Protective CD8+ T cell immunity requires that dendritic cells (DCs) cross-present the same peptide repertoire that infected or transformed cells present directly on MHC class I. Tabachnick-Cherny et al. (bioRxiv 2019; J Immunol 2020) showed that apoptosis, but not necrosis, of donor cells triggers p62-dependent global protein aggregation that captures stable proteins, and that these aggregates — including model polyglutamine (94Q) substrates — are a potent antigen source for DC cross-presentation in vitro and in vivo. The molecular pathway underlying this route, however, was left open: how apoptosis regulates aggregate formation in the donor cell, and how DCs recognize, internalize, de-aggregate, and proteolytically process aggregates to extract MHC-I peptides remain unknown, as does the possibility of exploiting immune clearance of aggregates in polyglutamine diseases. As of mid-2026 the aggregate-mediated cross-presentation route remains unanswered.

Background

Cytotoxic T lymphocytes recognize peptides of 8–10 amino acids bound to MHC class I molecules (the cell-surface proteins that display intracellular protein fragments to CD8+ T cells). Cells present their own proteins this way ('direct presentation'), but most tissues cannot activate naïve CD8+ T cells; that task belongs to dendritic cells (DCs), which can take up extracellular material and channel it onto MHC class I — a process called 'cross-presentation'. Effective immunity therefore requires an overlap between the repertoire a target cell presents directly and the repertoire a DC cross-presents. How this overlap was maintained was puzzling for stable, long-lived proteins: rapid direct presentation of such proteins is thought to rely on 'DRiPs' (defective ribosomal products — misfolded or truncated nascent polypeptides degraded almost immediately after synthesis), and such fleeting entities seemed hard to capture intact for transfer to DCs. Tabachnick-Cherny et al. (2019 preprint, DOI 10.1101/806414; published as J Immunol 2020, DOI 10.4049/jimmunol.1901535) addressed this with stable and unstable ovalbumin-based model antigens. They found that apoptosis (programmed cell death), but not heat-induced necrosis, causes a global, nonselective aggregation of cellular proteins in the donor cell, dependent on p62/SQSTM1 — an autophagy receptor protein that both clusters polyubiquitinated proteins into aggregates and can target them to lysosomes via autophagy. Aggregates from apoptotic donor cells were efficiently cross-presented by DCs in vitro and in vivo (using OT-I mice, whose CD8+ T cells recognize the ovalbumin SIINFEKL epitope, and bone-marrow chimeras — mice whose hematopoietic system has been replaced by donor-derived cells, which allows antigen-transfer routes to be traced in vivo), and polyglutamine ('polyQ') expansions — the amino-acid stretches that aggregate in Huntington's disease and spinocerebellar ataxias — fused to ovalbumin served directly as a potent antigen source, demonstrating an unusual capacity of DCs to process even a long 94Q aggregate, probably via lysosomal catabolism. The authors contrasted these stable donor-cell aggregates with DALIS (dendritic-cell aggresome-like induced structures — transient p62-based aggregates formed inside maturing DCs that transiently sequester self-ubiquitinated proteins and were previously implicated in favoring cross-presentation of exogenous antigens), concluding from prior DALIS studies together with their own findings that DCs use aggregation both to reduce the self MHC-I antigen load upon immunological challenge and to select relevant antigens in target cells for cross-presentation. Their Discussion explicitly states that detailed studies of 'the mechanisms that control aggregation in the donor cells and de-aggregation and processing in the APC' are needed, that aggregates are not the exclusive antigen source for cross-presentation (DCs also acquire intact antigens from necrotic debris, exosomes, and direct 'nibbling' of live cells), that p62 is a candidate lysosomal-targeting factor for apoptosis-related aggregates in DCs, and that a possible role of the immune system in clearing aggregates 'should be further studied and potentially could be exploited for therapy'.

Problem Statement

Determine the molecular pathway by which apoptosis-induced, p62-dependent protein aggregates mediate MHC class I cross-presentation. Concretely, following Tabachnick-Cherny et al. (J Immunol 2020): (1) identify the mechanisms that control global aggregate formation in donor cells during apoptosis, including how p62/SQSTM1-mediated aggregation is regulated at that stage; (2) identify how such aggregates are recognized and internalized by dendritic cells, and the lysosomal and proteasomal steps — including any de-aggregation or disaggregase activity and the candidate role of p62 as a lysosomal-targeting factor — required to extract MHC-I-binding peptides from aggregates as stable as a 94-glutamine polyQ substrate; and (3) as the explicitly raised translational facet: determine whether the immune system clears protein aggregates in vivo, including polyQ aggregates in glia and neurons of polyglutamine-disease models, and whether this can be exploited therapeutically. A complete answer to the core (1)–(2) mechanistic chain is the scientific objective; component (3) is a facet the same source poses rather than an independent objective.

References

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