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Article ; Online: Targeting tumor-stromal interactions in triple-negative breast cancer using a human vascularized micro-tumor model.

Hachey, Stephanie J / Hatch, Christopher J / Gaebler, Daniela / Mocherla, Aneela / Nee, Kevin / Kessenbrock, Kai / Hughes, Christopher C W

Breast cancer research : BCR

2024 Volume 26, Issue 1, Page(s) 5

Abstract: 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 ... ...

Abstract	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, 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 showed efficacy against TNBC. These data demonstrate the potential of inducing a favorable TME as a targeted therapeutic approach in TNBC.
MeSH term(s)	Humans ; Triple Negative Breast Neoplasms/drug therapy ; Triple Negative Breast Neoplasms/genetics ; Breast ; Paclitaxel ; Signal Transduction ; Stromal Cells ; Tumor Microenvironment/genetics
Chemical Substances	Paclitaxel (P88XT4IS4D)
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2015059-3
ISSN	1465-542X ; 1465-5411
ISSN (online)	1465-542X
ISSN	1465-5411
DOI	10.1186/s13058-023-01760-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Author Correction: Automated segmentation and tracking of mitochondria in live-cell time-lapse images.

Lefebvre, Austin E Y T / Ma, Dennis / Kessenbrock, Kai / Lawson, Devon A / Digman, Michelle A

Nature methods

2022 Volume 19, Issue 6, Page(s) 770

Language	English
Publishing date	2022-04-29
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-022-01506-2
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Article ; Online: scEpiLock: A Weakly Supervised Learning Framework for

Gong, Yanwen / Srinivasan, Shushrruth Sai / Zhang, Ruiyi / Kessenbrock, Kai / Zhang, Jing

Biomolecules

2022 Volume 12, Issue 7

Abstract: Recent advances in single-cell transposase-accessible chromatin using a sequencing assay (scATAC-seq) allow cellular heterogeneity dissection and regulatory landscape reconstruction with an unprecedented resolution. However, compared to bulk-sequencing, ... ...

Abstract	Recent advances in single-cell transposase-accessible chromatin using a sequencing assay (scATAC-seq) allow cellular heterogeneity dissection and regulatory landscape reconstruction with an unprecedented resolution. However, compared to bulk-sequencing, its ultra-high missingness remarkably reduces usable reads in each cell type, resulting in broader, fuzzier peak boundary definitions and limiting our ability to pinpoint functional regions and interpret variant impacts precisely. We propose a weakly supervised learning method, scEpiLock, to directly identify core functional regions from coarse peak labels and quantify variant impacts in a cell-type-specific manner. First, scEpiLock uses a multi-label classifier to predict chromatin accessibility via a deep convolutional neural network. Then, its weakly supervised object detection module further refines the peak boundary definition using gradient-weighted class activation mapping (Grad-CAM). Finally, scEpiLock provides cell-type-specific variant impacts within a given peak region. We applied scEpiLock to various scATAC-seq datasets and found that it achieves an area under receiver operating characteristic curve (AUC) of ~0.9 and an area under precision recall (AUPR) above 0.7. Besides, scEpiLock's object detection condenses coarse peaks to only ⅓ of their original size while still reporting higher conservation scores. In addition, we applied scEpiLock on brain scATAC-seq data and reported several genome-wide association studies (GWAS) variants disrupting regulatory elements around known risk genes for Alzheimer's disease, demonstrating its potential to provide cell-type-specific biological insights in disease studies.
MeSH term(s)	Chromatin/genetics ; Epigenesis, Genetic ; Epigenomics ; Genome-Wide Association Study ; Supervised Machine Learning
Chemical Substances	Chromatin
Language	English
Publishing date	2022-06-23
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12070874
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Article ; Online: Presentation of Human Neural Stem Cell Antigens Drives Regulatory T Cell Induction.

Greilach, Scott A / McIntyre, Laura L / Nguyen, Quy H / Silva, Jorge / Kessenbrock, Kai / Lane, Thomas E / Walsh, Craig M

Journal of immunology (Baltimore, Md. : 1950)

2023 Volume 210, Issue 11, Page(s) 1677–1686

Abstract: Transplantation of human neural stem cells (hNSCs) is a promising regenerative therapy to promote remyelination in patients with multiple sclerosis (MS). Transplantation of hNSCs has been shown to increase the number of CD4+CD25+Foxp3+ T regulatory cells ...

Abstract	Transplantation of human neural stem cells (hNSCs) is a promising regenerative therapy to promote remyelination in patients with multiple sclerosis (MS). Transplantation of hNSCs has been shown to increase the number of CD4+CD25+Foxp3+ T regulatory cells (Tregs) in the spinal cords of murine models of MS, which is correlated with a strong localized remyelination response. However, the mechanisms by which hNSC transplantation leads to an increase in Tregs in the CNS remains unclear. We report that hNSCs drive the conversion of T conventional (Tconv) cells into Tregs in vitro. Conversion of Tconv cells is Ag driven and fails to occur in the absence of TCR stimulation by cognate antigenic self-peptides. Furthermore, CNS Ags are sufficient to drive this conversion in the absence of hNSCs in vitro and in vivo. Importantly, only Ags presented in the thymus during T cell selection drive this Treg response. In this study, we investigate the mechanisms by which hNSC Ags drive the conversion of Tconv cells into Tregs and may provide key insight needed for the development of MS therapies.
MeSH term(s)	Humans ; Mice ; Animals ; T-Lymphocytes, Regulatory ; CD4-Positive T-Lymphocytes ; Multiple Sclerosis/therapy ; Lymphocyte Activation ; Neural Stem Cells ; Forkhead Transcription Factors ; CD4 Antigens
Chemical Substances	Forkhead Transcription Factors ; CD4 Antigens
Language	English
Publishing date	2023-06-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.2200798
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Ud II Zs.37: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Single-Cell Transcriptome Analysis Workflow for Splenic Myeloid-Derived Suppressor Cells from Murine Breast Cancer Models.

Alshetaiwi, Hamad / Pervolarakis, Nicholas / Nguyen, Quy H / Kessenbrock, Kai

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2236, Page(s) 177–187

Abstract: Single-cell transcriptomics is a powerful tool to study previously unrealized cellular heterogeneity at the resolution of individual cells. Most of the previous knowledge in cell biology is based on data generated by bulk analysis methods, which provide ... ...

Abstract	Single-cell transcriptomics is a powerful tool to study previously unrealized cellular heterogeneity at the resolution of individual cells. Most of the previous knowledge in cell biology is based on data generated by bulk analysis methods, which provide averaged readouts that usually mask cellular heterogeneity. This approach is challenging when the biological effect of interest is limited to a subpopulation within a cell type. This may particularly apply immune cell populations as these cells are highly mobile and swiftly respond to changes in cytokines or chemokines. For example, in cancer certain subset of myeloid immune cells may acquire immunosuppressive features to suppress antitumor immune responses, and thus described as myeloid-derived suppressor cells (MDSCs). Advances in single-cell RNA sequencing (scRNAseq) allowed scientists to overcome this limitation and enable in-depth interrogation of these subsets of immune cells including MDSCs. Here, we provide a detailed protocol for using scRNAseq to explore MDSCs in the context of splenic myeloid cells from breast tumor-bearing mice in comparison to wildtype controls to define the unique molecular features of immunosuppressive myeloid cells.
MeSH term(s)	Animals ; Computational Biology ; Female ; Gene Expression Profiling/methods ; Mammary Neoplasms, Animal/pathology ; Mice, Transgenic ; Myeloid-Derived Suppressor Cells/metabolism ; Quality Control ; Reproducibility of Results ; Single-Cell Analysis/methods ; Spleen/pathology ; Workflow
Language	English
Publishing date	2020-11-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1060-2_14
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Automated segmentation and tracking of mitochondria in live-cell time-lapse images.

Lefebvre, Austin E Y T / Ma, Dennis / Kessenbrock, Kai / Lawson, Devon A / Digman, Michelle A

Nature methods

2021 Volume 18, Issue 9, Page(s) 1091–1102

Abstract: Mitochondria display complex morphology and movements, which complicates their segmentation and tracking in time-lapse images. Here, we introduce Mitometer, an algorithm for fast, unbiased, and automated segmentation and tracking of mitochondria in live- ... ...

Abstract	Mitochondria display complex morphology and movements, which complicates their segmentation and tracking in time-lapse images. Here, we introduce Mitometer, an algorithm for fast, unbiased, and automated segmentation and tracking of mitochondria in live-cell two-dimensional and three-dimensional time-lapse images. Mitometer requires only the pixel size and the time between frames to identify mitochondrial motion and morphology, including fusion and fission events. The segmentation algorithm isolates individual mitochondria via a shape- and size-preserving background removal process. The tracking algorithm links mitochondria via differences in morphological features and displacement, followed by a gap-closing scheme. Using Mitometer, we show that mitochondria of triple-negative breast cancer cells are faster, more directional, and more elongated than those in their receptor-positive counterparts. Furthermore, we show that mitochondrial motility and morphology in breast cancer, but not in normal breast epithelia, correlate with metabolic activity. Mitometer is an unbiased and user-friendly tool that will help resolve fundamental questions regarding mitochondrial form and function.
MeSH term(s)	Algorithms ; Breast Neoplasms/metabolism ; Breast Neoplasms/pathology ; Cells, Cultured ; Female ; Humans ; Imaging, Three-Dimensional/methods ; Mammary Glands, Human/cytology ; Mitochondria/metabolism ; NAD/metabolism ; Reproducibility of Results ; Software ; Time-Lapse Imaging/methods ; Triple Negative Breast Neoplasms/pathology
Chemical Substances	NAD (0U46U6E8UK)
Language	English
Publishing date	2021-08-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-021-01234-z
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Zs.A 6022: Show issues

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Article ; Online: Microfluidic platform accelerates tissue processing into single cells for molecular analysis and primary culture models.

Lombardo, Jeremy A / Aliaghaei, Marzieh / Nguyen, Quy H / Kessenbrock, Kai / Haun, Jered B

Nature communications

2021 Volume 12, Issue 1, Page(s) 2858

Abstract: Tissues are complex mixtures of different cell subtypes, and this diversity is increasingly characterized using high-throughput single cell analysis methods. However, these efforts are hindered, as tissues must first be dissociated into single cell ... ...

Abstract	Tissues are complex mixtures of different cell subtypes, and this diversity is increasingly characterized using high-throughput single cell analysis methods. However, these efforts are hindered, as tissues must first be dissociated into single cell suspensions using methods that are often inefficient, labor-intensive, highly variable, and potentially biased towards certain cell subtypes. Here, we present a microfluidic platform consisting of three tissue processing technologies that combine tissue digestion, disaggregation, and filtration. The platform is evaluated using a diverse array of tissues. For kidney and mammary tumor, microfluidic processing produces 2.5-fold more single cells. Single cell RNA sequencing further reveals that endothelial cells, fibroblasts, and basal epithelium are enriched without affecting stress response. For liver and heart, processing time is dramatically reduced. We also demonstrate that recovery of cells from the system at periodic intervals during processing increases hepatocyte and cardiomyocyte numbers, as well as increases reproducibility from batch-to-batch for all tissues.
MeSH term(s)	Animals ; Cell Count ; Endothelial Cells/cytology ; Endothelial Cells/metabolism ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Hepatocytes/cytology ; Hepatocytes/metabolism ; Humans ; Kidney/cytology ; Kidney/metabolism ; Liver/cytology ; Liver/metabolism ; MCF-7 Cells ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Microfluidic Analytical Techniques/instrumentation ; Microfluidic Analytical Techniques/methods ; Myocardium/cytology ; Myocardium/metabolism ; Myocytes, Cardiac/cytology ; Myocytes, Cardiac/metabolism ; Reproducibility of Results ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Mice
Language	English
Publishing date	2021-05-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-23238-1
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Article ; Online: Let-7f miRNA regulates SDF-1α- and hypoxia-promoted migration of mesenchymal stem cells and attenuates mammary tumor growth upon exosomal release.

Egea, Virginia / Kessenbrock, Kai / Lawson, Devon / Bartelt, Alexander / Weber, Christian / Ries, Christian

Cell death & disease

2021 Volume 12, Issue 6, Page(s) 516

Abstract: Bone marrow-derived human mesenchymal stem cells (hMSCs) are recruited to damaged or inflamed tissues where they contribute to tissue repair. This multi-step process involves chemokine-directed invasion of hMSCs and on-site release of factors that ... ...

Abstract	Bone marrow-derived human mesenchymal stem cells (hMSCs) are recruited to damaged or inflamed tissues where they contribute to tissue repair. This multi-step process involves chemokine-directed invasion of hMSCs and on-site release of factors that influence target cells or tumor tissues. However, the underlying molecular mechanisms are largely unclear. Previously, we described that microRNA let-7f controls hMSC differentiation. Here, we investigated the role of let-7f in chemotactic invasion and paracrine anti-tumor effects. Incubation with stromal cell-derived factor-1α (SDF-1α) or inflammatory cytokines upregulated let-7f expression in hMSCs. Transfection of hMSCs with let-7f mimics enhanced CXCR4-dependent invasion by augmentation of pericellular proteolysis and release of matrix metalloproteinase-9. Hypoxia-induced stabilization of the hypoxia-inducible factor 1 alpha in hMSCs promoted cell invasion via let-7f and activation of autophagy. Dependent on its endogenous level, let-7f facilitated hMSC motility and invasion through regulation of the autophagic flux in these cells. In addition, secreted let-7f encapsulated in exosomes was increased upon upregulation of endogenous let-7f by treatment of the cells with SDF-1α, hypoxia, or induction of autophagy. In recipient 4T1 tumor cells, hMSC-derived exosomal let-7f attenuated proliferation and invasion. Moreover, implantation of 3D spheroids composed of hMSCs and 4T1 cells into a breast cancer mouse model demonstrated that hMSCs overexpressing let-7f inhibited tumor growth in vivo. Our findings provide evidence that let-7f is pivotal in the regulation of hMSC invasion in response to inflammation and hypoxia, suggesting that exosomal let-7f exhibits paracrine anti-tumor effects.
MeSH term(s)	Animals ; Cell Communication/physiology ; Cell Differentiation/physiology ; Cell Proliferation/physiology ; Chemokine CXCL12/metabolism ; Disease Models, Animal ; Female ; Humans ; Mammary Neoplasms, Experimental/genetics ; Mammary Neoplasms, Experimental/metabolism ; Mammary Neoplasms, Experimental/pathology ; Mesenchymal Stem Cells/metabolism ; Mesenchymal Stem Cells/pathology ; Mice ; Mice, Inbred BALB C ; MicroRNAs/biosynthesis ; MicroRNAs/genetics ; Transfection ; Tumor Hypoxia/physiology
Chemical Substances	Chemokine CXCL12 ; MicroRNAs ; mirnlet7 microRNA, human ; mirnlet7 microRNA, mouse
Language	English
Publishing date	2021-05-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2541626-1
ISSN	2041-4889 ; 2041-4889
ISSN (online)	2041-4889
ISSN	2041-4889
DOI	10.1038/s41419-021-03789-3
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Article ; Online: Wound healing in aged skin exhibits systems-level alterations in cellular composition and cell-cell communication.

Vu, Remy / Jin, Suoqin / Sun, Peng / Haensel, Daniel / Nguyen, Quy Hoa / Dragan, Morgan / Kessenbrock, Kai / Nie, Qing / Dai, Xing

Cell reports

2022 Volume 40, Issue 5, Page(s) 111155

Abstract: Delayed and often impaired wound healing in the elderly presents major medical and socioeconomic challenges. A comprehensive understanding of the cellular/molecular changes that shape complex cell-cell communications in aged skin wounds is lacking. Here, ...

Abstract	Delayed and often impaired wound healing in the elderly presents major medical and socioeconomic challenges. A comprehensive understanding of the cellular/molecular changes that shape complex cell-cell communications in aged skin wounds is lacking. Here, we use single-cell RNA sequencing to define the epithelial, fibroblast, immune cell types, and encompassing heterogeneities in young and aged skin during homeostasis and identify major changes in cell compositions, kinetics, and molecular profiles during wound healing. Our comparative study uncovers a more pronounced inflammatory phenotype in aged skin wounds, featuring neutrophil persistence and higher abundance of an inflammatory/glycolytic Arg1
MeSH term(s)	Cell Communication ; Fibroblasts/metabolism ; Macrophages/metabolism ; Signal Transduction ; Skin ; Wound Healing
Language	English
Publishing date	2022-08-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111155
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Article: Unraveling Heterogeneity in Epithelial Cell Fates of the Mammary Gland and Breast Cancer.

Samocha, Alexandr / Doh, Hanna / Kessenbrock, Kai / Roose, Jeroen P

Cancers

2019 Volume 11, Issue 10

Abstract: Fluidity in cell fate or heterogeneity in cell identity is an interesting cell biological phenomenon, which at the same time poses a significant obstacle for cancer therapy. The mammary gland seems a relatively straightforward organ with stromal cells ... ...

Abstract	Fluidity in cell fate or heterogeneity in cell identity is an interesting cell biological phenomenon, which at the same time poses a significant obstacle for cancer therapy. The mammary gland seems a relatively straightforward organ with stromal cells and basal- and luminal- epithelial cell types. In reality, the epithelial cell fates are much more complex and heterogeneous, which is the topic of this review. Part of the complexity comes from the dynamic nature of this organ: the primitive epithelial tree undergoes extensively remodeling and expansion during puberty, pregnancy, and lactation and, unlike most other organs, the bulk of mammary gland development occurs late, during puberty. An active cell biological debate has focused on lineage commitment to basal- and luminal- epithelial cell fates by epithelial progenitor and stem cells; processes that are also relevant to cancer biology. In this review, we discuss the current understanding of heterogeneity in mammary gland and recent insights obtained through lineage tracing, signaling assays, and organoid cultures. Lastly, we relate these insights to cancer and ongoing efforts to resolve heterogeneity in breast cancer with single-cell RNAseq approaches.
Language	English
Publishing date	2019-09-24
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers11101423
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