Biology subjects

Pineda, J. E.

Publications and source records attributed to Pineda, J. E..

4 recordsLinked to original sources

bioRxiv2026

Spatial immune hubs defined by conserved activated dendritic cells are remodeled by immunotherapy

Dendritic cells (DCs) orchestrate anti-tumor immune responses, yet the full extent of their phenotypic diversity, and spatial dynamics within the tumor microenvironment (TME) remains incompletely understood. Here, we constructed an integrated atlas of tumor-infiltrating DCs by harmonizing single-cell transcriptomic data from 12 murine tumor studies and 28 published human cancer datasets, together with newly generated single-cell-resolved multiplexed tissue imaging across immunotherapy conditions in a murine model. We noted conserved transcriptional states across species, including canonical conventional type 1 DCs (cDC1s), diverse type 2 DC (cDC2) subpopulations, and two activation states characterized by CCR7 expression (CCR7+ DCs) or interferon-stimulated gene expression (ISG DCs). Spatial transcriptomics analyses from human TMEs revealed that CCR7+ DCs and ISG DCs reside in distinct T cell-enriched regions that are embedded within distinct signaling environments. High-dimensional multiplexed proteomic imaging demonstrated that these DC-T cell niches undergo divergent remodeling across multiple immunotherapy conditions. Notably, this spatial reorganization occurred despite minimal detectable changes in DC transcriptional states. This study delineates conserved DC activation states and their spatial organization within tumors and captures the therapy-dependent remodeling, providing a framework for studying therapy-associated remodeling of DC immune programs in cancer.

immunology↗

bioRxiv2026

Antigen presentation requirements for effective cDC1-based cancer immunotherapy

Type 1 conventional dendritic cells (cDC1s) are important for generating and sustaining antitumor immunity. Accordingly, the abundance of cDC1s in human tumors correlates with improved outcomes in cancer. Capitalizing on this role, we previously demonstrated that vaccination with in vitro-derived murine cDC1s elicits durable tumor control in multiple preclinical models; however, the immunological mechanisms underlying the efficacy of cDC1 vaccination remain unclear. Here, we examined whether in vitro-derived cDC1s resemble tumor-infiltrating DC populations and whether MHC-I and MHC-II antigen presentation contribute to cDC1-mediated tumor control following vaccination in melanoma. As expected, MHC-I- or MHC-II-deficiency had minimal impact on the transcriptional state of cDC1s in homeostasis or following stimulation with the adjuvant poly dI:dC. Moreover, in vitro-derived cDC1s cultured under steady-state conditions closely resembled tumor-infiltrating cDC1s, whereas their poly dI:dC-stimulated counterparts resembled CCR7+ tumor-infiltrating DC populations, also referred to as mregDCs or LAMP3+ DCs. Our data further show that both MHC-I and MHC-II contribute to tumor control upon cDC1 vaccination, and coexpression of MHC-I and MHC-II on the same cDC1 is necessary for a robust vaccine response. We also identified an important function for host cDC1s in supporting the efficacy of vaccination with in vitro-derived cDC1s, as judged by impaired tumor control in Irf8+32-/- mice, which lack endogenous cDC1s. Overall, these results indicate that effective antitumor responses depend on MHC-I and MHC-II antigen presentation by vaccine-delivered cDC1s, with additional contributions from host cDC1s. Key pointsO_LIIn vitro-generated cDC1s resemble intratumoral DC populations found in mice and humans. C_LIO_LIMHC-I and MHC-II antigen presentation by vaccine-delivered cDC1s contribute to antitumor efficacy. C_LIO_LICoexpression of MHC-I and MHC-II on the same cDC1 enhances vaccine responses. C_LIO_LIAntitumor responses reflect the activity of vaccine and endogenous cDC1s. C_LI

immunology↗

bioRxiv2023

Overlapping and Distinct Mechanisms of Effective Neoantigen Cancer Vaccines and Immune Checkpoint Therapy

The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to eliminate cancer by expanding and/or sustaining T cells with anti-tumor capabilities. However, whether cancer vaccines and ICT enhance anti-tumor immunity by distinct or overlapping mechanisms remains unclear. Here, we compared effective therapeutic tumor-specific mutant neoantigen (NeoAg) cancer vaccines with anti-CTLA-4 and/or anti-PD-1 ICT in preclinical models. Both NeoAg vaccines and ICT induce expansion of intratumoral NeoAg-specific CD8 T cells, though the degree of expansion and acquisition of effector activity was much more substantial following NeoAg vaccination. Further, we found that NeoAg vaccines are particularly adept at inducing proliferating and stem-like NeoAg-specific CD8 T cells. Single cell T cell receptor (TCR) sequencing revealed that TCR clonotype expansion and diversity of NeoAg-specific CD8 T cells relates to their phenotype and functional state associated with specific immunotherapies employed. Effective NeoAg vaccines and ICT required both CD8 and CD4 T cells. While NeoAg vaccines and anti-PD-1 affected the CD4 T cell compartment, it was to less of an extent than observed with anti-CTLA-4, which notably induced ICOS+Bhlhe40+ Th1-like CD4 T cells and, when combined with anti-PD-1, a small subset of Th2-like CD4 T cells. Although effective NeoAg vaccines or ICT expanded intratumoral M1-like iNOS+ macrophages, NeoAg vaccines expanded rather than suppressed (as observed with ICT) M2-like CX3CR1+CD206+ macrophages, associated with the vaccine adjuvant. Further, combining NeoAg vaccination with ICT induced superior efficacy compared to either therapy in isolation, highlighting the utility of combining these modalities to eliminate cancer. HighlightsO_LINeoAg cancer vaccines utilize distinct mechanisms from CTLA-4 or PD-1 ICT C_LIO_LINeoAg vaccines induce TCF1+ stem-like and proliferating NeoAg-specific CD8 T cells C_LIO_LICD8 TCR clonotype expansion relates to phenotype and functional state associated with immunotherapy C_LIO_LINeoAg vaccines induce partially distinct macrophage remodeling from ICT C_LIO_LINeoAg vaccines synergize with ICT, exceeding combination CTLA-4/PD-1 ICT efficacy C_LI

immunology↗

bioRxiv2023

STAT3 protects HSCs from intrinsic interferon signaling and loss of long-term blood-forming activity

STAT3 function in hematopoietic stem and progenitor cells (HSPCs) has been difficult to discern as Stat3 deficiency in the hematopoietic system induces systemic inflammation, which can impact HSPC activity. To address this, we established mixed bone marrow (BM) chimeric mice with CreER-mediated Stat3 deletion in 20% of the hematopoietic compartment. Stat3-deficient HSPCs had impaired hematopoietic activity and failed to undergo expansion in BM in contrast to Stat3-sufficient (CreER) controls. Single-cell RNA sequencing of Lin-ckit+Sca1+ BM cells revealed altered transcriptional responses in Stat3-deficient hematopoietic stem cells (HSCs) and multipotent progenitors, including intrinsic activation of cell cycle, stress response, and interferon signaling pathways. Consistent with their deregulation, Stat3-deficient Lin-ckit+Sca1+ cells accumulated {gamma}H2AX over time. Following secondary BM transplantation, Stat3-deficient HSPCs failed to reconstitute peripheral blood effectively, indicating a severe functional defect in the HSC compartment. Our results reveal essential roles for STAT3 in HSCs and suggest the potential for using targeted synthetic lethal approaches with STAT3 inhibition to remove defective or diseased HSPCs. Key PointsO_LISTAT3 is critical for hematopoietic activity and hematopoietic stem cell maintenance in non-inflammatory conditions C_LIO_LISTAT3 has a cell-intrinsic role in the suppression of interferon signaling and myeloid-skewed transcription in hematopoietic stem cells C_LI

immunology↗