Biology subjects

Kessenbrock, K.

Publications and source records attributed to Kessenbrock, K..

15 recordsLinked to original sources

bioRxiv2026

Restoration of deficient IL-15 signaling enhances innate lymphoid cell immunity in brain metastasis

Natural killer (NK) cells and type 1 innate lymphoid cells (ILC1s), collectively known as group 1 innate lymphoid cells (ILCs), are critical mediators of anti-tumor immunity, yet their role in brain metastasis remains poorly defined. Using single-cell RNA sequencing and functional depletion models, we show that group 1 ILCs fail to provide adequate tumor control in breast cancer brain metastasis (BCBM). In contrast to the liver, where diverse, functionally competent group 1 ILC populations facilitate excellent metastatic control, group 1 ILCs in BCBM show limited diversity and profound tissue-specific dysfunction such that their depletion had no effect on tumor burden despite modest parenchymal infiltration. We attribute this group 1 ILC dysfunction to severely restricted IL-15 availability, with IL-15R protein detected at 500-fold lower concentration in the brain than in the liver. Local IL-15 complex administration restored group 1 ILC accumulation, cytotoxicity, and tissue residency, significantly reducing brain metastatic burden independent of T cells. Intracranial delivery of IL-15-secreting induced pluripotent stem-cell-derived (iPSC)-NK cells, already in clinical testing for non-small cell lung cancer, significantly reduced tumor burden. Collectively, these findings reveal how tissue-specific differences in cytokine availability shape group 1 ILC population diversity and disease response, establishing localized IL-15 signaling as a compelling strategy to unlock innate immunity against intracranial malignancies.

immunology↗

bioRxiv2026

Cell-of-origin shapes tumor subtype in BRCA1-associated triple-negative breast cancer

Pathogenic germline BRCA1 variants greatly increase lifetime breast cancer risk, with no targeted prevention. Accrual of mutations following DNA repair errors in luminal progenitors is considered the chief mechanism of triple-negative breast cancer (TNBC) initiation, which cannot explain the organ specificity nor the phenotypic spectrum of the disease. Here we show that TNBC also originates in basal-myoepithelial cells, and that the cell of origin shapes TNBC subtype through aberrant epithelial differentiation, likely due to pleiotropic role of BRCA1 in regulating hormone signaling. Single-cell RNA sequencing of 67,001 cells from Wap-Cre Brca1/p53 mice and reanalysis of published Blg-Cre data show that aberrant basal-myoepithelial differentiation (Wap-Cre) generates the mesenchymal subtype (TNBC-M) and aberrant luminal differentiation (Blg-Cre) the basal-like subtype (TNBC-BL1). We also show that both subtypes occur at comparable frequency in BRCA1 carriers. Aberrant basal-myoepithelial differentiation precedes tumor formation, and only tumors derived from transplanted basal cells reproduce the basal-containing phenotype of spontaneous tumors. Comparison with a developmental atlas identifies de-differentiation of myoepithelial cells into basal cells lacking myoepithelial markers, a fetal state, whereas experimental metastases shift toward luminal states while retaining a TNBC-M-like transcriptional program. These findings support the inclusion of basal-myoepithelial and luminal cells in targeted prevention strategies for BRCA1 carriers, and adoption of TNBC subtyping for patient stratification and improving outcomes.

cancer biology↗

bioRxiv2026

Single-cell profiling of synchronous multi-organ metastasis reveals a systemic CD74+ lipid-associated macrophage niche driving polymetastatic breast cancer

Systemic, multi-organ metastasis is the primary cause of breast cancer mortality, yet the biological mechanisms that allow disseminated tumor cells to simultaneously colonize physiologically diverse tissues remain poorly understood. Current paradigms focus on organ-specific tropism, largely overlooking the potential for systemic, conserved and synchronized programs that facilitate widespread colonization. Here, we present a high-resolution, multi-organ atlas of metastatic ecosystems and their niches using a synchronous model of brain, lung, liver, and bone metastasis combined with in vivo proximal niche labeling and single-cell RNA sequencing. We identify a remarkably conserved proximal niche program defined by the accumulation of CD74+ lipid-associated, metastasis-associated macrophages (LA-MAMs) across all metastatic sites. CD74+ LA-MAMs are characterized by a unique metabolic-immune signature and drive T cell suppression. We show that the cytokine Macrophage Migration Inhibitory Factor (MIF), secreted by metastatic cells, acts as the universal paracrine mediator that instructs the LA-MAM phenotype via the CD74 receptor. Interference of the MIF-CD74 axis effectively disrupts the LA-MAM niche, mitigates T cell exhaustion, and reduces metastatic burden across all organs. Analysis of a 100-patient cohort of metastasis samples from different sites confirms that the MIF-CD74 axis is a hallmark of human multi-organ colonization and independently predicts poor post-metastasis survival. Our findings define a synchronized and systemic metastatic niche that can be targeted, providing a mechanistic rationale for neutralizing the MIF-CD74 axis to treat polymetastatic breast cancer.

cancer biology↗

bioRxiv2025

PHLDA2 promotes breast cancer metastasis by co-opting a developmental program for placental vascular remodeling

Identifying drivers of metastasis is essential for developing new treatments for patients with advanced disease. Here, we identify PHLDA2 as a robust driver of breast cancer metastasis. Previous work established PHLDA2 as an imprinted gene expressed by trophoblasts which are critical for vascular remodeling during placental development. We find that hypomethylation of PHLDA2 in breast tumors correlates with increased gene expression, which is associated with metastasis and poor survival in breast cancer patients. RNA-sequencing showed that PHLDA2 overexpression results in upregulation of genes that control invasion, extracellular matrix assembly, and vascular remodeling, consistent with trophoblast functions in placental development. Using an in vitro vascularized microtumor (VMT) system, we find that PHLDA2 functions through SPARC, which promotes metastasis by inducing vascular permeability and enhancing tumor dissemination. These data suggest that increased expression of PHLDA2 through hypomethylation promotes metastasis by ectopic expression of a developmental program for vascular remodeling.

cancer biology↗

bioRxiv2024

Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model

Despite the major roles of choroid plexus epithelial cells (CPECs) in brain homeostasis and repair, their developmental lineage and diversity remain undefined. In simplified differentiations from human pluripotent stem cells, derived CPECs (dCPECs) displayed canonical properties and dynamic multiciliated phenotypes that interacted with A{beta} uptake. Single dCPEC transcriptomes over time correlated well with human organoid and fetal CPECs, while pseudotemporal and cell cycle analyses highlighted the direct CPEC origin from neuroepithelial cells. In addition, time series analyses defined metabolic (type 1) and ciliogenic dCPECs (type 2) at early timepoints, followed by type 1 diversification into anabolic-secretory (type 1a) and catabolic-absorptive subtypes (type 1b) as type 2 cells contracted. These temporal patterns were then confirmed in independent derivations and mapped to prenatal stages using human tissues. In addition to defining the prenatal lineage of human CPECs, these findings suggest new dynamic models of ChP support for the developing human brain.

neuroscience↗

bioRxiv2023

Targeting tumor-stromal interactions in triple-negative breast cancer using a human vascularized micro-tumor model

Triple-negative breast cancer (TNBC) is highly aggressive with limited available treatments. Stromal cells in the tumor microenvironment (TME) are crucial in TNBC progression; however, understanding the molecular basis of stromal cell activation and tumor-stromal crosstalk in TNBC is limited. To investigate therapeutic targets in the TNBC stromal niche, we used an advanced human in vitro microphysiological system called the vascularized micro-tumor (VMT). Using single-cell RNA sequencing (scRNA-seq), we revealed that normal breast-tissue stromal cells activate neoplastic signaling pathways in the TNBC TME. By comparing interactions in VMTs with clinical data, we identified therapeutic targets at the tumor-stromal interface with potential clinical significance. Combining treatments targeting Tie2 signaling with paclitaxel resulted in vessel normalization and increased efficacy of paclitaxel in the TNBC VMT. Dual inhibition of Her3 and Akt also demonstrated efficacy against TNBC. These data demonstrate the potential of inducing a favorable TME as a targeted therapeutic approach in TNBC.

cancer biology↗

bioRxiv2023

A spatially resolved single cell genomic atlas of the adult human breast

The adult human breast comprises an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue. While previous studies have mainly focused on the breast epithelial system, many of the non-epithelial cell types remain understudied. Here, we constructed a comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics data profiled 535,941 cells from 62 women, and 120,024 nuclei from 20 women, identifying 11 major cell types and 53 cell states. These data revealed abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Our spatial mapping using three technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells in the ducts and lobules, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide an unprecedented reference of adult normal breast tissue for studying mammary biology and disease states such as breast cancer.

genomics↗

bioRxiv2023

Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis

The monocytic/macrophage system is essential for skeletal muscle homeostasis, but its dysregulation contributes to the pathogenesis of muscle degenerative disorders. Despite our increasing knowledge of the role of macrophages in degenerative disease, it still remains unclear how macrophages contribute to muscle fibrosis. Here, we used single-cell transcriptomics to determine the molecular attributes of dystrophic and healthy muscle macrophages. We identified six novel clusters. Unexpectedly, none corresponded to traditional definitions of M1 or M2 macrophage activation. Rather, the predominant macrophage signature in dystrophic muscle was characterized by high expression of fibrotic factors, galectin-3 and spp1. Spatial transcriptomics and computational inferences of intercellular communication indicated that spp1 regulates stromal progenitor and macrophage interactions during muscular dystrophy. Galectin-3+ macrophages were chronically activated in dystrophic muscle and adoptive transfer assays showed that the galectin-3+ phenotype was the dominant molecular program induced within the dystrophic milieu. Histological examination of human muscle biopsies revealed that galectin-3+ macrophages were also elevated in multiple myopathies. These studies advance our understanding of macrophages in muscular dystrophy by defining the transcriptional programs induced in muscle macrophages, and reveal spp1 as a major regulator of macrophage and stromal progenitor interactions.

immunology↗

bioRxiv2021

Pre-neoplastic stromal cells drive BRCA1-mediated breast tumorigenesis

Women with germline mutations in BRCA1 (BRCA1+/mut) have increased risk for developing hereditary breast cancer1, 2. Cancer initiation in BRCA1+/mut is associated with pre-malignant changes in the breast epithelium including altered differentiation3-5, proliferative stress6 and genomic instability7. However, the role of the epithelium- associated stromal niche during BRCA1-driven tumor initiation remains unclear. Here, we show that the pre-malignant stromal niche promotes epithelial proliferation and BRCA1- driven cancer initiation in trans. Using single-cell RNAseq (scRNAseq) analysis of human pre-neoplastic BRCA1+/mut and control breast tissues, we show that stromal cells provide numerous pro-proliferative paracrine signals inducing epithelial proliferation. We identify a subpopulation of pre-cancer associated fibroblasts (pre-CAFs) that produces copious amounts of pro-tumorigenic factors including matrix metalloproteinase 3 (MMP3)8, 9, and promotes BRCA1-driven tumorigenesis in vivo. Our gene-signature analysis and mathematical modeling of epithelial differentiation reveals that stromal-induced proliferation leads to the accumulation of luminal progenitor cells with altered differentiation, and thus contributes to increased breast cancer risk in BRCA1+/mut. Our results demonstrate how alterations in cell-cell communication can induce imbalances in epithelial homeostasis ultimately leading to cancer initiation. We anticipate our results to form the foundation for novel disease monitoring and therapeutic strategies to improve patient management in hereditary breast cancer. For example, pre-CAF specific proteins may serve as biomarkers for pre-cancerous disease initiation to inform whether radical bilateral mastectomy is needed. In addition, MMP inhibitors could be re-indicated for primary cancer prevention treatment in women with high-risk BRCA1 mutations.

cancer biology↗

bioRxiv2020

Fine-tuning of Epithelial EGFR signals Supports Coordinated Mammary Gland Development

During puberty, robust morphogenesis occurs in the mammary gland; stem- and progenitor-cells develop into mature basal- and luminal-cells to form the ductal tree. The receptor signals that govern this process in mammary epithelial cells (MECs) are incompletely understood. The EGFR has been implicated and here we focused on EGFRs downstream pathway component Rasgrp1. We find that Rasgrp1 dampens EGF-triggered signals in MECs. Biochemically and in vitro, Rasgrp1 perturbation results in increased EGFR-Ras-PI3K-AKT and mTORC1-S6 kinase signals, increased EGF-induced proliferation, and aberrant branching-capacity in 3D cultures. However, in vivo, Rasgrp1 perturbation results in delayed ductal tree maturation with shortened branches and reduced cellularity. Rasgrp1-deficient MEC organoids revealed lower frequencies of basal cells, the compartment that incorporates stem cells. Molecularly, EGF effectively counteracts Wnt signal-driven stem cell gene signature in organoids. Collectively, these studies demonstrate the need for fine-tuning of EGFR signals to properly instruct mammary epithelium during puberty.

cell biology↗

bioRxiv2020

Patient-derived xenograft culture-transplant system for investigation of human breast cancer metastasis

Metastasis is a fatal disease where research progress has been hindered by a lack of authentic experimental models. Here, we develop a 3D tumor sphere culture-transplant system that facilitates the expansion and engineering of patient-derived xenograft (PDX) tumor cells for functional metastasis assays in vivo. Orthotopic transplantation and RNA sequencing analyses show that PDX tumor spheres maintain tumorigenic potential, and the molecular marker and global transcriptome signatures of native tumor cells. Tumor spheres display robust capacity for lentiviral engineering and dissemination in spontaneous and experimental metastasis assays in vivo. Inhibition of pathways previously reported to attenuate metastasis also inhibit metastasis after sphere culture, validating our approach for authentic investigations of metastasis. Finally, we demonstrate a new role for the metabolic enzyme NME1 in promoting breast cancer metastasis, providing proof-of-principle that our culture-transplant system can be used for authentic propagation and engineering of patient tumor cells for functional studies of metastasis.

cancer biology↗

bioRxiv2020

An In Vitro Vascularized Micro-Tumor Model of Human Colorectal Cancer Recapitulates In Vivo Drug Responses

Around 95% of anti-cancer drugs that show promise during preclinical study fail to gain FDA-approval for clinical use. This failure of the preclinical pipeline highlights the need for improved, physiologically-relevant in vitro models that can better serve as reliable drug-screening tools. The vascularized micro-tumor (VMT) is a novel three-dimensional model system that recapitulates the complex human tumor microenvironment, including perfused vasculature, within a transparent microfluidic device, allowing real-time study of drug responses and tumor-stromal interactions. Here we have validated the VMT platform for the study of colorectal cancer (CRC), the second leading cause of cancer-related deaths, by showing that gene expression, tumor heterogeneity, and treatment response in the VMT more closely model CRC tumor clinicopathology than current standard drug screening modalities, including 2-dimensional (2D) monolayer culture and 3-dimensional (3D) spheroids.

cancer biology↗

bioRxiv2019

Integrated single-cell transcriptomics and chromatin accessibility analysis reveals novel regulators of mammary epithelial cell identity

The mammary epithelial cell (MEC) system is a bi-layered ductal epithelial network consisting of luminal and basal cells, which is maintained by a lineage of stem and progenitor cell populations. Here, we used integrated single-cell transcriptomics and chromatin accessibility analysis to reconstruct the cell types of the mouse MEC system and their underlying gene regulatory features in an unbiased manner. We define previously unrealized differentiation states within the secretory type of luminal cells, which can be divided into distinct clusters of progenitor and mature secretory cells. By integrating single-cell transcriptomics and chromatin accessibility landscapes, we identified novel cis- and trans-regulatory elements that are differentially activated in the specific epithelial cell types and our newly defined luminal differentiation states. Our work provides an unprecedented resource to reveal novel cis/trans regulatory elements associated with MEC identity and differentiation that will serve as a valuable reference to determine how the chromatin accessibility landscape changes during breast cancer.

cell biology↗

bioRxiv2019

Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics

Myeloid-derived suppressor cells (MDSCs) are innate immune cells that acquire the capacity to suppress adaptive immune responses during cancer. It remains elusive how MDSCs differ from their normal myeloid counterparts, which limits our ability to specifically detect and therapeutically target MDSCs during cancer. Here, we used single-cell RNAseq to compare MDSC-containing splenic myeloid cells from breast tumor-bearing mice to wildtype controls. Our computational analysis of 14,646 single-cell transcriptomes reveals that MDSCs emerge through a previously unrealized aberrant neutrophil maturation trajectory in the spleen giving rise to a unique chemokine-responsive, immunosuppressive cell state that strongly differs from normal myeloid cells. We establish the first MDSC-specific gene signature and identify novel surface markers for improved detection and enrichment of MDSCs in murine and human samples. Our study provides the first single-cell transcriptional map defining the development of MDSCs, which will ultimately enable us to specifically target these cells in cancer patients.\n\nOne Sentence SummaryWe used single cell transcriptomics to identify the unique molecular features distinguishing myeloid-derived suppressor cells (MDSCs) from their normal, myeloid counterparts, which enabled us to reveal distinct transitory gene expression changes during their maturation in the spleen, and to identify novel cell surface markers for improved detection and isolation of MDSCs.

cancer biology↗

bioRxiv2018

Integrated single-cell potency and expression landscape in mammary epithelium reveals novel bipotent-like cells associated with breast cancer risk

The identification of progenitor and stem like cells in epithelial tissues, as well as those that may serve as the cell of origin for epithelial cancers, is an outstanding challenge. Here we present a novel algorithm, called LandSCENT, which constructs a 3-dimensional integrated landscape of cell-states, encompassing cell-potency and expression subtypes, to facilitate the identification of progenitor and stem-like cells. Application to thousands of single-cell RNA-Seq profiles from the normal mammary epithelium reveals a rare 5% subpopulation of highly potent single-cells. The integrated landscape naturally predicts that these cells define a bi-potent-like state, a result not obtainable via standard methods or without invoking prior assumptions. The bi-potent-like cells are overrepresented within the basal compartment but also overlap with an immature luminal phenotype. We characterize the transcriptome of these cells and show that is enriched for a mammary stem-cell module. We further identify YBX1, a regulator of breast cancer risk identified from GWAS, as the key transcription factor defining this candidate bi-potent cellular phenotype. We validate the putative bi-potency of YBX1-marked cells using independent FACS-sorted bulk expression data. In addition, YBX1 is overexpressed in basal breast cancer and correlates with clinical outcome. In summary, we here provide a novel computational framework which may serve to identify and prioritize candidate normal or cancer progenitor/stem-like single-cell phenotypes, for subsequent functional studies.

bioinformatics↗