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C1Q-associated adaptive myeloid remodelling accompanies early response to BCMA CAR-T therapy in multiple myeloma

Shubing Wang, Qian Wang, Yan-Ruide LiiD, Song LiiD

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Abstract

BCMA-directed chimeric antigen receptor T cells induce deep responses in multiple myeloma, yet the immune ecology accompanying early response remains incompletely resolved. We reanalysed 171,971 single-cell transcriptomes from 25 peripheral-blood and bone-marrow specimens from ten patients. At day 30, responders showed concordant enrichment of C1Q and IFN-{gamma} programmes in blood and marrow myeloid pseudobulk profiles. Antigen-presentation genes were enriched in blood, whereas TGF-{beta} and hypoxia programmes were depleted in responding marrow. Cholesterol-efflux genes were not enriched in responders or after treatment. A composite C1Q-cholesterol score showed nominal associations with response and CD8 dysfunction in selected compartments, but none survived study-wide correction. The pathway results support an adaptive, antigen-presenting C1Q-associated programme rather than a uniformly suppressive C1Q macrophage model. This state-contingent interpretation of early myeloid remodelling requires prospective, patient-level validation before biomarker or causal claims are warranted.

In-depth summary

Claude Opus 5.5 · xhigh effort · 7 Nov 2026 · from the full text of version 1 (25 Aug 2026) · CC BY 4.0

In a ten-patient multiple myeloma reanalysis, myeloid pseudobulk from day-30 BCMA CAR-T responders showed C1Q enrichment with interferon-γ signalling, not cholesterol efflux; patient-level composite scores stayed exploratory.

In diffuse large B-cell lymphoma, C1QB macrophages tracked progression and macrophage cholesterol efflux curbed CAR-T cytotoxicity in co-culture, yet those from complete responders expressed antigen-processing and interferon programmes, leaving C1Q's role unsettled. This reanalysis tests whether, about 30 days after BCMA CAR-T in multiple myeloma, response accompanies an adaptive rather than suppressive C1Q-associated myeloid state in blood and marrow, using patient-level pseudobulk.

Key results

  1. SuggestedAt day 30 in peripheral blood (PB), myeloid pseudobulk from complete responders was enriched for the C1Q, antigen-presentation and interferon-γ programmes and depleted for TGF-β signalling compared with nonresponders.

    Complete response (CR) vs nonCR, nine patients, normalized enrichment score (NES) with within-contrast false discovery rate (FDR): C1Q NES = 1.70 (FDR = 1.92 × 10^−5); antigen presentation NES = 1.99 (FDR = 3.96 × 10^−3); interferon-γ NES = 3.17 (FDR = 2.56 × 10^−30); TGF-β NES = −1.76 (FDR = 3.96 × 10^−3); hypoxia NES = −1.22 (FDR = 0.119). · Patient-level reanalysis resolves early blood…; Responding blood shows a C1Q-associated…

  2. SuggestedDay-30 bone marrow (BM) reproduced the responder C1Q and interferon-γ enrichment, with TGF-β and hypoxia programmes depleted; antigen presentation rose but did not pass correction.

    CR vs nonCR, six patients: C1Q NES = 1.70 (FDR = 1.33 × 10^−4); interferon-γ NES = 2.48 (FDR = 9.08 × 10^−14); TGF-β NES = −2.49 (FDR = 1.54 × 10^−7); hypoxia NES = −1.74 (FDR = 6.93 × 10^−4); antigen presentation NES = 1.49 (FDR = 0.0838). · Patient-level reanalysis resolves early blood…; Responding marrow recapitulates C1Q and…

  3. SuggestedResponders showed no positive enrichment of cholesterol-efflux genes (GO:0033344) in blood or marrow, and treatment did not raise them in paired blood, which argues against a joint C1Q and cholesterol-export state accompanying response.

    Cholesterol efflux NES = −1.08 (FDR = 0.365) in day-30 PB, NES = −0.91 (FDR = 0.586) in day-30 BM, and NES = −0.81 (FDR = 0.745) in the paired baseline-to-day-30 PB contrast. · Responding blood shows a C1Q-associated…; Responding marrow recapitulates C1Q and…; Longitudinal blood analysis supports…

  4. SuggestedIn paired blood samples, the C1Q, antigen-presentation and interferon-γ programmes rose from baseline to day 30, so the programme also reflects change after treatment and is not only a difference between response groups.

    Nine paired patients, edgeR with patient as blocking factor: C1Q NES = 1.72 (FDR = 3.57 × 10^−5); antigen presentation NES = 2.01 (FDR = 9.25 × 10^−4); interferon-γ NES = 2.79 (FDR = 1.72 × 10^−19); TGF-β and hypoxia not significant (FDR = 0.153 and 0.0804). · Patient-level reanalysis resolves early blood…; Longitudinal blood analysis supports…; Patient-level pseudobulk differential expression…

  5. SuggestedSample-level C1Q-cholesterol composite scores gave only nominal links to response and CD8 dysfunction, and none survived correction across the primary test family. Where a difference appeared, the score was higher in responders, the opposite of what a uniformly suppressive model predicts.

    Day-30 BM composite vs CD8 dysfunction: Spearman ρ = 0.943, permutation P = 0.0168, FDR = 0.247 (six patients); PB ρ = 0.167, P = 0.679 (nine patients). Composite CR minus nonCR: PB difference 0.954 (P = 0.0213, FDR = 0.247); BM 0.921 (P = 0.182, FDR = 0.528). · Patient-level composite scores remain…; Patient-level association tests

Methods, data and reproducibility

Secondary reanalysis of public scRNA-seq (GSE234261): per-sample QC, Scrublet and CellTypist annotation; counts summed by patient, specimen and compartment; edgeR quasi-likelihood tests (day-30 CR vs nonCR, blood and marrow separately; paired baseline vs day 30 in blood); gene-set enrichment analysis (GSEA) on six prespecified programmes; and 10,000-permutation tests on sample-level scores.

  • GSE234261 scRNA-seq of peripheral-blood and bone-marrow mononuclear cells from multiple myeloma patients before and about 30 days after BCMA CAR-T therapy · human · n = 25 specimens from ten patients; 171,971 of 179,876 cells retained after QC · GSE234261
  • Day-30 CR vs nonCR comparisons, analysed separately by tissue · human · n = nine patients (PB); six patients (BM) · GSE234261
  • Paired baseline vs day-30 peripheral blood · human · n = nine paired patients · GSE234261
  • Myeloid and CD8 T cells from broad CellTypist annotation · human · n = 86,830 myeloid cells; 31,653 CD8 T cells · GSE234261
  • Reference myeloma cohorts discussed but not used as independent clinical validation · GSE210079; GSE271915
Methods & tools
Scrublet, CellTypist (Immune_All_Low model), edgeR (trimmed mean of M-values normalization, robust quasi-likelihood GLM, filterByExpr), multilevel GSEA, MSigDB Hallmark gene sets, Gene Ontology (GO:0033344), NCBI GEO, BioPathfinder, Biomni
Reproducibility gaps
The GitHub link covers the general BioPathfinder workflow only. Analysis-specific scripts, the locked gene-set definitions and patient-level result tables are not yet public; the authors plan to deposit them in an archival repository before formal submission. No software versions are stated.
Limitations (6)
  • Ten patients in all: nine have day-30 blood profiles and six have day-30 marrow profiles. No power calculation was done, because every eligible public specimen was reused. · stated by the authors
  • The three-gene C1Q set can give extreme enrichment statistics when its genes rank together, which shows coordinated expression, not a new cell type. GSEA FDR was controlled within each contrast only. · stated by the authors
  • Pseudobulk over the whole myeloid compartment mixes monocytes, macrophages and dendritic cells, so the programme cannot be assigned to a C1Q-high macrophage subset. · stated by the authors
  • Response was early CR versus nonCR, not durable remission. The reference myeloma cohorts could not be mapped to the same endpoint, so there is no independent outcome-labelled validation. · stated by the authors
  • The design is observational: the data cannot tell a state that promotes response from one that follows falling tumour burden or simply reflects treatment exposure. · stated by the authors
  • The blood-marrow concordance comes from one ten-patient cohort with shared response labels, so it shows internal consistency, not independent replication. · noted in this summary

Read this if you study myeloid remodelling after CAR-T in myeloma, or want a template for patient-level pseudobulk testing of prespecified gene programmes in a small public scRNA-seq cohort.

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