Does pepinemab plus checkpoint inhibitors remodel melanoma tumors before surgery?

A biomarker endpoint, not a survival test

The question was whether blocking Semaphorin 4D (SEMA4D) with pepinemab changes the tumor microenvironment in a way that improves T effector cell infiltration when combined with checkpoint inhibitors. SEMA4D is a membrane-bound and secreted glycoprotein present on tumors and immune cells; its receptors, plexin B1/B2 and CD72, sit on tumor cells, B cells and myeloid antigen-presenting cells. Preclinical work cited by the authors proposed that blocking SEMA4D limits chemokine-driven recruitment of suppressive myeloid cells while reprogramming myeloid populations toward antigen presentation.

The trial enrolled patients with resectable stage IIIB/C/D melanoma who were immunotherapy naïve and had ECOG performance status 0 or 1. Thirty-eight patients were sequentially assigned to four treatment arms of eight each — pepinemab/nivolumab, pepinemab/ipilimumab, pepinemab/nivolumab/ipilimumab, and nivolumab alone — or a surgery-only arm of six. Two neoadjuvant doses were given on days 1 and 21, with surgery planned between days 35 and 49, followed by one year of adjuvant nivolumab. Sequential rather than randomized enrollment was chosen to reduce selection bias and avoid concentrating variables such as BRAF status in one arm.

The primary endpoint was modulation of tumor microenvironment phenotypes, not response rate or survival. Secondary endpoints covered safety and tolerability, pathological response and radiographic response. That hierarchy matters: the trial was designed as an integrated biomarker analysis and was not powered for definitive clinical efficacy, so the clinical observations reported as secondary endpoints are exploratory.

Toxicity tracked ipilimumab, and surgery was never delayed

Pepinemab-containing regimens were tolerated without toxicities beyond those expected from checkpoint inhibitor therapy alone, and no patient experienced toxicity that delayed or precluded planned curative-intent surgery. Among the 32 patients who received neoadjuvant therapy, 12 (37.5%) completed 13 cycles of adjuvant nivolumab, 11 (34.4%) stopped adjuvant therapy early because of recurrence, 7 (21.9%) stopped because of toxicity, and 2 (6.3%) were lost to follow-up after surgery.

Grade 3 adverse events clustered in the ipilimumab-containing arms: 5 of 8 patients on pepinemab/nivolumab/ipilimumab had grade 3 events including dermatitis, adrenal insufficiency, colitis, enteritis and nephritis, and 3 of 8 on pepinemab/ipilimumab had grade 3 events including adrenal insufficiency, thrombocytopenia and transaminitis. Only 1 of 16 patients treated without ipilimumab had a grade 3 event. No grade 4 or 5 adverse events occurred during neoadjuvant or adjuvant therapy.

Pathologic response, a secondary endpoint, was numerically higher with pepinemab plus nivolumab and ipilimumab, but the authors caution that small cohorts and the non-randomized design limit interpretation. This is the clearest place where a reader should resist converting a numeric trend into an efficacy claim.

Tumors shifted toward antigen presentation and recruitment

Transcriptional profiling of tumor samples found enrichment of transcripts associated with activated dendritic cells and immune recruitment pathways in patients receiving pepinemab-containing regimens. Consistent with that, circulating FLT3L protein — a regulator of dendritic cell development and cDC1 differentiation — was elevated in the same patients. Across treatment groups, tumors from patients with pathologic response showed enrichment of lymphoid-associated transcripts, including genes linked to B cells, T cells and dendritic cells, plus activated dendritic cell programs.

Comparisons within the trial add specificity. Pepinemab plus nivolumab was associated with enrichment of NF-κB, EMT and MAPK signaling transcripts relative to nivolumab alone. Among responders, the triplet regimen showed a distinct NF-κB pattern including non-canonical signaling involving the NFKB2/RelB complex. Differential expression also showed upregulation of FLT3, CXCR4, CCL21 and CCR7, which are linked to immune cell recruitment, alongside downregulation of MET, HGF, GREM1 and CCL2, which influence antigen-presenting cell migration and polarization.

These are associations in post-treatment tissue, not demonstrations that pepinemab caused the changes. The authors interpret the EMT- and MAPK-related shifts as possibly reflecting modulation of the MET–PlexinB1/2 axis after SEMA4D inhibition, a mechanism drawn from prior preclinical work rather than tested directly here.

Immune cells moved into the tumor bed, not just its margins

Multiplex immunohistochemistry on lymph node resection specimens validated the infiltration signal spatially. The tumor bed was identified by regions containing SOX10-expressing melanoma cells and/or evidence of regression such as fibrosis and altered lymph node architecture; the tumor periphery was defined as the region extending 1000 μm inward from the tumor bed edge, with the remainder designated the tumor core.

In this small cohort, tumors from patients treated with single-agent nivolumab appeared to show higher SEMA4D expression and features of immune exclusion at the margins. Tumors from patients receiving pepinemab plus nivolumab showed greater CD4⁺ and CD8⁺ T cell infiltration into the tumor bed, and foci of CD20⁺ B cells appeared within the tumor bed, whereas B cells were largely confined to tumor margins with nivolumab alone.

Myeloid composition shifted in the same direction: pepinemab plus nivolumab tumors had a higher proportion of HLA-DR⁺ antigen-presenting macrophages relative to PD-L1⁺ suppressive macrophages than nivolumab-alone tumors, producing a numerically increased HLA-DR:PD-L1 ratio, with a similar pattern for the triplet versus an external nivolumab-plus-ipilimumab comparator. The triplet also showed numerically higher conventional type 1 dendritic cell frequencies, significantly higher than the external comparator cohorts. Notably, overall abundance of CD4⁺ T cells, CD8⁺ T cells and B cells did not differ significantly across treatment groups; what differed was their spatial distribution. That distinction is central: the paper's claim is about organization and location, not simply more immune cells.

Mature lymphoid aggregates carried expanded T cell clones

The structural finding the authors emphasize most is the formation of mature lymphoid aggregates resembling tertiary lymphoid structures. These aggregates showed features of organized lymphoid tissue, including active germinal centers, compartmentalized B and T cell zones and follicular dendritic cells, and they contained clonally expanded T cell receptor repertoires. Patients with pathologic response showed oligoclonal B cell repertoires and more clonal, less diverse TCR repertoires within lymphoid aggregates relative to patients treated with checkpoint inhibitors alone.

The authors report that high density of mature lymphoid aggregates was associated with longer recurrence-free survival after neoadjuvant pepinemab combined with nivolumab and ipilimumab. Two measurement caveats sit beside this result. First, the repertoire analyses were limited by insufficient pretreatment tissue for paired BCR and TCR comparisons. Second, GeoMx spatial profiling was performed at the level of individual lymphoid aggregates rather than by patient, so aggregate-level sample counts differ from patient-level analyses and should not be pooled with them.

The authors also distinguish their observation from prior work showing immunotherapy can influence lymphoid aggregate abundance: their data suggest pepinemab plus checkpoint inhibitor treatment may additionally influence aggregate maturity. That is an interpretation of structure, not a demonstrated causal step.

External comparators widen context but weaken inference

The trial had no concurrent nivolumab-plus-ipilimumab-only control arm. To partially address this, the investigators incorporated samples from a similarly designed neoadjuvant melanoma study at MD Anderson Cancer Center (NCT02519322) as an independent contextual comparator, analyzed with harmonized multiplex immunohistochemistry methods. The authors themselves note that direct comparisons across independent clinical trials should be interpreted cautiously, even with comparable eligibility criteria.

Sample availability also varied by assay. Differences in tissue quality and specimen availability produced different numbers of evaluable samples across multiplex immunohistochemistry, bulk RNA profiling, GeoMx spatial profiling, immune repertoire sequencing and serum cytokine analyses. Pre-treatment research biopsy was not mandated, and archival tissue, mostly obtained by fine needle aspiration, was not suitable for spatial multiplex immunohistochemistry. Any per-assay denominator in this paper therefore describes a different subset of the 38 patients, and results should not be read as if they came from one uniform cohort.

Because analyses were limited to post-treatment specimens, the study cannot determine whether pepinemab contributes to de novo lymphoid aggregate formation. The authors state that future studies with matched pre- and post-treatment biopsies will be needed to answer that.

The priority is aggregate maturity, not response rate

Read together, the trial's most decision-relevant signal is not the numerically higher major pathologic response rate, which the authors flag as exploratory, but the convergence of three tissue-level measurements: transcriptional enrichment of activated dendritic cell and recruitment programs, spatial movement of T and B cells into the tumor bed with a higher HLA-DR:PD-L1 macrophage ratio, and mature lymphoid aggregates containing expanded T cell clones. The association between high mature lymphoid aggregate density and longer recurrence-free survival is the result that most directly justifies a larger randomized test.

The practical split the paper supports is between regimens. Grade 3 toxicity concentrated in ipilimumab-containing arms — 5 of 8 on the triplet and 3 of 8 on pepinemab/ipilimumab, versus 1 of 16 without ipilimumab — while the structural and antigen-presentation findings appeared across pepinemab-containing backbones. For anyone weighing whether SEMA4D blockade deserves further development in melanoma, the paper's own priority is clear: confirm in larger randomized trials whether pepinemab adds immune organization and durable benefit beyond checkpoint inhibitors alone, with matched pre- and post-treatment tissue to establish whether the aggregates are new.

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