Biology subjects

Coffer, P. J.

Publications and source records attributed to Coffer, P. J..

5 recordsLinked to original sources

bioRxiv2026

CD4+ T cell activation is dependent on a novel form of ULK1/2-independent autophagy

Autophagy is essential for CD4+ T cell activation and immune regulation. However, during activation both autophagy and anabolic signaling must be simultaneously sustained, challenging established models of pathway antagonism. Here, we show that T cell receptor signaling and co-stimulation induce a non-canonical form of autophagy required for proliferation and cytokine production. Pharmacological and genetic analyses reveal that this pathway is activated concurrently with mTORC1, and is dependent on PIK3C3, but occurs independently of the canonical regulators ULK1/2, AMPK, ATG13, and Beclin 1. Furthermore, immuno-electron microscopy demonstrates that activation generates smaller autophagic structures that associate with multivesicular bodies and exhibit a unique morphology. These findings uncover a fundamental rewiring of autophagy control in CD4+ T cells and identify a novel form of mechanistically and morphologically distinct non-canonical autophagy.

cell biology↗

bioRxiv2025

Site-dependent Treg cell transcriptional reprograming in a metastatic colorectal cancer model holds prognostic significance

In colorectal cancer (CRC), tumor-infiltrating regulatory T (Treg) cells suppress anti-tumor immunity, promoting immune evasion and tumor progression. Effective therapies require selectively targeting tumor-infiltrating Treg (TI-Treg) cells while preserving systemic Treg cells, necessitating insight into their adaptations within the tumor microenvironment. Here, CRC-organoids were implanted in the liver of Foxp3eGFP mice to investigate location-specific phenotypic differences in TI-Treg cells. Tumor tissue exhibited an increased proportion of Treg cells and a decrease of effector CD4 and CD8 T cells compared to matched healthy tissue. RNA sequencing of Treg cells isolated from the spleen, primary liver tumor transplant, or metastases identified gene expression profiles previously associated with CRC-related Treg cells in patients. Location-specific differences included elevated expression of WNT-pathway genes in peritoneal TI-Treg cells compared to liver counterparts. Higher expression of genes upregulated in liver TI-Treg cells correlated with poor CRC prognosis. Splenic Treg cells from tumor-bearing mice displayed distinct transcriptional profiles from both their healthy counterparts and TI-Treg cells, suggesting they represent a distinct CD4+ population. Taken together, these findings highlight TI-Treg cells heterogeneity across different tumor sites and the distinct nature of splenic Treg cells in tumor-bearing hosts.

immunology↗

bioRxiv2024

Tumor-derived colorectal cancer organoids induce a unique Treg cell population through direct modulation of CD4+ T cell differentiation.

In colorectal cancer (CRC), increased numbers of tumor-infiltrating CD4+ regulatory T (Treg) cells correlate with tumor development and immunotherapy failure, leading to poor prognosis. However, the molecular and cellular mechanisms governing Treg recruitment, expansion, or differentiation remain unclear. Here, we developed an in vitro co-culture system to assess the capacity of CRC tumors to directly modulate Treg cell differentiation. CD4+ T cells from Foxp3eGFP mice were co-cultured with murine tumor-derived CRC organoids, resulting in a significant increase in Treg cell numbers. This induction of Treg cells was not due to increased proliferation, but rather through differentiation of CD4+ T cells in a TGF{beta}-dependent manner. Human CRC tumor organoids similarly induced Treg cells that exhibited enhanced suppressive capacity compared to TGF{beta}-induced Treg cells. RNA-sequencing analysis identified distinct transcriptional profiles between CRC organoid-induced Treg cells and TGF{beta}-induced Treg cells, with upregulation of key functional signature genes linked to CRC Treg cells in vivo. High expression of genes upregulated in CRC organoid-induced Treg cells correlates with shorter progression free interval and overall survival of CRC patients, highlighting their prognostic potential. Taken together, CRC tumor organoids drive CD4+ differentiation to Treg cells with a phenotype resembling tumor-infiltrating Treg cells. This model can be applied to both understand the molecular mechanisms by which tumors can directly modulate CD4+ T cell differentiation and identify approaches to disrupt Treg cell function and stimulate anti-tumor immunity.

immunology↗

bioRxiv2024

IFNγ induces epithelial reprogramming driving CXCL11-mediated T cell migration

The cytokine interferon-gamma (IFN{gamma}) plays a multifaceted role in intestinal immune responses ranging from anti-to pro-inflammatory depending on the setting. Here, using a 3D co-culture system based on human intestinal epithelial organoids, we explore the capacity of IFN{gamma}-exposure to reprogram intestinal epithelia and thereby directly modulate lymphocyte responses. IFN{gamma} treatment of organoids led to transcriptional reprogramming, marked by a switch to a pro-inflammatory gene expression profile, including transcriptional upregulation of the chemokines CXCL9, CXCL10, and CXCL11. Proteomic analysis of organoid-conditioned medium post-treatment confirmed chemokine secretion. Furthermore, IFN{gamma}-treatment of organoids led to enhanced T cell migration in a CXCL11-dependent manner without affecting T cell activation status. Taken together, our results suggest a specific role for CXCL11 in T cell recruitment that can be targeted to prevent T cell trafficking to the inflamed intestine.

immunology↗

bioRxiv2023

Chemotherapy-induced intestinal injury promotes Galectin-9-driven modulation of T cell function

The intestine is vulnerable to chemotherapy-induced toxicity due to its high epithelial proliferative rate, making gut toxicity an off-target effect in several cancer treatments, including conditioning regimens for allogeneic hematopoietic cell transplantation (allo-HCT). In allo-HCT, intestinal damage is an important factor in the development of Graft-versus-Host Disease (GVHD), an immune complication in which donor immune cells attack the recipients tissues. Here, we developed a novel human intestinal organoid-based 3D model system to study the direct effect of chemotherapy-induced intestinal epithelial damage on T cell behavior. Chemotherapy treatment using busulfan, fludarabine, and clofarabine led to damage responses in organoids resulting in increased T cell migration, activation, and proliferation in ex-vivo co-culture assays. We identified galectin-9 (Gal-9), a beta-galactoside-binding lectin released by damaged organoids, as a key molecule mediating T cell responses to damage. Increased levels of Gal-9 were also found in the plasma of allo-HCT patients who later developed acute GVHD, supporting the predictive value of the model system in the clinical setting. This study highlights the potential contribution of chemotherapy-induced epithelial damage to the pathogenesis of intestinal GVHD through direct effects on T cell activation and trafficking promoted by galectin-9.

immunology↗