Antigen presentation, MHC and T-cell responses

At a glance

• T cells only see peptide bound to MHC (HLA in humans). CD8 T cells read class I (HLA-A, -B, -C) and kill. CD4 T cells read class II (HLA-DR, -DQ, -DP) and help.
• Naive T-cell activation needs three signals: antigen (TCR plus peptide-MHC), co-stimulation (CD28 with CD80/CD86) and cytokine (which sets the helper subset).
• CD4 subsets (Th1, Th2, Th17, Tfh, Treg) each match a type of pathogen and a family of immune diseases and biologics.
• HLA genes are the most polymorphic in the genome, which explains transplant matching, disease associations and pharmacogenetic drug reactions.
• Paper 1 tests mechanisms of immunosuppressants and checkpoint inhibitors, HLA-linked drug reactions, and immunodeficiency patterns. Worked numbers: a CD4 count from a differential, and an NNT for HLA screening.

Two presentation pathways

	MHC class I	MHC class II
Expressed on	All nucleated cells (not red cells)	Dendritic cells, macrophages, B cells; induced on others by interferon gamma
Peptide source	Cytosol: self, viral, tumour proteins	Endosomes: phagocytosed or endocytosed proteins
Processing	Proteasome, then TAP pumps peptides into the ER	Endosomal cathepsins; invariant chain and HLA-DM load the groove
Peptide length	8 to 10 amino acids	13 to 25 amino acids
Read by	CD8 T cells	CD4 T cells
Deficiency	TAP deficiency (bare lymphocyte type 1): chronic sinopulmonary infection, necrotising granulomatous skin lesions	Class II deficiency (type 2, CIITA or RFX): very low CD4 count, combined immunodeficiency

Cross-presentation. Specialised dendritic cells (cDC1) put exogenous antigen onto class I. That lets CD8 T cells respond to viruses that don't infect dendritic cells, and to tumours.

Dendritic cells link innate and adaptive immunity. Immature DCs sample tissue. PAMP signalling through TLRs (see innate immunity) makes them mature, upregulate CD80/CD86 and CCR7, and migrate to the lymph node. Antigen shown without these danger signals produces tolerance.

Pitfall: NK cells kill cells that have lost class I. CD8 T cells need class I to see their target. Viruses that downregulate HLA class I (CMV) escape CD8 cells but become NK targets.

Activating a naive T cell

1. Signal 1: TCR binds peptide-MHC. CD4 or CD8 binds the non-polymorphic part of the MHC. CD3 transmits the signal (ZAP-70, then calcium and calcineurin, NFAT, NF-kB, AP-1).
2. Signal 2: CD28 binds CD80/CD86. Without it the cell becomes anergic.
3. Signal 3: cytokines from the dendritic cell choose the subset.
4. IL-2 and CD25 (the high-affinity IL-2 receptor alpha chain) drive clonal expansion. One naive clone can expand 10,000-fold in a week.

Brakes: CTLA-4 is upregulated after activation and binds B7 with higher affinity than CD28. PD-1 binds PD-L1 and PD-L2 on tissue and tumour cells and dampens effector cells in the periphery.

Drugs mapped to the signals

Step	Drug	Mechanism
Signal 1	Anti-thymocyte globulin	Polyclonal depletion of T cells
Calcineurin	Tacrolimus, ciclosporin	Block NFAT dephosphorylation, so less IL-2
Signal 2	Abatacept (CTLA-4-Ig), belatacept	Bind CD80/CD86 and block CD28
IL-2 receptor	Basiliximab	Anti-CD25 induction in kidney transplant
Proliferation	Mycophenolate, azathioprine	Purine synthesis inhibition (IMPDH; thiopurine)
mTOR	Sirolimus, everolimus	Block IL-2 receptor signalling and cell cycle progression
Brakes released	Ipilimumab (CTLA-4), nivolumab, pembrolizumab (PD-1), atezolizumab, durvalumab (PD-L1)	Restore antitumour T-cell activity
Leucocyte trafficking	Natalizumab (alpha-4 integrin), fingolimod (S1P receptor)	Keep lymphocytes out of the CNS or in lymph nodes

Clinical consequences: immunosuppression complications, systemic therapy organ toxicity for immune-related adverse events, and rheumatoid arthritis for abatacept.

Pitfall: checkpoint inhibitor toxicity reflects the brake removed. Ipilimumab causes more colitis and hypophysitis; PD-1 inhibitors cause more thyroiditis and pneumonitis. The combination has the highest grade 3 to 4 rate (over 50% in CheckMate 067).

CD4 helper subsets

Subset	Driven by	Signature cytokines	Defends against	Disease when excessive	Targeted by
Th1	IL-12, IFN-gamma (STAT4, T-bet)	IFN-gamma, TNF	Intracellular bacteria, mycobacteria	Granulomas, type IV hypersensitivity	Anti-TNF, anti-IL-12/23
Th2	IL-4 (STAT6, GATA3)	IL-4, IL-5, IL-13	Helminths	Asthma, atopic dermatitis, eosinophilia	Dupilumab, mepolizumab
Th17	IL-6, TGF-beta, IL-23 (STAT3, ROR-gamma-t)	IL-17, IL-22	Extracellular bacteria, Candida	Psoriasis, spondyloarthritis	Secukinumab, ustekinumab, risankizumab
Tfh	IL-6, IL-21 (BCL6)	IL-21, CD40L	Help for B-cell germinal centres	Autoantibodies (SLE)
Treg	TGF-beta, IL-2 (FOXP3)	IL-10, TGF-beta	Self tolerance	Loss: IPEX syndrome (FOXP3)

Anti-TNF therapy breaks down granulomas, so latent TB reactivates. Screen with an interferon-gamma release assay before starting. Anti-IL-17 drugs raise mucocutaneous candidiasis rates, mirroring STAT3 deficiency (hyper-IgE syndrome) and AIRE deficiency (anti-IL-17 and IL-22 autoantibodies).

CD8 cytotoxicity

CD8 cells kill by perforin and granzymes and through Fas ligand. Perforin deficiency causes familial haemophagocytic lymphohistiocytosis: uncontrolled activation, ferritin often above 10,000 µg/L, cytopenias and hepatosplenomegaly. CD8 T cells mediate SJS/TEN through granulysin release (see SJS/TEN) and drive graft rejection and graft-versus-host disease.

Superantigens

Staphylococcal TSST-1 and enterotoxins, and streptococcal pyrogenic exotoxins, bind class II and the TCR V-beta region outside the peptide groove. Up to 20% of all T cells activate, compared with about 1 in 10^5 for a conventional antigen. The cytokine surge causes fever, shock and a desquamating rash. IVIG may neutralise toxin in streptococcal toxic shock, and clindamycin suppresses toxin synthesis.

Worked example 1: CD4 count from a differential

A man with newly diagnosed HIV has a white cell count of 3.8 × 10^9/L with 22% lymphocytes. Flow cytometry shows CD4 cells at 18% of lymphocytes.

• Lymphocytes: 3.8 × 0.22 = 0.84 × 10^9/L = 840 cells/µL.
• CD4 count: 840 × 0.18 = 151 cells/µL.

That is below 200, so he meets the PJP threshold even though his CD4 percentage (18%) is above the 14% backup threshold. He needs PJP prophylaxis (co-trimoxazole) as well as prompt ART. The percentage is more stable than the absolute count when the total white count changes, for example after splenectomy (raises it) or during acute illness (lowers it). Clinical management: acquired immunodeficiency.

Worked example 2: HLA screening NNT

HLA alleles present drugs or drug-modified peptides to T cells. In PREDICT-1 (Mallal, 2008, 1,956 patients), immunologically confirmed abacavir hypersensitivity occurred in 2.7% of the unscreened arm and 0% of the HLA-B*57:01-screened arm.

• Absolute risk reduction: 2.7% - 0% = 2.7%.
• NNT: 1 / 0.027 = about 37 patients screened to prevent one confirmed reaction.
• About half of HLA-B*57:01 carriers react (positive predictive value 48% in PREDICT-1), and the negative predictive value is close to 100%. A negative test means abacavir can be used.

Allele	Drug	Reaction	Highest-risk ancestry
HLA-B*57:01	Abacavir	Hypersensitivity syndrome	European (about 6%)
HLA-B*15:02	Carbamazepine, oxcarbazepine, phenytoin	SJS/TEN	Han Chinese, Thai, Malaysian
HLA-A*31:01	Carbamazepine	DRESS, maculopapular eruption	European, Japanese
HLA-B*58:01	Allopurinol	SJS/TEN, DRESS	Han Chinese, Thai, Korean

See drug allergy and DRESS. Disease associations work the same way: HLA-B27 with ankylosing spondylitis (see ankylosing spondylitis), HLA-DQ2 and DQ8 with coeliac disease (negative predictive value close to 100%), HLA-DR3 and DR4 with type 1 diabetes, and shared-epitope HLA-DRB1 with seropositive RA.

Thymic selection

T cells mature in the thymus. Positive selection keeps cells that bind self MHC weakly. Negative selection deletes cells that bind self peptide strongly. AIRE lets thymic epithelium express tissue-restricted proteins (insulin, thyroglobulin), so loss of AIRE causes APECED: candidiasis, hypoparathyroidism and adrenal failure. DiGeorge syndrome (22q11.2 deletion) gives a small or absent thymus and low T-cell numbers. See primary defects of cellular immunity and combined immunodeficiency.

How it's tested

• Mechanism of an immunosuppressant or checkpoint inhibitor, and the adverse effect that follows from it.
• HLA pharmacogenetics: which test before which drug, in which ancestry, and why a negative result matters.
• Matching an infection pattern to a T-cell defect: PJP and CMV (CD4 or combined), candidiasis (Th17), TB after anti-TNF.
• Calculating a CD4 count, or an NNT from screening data.

Pitfalls

• Pitfall: HLA-B*57:01 testing prevents immunological hypersensitivity, not all reactions. Clinically diagnosed reactions still occurred in the screened arm of PREDICT-1 (3.4%), mostly false positives.
• Pitfall: CD4 T cells read class II and CD8 T cells read class I. The product rule (4 × 2 = 8 × 1 = 8) is a quick check.
• Pitfall: abatacept blocks co-stimulation by binding CD80/CD86, not CD28.
• Pitfall: tacrolimus and ciclosporin don't kill T cells. They stop IL-2 production, and their toxicity (nephrotoxicity, hyperkalaemia, hypomagnesaemia, tremor) comes from calcineurin inhibition in other tissues.
• Pitfall: the CD4 percentage helps when the total white count is distorted. Don't stop PJP prophylaxis on a single count rising above 200.