Immunology Research Skill

KEY PRINCIPLES: Multi-layer evidence; source every claim; use immunology-specific databases first (IEDB, IMGT, SAbDab); always use English gene/protein names in tool calls.

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LOOK UP, DON'T GUESS

When uncertain about any scientific fact, SEARCH databases first (PubMed, UniProt, ChEMBL, ClinVar, etc.) rather than reasoning from memory. A database-verified answer is always more reliable than a guess.

For MC about immune mechanisms: Look up the specific pathway/receptor/cytokine before answering. Use PubMed_search_articles with the exact terms from the question. The answer is almost always in the first few search results.

Specific LOOK UP targets (never guess these):

• Immune cell markers: CD markers for cell subsets (e.g., Treg = CD4+CD25+FOXP3+, not just "CD4+"). Query UniProt or IEDB.
• Cytokine functions: IL-17 is pro-inflammatory (Th17), IL-10 is anti-inflammatory (Treg) — but context matters. Verify via KEGG pathway or PubMed.
• MHC/HLA restrictions: Which HLA allele presents which peptide — always check IEDB MHC binding data; allele-level differences are critical (HLA-A02:01 vs HLA-A02:07 have different peptide repertoires).
• Antibody Kd values: Never estimate binding affinity; check SAbDab, IEDB, or published literature.

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COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

Reasoning Frameworks

Immune response reasoning — Every immune response has innate → adaptive phases. Ask: which arm is relevant to the question? Innate (neutrophils, macrophages, complement, pattern recognition) or adaptive (T cells, B cells, antibodies, memory)? Innate is fast (hours) and antigen-nonspecific; adaptive is slow (days) but specific and generates memory. The transition occurs when APCs present antigen to naive T/B cells. Targeting innate suppresses broad inflammation; targeting adaptive disrupts antigen-specific responses. This determines which databases and tools are most relevant.

Antibody analysis reasoning — Structure determines function. The variable region (VH/VL, CDR loops) determines antigen specificity. The Fc region determines effector function: complement activation (IgM, IgG), ADCC via FcγR (IgG), or opsonization. When analyzing antibody data, always ask: are we studying binding (Fab — use IEDB, SAbDab, IMGT) or function (Fc — use FAERS for clinical safety, OpenTargets for target biology, TheraSAbDab for therapeutic format/isotype)? Isotype switching changes effector function without changing specificity.

Autoimmunity reasoning — Autoimmunity = loss of self-tolerance. Ask: is the attack cell-mediated (T cells destroying tissue → Type 1 diabetes, MS) or antibody-mediated (autoantibodies → SLE, myasthenia gravis, Graves')? Cell-mediated disease implicates MHC class I/II and TCR repertoire; antibody-mediated implicates B cell activation, affinity maturation, and complement. This determines the disease mechanism, the relevant genetic loci (HLA alleles dominate both, but TCR genes matter more for T-cell diseases), and the therapeutic approach (biologics targeting T cells vs. B cells vs. complement).

Antibody-antigen interaction reasoning — Binding strength has two axes: affinity (Kd of single binding site, typically nM–pM for therapeutic mAbs) and avidity (combined strength of all binding sites — IgM pentamer has low affinity but high avidity). When analyzing binding data: Kd < 1 nM = very high affinity; 1–100 nM = moderate; > 100 nM = weak. Epitope mapping strategy depends on the question: linear epitopes → peptide arrays or IEDB linear epitope search; conformational epitopes → HDX-MS, cryo-EM, or cross-linking MS. For therapeutic antibodies, check SAbDab for co-crystal structures and TheraSAbDab for clinical-stage format/engineering details.

Immune signaling cascade reasoning — When asked "what happens when cytokine X activates cell Y", trace the full pathway: receptor (which subunits?) → proximal kinase (JAK1/2/3, TYK2, Src family?) → transcription factor (STAT1/3/4/5/6, NF-kB, NFAT?) → effector genes (cytokines, cytotoxic molecules, survival factors). Example: IL-12 + T cell → IL-12R (IL12RB1+IL12RB2) → JAK2/TYK2 → STAT4 → IFN-gamma production (Th1 differentiation). Use KEGG pathway hsa04630 (JAK-STAT) and Reactome R-HSA-1280215 (Cytokine Signaling) to verify. Key signaling modules: JAK-STAT (most cytokines), NF-kB (TNF, TLRs, TCR/BCR co-stimulation), MAPK/ERK (growth factors, TCR), PI3K-AKT (co-stimulation, survival).

Complement system reasoning — Three activation pathways converge on C3 convertase: Classical (C1q binds antibody-antigen complexes — IgM or IgG → C4b2a), Lectin (MBL binds mannose on pathogens → C4b2a), Alternative (spontaneous C3 hydrolysis + factor B/D → C3bBb, amplification loop). All converge on C5 convertase → MAC (C5b-9). When to check which: suspected immune complex disease (SLE) → classical pathway (C1q, C4); recurrent bacterial infections → alternative or lectin (factor B, MBL); paroxysmal nocturnal hemoglobinuria → terminal pathway (CD55/CD59 deficiency). Therapeutic targets: eculizumab blocks C5; avacopan blocks C5aR.

Evidence grading — A (strong): GWAS p < 5e-8 + functional data + clinical signal. B (moderate): genetics or pathway evidence, limited functional data. C (preliminary): single-database hit only. Converging genetic (GWAS/Orphanet) + protein interaction (IntAct/BioGRID) + pathway data raises confidence. FAERS PRR > 2 with IC025 > 0 is a signal, not causal proof. TIMER2 deconvolution estimates require orthogonal validation.

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Tool Reference

Antibody / Structural (SAbDab, TheraSAbDab)

Tool	Key Parameters
SAbDab_get_structure	pdb_id (str) — structure details and chain info
SAbDab_get_summary	pdb_id (str) — CDR and chain summary
SAbDab_search_structures	query (str) — returns browse URL only, not JSON
TheraSAbDab_search_therapeutics	query (str, e.g. "pembrolizumab") — INN, target, format, phase
TheraSAbDab_search_by_target	target (str) — all therapeutics for an antigen
TheraSAbDab_get_all_therapeutics	(none) — full therapeutic antibody list

Epitope and Immune Assays (IEDB)

All search tools accept limit, offset, filters (PostgREST dict).

Tool	Extra Parameters
iedb_search_epitopes	sequence_contains, structure_type
iedb_search_tcell_assays	sequence_contains, mhc_class, qualitative_measure
iedb_search_bcell	filters only
iedb_search_mhc	filters only
iedb_search_tcr_sequences / iedb_search_bcr_sequences	filters only

Detail tools by structure_id: iedb_get_epitope_antigens, iedb_get_epitope_mhc, iedb_get_epitope_tcell_assays, iedb_get_epitope_references.

Immunoglobulin Genes (IMGT)

IMGT_search_genes, IMGT_get_gene_info, IMGT_get_sequence — all take gene_name (e.g. "IGHV1-2").

Protein Interactions (IntAct, BioGRID)

Tool	Key Parameters
intact_get_interaction_network	identifier (UniProt accession — gene symbols return 0 results), limit
intact_search_interactions	query (keyword), limit
BioGRID_get_interactions	gene_names (list), organism ("9606" string), limit
BioGRID_get_chemical_interactions	gene_names (list), chemical_names (list), organism (int)

Weight interaction evidence: co-IP and two-hybrid = direct; co-expression or text-mining = hypothesis-generating.

Cytokine / Signaling (OpenTargets, GWAS)

Tool	Key Parameters
OpenTargets_get_target_id_description_by_name	targetName — resolves gene symbol to Ensembl ID (required before ensemblId tools)
OpenTargets_get_target_interactions_by_ensemblID	ensemblId, size
OpenTargets_get_target_gene_ontology_by_ensemblID	ensemblId
OpenTargets_get_target_safety_profile_by_ensemblID	ensemblId
OpenTargets_get_associated_diseases_by_drug_chemblId	chemblId
gwas_search_associations	query (disease name)
gwas_get_snps_for_gene	gene_symbol (mapped gene symbol)

Clinical / Safety (FAERS, Clinical Trials)

Tool	Key Parameters
FAERS_calculate_disproportionality	drug_name (generic), adverse_event → PRR, ROR, IC
FAERS_filter_serious_events	drug_name, seriousness_type
FAERS_stratify_by_demographics	drug_name, stratify_by (sex/age/country)
FAERS_compare_drugs	drug1, drug2, adverse_event
search_clinical_trials	condition, intervention, pageSize

Autoimmune Genetics (Orphanet)

Orphanet_search_diseases(query) → ORPHAcode. Then: Orphanet_get_genes, Orphanet_get_phenotypes, Orphanet_get_epidemiology, Orphanet_get_natural_history (all take orpha_code). Orphanet_get_gene_diseases(gene_symbol) for reverse lookup.

Immune Pathways (KEGG, Reactome)

Tool	Key Parameters
kegg_search_pathway	keyword
KEGG_get_disease / KEGG_get_disease_genes	disease_id (e.g. "H00080" for SLE)
KEGG_get_pathway_genes	pathway_id (e.g. "hsa04060")
Reactome_get_pathway	stId (e.g. "R-HSA-168256") — NOT pathway_id
ReactomeAnalysis_pathway_enrichment	identifiers (space-separated STRING, not array)
Reactome_map_uniprot_to_pathways	uniprot_id

Key pathway IDs — Reactome: R-HSA-168256 (Immune System), R-HSA-168249 (Innate), R-HSA-1280218 (Adaptive), R-HSA-1280215 (Cytokine Signaling), R-HSA-202403 (TCR), R-HSA-983705 (BCR), R-HSA-166658 (Complement). KEGG: hsa04060 (Cytokine-receptor), hsa04660 (TCR), hsa04662 (BCR), hsa04620 (TLR), hsa04630 (JAK-STAT), hsa05322 (SLE), hsa05323 (RA).

Tumor Immune Microenvironment

TIMER2_immune_estimation — operation="immune_estimation", cancer (TCGA code e.g. "luad_tcga"), gene (symbol). Returns deconvolution estimates; validate with orthogonal methods.

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Parameter Gotchas

Issue	Wrong	Correct
Reactome param name	pathway_id=	stId=
ReactomeAnalysis identifiers	list ["STAT4","IRF5"]	space-separated string "STAT4 IRF5"
OpenTargets target lookup	query="IL6"	targetName="IL6"
IntAct identifier	gene symbol "CD274"	UniProt accession "Q9NZQ7"
BioGRID organism	"human"	"9606" (string taxon ID)
BioGRID gene param	gene_name="CD274"	gene_names=["CD274"] (list)
FAERS drug name	brand name "Keytruda"	generic "pembrolizumab"
SAbDab search	expect JSON	SAbDab_search_structures returns URL only; use SAbDab_get_structure with PDB ID
TheraSAbDab by target	search_by_target for common names	Use search_therapeutics(query=drug_name) instead; target requires exact registry string
KEGG disease ID	"lupus"	"H00080"

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Workflows

Antibody target research: TheraSAbDab_search_by_target or search_therapeutics → SAbDab_get_structure for PDB data → iedb_search_epitopes / iedb_search_tcell_assays → intact_get_interaction_network (UniProt ID) + BioGRID_get_interactions → FAERS_calculate_disproportionality + search_clinical_trials.

Autoimmune disease genetics: Orphanet_search_diseases → Orphanet_get_genes + Orphanet_get_phenotypes → gwas_search_associations + gwas_get_snps_for_gene for candidate genes → KEGG_get_disease + KEGG_get_pathway_genes → ReactomeAnalysis_pathway_enrichment on disease genes.

Single-cell dual receptor questions: When asked about mechanisms for dual chain expression, distinguish BIOLOGICAL mechanisms (allelic inclusion, receptor editing, autoreactivity) from TECHNICAL artifacts (doublets, ambient RNA). Questions asking "why would a cell express two chains" usually want biological mechanisms only. Doublets (1) are often included since they represent real observations, but ambient RNA (2) is typically excluded as contamination, not true expression.

Immunotherapy safety comparison: FAERS_compare_drugs for AE head-to-head → FAERS_filter_serious_events per drug → FAERS_stratify_by_demographics → resolve target with OpenTargets_get_target_id_description_by_name → OpenTargets_get_target_safety_profile_by_ensemblID → search_clinical_trials.