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Cancer Immunology Research

American Association for Cancer Research (AACR)

Preprints posted in the last 90 days, ranked by how well they match Cancer Immunology Research's content profile, based on 35 papers previously published here. The average preprint has a 0.04% match score for this journal, so anything above that is already an above-average fit.

1
Dual targeting of CCR2+ monocytes and neutrophils enhances anti-tumor immunity

Fjaestad, K. Y.; Johansen, A. Z.; Linder, H.; Carretta, M.; Siersbaek, M.; Baker, K. J.; Thorseth, M.-L.; Hübbe, M. L.; Hald Andersen, M.; Grontved, L.; Madsen, D. H.

2026-05-15 cancer biology 10.64898/2026.05.13.723724 medRxiv
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Targeting immunosuppressive tumor-associated myeloid populations has emerged as a promising strategy to enhance anti-tumor immunity. The CCL2-CCR2 axis plays a central role in the recruitment of monocytes that differentiate into tumor-associated macrophages (TAMs), yet the therapeutic potential of CCR2 targeting remains limited. Using transgenic CCR2-DTR mice, we show that depletion of CCR2+ monocytes and TAMs reduced tumor growth across multiple models, accompanied by remodeling of the tumor microenvironment (TME). Residual CCR2-independent TAMs exhibited a pro-inflammatory and less immunosuppressive phenotype, and expressed the alternative recruitment receptor CCR3. Concomitantly, CCR2 depletion markedly enhanced anti-tumor immunity by increasing infiltration of activated CD8+ T cells. Splenocytes from tumor-bearing CCR2-DTR mice showed an increased IFN{gamma} response to a cancer-associated antigen. Furthermore, CCR2 depletion synergized with immune checkpoint blockade to enhance tumor control. Despite these effects, compensatory tumor infiltration of neutrophils following CCR2 targeting limited therapeutic benefit. These neutrophils exhibited a terminally differentiated, immunosuppressive phenotype and were associated with increased cancer cell-intrinsic expression of the neutrophil-recruiting chemokines Cxcl2 and Cxcl5. Importantly, combined depletion of CCR2+ cells and neutrophils overcame this resistance mechanism, resulting in reduced tumor growth, prolonged survival, and complete tumor clearance in 25% of the mice. Dual depletion of CCR2+ cells and neutrophils was also associated with a synergistic increase in circulating CD8+ T cells. These findings highlight the dynamic remodeling of the TME upon CCR2 depletion and suggest that combinatorial strategies addressing immunosuppressive neutrophil infiltration may improve the efficacy of CCR2 targeting therapies.

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Spatiotemporal dynamics of adoptively transferred stem-like CD8+ T cells in the tumor microenvironment following vaccination

Hermans, D.; Fussell, S. C.; Ramirez-Valdez, A.; Shepard, S.; Poulard, R.; Zumalave, S.; Sievers, B.; Garliss, C. M.; Coble, V. L.; Lynn, G. M.; Ishizuka, A. S.; Cortes-Ciriano, I.; Seder, R. A.

2026-05-14 immunology 10.64898/2026.05.12.724323 medRxiv
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Adoptive cell therapy (ACT) of tumor-specific T cells can improve survival in a subset of cancer patients. Current ACT approaches may be limited by using highly differentiated T cells which can be inhibited by an immunosuppressive tumor microenvironment (TME). Here, we developed an approach to optimize ACT and used spatial transcriptomics to show how stem-like and effector CD8+ T cells differentially mediate tumor control following vaccination. Spatial transcriptomic profiling of the TME showed that ACT with stem-like T cells followed by intravenous vaccination prevented immune exclusion, increased infiltration of pro-inflammatory macrophages, and reprogrammed tumor cells to upregulate Type I and Type II IFN signaling and apoptotic gene programs. The protective transcriptomic signature of the TME in this ACT model contained overlapping biomarkers with patients who responded to ACT therapy. This approach demonstrates synergy between transferred stem-like T cells and intravenous vaccination to transcriptionally remodel the TME and enhance tumor control.

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Monocytes promote intraepithelial infiltration of effector memory CD8+ T cells in regressing tumors

Vermare, A.; Ventura, A.; Rouault Montecino, A.; Simula, L.; Seradj, M.; Lhuillier, L.; Weber-Delacroix, E.; Mulder, K.; Vimeux, L.; Espie, D.; Bailly, K.; Izac, B.; Saintpierre, B.; Zeitouni, W.; Jolly, A.; Delagrange, P.; Guerin, M. v.; Donnadieu, E.; Pendino, F.; Dutertre, C.-A.; Boissonnas, A.; Prevost-Blondel, A.; Peranzoni, E.; Bercovici, N.

2026-05-29 immunology 10.64898/2026.05.28.728475 medRxiv
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Despite the clinical success of cancer immunotherapies, the cellular interactions driving tumor regression remain incompletely understood. Here, we investigated the dynamic remodeling of the tumor immune microenvironment during regression of transplanted PyMT mammary tumors following STING agonist treatment. Using scRNA-seq of sorted CD8+ T cells and myeloid cells, combined with imaging approaches, we identified major changes in both lymphoid and myeloid compartments during tumor regression. Regressing tumors showed a transient accumulation of Ly6Chi monocyte populations associated with a decline in macrophage subsets, while effector and memory CD8+ T-cell populations increased at the expense of exhausted T cells. Interaction analyses predicted enhanced chemotactic and adhesion interactions between CXCL9+ Ly6Chi monocytes and effector CD8+ T cells. Consistently, dynamic imaging revealed increased CD8+ T-cell motility and infiltration into tumor cores following treatment. In particular, CXCR6+ effector CD8+ T cells transiently accumulated within tumor islets during regression before relocalizing to stromal regions. Together, these findings reveal a coordinated spatiotemporal remodeling of myeloid and CD8+ T-cell populations during immunotherapy-induced tumor regression and highlight cooperative interactions that may promote durable anti-tumor immunity.

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Targeting DNMT1 augments anti-tumor CD8⁺ T cell function

Deshmukh, M.; Sohai, D.; Obbad, K.; Park, K.; Milette, S.; Gu, P.; Nam, H.; Daniels, A.; Spasov, K.; Hurwitz, M.; Katz, S. G.; Flavell, R. A.; Anderson, K.; Bosenberg, M.; Micevic, G.

2026-07-06 immunology 10.64898/2026.07.03.736412 medRxiv
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Chronic stimulation of CD8 T cells within the tumor microenvironment (TME) induces a hypofunctional state characterized by diminished cytotoxicity and functionally impaired anti-tumor function, known as exhaustion. Exhaustion is associated with epigenetic changes that remain relatively stable despite interventions like immune checkpoint inhibition (ICI). Although epigenetic changes are potentially reversible, reports of therapeutic strategies to effectively restore function in exhausted CD8 T cells remain limited. Here, we report DNA methyltransferase 1 (DNMT1) inhibition (DNMT1i) in counteracting CD8+ T cell dysfunction during the anti-tumor response. We show that DNMT1i synergizes with ICI to rescue the tumor cell killing activity of chronically stimulated CD8 T cells in a melanoma model. DNMT1i mitigates transcriptional features of exhaustion while inducing a divergent effector program. DNMT1i attenuates the global increase in chromatin accessibility associated with exhaustion and enables epigenetic remodeling of the exhausted chromatin landscape upon restimulation. Finally, DNMT1i enhances the effector function of melanoma patient-derived tumor infiltrating lymphocytes after prolonged ex vivo expansion. These studies establish DNMT1 targeting as a promising strategy to counteract CD8 T cell exhaustion and potentiate ICI efficacy.

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Conventional dendritic cells type I with an enhanced type-I-IFN signaling underpin anti-tumor immune responses in brain metastases

James, F.; Revalova, A.; Fife, C.; Williams, J.; Guglietta, D. V.; Hadi, Z.; Vasconcelos, E. J. R.; Sunderland, A.; Mallett, G.; Ingram, N.; Kaisho, T.; Brackenbury, W. J.; Lawrence, M.; Westhead, D. R.; MacDonald, A. S.; Lorger, M.

2026-07-08 cancer biology 10.64898/2026.07.08.737181 medRxiv
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Brain metastases (BrM) are associated with poor prognosis. A better understanding of anti-tumor immune responses in the context of immune specialized microenvironment of the brain is required to develop improved therapeutic strategies for this disease. We demonstrate that the conventional dendritic cells type 1 (cDC1) gene signature positively correlates with a prolonged BrM-dependent survival in melanoma and breast cancer patients. Furthermore, intracranial anti-tumor immune responses in preclinical BrM models consistently rely on cDC1s for tumor growth control, BrM-dependent survival and maintenance of the intra-tumoral CD8+ T cell pool, in contrast to variable, cancer type-dependent cDC1 roles in extracranial tumors. This is underpinned by tumor site-specific cDC1 molecular profiles with distinct Toll like receptor repertoires, upregulation of co-stimulatory molecules and IL-12, and enhanced type-I-IFN signaling in intracranial cDC1s, with the latter driving increased cDC1 activation. cDC1s also promote the conversion of progenitor exhausted CD8+ T cells to transient effectors, which is further enhanced by immune checkpoint blockade therapy. These findings pinpoint cDC1s as a major cell population of interest in the development of future immunotherapies for BrM.

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PSGL-1 blockade delays relapse to BRAF/MEK inhibition in cutaneous melanoma

El Naggar, O. S.; Ha, B. N.; Rakoto, M. L.; Cort, L.; Amirfallah, A.; Haglund, E. A.; Urquiza, P.; Hetrick, H. A. F.; Bradley, L. M.; Hartsough, E. J.; Hope, J. L.; Romano, G.

2026-07-07 immunology 10.64898/2026.07.02.736105 medRxiv
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Advanced BRAF-mutant cutaneous melanoma can be treated with targeted therapy when immune checkpoint inhibitors (ICIs) fail or are not a feasible option. Nevertheless, most patients do not achieve a durable response, highlighting the critical need for therapeutic partners that enhance the long-term efficacy of targeted therapy. Transcriptomic analysis of a BRAF-mutant melanoma model of acquired resistance identified P-selectin glycoprotein ligand-1 (PSGL-1) as a top-upregulated immune mediator upon resistance acquisition. PSGL-1 is a key regulator of CD8+ T cell exhaustion and differentiation, and its inhibition has been shown to enhance T cell function across multiple disease models. Based on these observations, we hypothesized that combined targeting of BRAF/MEK and PSGL-1 would improve anti-tumor responses. Here, we demonstrate that dual inhibition of BRAF/MEK and PSGL-1 elicits durable tumor control in a preclinical model of PD-1-refractory cutaneous melanoma. Single-cell RNA sequencing of the tumor microenvironment reveals robust reprogramming of intratumoral CD8+ T cells toward a less terminally differentiated, memory-like phenotype following combined BRAF/MEK and PSGL-1 targeting. Consistent with these findings, CD8+ T cells in the tumor-draining lymph nodes of PSGL-1-/- mice exhibit enhanced functionality and a less differentiated state of exhaustion when compared with wild-type mice. To extend these observations to a translationally relevant setting, we further show that antibody-mediated blockade of PSGL-1, in combination with BRAF/MEK inhibition, yields superior anti-tumor activity compared with either monotherapy. Collectively, these findings identify PSGL-1 as a promising therapeutic target to enhance the durability of targeted therapy and provide a strong rationale for future clinical evaluation.

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PD-L1 deletion or blockade regulate macrophage antigen presentation and checkpoint molecule surface levels

Waddell, T. Q.; Dong, H.; Roh-Johnson, M.; Lancaster, J. N.

2026-06-29 immunology 10.64898/2026.06.23.734016 medRxiv
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Macrophages in the tumor microenvironment are known to upregulate PD-L1 expression, thereby suppressing T cells through PD-1 ligation. However, the manner in which PD-L1 expression intrinsically impacts macrophages and their immunomodulatory phenotype is less clear. Clarifying this knowledge gap would yield insight into the mechanisms of immunosuppression within the tumor microenvironment. To characterize the macrophage intrinsic role of PD-L1, we used complementary genetic and pharmacological approaches by analyzing primary murine bone marrow-derived macrophages (BMDMs) with complete genetic PD-L1 deletion and wildtype BMDMs treated with anti-PD-L1 blocking antibodies. Macrophages were evaluated across naive, pro-inflammatory (M1), and tumor conditioned (TCM) polarization states in vitro. Unlike prior reports, neither genetic deletion nor antibody blockade dramatically altered the expression of macrophage polarization markers or in vitro phagocytic capacity. Both conditions consistently reduced surface levels of the M1-associated costimulatory molecule CD80, prompting further analysis of T cell interacting and antigen presenting proteins, in which we revealed disparate effects of genetic deletion and antibody blockade on the surface levels of MHCI, MHCII, PD-1, and PD-L2. These findings suggest that PD-L1 deletion and antibody-mediated blockade contribute to macrophage immune regulatory profiles in distinct manners. This difference supports a model in which PD-L1 functions in macrophages beyond its canonical role as a ligand for PD-1, influencing antigen presentation and checkpoint molecule levels and playing a broader role in immune regulation in the tumor microenvironment.

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Reprogramming tumour-associated macrophages from immune suppressive to inflammatory state by Checkpoint kinase 1 inhibitor combination treatment

Zeng, Z.; Gandini, A.; Bhatt, R.; Proctor, M.; Guo, J.; Millard, S.; Wu, S. Y.; Dolcetti, R.; Wells, J. W.; Gonzalez Cruz, J.; Irvine, K. M.; Gabrielli, B.

2026-05-17 cancer biology 10.64898/2026.05.13.724422 medRxiv
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BackgroundTumour-associated macrophages (TAMs) play critical roles within the tumour microenvironment regulating immune evasion and therapeutic response. Previously, we have shown that the combination of Checkpoint kinase 1 inhibitor (CHK1i) with a subclinical dose of hydroxyurea (LDHU) reprograms the tumour immune microenvironment to a pro-inflammatory status. MethodsWe investigated a tumour-restricted Fcgr4 (Cd16.2) expressing macrophage population in multiple murine tumour models and the impact of CHK1i+LDHU on this population, using conventional and imaging flow cytometry as well as single-cell sequencing. ResultsTranscriptional profiling using CITE-seq and single-cell RNA sequencing reveals that Fcgr4 TAMs closely resemble Fcgr4- TAMs but display modest enrichment of interferon-associated and inflammatory gene programs, consistent with a functionally biased state rather than a distinct lineage. Importantly, we show that a highly tumour selective CHK1i+LDHU therapy shifts TAMs toward a more inflammatory phenotype while preserving dominant immunosuppressive features. Depletion of CSF1R macrophages enhanced CD8 T cell activation without influencing tumour growth but significantly augmented therapeutic efficacy of CHK1i+LDHU. ConclusionTogether, these findings define a novel TAM population and establish how targeted therapy reshapes, but does not fully overcome, TAM-mediated immune regulation.

9
In vivo CRISPR-based screen identifies ZC3H12C as a mediator of CAR-T cell dysfunction in solid tumors

Barbao, P.; Rodriguez-Garcia, A.; Galindo-Albarran, A.; Gimenez-Alejandre, M.; Clavero, P.; Lobo-Jarne, T.; Botas, M.; Colell, G.; Castellsague, J.; Cascallo, G.; Andreu-Saumell, I.; Soria-Castellano, M.; Colell, S.; Marzal, B.; Martin-Mur, B.; Esteve-Codina, A.; Urbano-Ispizua, A.; Prat, A.; Gattinoni, L.; Mendoza-Parra, M.; Guedan, S.

2026-05-02 immunology 10.64898/2026.04.30.721530 medRxiv
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CAR-T cell therapy has shown limited efficacy in solid tumors, largely due to T cell dysfunction driven by chronic antigen exposure. To uncover mediators of this dysfunction, we developed an in vivo screening platform using an ovarian xenograft tumor model in which CD28-based CAR-T cells undergo exhaustion leading to tumor escape. Transcriptomic profiling of tumor-infiltrating CAR-T cells at different stages revealed dynamic upregulation of exhaustion-associated genes. We used this data to design a focused CRISPR/Cas9 library and performed an in vivo screen. We identified 14 significantly enriched candidate genes, among which ZC3H12C emerged as the top hit. Single-cell RNA and ATAC-seq confirmed ZC3H12C expression in CAR-T cells undergoing early exhaustion in vivo. ZC3H12C disruption enhanced CAR-T cell persistence and antitumor efficacy while reducing exhaustion, across both CD28- and 4-1BB-based CARs targeting distinct antigens. These results highlight ZC3H12C as a promising target to improve CAR-T therapy in solid tumors.

10
Decoding molecular programs that define macrophage responses to tumor-derived cues

Sribike, K.; Haeuser, L. J.; Acedo-Terrades, A.; Riudavets-Puig, R.; Hau, J.; Totu, T.; Bossart, J.; Patterson, A. B.; Krymova, E.; Ayala-Nunez, V.; Rottmar, M.; Maniura-Weber, K.; Tugues, S.; Neidert, M.; Sobottka, B.; Buljan, M.

2026-06-09 immunology 10.64898/2026.06.05.730376 medRxiv
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Tumor-associated macrophages (TAMs) comprise functionally diverse states that can suppress anti-tumor immunity and promote tumor progression, yet the tumor microenvironmental cues and signaling programs that generate these states remain incompletely defined. Here, we systematically stimulate primary human monocyte-derived macrophages with a panel of cytokines and metabolites abundant in the tumor microenvironment (TME), and profile their transcriptomic and phosphoproteomic responses to resolve stimulus-specific molecular programs. We observe that potassium (K+) and adenosine (Ado) stimulation, which accumulate in necrotic tumor cores, downregulate antigen-presentation genes and their master regulator CIITA. K+ stimulation results in the upregulated fibronectin 1 expression, associated with immunosuppressive, metastasis-promoting TAM subsets. Ado induces upregulated expression of tryptophan (Trp) catabolism genes, myeloid checkpoints and metallothioneins (MTs). Although MT-high TAM states have been recurrently observed across tumor single cell RNA sequencing studies, their function remains poorly defined. We show that elevated MT expression in tumor tissue is associated with shorter overall survival. By aligning in vitro transcriptomes with single-cell RNA sequencing (scRNA-seq) signatures from a pan-cancer TAM atlas, we identify significant similarities between several in vitro states and clinically observed TAM populations, with Ado-stimulated macrophages closely resembling a MT-expressing TAM cluster. Overall, this work provides a systematic molecular context linking tumor microenvironmental cues to clinically relevant TAM states and offers a framework for recapitulating their functions in vitro. STATEMENT OF SIGNIFICANCEThis study explores how cytokines and metabolites from the tumor microenvironment shape macrophage molecular phenotypes and lead to the upregulation of clinically relevant marker genes and recapitulation of functional states of interest.

11
Humanized patient-derived xenografts preserve tumour-specific immune microenvironments

Stueckmann, D.; Meens, J.; Pfeil, J. Q.; Sivapatham, S.; Chevrier, S.; Hui, S.; Karamboulas, C.; Gill, R.; Zhang, X.; Martin, L.; Komisarenko, M.; Dube, P.; Prendeville, S.; Jackson, H. W.; Finelli, A.; Bader, G. D.; Bodenmiller, B.; Ailles, L.; Lawson, K. A.

2026-05-19 cancer biology 10.64898/2026.05.15.724697 medRxiv
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Defining the genetic and cellular programs that allow solid tumours to evade immune control requires preclinical models that preserve the complexity of the human tumour immune microenvironment. Most available systems capture only part of this biology. Organoid cultures and ex vivo tumour fragments can retain patient-derived tumour architecture and associated immune cells, but immune populations are typically maintained only for short periods. These models also cannot capture antitumour immune responses in the physiological setting of a living organism. Patient-derived xenografts propagated in humanized mice offer a potential path to overcome these limitations by combining patient-derived tumour tissue with a reconstituted human immune system. However, few studies have systematically tested whether these models reproduce the diverse immune cell phenotypes present in the parental tumours from which they are derived. This has limited their use for studying tumour-intrinsic mechanisms that shape immune composition and promote immune evasion. To address this gap, we profiled tumour-infiltrating, splenic, and bone marrow immune cells from ovarian, head and neck, and renal PDX models propagated in CD34+ hematopoietic stem cell (HSC)-derived huNOG-EXL mice expressing human IL-3 and GM-CSF. By comparing tumours grown across distinct HSC donor backgrounds with their matched primary tumour samples, we found that tumour-intrinsic factors are a dominant determinant of immune composition in humanized PDX tumours. Across models, these immune infiltrates generally resembled those of the corresponding parental tumours. These findings support humanized PDX models as a platform for functionally interrogating tumour-intrinsic drivers of immune composition and immune evasion in solid tumours.

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IL-36γ Drives Th9 cell Differentiation via IκBζ to Sustain Antitumor Immunity

WANG, X.; Zhu, Q.; Chen, Y.; Gao, J.; Tang, P.; Ma, Z.; Li, X.; Jiang, H.; Huang, Z.; Zang, Y.; Zhao, X.; Zhang, J.

2026-05-04 immunology 10.64898/2026.04.29.721605 medRxiv
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Th9/Tc9 cells polarized with TGF-{beta} and IL-4 exhibit superior antitumor efficacy, prompting extensive efforts to optimize their differentiation protocols and augment therapeutic potency. In the current study, we identified IL-36{gamma} as a potent cytokine that synergizes with TGF-{beta} to robustly drive Th9 differentiation both in the presence and absence of IL-4. IL-36{gamma}-programmed Th9 cell subsets exhibited phenotypic and transcriptional profiles identical to classic Th9 cells. Mechanistically, IL-36{gamma} drove Th9 cell differentiation through amplifying key signaling pathways such as STAT6, STAT5, and NF-{kappa}B that are essential for classic Th9 programming. Notably, we uncovered a novel regulatory axis wherein IL-36{gamma} upregulates the transactivation factor I{kappa}B{zeta}, which directly governs Th9 lineage specification. In in adoptive cell therapy (ACT) models, IL-36{gamma}-polarized Th9 cell subsets demonstrated enhanced antitumor efficacy, attributable to their sustained persistence, reduced exhaustion markers and stem-like/memory properties. Collectively, this study elucidates a previously unrecognized I{kappa}B{zeta}-dependent mechanism underpinning Th9 differentiation and highlights the translational potential of IL-36{gamma}-engineered Th9 cells as a valuable ACT strategy for refractory tumors.

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CMAS dampens anti-tumor immunity and associates with response to neoadjuvant immunotherapy in melanoma

Coccimiglio, M.; Ibanez-Molero, S.; Springer, B. O.; Goossens-Kruijssen, L.; Clayton, G.; Davison, R.; Zhang, T.; Wijnen, S.; Rodriguez, E.; Olesek, K.; Veenstra, S. P. G. R.; van den Brekel, T.; Nardini, E.; van Elk, J.; Keuning, E.; Garcia-Garcia, S.; Boelaars, K.; de Haan, N.; Labots, M.; de Gruijl, T. D.; Blank, C.; Chiodo, F.; van Kooyk, Y.

2026-04-29 cancer biology 10.64898/2026.04.27.719251 medRxiv
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Identifying immune-regulatory pathways to predict response is crucial for the efficacy of immune checkpoint blockade (ICB) immunotherapies. Sialylation is upregulated in tumor cells and modulates immune responses in cancer, yet its impact on patient clinical outcome and the spatial organization of the tumor microenvironment remain unclear. Here, using publicly available single-cell RNA sequencing data we show that expression of the sialylation master regulator CMAS in melanoma cells correlates with poorer patient survival. Using a murine melanoma model, we demonstrate that Cmas deletion in tumor cells severely impaired tumor growth and improved anti-tumor lymphoid and myeloid cell responses, increasing tumor cell-intrinsic susceptibility to interferon-gamma-, CD4+ T cell-, and macrophage-mediated killing. Single-cell spatial transcriptomics on neoadjuvant ICB-treated melanoma patient tumor biopsies revealed that CMAS expression in tumor cells inversely correlated with tumor cell proximity to and activation status of T cells and macrophages. Furthermore, expression of CMAS in tumor cells was increased in patients who did not respond to immunotherapy, compared to responders. Overall, our work identifies CMAS as a key modulator of tumor-immune dynamics associated with survival and response to neoadjuvant ICB immunotherapy in melanoma patients.

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High immune receptor clonality in melanoma-draining lymph nodes associates with immune dysfunction and poor survival

Walter, V.; Herold, J.; Feuchter, S. A.; Thomae, S.; Venohr, M.; Vogelsberg, A.; Kilic, M.; Berner, F.; Nanz, L.; Leiter-Stoeppke, U.; Sinnberg, T.; Schuerch, C. M.; Ulmer, A.; Buerkner, P.-C.; Flatz, L.

2026-06-10 immunology 10.64898/2026.06.09.729531 medRxiv
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Tumor-draining lymph nodes (tdLNs) are critical hubs of anti-tumor immunity but are also vulnerable to tumor-mediated immunosuppression. We analyzed T cell and B cell receptor (TCR/BCR) repertoires and transcriptomes from sentinel and non-sentinel lymph nodes of patients with melanoma from a historical pre-immune checkpoint inhibitor cohort (1994-2002) and an independent contemporary validation cohort (2022-2024). Melanoma-positive lymph nodes exhibited increased immune receptor clonality compared with tumor-free nodes. While average clonality showed no consistent association with outcome, the presence of extreme high-clonality outliers in individual lymph nodes was strongly associated with poor melanoma-specific survival. These outliers were characterized by a loss of lymphocyte-related genes and activation markers, an enrichment of melanocytic transcripts, and the suppression of immune signaling pathways, consistent with local immune dysfunction. Increased clonality was confined to lymph nodes and not observed in the peripheral blood. T cell responses to melanocyte differentiation antigens were infre-quently shared between lymph nodes and peripheral blood, highlighting immune compartmentalization.

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The initial melanoma T cell infiltrate is defined by tissue-resident programs restrained by regulatory T cells

Williams, J. B.; Pant, S. M.; Kley, A. L.; Rajmalani, B. A.; Yapp, C.; Zhang, J.; Rotrosen, E.; Sales, A.; Sorger, P. K.; Kupper, T. S.

2026-06-18 immunology 10.1101/2025.10.21.683143 medRxiv
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How the immune system surveys nascent tumors and how this surveillance is subverted remain poorly understood. Using high-plex cyclic immunofluorescence and 3D imaging, we identified regulatory T (Treg) cells that co-localize with tissue-resident memory (TRM)-like T cells in early-stage human melanoma. In an autochthonous Braf/PTEN melanoma model expressing a defined tumor antigen, the initial CD8+ T cell infiltrate adopts a CD103+CD101+ TRM-like fate, establishing active immunosurveillance within nascent lesions. TRM-like cells dominate early tumors, occupy a stable epidermal niche, express effector molecules, and initiate T cell recruitment. However, Treg cells adopt a parallel tissue-resident phenotype, co-localizing with TRM-like cells and restraining both cytotoxic and sentinel functions. Tumor-site-specific Treg depletion reactivated TRM-like cells, drove robust T cell recruitment, expanded tumor-specific responses, and limited tumor growth. These findings reveal how early immunosurveillance is established through tissue-resident programs and identify Treg co-option of this response as a critical mechanism of tumor immune evasion. One Sentence SummaryNascent melanoma imprints a tissue-resident program on the initial CD8+ T cell infiltrate, which is suppressed by regulatory T cells as a critical checkpoint in immune evasion.

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Single-cell characterization of tumor immune landscapes in colorectal cancer humanized mice

Bootsma, S.; Saris, J.; Li Yim, A. Y.; Lenos, K. J.; Vieira Braga, F. A.; Grootjans, J.; Vermeulen, L.

2026-06-04 cancer biology 10.64898/2026.06.01.729295 medRxiv
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Colorectal cancer (CRC) displays inter-patient heterogeneity in molecular tumor features and immune cell composition, which influence therapy response. Humanized immune system (HIS) mouse models offer a promising in vivo model to study human tumor-immune interactions, yet their ability to recapitulate the CRC tumor immune microenvironment at single-cell resolution remains incompletely defined. Here, we performed single-cell RNA sequencing of systemic and tumor-infiltrating human immune cells in HIS mice bearing human CRC tumors and benchmarked these data against reference datasets of healthy human spleens and primary CRC tumors. Major immune lineages and transcriptional programs characteristic of the human systemic immune compartment were identified, and HIS mouse tumors developed complex, human-like immune infiltrates. Tumor-infiltrating immune cells comprised diverse T cell, myeloid, natural killer, and B cell populations, including exhausted T cell states marked by expression of PDCD1, TIGIT, HAVCR2, LAG3, and CTLA4. We further demonstrate CRC consensus molecular subtype-associated spatial differences in immune infiltration. Collectively, our findings support the use of HIS mice as a relevant model for studying CRC immune landscapes and preclinical evaluation of immunomodulatory therapies.

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Inhibition of integrin αvβ8-mediated TGFβ activation and active-TGFβ blockade promote anti-tumor immunity through distinct biological mechanisms

Williams, K.; Mittman, S.; Firmino, N.; Larrick, J. W.; Zhang, Z.; Whitty, C.; Ma, H.-Y.; Ren, X.; Chiu, C.; Yang, Y.; Zhang, J.; Thai, M.; Paidassi, H.; Masureel, M.; Loyet, K.; Liang, W.-C.; Koerber, J. T.; Cubas, R.; Wu, Y.; Turley, S. J.; Mellman, I.; West, N. R.; Muller, S.; Qu, Y.; Sheppard, D.; Castiglioni, A.

2026-07-09 immunology 10.64898/2026.07.06.735099 medRxiv
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Transforming Growth Factor {beta} (TGF{beta}) is a potent immunosuppressor and a primary driver of resistance to cancer immunotherapy. While preclinical models have long suggested that TGF{beta} inhibition could synergize with immune checkpoint inhibitors, these effects have proven difficult to replicate in clinical settings. The highly regulated TGF{beta} pathway can be inhibited through various mechanisms, including neutralizing activated ligands or inhibiting upstream activators, such as integrins. Recent structural data demonstrated that integrin v{beta}8 can enable TGF{beta}1/3 signaling without releasing the active cytokines from their Latency-Associated Peptides , suggesting that ligand-blocking antibodies may have limited access to their epitopes. Here, we show that integrin v{beta}8 blockade, while achieving anti-tumor responses similar to those of anti-TGF{beta} antibodies, does so through a distinct mechanism of action. Anti-v{beta}8 is 3 orders of magnitude more potent at inhibiting v{beta}8-mediated TGF{beta} activity than a commonly used antibody against the mature form of the cytokine. Whereas TGF{beta} ligand inhibition has little effect on TGF{beta} signaling in tumor-draining lymph nodes (tdLN) and requires IFN{gamma}for its anti-tumor effects, v{beta}8 blockade strongly inhibits TGF{beta} signaling in tdLN and, in combination with PD-L1 blockade, drives tumor control through an IFN{gamma} -independent mechanism that strictly requires T cell egress from tdLN. Combined v{beta}8 and anti-PD-L1 blockade enhances antigen presentation in dendritic cells (DCs) and, unlike TGF{beta} ligand blockade, improves the efficiency of DC-induced T cell activation in response to cross-presented antigen. These findings suggest that v{beta}8 blockade can disable an immunologically critical source of TGF{beta} signaling that is not addressed by antibodies targeting TGF{beta} ligands, suggesting a promising new approach to TGF{beta} pathway modulation.

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High-avidity TCR signaling induces a distinct KLR-positive exhaustion state in human tumor-infiltrating CD8 T cells associated with immunotherapy response

Mullins, R. D. Z.; Zaretsky, J. M.; Barrett, T. F.; Stoller, E.; Bischoff, P.; Egloff, A. M.; Huffman, C.; Ramadan, S.; Ramadan, A.; Ley, J.; Schwetye, K.; Miller, D.; De Los Santos, J.; Apicelli, A. J.; Rammohan, N.; Thorstad, W.; Oppelt, P.; Knapp, B. J.; Auberle, C.; Wahle, B.; Rich, J. T.; Jackson, R. S.; Pipkorn, P.; Zolkind, P. A.; Harbison, R. A.; Egawa, T.; Singh, N.; Mitra, R. D.; Karam, S. D.; Uppaluri, R.; Adkins, D. R.; Puram, S. V.

2026-06-02 immunology 10.64898/2026.05.29.728765 medRxiv
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Tumor-specific exhausted CD8 T cells (Tex) adopt diverse phenotypes across human cancers, but the drivers of this heterogeneity remain poorly understood. Using flow cytometry and single-cell RNA and T cell receptor (TCR) sequencing of 106,667 tumor-infiltrating CD8 T cells from head and neck squamous cell carcinoma (HNSCC) tumors, we identified and validated three Tex subsets, each with distinct clonotypes: (1) Tex-Conv, expressing conventional exhaustion genes; (2) Tex-CCR6, distinguished by CCR6 and Tc17-like genes; and (3) Tex-KLR, marked by killer cell lectin-like receptors (KLRs) and particularly high immune checkpoint expression. Through multiplexed immunofluorescence, we found that Tex-KLR cells preferentially localized within tumor nests in direct contact with malignant cells. Due to the elevated checkpoint expression, unique clonotypes, and intra-tumoral localization of Tex-KLR cells, we hypothesized that high-avidity TCR signaling induces this state. We therefore developed an in vitro co-culture system to model TCR avidity in primary human CD8 T cells and identified high-avidity, NFAT-dependent TCR signaling as a key driver of the Tex-KLR signature. Strikingly, in HNSCC and breast cancer patients, we found that Tex-KLR cells are associated with response to neoadjuvant anti-PD-1 therapy. Together, our findings demonstrate that high-avidity, NFAT-dependent TCR signaling shapes Tex phenotypes and promotes the Tex-KLR signature. These data support further investigation of the Tex-KLR subtype and its role, dynamics, and targetable translational applications to cancer immunotherapy.

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Organoid-T cell co-cultures functionally stratify tumor-reactive T cells and their responses to immune checkpoint inhibitors

Merritt, E.; Cavallo-Fleming, J.-A.; Lara Granados, G.; Nath, S.; Lee, W.; Sritharan, R.; Sridhar, S.; Zuluaga, L.; Ariztia, E. V.; Hirsch, F. R.; Walsh, M.; Sfakianos, J. P.; Badani, K.; Brody, R.; Horowitz, A.; Tsankov, A. M.; Sia, D.; Hopkins, B.; Tocheva, A. S.

2026-05-31 immunology 10.64898/2026.05.27.727968 medRxiv
Top 0.2%
5.1%
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Tumor-reactive T cells (TRTs) are critical for anti-tumor immunity but are incompletely captured by current assays, which fail to reproduce tumor-specific antigen diversity. Here, we show that multiplex functional profiling of patient-derived tumor organoid-T cell co-cultures (PDOTs) enables robust identification of TRTs across CD8, CD4, and double-negative (DN) T cell populations. Single activation markers underestimated TRT responses, whereas integrated analysis revealed broader functional repertoire. MHCI blockade abrogated CD8 and DN TRT responses while preserving CD4 reactivity, supporting antigen-dependent recognition across T cell lineages. Tumor PDO expressed MHCI and MHCII, and PDOTs enabled generation and detection of TRTs from peripheral blood. PD1 blockade induced heterogeneous responses, enhancing CD8 and DN activity and unexpectedly augmenting CD4 reactivity. PDOTs further identified additional inhibitory pathways whose therapeutic targeting in combination with PD1 blockade increased TRT responses. These findings establish PDOTs as a platform to identify TRTs and functionally stratify patient-specific tumor-T cell responses to checkpoint immunotherapy.

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PD-1 blockade drug holiday improves exhausted progenitor CD8 T cell (Tpex) reinvigoration by avoiding Tpex adaptive resistance

Wherry, E. J.; Ngiow, S. F.

2026-05-18 immunology 10.64898/2026.05.14.725199 medRxiv
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4.7%
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Blocking the programmed cell death 1 (PD-1) pathway using monoclonal antibodies reinvigorates exhausted T cells (Tex), enhancing control of chronic viral infections and cancer. Considerable effort has focused on evaluating different PD-1 blockade agents in preclinical and clinical cancer settings, but relatively little information exists on how to optimize the pharmacodynamic effects of PD-1 pathway blockade on reinvigorating Tex. To address this question, we performed longitudinal tracking of Tex reinvigoration during chronic infection with lymphocytic choriomeningitis virus (LCMV) following different regimens of PD-1 blockade. We compared single-cycle (2 weeks of treatment), long-term continuous PD-1 pathway blockade (i.e. 3 months), or blockade followed by a drug holiday and then re-blockade (intermittent treatment). These studies revealed little benefit of continuous versus single-cycle PD-1 blockade, with both resulting in a single peak of Tex reinvigoration and similar effects on viral replication. In contrast, intermittent blockade resulted in a new cycle of secondary Tex reinvigoration upon redosing after a washout and this secondary Tex reinvigoration improved disease control. Mechanistically, long-term blockade eroded the ability of Tex progenitor cells (Tpex) to give rise to downstream, more functional Tex intermediate (Tex-Int) progeny, whereas the drug holiday restored this Tpex proliferative and differentiation capacity. Tpex from long-term treated mice showed evidence of adaptive resistance and additional layers of negative regulation, including sustained expression of the inhibitory receptor CD22. Indeed, co-blockade of PD-1 and CD22 using combination antibodies or bispecific antibody approaches improved disease control and reinvigoration of Tex. These data have implications for clinical immune pharmacodynamics of PD-1 blockade and provide insights into the biology of Tex reinvigoration. One Sentence SummaryModifying the immunopharmacology of PD-1 blockade reveals a benefit of a drug holiday and identifies mechanisms of Tex progenitor deficiency provoked by prolonged loss of PD-1 signals including the inhibitory receptor CD22.