Biology subjects

Cuenca, A. G.

Publications and source records attributed to Cuenca, A. G..

3 recordsLinked to original sources

bioRxiv2026

HLiCA: An integrated cell atlas of the healthy human liver

The human liver is composed of a heterogeneous mix of cell types. How these distinct populations contribute individually and collectively to liver function remains poorly understood. Although single-cell technologies have advanced our understanding of liver biology, individual studies have often been limited by small donor cohorts and inconsistent cell type annotations. Integrating multiple datasets can overcome these challenges and better capture biological variability. We present the Human Liver Cell Atlas (HLiCA), an integrated reference of non-disease liver cells assembled from eight datasets across six research centers, encompassing more than 525,000 cells from 110 donors. Developed in collaboration with the Human Cell Atlas Liver Bionetwork, the HLiCA incorporates expert-curated cell annotations refined through community feedback and dedicated cell type annotation meetings. The HLiCA classifies cells into six lineages and expands the cell type resolution to include 47 distinct cell types. Starting from raw sequencing reads, we realigned all data and performed rigorous benchmarking to ensure robust integration across technical and biological variables. Genetic ancestry was inferred for all samples to evaluate the range of ancestral backgrounds represented in the atlas. The expanded cell type annotation enabled identification of previously unrecognized liver cell types, including NRXN1+ stromal cells. Their presence was validated using spatial transcriptomics, which localized NRXN1+ stromal cells to periportal regions. With the number of donors included in the HLiCA we were able to examine cell type specific associations with demographic covariates. In hepatocytes, drug metabolism genes showed differential expression between sexes, and in cholangiocytes, mucus-production genes varied with age. As the largest and most genetically diverse human liver cell atlas to date, the HLiCA provides a comprehensive, well-annotated reference for the field, annotated by expert consensus. This resource will enable deeper interrogation of liver cellular diversity, architecture, and function in the healthy human liver and serve as a reference to understand changes that occur with disease.

genomics↗

bioRxiv2025

Group 2 Innate lymphoid cells promote allograft survival by constraining and inducing anergy in alloreactive CD4+ T cells

Although solid organ transplant outcomes have dramatically improved over the last several decades, incomplete understanding of the immune interface between the donor organ and the recipients immune system has impaired our ability to induce immune tolerance in most transplant recipients. Since group 2 innate lymphoid cells (ILC2s) reside in all transplanted solid organs, participate in wound healing, and coordinate other immunoregulatory cell populations, we investigated their role in the alloimmune response. Using a mouse heterotopic cardiac transplant model, we show that recipient ILC2s replace donors ILC2s, upregulate MHCII without expressing costimulatory molecules. In addition, recipient derived ILC2s process and present alloantigen, inducing CD4+ T cell anergy via Caspase-3 pathway. When recipient-derived ILC2s are not present, we observed a significant increase in infiltrating donor reactive CD4+ T cells and worsened allograft survival. Additionally, expansion of ILC2s in vivo through IL33 administration prolonged the survival of murine heart allografts. Overall, these data highlight a critical and novel immunoregulatory role of host-derived ILC2s in solid organ transplant, where they induce anergy in alloreactive CD4+ T cells, promoting the induction of alloimmune tolerance.

immunology↗

bioRxiv2024

Adjuvant conditioning shapes the adaptive immune response and promotes trained immunotolerance via NLRP3/IL-1

Trained immunity enhances responsiveness of the innate immune system upon restimulation. Although adjuvants are used to enhance immune responses, we showed that repeated administration of alum, termed adjuvant conditioning (AC), establishes an immunosuppressive environment that delays allogeneic graft rejection by expanding myeloid-derived suppressor cells (MDSCs). Here, we show that AC-induced MDSCs suppress antigen specific adaptive responses both in vitro and in vivo, and that the immunosuppression is abolished in the absence of NLRP3 and IL-1 signaling. Allogeneic pancreatic islets transplanted into AC-treated NLRP3-/- mice are not protected, demonstrating that AC requires NLRP3 signaling. Finally, AC also has an immunosuppressive effect on human cells. Overall, our data show that AC establishes an immunosuppressive milieu via the NLRP3/IL-1 axis, leading to trained immunosuppression, or trained tolerance. Our findings give a potent mandate to explore the possibility to target the NLRP3/IL-1 pathway as a new promising strategy to condition transplant recipients and promote allograft tolerance.

immunology↗