 'evidence_for': "{'pmid': '25609778', 'year': '2015', 'claim': 'TREM2 signaling through TYROBP is essential for microglial survival and amyloid containment in AD models', 'source': 'Neuron'}; {'pmid': '37952199', 'year': '2023', 'claim':", 'evidence_against': "{'pmid': 'none', 'claim': 'TYROBP lacks druggable pockets for selective negative allosteric modulation (scaffold protein)'}; {'pmid': '24250719', 'claim': 'Pharmacological TYROBP inhibition would recreate TREM2 R47H loss"}, {'id': 'h-887bddf5', 'title': 'AQP4 Water Channel Normalization as Surrogate Marker and Therapeutic Target', 'type': '', 'disease': 'neurodegeneration', 'composite_score': 0.105, 'confidence_score': 0.5, 'evidence_for': "{'pmid': '23164577', 'claim': 'AQP4 deletion accelerates amyloid plaque deposition in APP/PS1 mice'}; {'pmid': '36732336', 'claim': 'Perivascular AQP4 localization is impaired in AD brains and correlates with sleep disru", 'evidence_against': "{'pmid': 'none', 'claim': 'Multiple laboratories have failed to replicate the original glymphatic imaging findings'}; {'pmid': 'none', 'claim': 'AQP4 deletion does not consistently affect amyloid burden in all APP models"}]
hyp_df = pd.DataFrame(hyp_rows)
hyp_df
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| id | title | type | disease | composite_score | confidence_score | evidence_for | evidence_against | |
|---|---|---|---|---|---|---|---|---|
| 0 | h-b9c26a65 | TREM2 Agonism with CX3CR1 Antagonism for Micro... | neurodegeneration | 0.105 | 0.5 | {'pmid': '24250719', 'claim': 'TREM2 R47H vari... | {'pmid': '29328995', 'claim': 'TREM2 agonism w... | |
| 1 | h-dacf4657 | NLRP3 Inflammasome Suppression via Selective C... | neurodegeneration | 0.105 | 0.5 | {'pmid': '23974753', 'claim': 'NLRP3 inflammas... | {'pmid': '31289364', 'claim': 'MCC950 and dapa... | |
| 2 | h-1ed9eec4 | CD300f Immunoglobulin Receptor as Neuroinflamm... | neurodegeneration | 0.105 | 0.5 | {'pmid': '26928465', 'claim': 'CD300f negative... | {'pmid': 'none', 'claim': 'No physiological li... | |
| 3 | h-f886036d | P2RX7-PANX1 Channel Blockade for Neuroinflamma... | neurodegeneration | 0.105 | 0.5 | {'pmid': '26887441', 'year': '2015', 'claim': ... | {'pmid': 'none', 'claim': 'CE-224,535 (Pfizer)... | |
| 4 | h-5e0c4ddf | IL-33/ST2 Axis Augmentation for Synaptic Prote... | neurodegeneration | 0.105 | 0.5 | {'pmid': '25240225', 'year': '2014', 'claim': ... | {'pmid': '31296952', 'claim': 'IL-33 administr... | |
| 5 | h-9e51501a | TYROBP Causal Network Inhibition for Microglia... | neurodegeneration | 0.105 | 0.5 | {'pmid': '25609778', 'year': '2015', 'claim': ... | {'pmid': 'none', 'claim': 'TYROBP lacks drugga... | |
| 6 | h-887bddf5 | AQP4 Water Channel Normalization as Surrogate ... | neurodegeneration | 0.105 | 0.5 | {'pmid': '23164577', 'claim': 'AQP4 deletion a... | {'pmid': 'none', 'claim': 'Multiple laboratori... |
if len(hyp_df):
ranked = hyp_df.sort_values('composite_score')
fig, ax = plt.subplots(figsize=(9, max(4, len(ranked) * 0.45)))
ax.barh(ranked['title'], ranked['composite_score'], color='#26a69a')
ax.set_xlabel('Composite score')
ax.set_title('Scored hypotheses')
ax.grid(axis='x', alpha=0.25)
plt.tight_layout(); plt.show()
2. Score dimension heatmap¶
dims = ['confidence_score', 'novelty_score', 'feasibility_score', 'impact_score', 'mechanistic_plausibility_score', 'clinical_relevance_score', 'data_availability_score', 'reproducibility_score', 'druggability_score', 'safety_profile_score']
labels = ['TREM2 Agonism with CX3CR1 Antagonism for Microgl', 'NLRP3 Inflammasome Suppression via Selective Cas', 'CD300f Immunoglobulin Receptor as Neuroinflammat', 'P2RX7-PANX1 Channel Blockade for Neuroinflammato', 'IL-33/ST2 Axis Augmentation for Synaptic Protect', 'TYROBP Causal Network Inhibition for Microglial ', 'AQP4 Water Channel Normalization as Surrogate Ma']
matrix = np.array([[0.5, 0.5, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.5], [0.5, 0.5, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.5], [0.5, 0.5, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.5], [0.5, 0.5, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.5], [0.5, 0.5, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.5], [0.5, 0.5, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.5], [0.5, 0.5, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.5]])
if matrix.size:
fig, ax = plt.subplots(figsize=(10, max(4, len(labels) * 0.4)))
im = ax.imshow(matrix, cmap='viridis', aspect='auto', vmin=0, vmax=1)
ax.set_xticks(range(len(dims)))
ax.set_xticklabels([d.replace('_score','').replace('_',' ').title() for d in dims], rotation=45, ha='right', fontsize=8)
ax.set_yticks(range(len(labels)))
ax.set_yticklabels(labels, fontsize=7)
ax.set_title('Hypothesis scoring dimensions')
plt.colorbar(im, ax=ax, shrink=0.8)
plt.tight_layout(); plt.show()
else:
print('No score matrix available')
3. PubMed literature context (Forge PubMed Search)¶
lit_rows = [{'hypothesis': 'NLRP3 Inflammasome Suppression via Selective Caspase-1 Inhibition', 'year': '2025', 'journal': 'Cell Death Discov', 'title': 'Hydrogen sulfide protects against spinal cord pyroptosis via persulfidation of Rac1 after lumbosacra', 'pmid': '41053008'}, {'hypothesis': 'AQP4 Water Channel Normalization as Surrogate Marker and Therapeutic T', 'year': '2025', 'journal': 'Neurobiol Dis', 'title': 'Glymphatic dysfunction and neurodegeneration in ALS: Longitudinal insights from rNLS8 TDP-43 mice.', 'pmid': '39914774'}]
if lit_rows:
pd.DataFrame(lit_rows)
else:
print('No PubMed literature rows returned')
4. Debate and KG context¶
debate_info = {'num_rounds': 4, 'quality_score': 0.5}
edge_data = []
print('Debate:', debate_info)
if edge_data:
display(pd.DataFrame(edge_data))
else:
print('No KG edges recorded for this analysis')
Debate: {'num_rounds': 4, 'quality_score': 0.5}
No KG edges recorded for this analysis
Interpretation¶
This analysis has enough scored hypothesis data to support a real notebook, but it needs a future extraction pass to normalize target genes before STRING, Reactome, and enrichment analyses can be run responsibly.