Biology subjects

Freud, A. G.

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

10 recordsLinked to original sources

bioRxiv2026

CDK4/6 inhibition sensitizes breast cancer to NK cell therapy by inducing immune-interactive surface proteins

CDK4/6 inhibitors are standard-of-care for metastatic estrogen receptor-positive (ER+) breast cancer, yet the development of resistance remains a significant clinical hurdle. While CDK4/6 inhibitors are primarily recognized for their ability to induce cytostasis, their role in modulating innate immune responses remains poorly defined. Here, we demonstrated that CDK4/6i treatment remodels the tumor cell surface to favor recognition and elimination by Natural Killer (NK) cells. Using a diverse biobank of patient-derived organoids (PDOs), we found that CDK4/6 inhibition robustly upregulated the adhesion molecule ICAM-1 and the NKG2D stress ligands (ULBP2/5/6 and MICA/B). This NK-engaging cell surface phenotype was driven by a bifurcated signaling network: NF-{kappa}B signaling orchestrated ICAM-1 induction, while the PI3K/mTOR pathway regulated the expression of stress ligands. Functional assays confirmed that these ligands were indispensable for NK cell-mediated elimination of breast cancer cells. In vivo studies using ER+ PDX models revealed that a brief seven-day primer treatment with the CDK4/6 inhibitor abemaciclib was sufficient to sensitize tumors to NK cell therapy, significantly inhibiting tumor growth and prolonging survival. We also observed efficacy with a concurrent dosing strategy that delayed the onset of acquired resistance. These findings provide a mechanistic rationale for combining CDK4/6 inhibitors with NK cell therapy. This "prime and kill" approach offers a promising strategy to overcome therapeutic resistance and improve outcomes for patients with metastatic ER+ breast cancer.

cancer biology↗

bioRxiv2025

A developmental program of early residency promotes the differentiation of divergent uterine NK cell subsets in humans

Human uterine natural killer cells (uNKs) are a tissue-resident, innate lymphocyte population that have critical roles in supporting pregnancy health. uNKs derive from circulatory cells in the peripheral blood which immigrate into the endometrium and become resident as they reconstitute the uterine lining after menses. How tissue-resident uterine NK cells arise from blood-based precursor cells is unknown. Here, we identify early tissue immigrants, developmental intermediates, and mature effector states in human endometrium. We also uncover a transcriptional program of TGF-{beta} responsive genes that is upregulated in recent tissue immigrants prior to expression of effector molecules. Differences in TGF-{beta} responsiveness of uNK precursors promote differential expression of divergent effector uNK subsets, resulting in either repression or preservation of cytotoxic effector potential. Collectively, these data suggest a molecular mechanism of tissue-resident uNK maturation that links tissue residency with the acquisition of divergent effector functions in human endometrium.

immunology↗

bioRxiv2024

Cell fate determination is associated with changes in competing transcriptional units in the human GATA1 and GATA2 lineage-determining transcription factors

The GATA1 and GATA2 transcription factors play a central role in early cell fate decisions in hematopoietic progenitor cells. Although the switch from GATA2 to GATA1 occupancy at GATA-binding sites in erythroblast-specific genes has been extensively studied, the underlying molecular mechanisms controlling this switch are not fully elucidated. An antisense promoter in the 5 region of the GATA2 gene produces a long non-coding RNA that has been shown to affect GATA2 transcription and erythroblast differentiation. The recent identification of an antisense promoter in the first intron of the GATA1 gene indicates that similar promoter competition mechanisms operate in these genes, potentially controlling GATA1/GATA2 levels in a probabilistic manner. In the current study we perform a comprehensive evaluation of GATA1 and GATA2 transcripts in human CD34+ progenitors either freshly isolated or differentiated in vitro and the human leukemia cell lines K562 and HL60. The ratio of competing sense and antisense transcripts varied significantly with differentiation status, suggesting that promoter competition controls cell fate decisions. Treatment of HL60 cells with differentiating agents resulted in significant changes in the ratio of GATA2 sense to antisense promoter activity, in agreement with previous results showing that sense and antisense transcription are associated with distinct cellular phenotypes.

developmental biology↗

bioRxiv2024

Inhibition of NFAT promotes loss of tissue resident uterine natural killer cells and attendant pregnancy complications in humans

Uterine natural killer cells (uNKs) are a tissue resident lymphocyte population that are critical for pregnancy success. Although mouse models have demonstrated that NK deficiency results in abnormal placentation and poor pregnancy outcomes, the generalizability of this knowledge to humans remains unclear. Here we identify uterus transplant (UTx) recipients as a human population with reduced uNK cells and altered pregnancy phenotypes. We show that the NK reduction in UTx correlates with impaired transcriptional programming of NK tissue residency arising from the inhibition of NFAT-mediated signaling. Our observations suggest that NFAT-dependent genes modulate multiple molecular tissue residency programs in uNKs. These include early residency programs involving AP-1-family transcription factors and TGF-{beta}-mediated upregulation of surface integrins. Collectively, our data identify a previously undescribed role for NFAT in uterine NK tissue residency and provide novel mechanistic insights into the biologic basis of pregnancy complications due to alteration of tissue resident NK subsets in humans. One Sentence SummaryRole of NFAT in uterine NK cell tissue residency

immunology↗

bioRxiv2024

Rapid Identification of Genomic Alterations in Tumors affecting lymphocyte Infiltration (RIGATonI)

Tumor genomic alterations have been associated with altered tumor immune microenvironments and therapeutic outcomes. These studies raise a critical question: are there additional genomic variations altering the immune microenvironment in tumors that can provide insight into mechanisms of immune evasion? This question is the backbone of precision immuno-oncology. Current computational approaches to estimate immunity in bulk RNA sequencing (RNAseq) from tumors include gene set enrichment analysis and cellular deconvolution, but these techniques do not consider the spatial organization of lymphocytes or connect immune phenotypes with gene activity. Our new software package, Rapid Identification of Genomic Alterations in Tumors affecting lymphocyte Infiltration (RIGATonI), addresses these two gaps in separate modules: the Immunity Module and the Function Module. Using pathologist-reviewed histology slides and paired bulk RNAseq expression data, we trained a machine learning algorithm to detect high, medium, and low levels of immune infiltration (Immunity Module). We validated this technique using a subset of pathologist-reviewed slides not included in the training data, multiplex immunohistochemistry, flow cytometry, and digital staining of The Cancer Genome Atlas (TCGA). In addition to immune infiltrate classification, RIGATonI leverages another novel machine learning algorithm for the prediction of gain- and loss-of-function genomic alterations (Function Module). We validated this approach using clinically relevant and function-impacting genomic alterations from the OncoKB database. Combining these two modules, we analyzed all genomic alterations present in solid tumors in TCGA for their resulting protein function and immune phenotype. We visualized these results on a publicly available website. To illustrate RIGATonIs potential to identify novel genomic variants with associated altered immune phenotypes, we describe increased anti-tumor immunity in renal cell carcinoma tumors harboring 14q deletions and confirmed these results with previously published single-cell RNA sequencing. Thus, we present our R package and online database, RIGATonI: an innovative software for precision immuno-oncology research.

bioinformatics↗

bioRxiv2024

Sequential Transcriptional Programs of Tissue Residency Drive Human Uterine NK Cell Development

Uterine natural killer cells are critical for pregnancy success, but the origin and development of these cells in humans remain unclear. Here we use various single cell approaches to identify the transcriptional programs governing uterine NK cell development in humans. These analyses suggest a developmental continuum which begins with seeding of the endometrium with blood immature CD56bright precursors, evolves through CD56bright endometrial founder NK cells, and ends with tissue resident decidual NK cells during pregnancy which possess non-cytotoxic functions. Our work identifies a role for sequential programs of tissue residency in the differentiation of these cells, as differentiating endometrial tissue resident NK (trNK) cells acquire early and late transcriptional programs of residency which coincide with acquisition of unique non-cytotoxic effector programs. Notably, we identified early residency programs in human endometrial trNKs by expression of NR4A2, AP-1 transcription factors, and other immediate early response genes that were shared with CD8 tissue resident memory T cells in mice, suggesting conservation of transcriptional programs of early tissue residency programs across species and cell types. Late residency programs were guided by TGF{beta}, which promoted expression of various integrins and trNK subset diversification within the non-pregnant endometrium. Altogether, these data identify the molecular foundations for endometrial trNK heterogeneity and suggest that the uterine NK diversity observed during pregnancy is established before embryo implantation and intimately tied to residency programming.

immunology↗

bioRxiv2023

Mapping human natural killer cell development in pediatric tonsil by imaging mass cytometry & high-resolution microscopy

Natural killer (NK) cells develop from CD34+ progenitors in a stage-specific manner defined by changes in cell surface receptor expression and function. Secondary lymphoid tissues, including tonsil, are sites of human NK cell development. Here we present new insights into human NK cell development in pediatric tonsil using cyclic immunofluorescence and imaging mass cytometry. We show that NK cell subset localization and interactions are dependent on NK cell developmental stage and tissue residency. NK cell progenitors are found in the interfollicular domain in proximity to cytokine-expressing stromal cells that promote proliferation and maturation. Mature NK cells are primarily found in the T-cell rich parafollicular domain engaging in cell-cell interactions that differ depending on their stage and tissue residency. The presence of local inflammation results in changes in NK cell interactions, abundance, and localization. This study provides the first comprehensive atlas of human NK cell development in secondary lymphoid tissue.

immunology↗

bioRxiv2022

Aiolos modulates the TFH and CD4-CTL differentiation programs via reciprocal regulation of the Zfp831/TCF-1/Bcl-6 axis and CD25

Effective immunity to influenza virus and other respiratory viruses requires the generation of CD4+ T cell subsets that coordinate multiple aspects of the immune response. These subsets include T follicular helper (TFH) and T helper 1 (TH1) cells, which promote humoral and cell-mediated responses, respectively. A third population, CD4+ cytotoxic T lymphocytes (CD4-CTLs) facilitates clearance of infection via mechanisms normally associated with CD8+ T cells. Here, we identify the transcription factor Aiolos as a regulator of TFH and CD4-CTL responses. We demonstrate that Aiolos deficiency compromises TFH differentiation and antibody production during influenza virus infection. Conversely, we find that CD4+ T cells acquire a cytotoxic-like program in the absence of Aiolos, including increased expression of the CTL-associated transcription factors Eomes and Blimp-1. We further show that while Aiolos positively regulates the TFH transcriptional regulators Zfp831, TCF-1 and Bcl-6, it also directly represses expression of IL-2R and IL-2/STAT5-driven expression of the cytotoxic gene program. Thus, our findings identify Aiolos as a pivotal regulator of TFH and CD4-CTL differentiation and highlight its potential as a target for manipulating CD4+ T cell humoral and cytotoxic responses.

immunology↗

bioRxiv2020

Differential integrin adhesome expression defines human natural killer cell residency and developmental stage

Natural killer (NK) cells are innate immune cells that reside within tissue and circulate in peripheral blood. As such, they interact with a variety of complex microenvironments, yet how NK cells engage with these varied microenvironments is not well documented. The integrin adhesome represents a molecular network of defined and predicted integrin-mediated signaling interactions. Here, we define the integrin adhesome expression profile of NK cells from tonsil, peripheral blood and those derived from hematopoietic precursors through stromal cell coculture systems. We report that the site of cell isolation and NK cell developmental stage dictate differences in expression of adhesome associated genes and proteins. Furthermore, we define differences in cortical actin content associated with differential expression of actin regulating proteins, suggesting that differences in adhesome expression are associated with differences in cortical actin homeostasis. Together, these data provide new understanding into the diversity of human NK cell populations and how they engage with their microenvironment.

cell biology↗

bioRxiv2020

Gut Dysbiosis with a Pathobiont Shifts the Intestinal Microbiota Profile and Accelerates Lupus Nephritis

The gut microbiota (GM) exerts a strong influence over the host immune system and dysbiosis of this microbial community can affect the clinical phenotype in chronic inflammatory conditions. To explore the role of the GM in lupus nephritis, we colonized NZM2410 mice with Segmented Filamentous Bacteria (SFB). Gut colonization with SFB was associated with worsening glomerulonephritis, glomerular and tubular immune complex deposition and interstitial inflammation compared to NZM2410 mice free of SFB. With SFB colonization mice experienced an increase in small intestinal lamina propria Th17 cells and group 3 innate lymphoid cells (ILC3s). However, although serum IL-17A expression was elevated in these mice, Th17 cells and ILC3s were not detected in the inflammatory infiltrate in the kidney. In contrast, serum and kidney tissue expression of the macrophage chemoattractants MCP-1 and CXCL1 were significantly elevated in SFB colonized mice. Furthermore, kidney infiltrating F4/80+CD206+ M2-like macrophages were significantly increased in these mice. Evidence of increased gut permeability or "leakiness" was detected in SFB colonized mice. Finally, the intestinal microbiome of SFB colonized mice at 15 and 30 weeks of age exhibited dysbiosis when compared to uncolonized mice at the same time points. Both microbial relative abundance as well as biodiversity of colonized mice was found to be altered. Collectively, SFB gut colonization in the NZM2410 mouse exacerbates kidney disease, promotes kidney M2-like macrophage infiltration and overall intestinal microbiota dysbiosis.

immunology↗