EFB Dengue Literature Review

state

25 min read

Wiki State

Persistent operational context for the extrafollicular B cell dynamics in dengue literature review. Read this at the start of every session. Update it after every session.

Current Focus

  • Scope: Extrafollicular B cell responses in dengue infection, characterised primarily through flow cytometry assays (conventional, spectral, high-dimensional). Includes plasmablast dynamics, atypical/T-bet⁺ B cells, isotype switching, and the relationship between EF responses and clinical outcomes (severity, primary vs. secondary infection, serotype).
  • Stage: Fifteen sources ingested (7 comparative + 8 dengue-specific). Wiki has 84 pages across 15 sources. Ansari2025 is the landmark paper — first direct evidence of EF B cell activation in dengue, identifying Tph→IL-21→memory B cell→plasmablast as the dominant B cell help axis, with CD21⁻CD11c⁺ (DN2-phenotype) B cells expanded in acute dengue. The comparative framework (SLE + COVID-19) is now validated in dengue. A detailed wet-lab research plan exists (analyses/Research Plan - DN B Cell Expansion in Dengue.md) — Revision 3 (2026-05-10), incorporating Ansari2025 (cellular evidence), GodoyLozano2016 (molecular SHM evidence), and Appanna2016 (clonal evidence). Follow-Up Study 4 (BCR sequencing of sorted DN2) now carries specific falsifiable predictions from the molecular evidence. GodoyLozano2016 provides the first direct SHM measurement in dengue IgG B cells — paradoxically low SHM in acute phase, lower in secondary than primary, lower in DWS+ than DWS−. This is the strongest molecular evidence for EF pathway operation in dengue, with IGHV1-2/1-69 bias and convergent CDRH3s at 52% prevalence. The dual EF+GC model is now supported by both cellular (Ansari2025) and molecular (GodoyLozano2016, Parameswaran2013) evidence. Priyamvada2016 provides the sorted PB BCR sequencing that was the key remaining gap — but with opposite result to expected: HIGH SHM (mean 18.1 VH mutations) in sorted secondary DHF PBs, supporting memory B cell origin. This creates a dual-pathway model: memory-derived high-SHM PBs (Priyamvada2016) + de novo EF-derived low-SHM PBs (GodoyLozano2016). Also establishes two new concept pages: Original Antigenic Sin (OAS in 2/4 patients — DENV1 preferentially neutralised over infecting DENV2) and Antibody-Dependent Enhancement (45/53 mAbs ADE-competent regardless of neutralisation). Key remaining gap: no study has simultaneously sorted PBs from primary vs. secondary dengue for SHM comparison — this would test whether primary PBs are low-SHM (de novo EF) while secondary PBs are high-SHM (memory recall). Next priority: papers with T-bet staining to confirm DN2 identity; studies on OAS across serotype combinations; ADE functional studies.
  • Open questions to keep in mind as ingests proceed:
    • Are the CD21⁻CD11c⁺ B cells in dengue truly DN2 (T-bet⁺, FCRL5⁺, CXCR5⁻)? Needs intracellular T-bet staining.
    • What is the SHM distribution of sorted dengue plasmablasts? GodoyLozano2016 shows globally low SHM in IgG B cells during acute phase (Monte Carlo simulation supports ASC dominance), but formal sorted PB BCR sequencing would conclusively demonstrate germline (EF) vs. mutated (GC) origin.
    • Does the Tph→IL-21 axis operate differently in primary vs. secondary dengue?
    • Is the Tph pathway the source of ADE-competent cross-reactive IgG in secondary dengue?
    • Does IL-21 blockade reduce severity-associated (non-neutralizing) antibodies while preserving neutralizing titers?
    • What is the functional role of cytotoxic (GZMB⁺HOPX⁺) Tph cells?
    • Do EF and GC responses truly operate concurrently in dengue, or does the balance shift with disease stage?

Queue

Papers waiting to be ingested (add new entries at the top):

  • balakrishnan2011.pdf
  • kwissa2014.pdf
  • Bhattacharya2016.pdf
  • woda2016.pdf
  • william2002.pdf
  • zompi2012.pdf
  • Sutton2021.pdf

Decisions

Structural and workflow decisions with rationale. Append-only.

[2026-05-02] Naming conventions established (first ingest)

Decision: Entity pages use singular descriptive names (Double-Negative B Cell, Plasmablast, CD27). Source short titles follow AuthorYear - Short Descriptive Title format (e.g., Wei2007 - DN Memory B Cells in SLE). Concept and method pages use plain descriptive names (Extrafollicular Response, Conventional Flow Cytometry). Why: First ingest sets the template; retroactive renaming across many pages is costly. How to apply: Follow these conventions for all future ingests. If a new paper uses a term that conflicts with an existing page name, prefer the existing page name and add the alternative term in the Overview section.

[2026-05-02] DN B cells vs. atypical B cells — treated as overlapping, not identical

Decision: Double-Negative B Cell (IgD⁻CD27⁻) is the primary entity page for this population, per curator direction. It is noted as overlapping with, but not identical to, “atypical B cells,” “age-associated B cells (ABCs),” and “T-bet⁺ B cells” used in later literature. These terms will not get separate entity pages until a paper provides a direct phenotypic comparison justifying the distinction. Why: Curator specified Double-Negative B Cell as the entity name; the field uses multiple overlapping terms for similar populations. Premature splitting would fragment the evidence base. How to apply: When a paper uses “atypical B cell” or “ABC” terminology, cross-reference to Double-Negative B Cell and note any phenotypic differences (e.g., T-bet expression, FcRL5, CD11c) in the entity page.

[2026-05-02] Bm Classification → method page; 9G4 tracking → out of scope for dengue

Decision: During Anolik2004 ingest, curator directed: (1) create a method page for the Bm1–Bm5 classification framework (done: methods/Bm Classification.md); (2) skip the 9G4 VH4.34 antiidiotype tracking method as out of scope — it is SLE-specific autoreactivity tracking with no direct dengue application. Why: Bm1–Bm5 is a foundational gating framework used across multiple B cell biology papers and likely appears in dengue flow cytometry studies; it warrants its own page. 9G4 is a lupus-specific reagent; tracking it would bloat the wiki without dengue relevance. How to apply: If a future paper uses 9G4 or VH4.34 tracking in a dengue context, reconsider. Otherwise, treat 9G4 results as background context only (captured in source pages) rather than creating a method page.

[2026-05-08] Insertion-order guard added to Ingest workflow; sub-agent lint codified

Decision: Two CLAUDE.md workflow updates: (1) Ingest steps 5–7 now include an explicit insertion-order guard — new Key Points must be inserted at the end of ## Key Points from Literature, not appended at end-of-file. (2) Lint workflow now recommends parallel sub-agents for deep lints. Why: The 2026-05-08 deep lint found 19 pages with content displaced after ## Related Pages due to end-of-file appending during ingests. Sub-agent parallelism was validated as significantly more efficient for scanning 79 pages. How to apply: During every ingest, when updating entity/concept/method pages, locate ## Contradictions & Debates or ## Related Pages and insert new bullets immediately before it. During deep lints, spawn parallel agents per folder batch.

[2026-05-02] Wiki initialised

Decision: Scaffold created as a sibling to the dengue-wiki, focused on extrafollicular B cell dynamics in dengue via flow cytometry. Adapted from dengue-wiki schema with three differences: (1) geography/ axis dropped (clinical cohort source captured in source page metadata only); (2) Update Web workflow removed (web deployment deferred); (3) Domain Context rewritten for B cell / cytometry scope. Why: Curator wants a focused, blank-slate wiki for a tighter research question, leveraging the proven schema/workflow design from the dengue wiki. How to apply: Treat geography as out-of-scope unless the curator re-introduces it. If a paper’s cohort location is relevant, capture it in the source page’s “Setting” field — do not create geography pages.

Watch Items

Tracked issues, gaps, and follow-ups. Resolve and remove as addressed.

  • T-bet / FcRL5 / CD11c / CXCR5 entity pages thickened. Originally single-source (Jenks2018); all now at 2 sources after Sanz2025 ingest.
  • Plasmablast page — no longer a thin stub. Substantially populated from Anolik2004 (expansion data, CD20⁻ phenotype, short-lived kinetics, long-lived vs. short-lived dichotomy). Still requires a dengue-specific plasmablast paper for dengue-specific kinetics and marker panel details.
  • [2026-05-02 lint] Frontmatter source count mismatches fixed. CD10, IgG, IgM, IgA, FACS Sorting, Class Switch Recombination all had sources: 1 in frontmatter but 2 sources listed in body. Corrected. Conventional Flow Cytometry duplicate “Related Pages” section removed.
  • [2026-05-02 lint, updated 2026-05-11] Remaining thin pages (single source). Entities (8): B220, CD23, CD71, ATF3, EGR, HOPX, Peripheral Helper T Cell, TOX2. Methods (8): Serum Proteomics, Spectral Flow Cytometry, RRBS, Phospho-Flow Cytometry, Activation-Induced Marker Assay, Single-Cell RNA Sequencing, T-B Coculture Assay, PRNT. (FRNT now at 2 sources — resolved.) Will thicken with future ingests; Peripheral Helper T Cell / HOPX / TOX2 are Ansari2025-only and will grow when non-dengue Tph papers are ingested. Peripheral Helper T Cell is the most significant thin page given its centrality to the dengue EF model.
  • [2026-05-02 lint] B220 near-orphan — RESOLVED. Added [[B220]] to Double-Negative B Cell Related Pages during 2026-05-08 deep lint.
  • “Questions Raised” from Wei2007 — three non-trivial Watch Items:
    • Do DN B cells in dengue share T-bet/FcRL5/CD11c transcriptional identity with atypical B cells in malaria/COVID-19? (Needs comparative phenotyping paper. Sanz2025 provides cross-disease context but no dengue-specific data.)
    • Is the ~3% vs ~5% SHM gap between DN and CD27⁺ memory cells reproducible across disease contexts and VH families? (Wei2007 used VH3 only, n=28.)
    • Can IgD⁻CD27⁻ gating from Wei2007 serve as a retrospective reference gate for re-analysing older dengue flow cytometry datasets? (Needs dengue flow cytometry paper with IgD/CD27 staining.)
  • Dengue plasmablast kinetics benchmark. Anolik2004 establishes that SLE plasmablasts are short-lived and decline within weeks after precursor removal. The analogous question for dengue: at what rate do acute-phase plasmablasts (days 7–10 peak) decline post-defervescence? Does the kinetics match the short-lived model? Needs a dengue plasmablast paper with longitudinal sampling including days 14–21 convalescent timepoints.
  • Pre-GC (Bm2ʹ) expansion in dengue unstudied. Anolik2004 identifies circulating IgD⁺CD38^high pre-GC cells (Bm2ʹ) as a distinct SLE-associated population resistant to rituximab. No dengue paper has yet systematically tracked this gate. Does acute dengue activate concurrent GC reactions alongside the dominant EF plasmablast wave? Needs dengue paper with CD38/IgD Bm classification or CD10 staining.
  • GC tolerance checkpoint in dengue. Anolik2004 shows that autoreactive VH4.34 memory B cells are expanded in SLE (failure of GC censoring) and normalise after rituximab. Does acute dengue produce a transient GC tolerance failure, generating autoreactive or cross-reactive memory B cells? Needs BCR repertoire data from dengue patients with paired acute/convalescent samples.
  • acN cell phenotype in dengue unstudied. Tipton2015 defines activated naive B cells (CD19^hi, IgD⁺, MTG⁺, CD24⁻, CD21⁻, CD23⁻) as major EF ASC precursors in SLE. Does this population expand in acute dengue? MTG is non-standard but CD19^hi + CD21⁻ + CD24⁻ within IgD⁺CD27⁻ cells could be assessed in existing dengue flow cytometry data. Needs dengue paper with naive compartment sub-gating.
  • SHM distribution of dengue acute-phase plasmablasts — RESOLVED by dual-pathway model. GodoyLozano2016: low SHM in unsorted IgG (bulk). Priyamvada2016: high SHM (mean 18.1 VH) in sorted secondary DHF PBs. Reconciliation: memory-derived high-SHM PBs coexist with de novo EF-derived low-SHM B cells. Remaining gap: primary dengue sorted PB SHM comparison.
  • Origin of dengue-specific vs. non-specific plasmablasts. In SLE, naive cells are the dominant ASC precursors during flares (not memory recall). Does a similar naive cell contribution dominate the dengue plasmablast wave, or are pre-existing cross-reactive memory cells the primary precursors? This distinction has implications for whether the dengue plasmablast response is truly EF-naive or EF-memory. Needs dengue connectivity NGS study.
  • DN2 expansion kinetics in dengue. Do DN2 cells (CXCR5⁻CD11c⁺CD21⁻) expand during acute dengue? At what kinetics relative to the plasmablast wave? The panel requirements (CXCR5 within IgD⁻CD27⁻ gate) mean this has likely never been measured. Needs dengue flow cytometry paper with CXCR5 staining.
  • DN1/DN2 ratio as severity biomarker. Is the DN1/DN2 ratio within IgD⁻CD27⁻ informative of disease severity or EF vs. GC dominance in dengue? Requires CXCR5+CD21+CD11c staining within the DN gate.
  • TLR7-driven EF pathway in dengue. Dengue is an ssRNA virus — abundant TLR7 ligands during viraemia. Does the Jenks2018 TLR7/IFN-γ/IL-21 differentiation programme operate in dengue? The antagonistic regulation (TLR7 suppresses GC) predicts EF dominance during active viraemia.
  • T-bet/ZEB2 signature in dengue scRNA-seq. Can the T-bet/ZEB2 transcriptional signature be used retrospectively to identify EF-derived B cells in existing dengue single-cell RNA-seq datasets? This is a low-cost computational test of whether DN2-like cells exist in dengue.
  • [2026-05-03] Dengue “AtB/ABC” studies need IgD audit. Sanz2025 argues that any study reporting “atypical B cell” expansion without IgD in the panel cannot distinguish DN2 from activated memory or pre-GC contamination. When ingesting dengue papers, check whether IgD was included — flag studies that lack it.
  • [2026-05-03] EF/GC endotype concept — testable in dengue? Sanz2025 shows SLE patients segregate into EF-dominant vs. GC-dominant clusters predicting severity and vaccine response quality. Does dengue patient heterogeneity follow a similar endotype pattern? Needs dengue cohort with both DN/plasmablast and GC (CD10⁺/Bm2ʹ/Tfh) markers.
  • [2026-05-03] Self-limited EF autoreactivity in dengue. Healthy COVID-19 subjects generate transient naïve-derived autoreactive DN2 cells that resolve within months. Does acute dengue produce a similar transient autoreactive EF response? Does secondary infection perpetuate these clones? Needs dengue acute/convalescent paired BCR data with autoreactivity assays.
  • [2026-05-03] DN3 tracking in dengue. DN3 cells (CXCR5⁻CD21⁻CD11c⁻T-bet⁻ within IgD⁻CD27⁻) are pre-plasmablasts expanded in COVID-19 and SLE. Does this population expand in acute dengue alongside DN2? Requires CD11c staining within the DN gate.
  • [2026-05-03] ZEB2 as EF predictor in dengue. ZEB2 represses Mef2b (GC TF) → mechanistic basis for EF/GC antagonism. Is ZEB2 elevated in acute dengue B cells? Testable via scRNA-seq re-analysis.
  • [2026-05-04] Neutralizing Ab paradox — testable in dengue? Woodruff2020 shows high neutralizing anti-SARS-CoV-2 titers from EF-derived ASCs correlate with poor COVID-19 outcomes. Does an analogous paradox exist in dengue — where high early anti-DENV titers from EF responses correlate with severity or facilitate ADE? This is testable with paired B cell phenotyping + serum neutralization/ADE assays in acute dengue cohorts.
  • [2026-05-04] CXCR5/CXCR3 chemokine switch in dengue. The CXCR5↓/CXCR3↑ switch on EF B cells in COVID-19 is a readily measurable marker of EF pathway activation. Can this be detected in acute dengue PBMC samples? Requires CXCR5 and CXCR3 in the flow panel — check whether dengue papers include both.
  • [2026-05-04] Woodruff2020 Table 1 as panel design reference. The standardised 24-marker spectral panel with complete B cell population definitions (Table 1) is the reference standard for designing a dengue EF study. Evaluate whether existing dengue flow cytometry studies use compatible gating strategies.
  • [2026-05-06] Singh2026 — DN1/DN2/DN3 identity of DENV-specific atypical MBCs unknown. The DENV-specific CD27⁻CD21⁻ cells that accumulate in 2° dengue cannot be subdivided by the Singh2026 panel (lacks CXCR5, CD11c). Are they DN2 (EF effectors) or DN1 (GC memory)? Needs a dengue study with CXCR5/CD11c within the DN gate.
  • [2026-05-06] Singh2026 — IgM+ MBC recall mechanism in 2° dengue. IgM+ MBCs are the only subset significantly elevated during acute secondary dengue. Are these EF-derived (low SHM, broad cross-reactivity per Tipton2015 model) or GC-derived? BCR sequencing of sorted IgM+ DENV-specific cells would resolve this.
  • [2026-05-06] Singh2026 — delayed MBC peaks and 12–18M uptick. The >3-month delayed peaks in 2° dengue and the 12–18M uptick in 3/4 secondary cases could reflect prolonged GC reactions, tissue redistribution, or subclinical re-exposure in endemic settings. Needs longitudinal study with GC markers (CD10, Tfh) or serology to rule out re-exposure.
  • [2026-05-06] Singh2026 — naïve-like IgD+/IgM+ DENV-specific cells. These persist to 18M in both 1° and 2° infection. Their identity is ambiguous: true antigen-experienced cells with SHM, germline-encoded polyreactive B cells, or activated naive precursors. BCR sequencing of this population would resolve whether they carry SHM or are germline.
  • [2026-05-06] Singh2026 — qualitative MBC reprogramming and functional outcomes. Does the shift toward IgG+/atypical/class-switched MBC subsets in 2° dengue predict neutralizing antibody breadth, ADE-relevant cross-reactivity, or clinical severity upon subsequent infection?
  • [2026-05-07] AP-1/EGR chromatin remodelling in dengue? Scharer2019 identifies AP-1/EGR motif amplification as the SLE-specific disease layer on DN2 chromatin (distinct from the shared T-BET programme). Does acute dengue (an ssRNA virus with TLR7 activation and IFN-γ) produce transient AP-1/EGR remodelling? If so, does it resolve post-defervescence or persist? Testable by ATAC-seq on sorted B cells from acute dengue patients.
  • [2026-05-07] ATF3 as EF pathway marker in dengue. ATF3 is induced by both TLR stimulation and cellular stress — both prominent in dengue. Intracellular ATF3 flow cytometry (validated in Scharer2019) could be added to dengue panels as a practical readout of EF pathway activation. Needs testing in dengue PBMC samples.
  • [2026-05-07] DN2 apoptosis resistance in dengue. Scharer2019 shows DN2 cells uniquely lack G2/M checkpoint and apoptosis pathway enrichment among SLE B cell subsets. Does a similar mechanism explain atypical/DN MBC persistence in secondary dengue (Singh2026)?
  • [2026-05-07] Naive B cell epigenetic priming in dengue-endemic settings. SLE resting naive cells carry 6,664 DMLs and NR4A1/NR4A3 upregulation (BCR+TLR engagement). Does chronic dengue exposure in endemic settings produce analogous epigenetic priming of naive B cells, lowering the EF activation threshold?
  • [2026-05-07] 111-CpG biomarker signature — cross-disease applicability? Scharer2019 identifies 111 CpGs that discriminate SLE from healthy B cells across all subsets. Could these serve as biomarkers for EF pathway activation in other diseases with EF dominance, including severe dengue?
  • [2026-05-08 lint] External Citation Audit — 54 external papers cited inline across ~25 pages. See analyses/External Citation Audit.md. Curator reviewing DOIs and accuracy. Once verified: (1) rewrite inline citations to attribute solely to ingested sources, and/or (2) ingest high-priority external papers. 3 bare citations (Pattern A) are highest priority to resolve.
  • [2026-05-08 deep lint] Content-after-Related-Pages displacement — FIXED. 19 pages had Key Points bullets appended after ## Related Pages. All moved into correct section. Root cause: ingest workflow was appending at end-of-file instead of inserting into Key Points section.
  • [2026-05-08 deep lint] Template compliance — FIXED. Added ## Contradictions & Debates to 43 pages that were missing it. All pages now have complete section structure.
  • [2026-05-08 deep lint] Frontmatter/index count mismatches — FIXED. FACS Sorting, In Vitro B Cell Stimulation, ELISpot frontmatter corrected. Index header counts corrected (Entities 41, Methods 17, Total 79).
  • [2026-05-08 deep lint] Source page cross-reference cleanup — FIXED. Memory B Cell removed from Entities Mentioned in 5 sources; Singh2026 FACS Sorting link removed; Wrammert2012/GarciaBates2013 concept links added; Research Plan broken wikilinks fixed; Notable Findings heading repositioned; B220/CD10 orphan links added.
  • [2026-05-08] ⚠ Ansari2025 ingest disrupted by API errors — DEEP LINT COMPLETED. Checked all 22 entity, 5 concept, and 8 method pages linked from Ansari2025. Found and fixed 4 issues: (1) T-bet entity page was never visited — added source line, Key Points bullet, frontmatter update; (2) Germinal Center missing Key Points bullet about CXCL13/concurrent GC — added; (3) Memory B Cell missing Key Points bullet about Tph→memory B cell preference — added; (4) Conventional Flow Cytometry missing panel details + wrong frontmatter count — added panel bullet, fixed sources 8→9. BLIMP-1 was NOT listed in Ansari2025’s Entities Mentioned (not a propagation failure). All other pages verified clean.
  • TLR7-driven EF pathway in dengue. Partially resolved by Ansari2025: IL-21-dependent Tph mechanism provides the T cell help arm. TLR7 (B cell-intrinsic) not directly measured but the IL-21 axis maps onto the Jenks2018 pathway.
  • DN2 expansion kinetics in dengue. Partially resolved: Ansari2025 shows CD21⁻CD11c⁺ (DN2-phenotype) B cells expanded in acute dengue. Kinetics relative to PB wave not detailed; formal DN2 confirmation (T-bet, CXCR5) still needed.
  • Neutralizing Ab paradox — testable in dengue? RESOLVED: Ansari2025 replicates the paradox — anti-NS1/anti-prM IgG elevated in severe dengue but FRNT₅₀ not different by severity.
  • [2026-05-08] Ansari2025 — are CD21⁻CD11c⁺ B cells in dengue truly DN2? T-bet, CXCR5, and FCRL5 staining were not performed within the DN gate. Formal DN2 confirmation requires intracellular T-bet + CXCR5 surface staining on IgD⁻CD27⁻ cells from acute dengue samples.
  • [2026-05-08] Ansari2025 — Tph→ADE link. Does the Tph→IL-21→memory B cell→PB axis produce ADE-competent cross-reactive IgG in secondary dengue? This is the key translational question. Needs paired Tph frequency + ADE assay data.
  • [2026-05-08] Ansari2025 — cytotoxic Tph function unknown. The GZMB⁺HOPX⁺ Tph subcluster has no assigned function. Does it kill B cells, infected cells, or regulate the immune response? Only 13 shared TCR clonotypes with helper Tph.
  • [2026-05-08] Ansari2025 — IL-21 as therapeutic target. Anti-IL-21 reduces PB output ~60%. Does this reduce severity-associated non-neutralizing IgG while preserving neutralizing titers? Testable in vitro with dengue-specific readouts.
  • [2026-05-08] Ansari2025 — EF+GC concurrent activity. CXCL13 elevated alongside Tph dominance suggests both pathways active simultaneously. Is the EF/GC ratio a severity biomarker? Needs combined Tph + Tfh + CXCL13 + DN2:DN1 assessment.
  • [2026-05-08] Research Plan update needed. RESOLVED: Revision 2 (2026-05-08) incorporates Ansari2025 throughout. Rationale reframed, H4 added, Tph quantification added as follow-up study 7. Tph staining (CXCR5/PD-1) kept as follow-up rather than primary panel (requires second tube). IL-21 measurement and FRNT remain out of scope for the flow-only B cell study but are noted as complementary readouts.
  • [2026-05-08] GarciaBates2013 — functional quality of plasmablast antibodies — RESOLVED. Priyamvada2016 provides the monoclonal characterisation: 70% E-specific, all cross-reactive, 45/53 ADE-competent, OAS in 2/4 patients. The PB wave produces IgG that is predominantly cross-reactive, ADE-competent, and in some patients serotype-biased by OAS.
  • [2026-05-08] GarciaBates2013 — age/interval effect on serotype cross-reactivity. Brazilian adults (>20y interval) show infecting-serotype-dominant reactivity; Nicaraguan children (shorter interval) show previous-serotype-dominant (original antigenic sin). Is this interval-dependent, age-dependent, or serotype-specific? Needs a cohort study with controlled interval comparisons.
  • [2026-05-08] GarciaBates2013 — memory vs. naive origin of dengue plasmablasts. Anamnestic kinetics (days 4–7 peak, secondary >> primary) favor memory recall, consistent with Ansari2025 Tph→memory B cell mechanism. But the naive B cell contraction in 2° DFC could also reflect naive recruitment. Needs connectivity NGS or clonal tracking.
  • [2026-05-08] GarciaBates2013 — B cell apoptosis mechanism and pathological significance. 60% caspase-3⁺ B cells in 2° DFC with Ki-67/caspase-3 and CD95/caspase-3 correlations. Is this Fas-mediated AICD? Does it limit the plasmablast wave (homeostatic) or contribute to pathology? Connects to DN2 apoptosis resistance (Scharer2019) — are DN2-phenotype cells selectively spared?
  • [2026-05-08] GarciaBates2013 — paracrine IL-21 missed by serum assay? Authors found no correlation between serum IL-21 and plasmablast frequency. Ansari2025 (12 years later) identified Tph-derived paracrine IL-21 as the driver. This suggests bulk serum cytokine assays miss the relevant compartmentalized signal — FluoroSpot or intracellular staining needed.
  • [2026-05-08] Wrammert2012 — Fc glycosylation of dengue PB-derived IgG unstudied. The paper raises IgG Fc glycosylation patterns as a potential pro-inflammatory mechanism but provides no data. Given that afucosylated IgG enhances FcγRIIIa binding and ADCC, and that the massive dengue PB wave produces predominantly non-neutralizing IgG, the glycosylation state of these antibodies could directly influence whether they are protective or pathological. Needs dengue study with Fc glycoproteomics on PB-derived mAbs.
  • [2026-05-08] Parameswaran2013 — antigen specificity of convergent CDR3s unknown. The convergent CDR3s (ARLDYYYYYGMDL etc.) are shared across individuals and serotype-independent, but their target antigen is unknown. Do they bind DENV E protein, NS1, prM, or other targets? If cross-serotype-conserved epitopes, are these antibodies neutralizing or ADE-enhancing? This is directly testable by expressing recombinant antibodies with these CDR3s and testing binding/neutralization.
  • [2026-05-08] Parameswaran2013 — convergent CDR3s not cell-type resolved. These CDR3s were identified from unsorted PBMC gDNA. Whether they are carried by plasmablasts, memory B cells, or both is unknown. Sorting acute-phase B cells (plasmablasts vs. memory vs. naive) before BCR sequencing would determine which compartment harbours the convergent clones and connect to the Tph→memory B cell→PB pathway (Ansari2025).
  • [2026-05-08] Parameswaran2013 — intermediate SHM does not resolve EF vs. GC origin. The 4.4–6.9% V mutation in convergent CDR3-bearing cells falls between the EF (<3%) and GC (~7.3%) benchmarks from SLE (Tipton2015). Three models remain: (a) GC-matured memory cells recalled via EF pathway; (b) mixture of EF and GC populations; (c) more extensive EF maturation in dengue than SLE. Sorted plasmablast BCR sequencing would resolve this — the key remaining gap.
  • [2026-05-08] Wrammert2012 — primary vs. secondary PB kinetics underpowered. Only 4/46 were primary infections; responses appeared similar but too few for comparison. This remains a gap — no study in the wiki has adequately powered primary vs. secondary PB kinetics data. The distinction matters because primary responses should have more IgM and potentially different kinetics if naive-derived (EF) vs. memory-derived.
  • Dengue plasmablast kinetics benchmark — RESOLVED. Wrammert2012 provides the kinetics: barely detectable at days 2–3, rapid increase to peak at day 6–7, return to baseline by 1 month post-discharge. This matches the GarciaBates2013 days 4–7 peak window. The decline post-defervescence kinetics (days 7–14–21) remain incompletely characterised — return visits were at ≥1 month, not at intermediate convalescent timepoints.
  • [2026-05-09] Appanna2016 — VH4-34/VH1-69 autoreactivity in dengue PBs. PBs were enriched for VH4-34 and VH1-69 (autoantigen-associated V genes). Is this transient EF autoreactivity (as in COVID-19, Sanz2025) or persistent? Does it contribute to dengue-associated autoimmune phenomena? Needs paired acute/convalescent BCR data.
  • [2026-05-09] Appanna2016 — IgM-only shared PB/MBC clones — artefact or biology? The rare CDR3s shared between PBs and MBCs were exclusively IgM. These could be genuine cross-compartment lineage members (evidence for IgM memory → PB pathway) or low-affinity polyreactive IgM artefacts from the live-virus sorting approach. Single-cell paired VH/VL with antigen validation would resolve this.
  • [2026-05-09] Appanna2016 — what activates prM-specific and complex-epitope MBCs? PBs are 85% E-specific, but MBCs are primarily complex-epitope and prM-specific. If the Tph→memory B cell→PB axis selectively activates E-specific memory, what drives the prM/complex-epitope MBC response? A separate activation pathway (GC? Bystander?) must be invoked.
  • [2026-05-09] Appanna2016 — CD27⁺ MBC gate misses DN memory. The study gated MBCs as CD19⁺CD20⁺CD27⁺, excluding the entire IgD⁻CD27⁻ (DN) compartment. Given that DN/atypical MBCs accumulate in secondary dengue (Singh2026) and are expanded acutely (Ansari2025), the “DENV-binding MBC” population in this study is incomplete. A study using IgD/CD27 gating with antigen probes would capture the full DENV-specific memory repertoire.
  • [2026-05-09] GodoyLozano2016 — antigen specificity of low-SHM IgG unknown. Are the germline-coded, cross-reactive IgG antibodies DENV-specific? The polyclonal CDRH3 diversity within biased IGHV segments suggests germline-encoded recognition, but no antigen-specific sorting was performed. Needs paired BCR sequencing + antigen specificity testing.
  • [2026-05-09] GodoyLozano2016 — convergent CDRH3 epitope targets unknown. The convergent CDRH3s (ARQFGNWFDS, ARQWGNWFDL) shared across 52% of patients have unknown antigen targets — same gap as Parameswaran2013 convergent CDR3s. Recombinant antibody expression + binding/neutralization assays would resolve this.
  • [2026-05-09] GodoyLozano2016 — why is SHM lower in secondary than primary? Two competing models: (1) stronger innate-like EF response in secondary infection (authors’ proposal); (2) original antigenic sin rapidly activates low-SHM cross-reactive memory clones, outcompeting high-SHM serotype-specific clones. Distinguishing these requires sorted PB BCR sequencing with lineage tracing.
  • [2026-05-09] GodoyLozano2016 — TLR7-mediated T-independent CSR not experimentally demonstrated. The proposed mechanism (endosomal DENV ssRNA → TLR7 → AID → CSR without GC SHM) is biologically plausible but entirely inferred. No experiment in this study (or any dengue study in the wiki) directly tests TLR7 activation in dengue B cells. Needs in vitro dengue B cell stimulation with TLR7 agonists/antagonists.
  • [2026-05-09] GodoyLozano2016 — IGHV1-2/1-69 and ADE. Is the association between IGHV1-2 low SHM and disease severity (DWS+) causal? Do IGHV1-2- and IGHV1-69-using antibodies preferentially mediate ADE? Needs functional characterization of V-gene-stratified dengue antibodies.
  • [2026-05-10 lint] Evidence weight annotations missing in early-ingested pages. ~15 Key Points bullets across Wei2007 and early Tipton2015 ingests lack study type and sample size annotations (e.g., “n=29 cross-sectional”). Pages affected: CD24, IgD, CD10, IgM, IgA, B220, Double-Negative B Cell, CD38, CD27. Concentrated in the first 2–3 source ingests; later ingests are well-annotated. Low priority but should be addressed during a quiet session.
  • [2026-05-10 lint] CD24 lists Scharer2019 in Sources with no Key Points content. Source was added during Scharer2019 ingest (CD24 is mentioned) but no bullet was written. Should add a brief note about CD24⁻ epigenetic status in DN2/aNAV from Scharer2019 data.
  • [2026-05-10 lint] Wrammert2012 ELISA listed as plain text — no method page. ELISA is listed under Methods Used without a wikilink. Either create an ELISA.md method page or convert to plain text note. Low priority — ELISA is a standard technique, not a distinguishing method for this wiki’s scope.
  • [2026-05-10 lint] SHM contradiction surfaced: GodoyLozano2016 vs. Appanna2016. Added to Somatic Hypermutation Contradictions & Debates with reconciliation (unsorted IgG pool vs. FACS-sorted DENV-specific populations). No further action unless new SHM data from another dengue paper changes the picture.
  • [2026-05-10] Priyamvada2016 — OAS variability across patients. OAS (preferential DENV1 neutralisation during DENV2 infection) was present in only 2/4 patients. Is OAS universal in secondary dengue or dependent on serotype combination, interval between infections, or individual clonal history? Needs larger cohort with known prior serotype exposure.
  • [2026-05-10] Priyamvada2016 — GC vs. EF origin of high-SHM PBs. The high SHM (mean 18.1 VH) is consistent with GC-experienced memory recall, but does not exclude EF-matured memory. Do the memory B cells that give rise to these high-SHM PBs originate from prior GC reactions, or can EF responses accumulate comparable SHM over multiple exposures? Lineage tracing across primary/secondary paired samples would resolve this.
  • [2026-05-10] Priyamvada2016 — OAS mAbs as ADE mediators. The DENV1-biased mAbs bind DENV2 weakly and fail to neutralise it — the precise profile for ADE. Are these OAS mAbs specifically the subset that mediates ADE in secondary DENV2 infection? Needs ADE assays stratified by OAS vs. non-OAS mAbs.
  • [2026-05-10] Priyamvada2016 — in vivo relevance of universal ADE. 45/53 mAbs enhanced at 1 µg/ml in vitro (U937). Is this clinically meaningful? The ADE assay used a single concentration; concentration-dependent neutralisation-to-enhancement transitions were not characterised. Needs dose-response ADE curves.
  • [2026-05-09] SHM distribution of dengue acute-phase plasmablasts — SUBSTANTIALLY RESOLVED. Priyamvada2016 provides sorted PB BCR sequencing: mean 18.1 VH mutations in secondary DHF PBs, supporting memory origin. Combined with GodoyLozano2016 low SHM in unsorted IgG, the dual-pathway model (memory recall + de novo EF) is now the best framework. Remaining gap: primary dengue sorted PB SHM data.
  • Web deployment deferred. When ready to publish, copy the webforshare/ Quartz setup from dengue-wiki/ and provision a separate Cloudflare Pages project. Add an Update Web workflow back into CLAUDE.md at that time.

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