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Mérignac-Lacombe J, Kornbausch N, Sivarajan R, Boichot V, Berg K, Oberwinkler H, Saliba AE, Loos HM, Ehret Kasemo T, Scherzad A, Bodem J, Buettner A, Neiers F, Erhard F, Hackenberg S, Heydel JM, Steinke M. Characterization of a Human Respiratory Mucosa Model to Study Odorant Metabolism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12696-12706. [PMID: 38775624 DOI: 10.1021/acs.jafc.4c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Nasal xenobiotic metabolizing enzymes (XMEs) are important for the sense of smell because they influence odorant availability and quality. Since the major part of the human nasal cavity is lined by a respiratory mucosa, we hypothesized that this tissue contributed to nasal odorant metabolism through XME activity. Thus, we built human respiratory tissue models and characterized the XME profiles using single-cell RNA sequencing. We focused on the XMEs dicarbonyl and l-xylulose reductase, aldehyde dehydrogenase (ALDH) 1A1, and ALDH3A1, which play a role in food odorant metabolism. We demonstrated protein abundance and localization in the tissue models and showed the metabolic activity of the corresponding enzyme families by exposing the models to the odorants 3,4-hexandione and benzaldehyde. Using gas chromatography coupled with mass spectrometry, we observed, for example, a significantly higher formation of the corresponding metabolites 4-hydroxy-3-hexanone (39.03 ± 1.5%, p = 0.0022), benzyl alcohol (10.05 ± 0.88%, p = 0.0008), and benzoic acid (8.49 ± 0.57%, p = 0.0004) in odorant-treated tissue models compared to untreated controls (0 ± 0, 0.12 ± 0.12, and 0.18 ± 0.18%, respectively). This is the first study that reveals the XME profile of tissue-engineered human respiratory mucosa models and demonstrates their suitability to study nasal odorant metabolism.
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Affiliation(s)
- Jeanne Mérignac-Lacombe
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, 9 E bd Jeanne d'Arc, 21000 Dijon, France
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Nicole Kornbausch
- Chair of Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 9, 91054 Erlangen, Germany
| | - Rinu Sivarajan
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Valentin Boichot
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, 9 E bd Jeanne d'Arc, 21000 Dijon, France
| | - Kevin Berg
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstraße 4, 93053 Regensburg, Germany
| | - Heike Oberwinkler
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research (HZI), Josef-Schneider-Straße 2, 97080 Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Helene M Loos
- Chair of Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 9, 91054 Erlangen, Germany
- Fraunhofer Institute for Process Engineering and Packaging IVV, Giggenhauser Str. 35, 85354 Freising, Germany
- FAU Research Center "New Bioactive Compounds", Schlossplatz 4, 91054 Erlangen, Germany
| | - Totta Ehret Kasemo
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
| | - Agmal Scherzad
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
| | - Jochen Bodem
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Andrea Buettner
- Chair of Aroma and Smell Research, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 9, 91054 Erlangen, Germany
- Fraunhofer Institute for Process Engineering and Packaging IVV, Giggenhauser Str. 35, 85354 Freising, Germany
- FAU Research Center "New Bioactive Compounds", Schlossplatz 4, 91054 Erlangen, Germany
| | - Fabrice Neiers
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, 9 E bd Jeanne d'Arc, 21000 Dijon, France
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstraße 4, 93053 Regensburg, Germany
| | - Stephan Hackenberg
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
| | - Jean-Marie Heydel
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, 9 E bd Jeanne d'Arc, 21000 Dijon, France
| | - Maria Steinke
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
- Fraunhofer Institute for Silicate Research ISC, Röntgenring 12, 97070 Würzburg, Germany
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Dai L, Fan G, Xie T, Li L, Tang L, Chen H, Shi Y, Han X. Single-cell and spatial transcriptomics reveal a high glycolysis B cell and tumor-associated macrophages cluster correlated with poor prognosis and exhausted immune microenvironment in diffuse large B-cell lymphoma. Biomark Res 2024; 12:58. [PMID: 38840205 PMCID: PMC11155084 DOI: 10.1186/s40364-024-00605-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous malignancy characterized by varied responses to treatment and prognoses. Understanding the metabolic characteristics driving DLBCL progression is crucial for developing personalized therapies. METHODS This study utilized multiple omics technologies including single-cell transcriptomics (n = 5), bulk transcriptomics (n = 966), spatial transcriptomics (n = 10), immunohistochemistry (n = 34), multiple immunofluorescence (n = 20) and to elucidate the metabolic features of highly malignant DLBCL cells and tumor-associated macrophages (TAMs), along with their associated tumor microenvironment. Metabolic pathway analysis facilitated by scMetabolism, and integrated analysis via hdWGCNA, identified glycolysis genes correlating with malignancy, and the prognostic value of glycolysis genes (STMN1, ENO1, PKM, and CDK1) and TAMs were verified. RESULTS High-glycolysis malignant DLBCL tissues exhibited an immunosuppressive microenvironment characterized by abundant IFN_TAMs (CD68+CXCL10+PD-L1+) and diminished CD8+ T cell infiltration. Glycolysis genes were positively correlated with malignancy degree. IFN_TAMs exhibited high glycolysis activity and closely communicating with high-malignancy DLBCL cells identified within datasets. The glycolysis score, evaluated by seven genes, emerged as an independent prognostic factor (HR = 1.796, 95% CI: 1.077-2.995, p = 0.025 and HR = 2.631, 95% CI: 1.207-5.735, p = 0.015) along with IFN_TAMs were positively correlated with poor survival (p < 0.05) in DLBCL. Immunohistochemical validation of glycolysis markers (STMN1, ENO1, PKM, and CDK1) and multiple immunofluorescence validation of IFN_TAMs underscored their prognostic value (p < 0.05) in DLBCL. CONCLUSIONS This study underscores the significance of glycolysis in tumor progression and modulation of the immune microenvironment. The identified glycolysis genes and IFN_TAMs represent potential prognostic markers and therapeutic targets in DLBCL.
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Affiliation(s)
- Liyuan Dai
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Guangyu Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Tongji Xie
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Lin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Le Tang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Haizhu Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Breast Tumor Centre, Department of Medical Oncology, Phase I Clinical Trial Centre, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, P. R. China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
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Bramel EE, Camejo WAE, Creamer TJ, Restrepo L, Saqib M, Bagirzadeh R, Zeng A, Mitchell JT, Stein-O’Brien GL, Pedroza AJ, Fischbein MP, Dietz HC, MacFarlane EG. Intrinsic Gata4 expression sensitizes the aortic root to dilation in a Loeys-Dietz syndrome mouse model. RESEARCH SQUARE 2024:rs.3.rs-4420617. [PMID: 38883722 PMCID: PMC11177966 DOI: 10.21203/rs.3.rs-4420617/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Loeys-Dietz syndrome (LDS) is an aneurysm disorder caused by mutations that decrease transforming growth factor-β (TGF-β) signaling. Although aneurysms develop throughout the arterial tree, the aortic root is a site of heightened risk. To identify molecular determinants of this vulnerability, we investigated the heterogeneity of vascular smooth muscle cells (VSMCs) in the aorta of Tgfbr1 M318R/+ LDS mice by single cell and spatial transcriptomics. Reduced expression of components of the extracellular matrix-receptor apparatus and upregulation of stress and inflammatory pathways were observed in all LDS VSMCs. However, regardless of genotype, a subset of Gata4-expressing VSMCs predominantly located in the aortic root intrinsically displayed a less differentiated, proinflammatory profile. A similar population was also identified among aortic VSMCs in a human scRNAseq dataset. Postnatal VSMC-specific Gata4 deletion reduced aortic root dilation in LDS mice, suggesting that this factor sensitizes the aortic root to the effects of impaired TGF-β signaling.
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Affiliation(s)
- Emily E. Bramel
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Predoctoral Training in Human Genetics and Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wendy A. Espinoza Camejo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Predoctoral Training in Human Genetics and Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tyler J. Creamer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leda Restrepo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Muzna Saqib
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rustam Bagirzadeh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anthony Zeng
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacob T. Mitchell
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Predoctoral Training in Human Genetics and Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Genevieve L. Stein-O’Brien
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Albert J. Pedroza
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Michael P. Fischbein
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Harry C. Dietz
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elena Gallo MacFarlane
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Huang R, Kratka CE, Pea J, McCann C, Nelson J, Bryan JP, Zhou LT, Russo DD, Zaniker EJ, Gandhi AH, Shalek AK, Cleary B, Farhi SL, Duncan FE, Goods BA. Single-cell and spatiotemporal profile of ovulation in the mouse ovary. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.594719. [PMID: 38826447 PMCID: PMC11142086 DOI: 10.1101/2024.05.20.594719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Ovulation is a spatiotemporally coordinated process that involves several tightly controlled events, including oocyte meiotic maturation, cumulus expansion, follicle wall rupture and repair, and ovarian stroma remodeling. To date, no studies have detailed the precise window of ovulation at single-cell resolution. Here, we performed parallel single-cell RNA-seq and spatial transcriptomics on paired mouse ovaries across an ovulation time course to map the spatiotemporal profile of ovarian cell types. We show that major ovarian cell types exhibit time-dependent transcriptional states enriched for distinct functions and have specific localization profiles within the ovary. We also identified gene markers for ovulation-dependent cell states and validated these using orthogonal methods. Finally, we performed cell-cell interaction analyses to identify ligand-receptor pairs that may drive ovulation, revealing previously unappreciated interactions. Taken together, our data provides a rich and comprehensive resource of murine ovulation that can be mined for discovery by the scientific community.
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Huo Q, Song R, Ma Z. Recent advances in exploring transcriptional regulatory landscape of crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1421503. [PMID: 38903438 PMCID: PMC11188431 DOI: 10.3389/fpls.2024.1421503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.
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Affiliation(s)
| | | | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Tran KM, Kwang N, Gomez-Arboledas A, Kawauchi S, Mar C, Chao D, Da Cunha C, Wang S, Collins S, Walker A, Shi KX, Alcantara JA, Neumann J, Tenner AJ, LaFerla FM, Hohsfield LA, Swarup V, MacGregor GR, Green KN. APOE Christchurch enhances a disease-associated microglial response to plaque but suppresses response to tau pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597211. [PMID: 38895362 PMCID: PMC11185750 DOI: 10.1101/2024.06.03.597211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background Apolipoprotein E ε4 (APOE4) is the strongest genetic risk factor for late-onset Alzheimer's disease (LOAD). A recent case report identified a rare variant in APOE, APOE3-R136S (Christchurch), proposed to confer resistance to autosomal dominant Alzheimer's Disease (AD). However, it remains unclear whether and how this variant exerts its protective effects. Methods We introduced the R136S variant into mouse Apoe (ApoeCh) and investigated its effect on the development of AD-related pathology using the 5xFAD model of amyloidosis and the PS19 model of tauopathy. We used immunohistochemical and biochemical analysis along with single-cell spatial transcriptomics and proteomics to explore the impact of the ApoeCh variant on AD pathological development and the brain's response to plaques and tau. Results In 5xFAD mice, ApoeCh enhances a Disease-Associated Microglia (DAM) phenotype in microglia surrounding plaques, and reduces plaque load, dystrophic neurites, and plasma neurofilament light chain. By contrast, in PS19 mice, ApoeCh suppresses the microglial and astrocytic responses to tau-laden neurons and does not reduce tau accumulation or phosphorylation, but partially rescues tau-induced synaptic and myelin loss. We compared how microglia responses differ between the two mouse models to elucidate the distinct DAM signatures induced by ApoeCh. We identified upregulation of antigen presentation-related genes in the DAM response in a PS19 compared to a 5xFAD background, suggesting a differential response to amyloid versus tau pathology that is modulated by the presence of ApoeCh. Conclusions These findings highlight the ability of the ApoeCh variant to modulate microglial responses based on the type of pathology, enhancing DAM reactivity in amyloid models and dampening neuroinflammation to promote protection in tau models. This suggests that the Christchurch variant's protective effects likely involve multiple mechanisms, including changes in receptor binding and microglial programming.
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Affiliation(s)
- Kristine M. Tran
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Nellie Kwang
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Angela Gomez-Arboledas
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Shimako Kawauchi
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Transgenic Mouse Facility, ULAR, Office of Research, University of California, Irvine, CA 92697, USA
| | - Cassandra Mar
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Donna Chao
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Celia Da Cunha
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Shuling Wang
- Transgenic Mouse Facility, ULAR, Office of Research, University of California, Irvine, CA 92697, USA
| | - Sherilyn Collins
- Transgenic Mouse Facility, ULAR, Office of Research, University of California, Irvine, CA 92697, USA
| | - Amber Walker
- Transgenic Mouse Facility, ULAR, Office of Research, University of California, Irvine, CA 92697, USA
| | - Kai-Xuan Shi
- Transgenic Mouse Facility, ULAR, Office of Research, University of California, Irvine, CA 92697, USA
| | - Joshua A. Alcantara
- Transgenic Mouse Facility, ULAR, Office of Research, University of California, Irvine, CA 92697, USA
| | - Jonathan Neumann
- Transgenic Mouse Facility, ULAR, Office of Research, University of California, Irvine, CA 92697, USA
| | - Andrea J. Tenner
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Frank M. LaFerla
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Lindsay A. Hohsfield
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Grant R. MacGregor
- Transgenic Mouse Facility, ULAR, Office of Research, University of California, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Kim N. Green
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
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Ye D, Walsh JT, Junker IP, Ding Y. Changes in the cellular makeup of motor patterning circuits drive courtship song evolution in Drosophila. Curr Biol 2024; 34:2319-2329.e6. [PMID: 38688283 DOI: 10.1016/j.cub.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
How evolutionary changes in genes and neurons encode species variation in complex motor behaviors is largely unknown. Here, we develop genetic tools that permit a neural circuit comparison between the model species Drosophila melanogaster and the closely related species D. yakuba, which has undergone a lineage-specific loss of sine song, one of the two major types of male courtship song in Drosophila. Neuroanatomical comparison of song-patterning neurons called TN1 across the phylogeny demonstrates a link between the loss of sine song and a reduction both in the number of TN1 neurons and the neurites supporting the sine circuit connectivity. Optogenetic activation confirms that TN1 neurons in D. yakuba have lost the ability to drive sine song, although they have maintained the ability to drive the singing wing posture. Single-cell transcriptomic comparison shows that D. yakuba specifically lacks a cell type corresponding to TN1A neurons, the TN1 subtype that is essential for sine song. Genetic and developmental manipulation reveals a functional divergence of the sex determination gene doublesex in D. yakuba to reduce TN1 number by promoting apoptosis. Our work illustrates the contribution of motor patterning circuits and cell type changes in behavioral evolution and uncovers the evolutionary lability of sex determination genes to reconfigure the cellular makeup of neural circuits.
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Affiliation(s)
- Dajia Ye
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Justin T Walsh
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian P Junker
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yun Ding
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Huynh KLA, Tyc KM, Matuck BF, Easter QT, Pratapa A, Kumar NV, Pérez P, Kulchar R, Pranzatelli T, de Souza D, Weaver TM, Qu X, Valente Soares LA, Dolhnokoff M, Kleiner DE, Hewitt SM, da Silva LFF, Rocha VG, Warner BM, Byrd KM, Liu J. Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596861. [PMID: 38895230 PMCID: PMC11185514 DOI: 10.1101/2024.05.31.596861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Identifying cell types and states remains a time-consuming and error-prone challenge for spatial biology. While deep learning is increasingly used, it is difficult to generalize due to variability at the level of cells, neighborhoods, and niches in health and disease. To address this, we developed TACIT, an unsupervised algorithm for cell annotation using predefined signatures that operates without training data, using unbiased thresholding to distinguish positive cells from background, focusing on relevant markers to identify ambiguous cells in multiomic assays. Using five datasets (5,000,000-cells; 51-cell types) from three niches (brain, intestine, gland), TACIT outperformed existing unsupervised methods in accuracy and scalability. Integration of TACIT-identified cell with a novel Shiny app revealed new phenotypes in two inflammatory gland diseases. Finally, using combined spatial transcriptomics and proteomics, we discover under- and overrepresented immune cell types and states in regions of interest, suggesting multimodality is essential for translating spatial biology to clinical applications.
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Affiliation(s)
- Khoa L. A. Huynh
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Katarzyna M. Tyc
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
- Massey Cancer Center, Richmond VA, USA
| | - Bruno F. Matuck
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
| | - Quinn T. Easter
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
| | - Aditya Pratapa
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Nikhil V. Kumar
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
| | - Paola Pérez
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Rachel Kulchar
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Pranzatelli
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Deiziane de Souza
- Department of Pathology, Medicine School of University of Sao Paulo, SP, BR
| | - Theresa M. Weaver
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
| | - Xufeng Qu
- Massey Cancer Center, Richmond VA, USA
| | | | - Marisa Dolhnokoff
- Department of Pathology, Medicine School of University of Sao Paulo, SP, BR
| | - David E. Kleiner
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Vanderson Geraldo Rocha
- Department of Hematology, Transfusion and Cell Therapy Service, University of Sao Paulo, Sao Paulo, Brazil
| | - Blake M. Warner
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Kevin M. Byrd
- Lab of Oral & Craniofacial Innovation (LOCI), Department of Innovation & Technology Research, ADA Science & Research Institute, Gaithersburg, MD, USA
- Salivary Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jinze Liu
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
- Massey Cancer Center, Richmond VA, USA
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59
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Hakobyan M, Binder H, Arakelyan A. Pan-cancer analysis of telomere maintenance mechanisms. J Biol Chem 2024; 300:107392. [PMID: 38763334 PMCID: PMC11225560 DOI: 10.1016/j.jbc.2024.107392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/28/2024] [Accepted: 05/13/2024] [Indexed: 05/21/2024] Open
Abstract
Telomeres, protective caps at chromosome ends, maintain genomic stability and control cell lifespan. Dysregulated telomere maintenance mechanisms (TMMs) are cancer hallmarks, enabling unchecked cell proliferation. We conducted a pan-cancer evaluation of TMM using RNA sequencing data from The Cancer Genome Atlas for 33 different cancer types and analyzed the activities of telomerase-dependent (TEL) and alternative lengthening of telomeres (ALT) TMM pathways in detail. To further characterize the TMM profiles, we categorized the tumors based on their ALT and TEL TMM pathway activities into five major phenotypes: ALT high TEL low, ALT low TEL low, ALT middle TEL middle, ALT high TEL high, and ALT low TEL high. These phenotypes refer to variations in telomere maintenance strategies, shedding light on the heterogeneous nature of telomere regulation in cancer. Moreover, we investigated the clinical implications of TMM phenotypes by examining their associations with clinical characteristics and patient outcomes. Specific TMM profiles were linked to specific survival patterns, emphasizing the potential of TMM profiling as a prognostic indicator and aiding in personalized cancer treatment strategies. Gene ontology analysis of the TMM phenotypes unveiled enriched biological processes associated with cell cycle regulation (both TEL and ALT), DNA replication (TEL), and chromosome dynamics (ALT) showing that telomere maintenance is tightly intertwined with cellular processes governing proliferation and genomic stability. Overall, our study provides an overview of the complexity of transcriptional regulation of telomere maintenance mechanisms in cancer.
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Affiliation(s)
- Meline Hakobyan
- Bioinformatics Group, Institute of Molecular Biology NAS RA, Yerevan, Armenia.
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany; Armenian Bioinformatics Institute, Yerevan, Armenia
| | - Arsen Arakelyan
- Bioinformatics Group, Institute of Molecular Biology NAS RA, Yerevan, Armenia
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Zheng X, Lei W, Zhang Y, Jin H, Han C, Wu F, Jia C, Zeng R, Chen Z, Zhang Y, Wang H, Liu Q, Yao Z, Yu Y, Zhou J. Neuropilin-1 high monocytes protect against neonatal inflammation. Cell Mol Immunol 2024; 21:575-588. [PMID: 38632385 PMCID: PMC11143335 DOI: 10.1038/s41423-024-01157-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Neonates are susceptible to inflammatory disorders such as necrotizing enterocolitis (NEC) due to their immature immune system. The timely appearance of regulatory immune cells in early life contributes to the control of inflammation in neonates, yet the underlying mechanisms of which remain poorly understood. In this study, we identified a subset of neonatal monocytes characterized by high levels of neuropilin-1 (Nrp1), termed Nrp1high monocytes. Compared with their Nrp1low counterparts, Nrp1high monocytes displayed potent immunosuppressive activity. Nrp1 deficiency in myeloid cells aggravated the severity of NEC, whereas adoptive transfer of Nrp1high monocytes led to remission of NEC. Mechanistic studies showed that Nrp1, by binding to its ligand Sema4a, induced intracellular p38-MAPK/mTOR signaling and activated the transcription factor KLF4. KLF4 transactivated Nos2 and enhanced the production of nitric oxide (NO), a key mediator of immunosuppression in monocytes. These findings reveal an important immunosuppressive axis in neonatal monocytes and provide a potential therapeutic strategy for treating inflammatory disorders in neonates.
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Affiliation(s)
- Xiaoqing Zheng
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
- Institute of Pediatric Health and Disease, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Department of Immunology, Hebei Medical University, Shijiazhuang, 050017, China
| | - Wen Lei
- Pediatric Immunity and Healthcare Biomedical Co., Ltd, Guangzhou, 510320, China
| | - Yongmei Zhang
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
| | - Han Jin
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Cha Han
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Fan Wu
- Institute of Pediatric Health and Disease, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Neonatology, Guangzhou Key Laboratory of Neonatal Intestinal Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Chonghong Jia
- Institute of Pediatric Health and Disease, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Neonatology, Guangzhou Key Laboratory of Neonatal Intestinal Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Ruihong Zeng
- Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Department of Immunology, Hebei Medical University, Shijiazhuang, 050017, China
| | - Zhanghua Chen
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Yuxia Zhang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Haitao Wang
- Department of oncology, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Precision Medicine for Sex Hormones and Diseases, Tianjin, 300211, China
| | - Qiang Liu
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Zhi Yao
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China
| | - Ying Yu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jie Zhou
- Tianjin Institute of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), State Key Laboratory of Experimental Hematology, Department of Immunology, Tianjin Medical University, Tianjin, 300070, China.
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61
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Zhang L, Bartosovic M. Single-cell mapping of cell-type specific chromatin architecture in the central nervous system. Curr Opin Struct Biol 2024; 86:102824. [PMID: 38723561 DOI: 10.1016/j.sbi.2024.102824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/22/2024] [Accepted: 04/08/2024] [Indexed: 05/19/2024]
Abstract
Determining how chromatin is structured in the nucleus is critical to studying its role in gene regulation. Recent advances in the analysis of single-cell chromatin architecture have considerably improved our understanding of cell-type-specific chromosome conformation and nuclear architecture. In this review, we discuss the methods used for analysis of 3D chromatin conformation, including sequencing-based methods, imaging-based techniques, and computational approaches. We further review the application of these methods in the study of the role of chromatin topology in neural development and disorders.
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Affiliation(s)
- Letian Zhang
- Department of Biochemistry and Biophysics, Svante Arrhenius väg 16C, 162 53, Stockholm, Sweden. https://twitter.com/LetianZHANG_
| | - Marek Bartosovic
- Department of Biochemistry and Biophysics, Svante Arrhenius väg 16C, 162 53, Stockholm, Sweden.
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62
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Hu H, Wang C, Tao R, Liu B, Peng D, Chen Y, Zhang W. Evidences of neurological injury caused by COVID-19 from glioma tissues and glioma organoids. CNS Neurosci Ther 2024; 30:e14822. [PMID: 38923860 PMCID: PMC11199819 DOI: 10.1111/cns.14822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION Despite the extensive neurological symptoms induced by COVID-19 and the identification of SARS-CoV-2 in post-mortem brain samples from COVID-19 patients months after death, the precise mechanisms of SARS-CoV-2 invasion into the central nervous system remain unclear due to the lack of research models. METHODS We collected glioma tissue samples from glioma patients who had a recent history of COVID-19 and examined the presence of the SARS-CoV-2 spike protein. Subsequently, spatial transcriptomic analyses were conducted on normal brain tissues, glioma tissues, and glioma tissues from glioma patients with recent COVID-19 history. Additionally, single-cell sequencing data from both glioma tissues and glioma organoids were collected and analyzed. Glioma organoids were utilized to evaluate the efficacy of potential COVID-19 blocking agents. RESULTS Glioma tissues from glioma patients with recent COVID-19 history exhibited the presence of the SARS-CoV-2 spike protein. Differences between glioma tissues from glioma patients who had a recent history of COVID-19 and healthy brain tissues primarily manifested in neuronal cells. Notably, neuronal cells within glioma tissues of COVID-19 history demonstrated heightened susceptibility to Alzheimer's disease, depression, and synaptic dysfunction, indicative of neuronal aberrations. Expressions of SARS-CoV-2 entry factors were confirmed in both glioma tissues and glioma organoids. Moreover, glioma organoids were susceptible to pseudo-SARS-CoV-2 infection and the infections could be partly blocked by the potential COVID-19 drugs. CONCLUSIONS Gliomas had inherent traits that render them susceptible to SARS-CoV-2 infection, leading to their representability of COVID-19 neurological symptoms. This established a biological foundation for the rationality and feasibility of utilization of glioma organoids as research and blocking drug testing model in SARS-CoV-2 infection within the central nervous system.
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Affiliation(s)
- Huimin Hu
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Chen Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Rui Tao
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Bohan Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Dazhao Peng
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Yankun Chen
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
| | - Wei Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Center of Brain Tumor, Beijing Institute for Brain DisordersBeijingChina
- China National Clinical Research Center for Neurological DiseasesBeijingChina
- Chinese Glioma Genome Atlas Network (CGGA)BeijingChina
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63
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Quek YJ, Tay A. Nanoscale Methods for Longitudinal Extraction of Intracellular Contents. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2314184. [PMID: 38459829 DOI: 10.1002/adma.202314184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Longitudinal analysis of intracellular contents including gene and protein expression is crucial for deciphering the fundamentally dynamic nature of cells. This offers invaluable insights into complex tissue composition and behavior, and drives progress in disease diagnosis, biomarker discovery, and drug development. Traditional longitudinal analysis workflows, involving the destruction of cells at various timepoints, limit insights to singular moments and fail to account for cellular heterogeneity. Current non-destructive approaches, like temporal modeling with single-cell ribonucleic acid sequencing (RNA-seq) and live-cell fluorescence imaging, either rely on biological assumptions or possess the risk of cellular perturbation. Recent advances in nanoscale technologies for non-destructive intracellular content extraction offer a promising solution to these challenges. These novel methods work at the nanoscale to non-destructively access cellular membranes and can be broadly classified into three mechanisms: tip-facilitated aspiration, membrane-based, and probe-based methods. This perspective focuses on these emerging nanotechnologies for repeated intracellular content extraction. Their potential in longitudinal analysis is discussed, the critical requirements for effective repeated sampling are addressed, and the suitability of each technique for various applications is explored. Furthermore, unresolved challenges in repeated sampling are highlighted to encourage further research in this growing field.
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Affiliation(s)
- Ying Jie Quek
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, 138648, Singapore
| | - Andy Tay
- Department of Biomedical Engineering, National University of Singapore, Singapore, 117583, Singapore
- Institute for Health Innovation & Technology, National University of Singapore, Singapore, 117599, Singapore
- Tissue Engineering Programme, National University of Singapore, Singapore, 117510, Singapore
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64
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Parrish AG, Arora S, Thirimanne HN, Rudoy D, Schmid S, Sievers P, Sahm F, Holland EC, Szulzewsky F. Aggressive high-grade NF2 mutant meningiomas downregulate oncogenic YAP signaling via the upregulation of VGLL4 and FAT3/4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596719. [PMID: 38854109 PMCID: PMC11160807 DOI: 10.1101/2024.05.30.596719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Meningiomas are the most common primary brain tumors in adults. Although generally benign, a subset of meningiomas is of higher grade, shows aggressive growth behavior and recurs even after multiple surgeries. Around half of all meningiomas harbor inactivating mutations in NF2. While benign low-grade NF2 mutant meningiomas exhibit few genetic events in addition to NF2 inactivation, aggressive high-grade NF2 mutant meningiomas frequently harbor a highly aberrant genome. We and others have previously shown that NF2 inactivation leads to YAP1 activation and that YAP1 acts as the pivotal oncogenic driver in benign NF2 mutant meningiomas. Using bulk and single-cell RNA-Seq data from a large cohort of human meningiomas, we show that aggressive NF2 mutant meningiomas harbor decreased levels YAP1 activity compared to their benign counterparts. Decreased expression levels of YAP target genes are significantly associated with an increased risk of recurrence. We then identify the increased expression of the YAP1 competitor VGLL4 as well as the YAP1 upstream regulators FAT3/4 as a potential mechanism for the downregulation of YAP activity in aggressive NF2 mutant meningiomas. High expression of these genes is significantly associated with an increased risk of recurrence. In vitro, overexpression of VGLL4 resulted in the downregulation of YAP activity in benign NF2 mutant meningioma cells, confirming the direct link between VGLL4 expression and decreased levels of YAP activity observed in aggressive NF2 mutant meningiomas. Our results shed new insight on the biology of benign and aggressive NF2 mutant meningiomas and may have important implications for the efficacy of therapies targeting oncogenic YAP1 activity in NF2 mutant meningiomas.
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Affiliation(s)
- Abigail G Parrish
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Dmytro Rudoy
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sebastian Schmid
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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Guo N, Vargas J, Reynoso S, Fritz D, Krishna R, Wang C, Zhang F. Uncover spatially informed variations for single-cell spatial transcriptomics with STew. BIOINFORMATICS ADVANCES 2024; 4:vbae064. [PMID: 38827413 PMCID: PMC11142628 DOI: 10.1093/bioadv/vbae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/06/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024]
Abstract
Motivation The recent spatial transcriptomics (ST) technologies have enabled characterization of gene expression patterns and spatial information, advancing our understanding of cell lineages within diseased tissues. Several analytical approaches have been proposed for ST data, but effectively utilizing spatial information to unveil the shared variation with gene expression remains a challenge. Results We introduce STew, a Spatial Transcriptomic multi-viEW representation learning method, to jointly analyze spatial information and gene expression in a scalable manner, followed by a data-driven statistical framework to measure the goodness of model fit. Through benchmarking using human dorsolateral prefrontal cortex and mouse main olfactory bulb data with true manual annotations, STew achieved superior performance in both clustering accuracy and continuity of identified spatial domains compared with other methods. STew is also robust to generate consistent results insensitive to model parameters, including sparsity constraints. We next applied STew to various ST data acquired from 10× Visium, Slide-seqV2, and 10× Xenium, encompassing single-cell and multi-cellular resolution ST technologies, which revealed spatially informed cell type clusters and biologically meaningful axes. In particular, we identified a proinflammatory fibroblast spatial niche using ST data from psoriatic skins. Moreover, STew scales almost linearly with the number of spatial locations, guaranteeing its applicability to datasets with thousands of spatial locations to capture disease-relevant niches in complex tissues. Availability and implementation Source code and the R software tool STew are available from github.com/fanzhanglab/STew.
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Affiliation(s)
- Nanxi Guo
- Biostatistics and Informatics PhD Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
- Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Juan Vargas
- Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
- MPH Biostatistics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Samantha Reynoso
- Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
- Computational Bioscience PhD Program, University of Colorado School of Medicine, Aurora, CO 80045, United States
| | - Douglas Fritz
- Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Revanth Krishna
- Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Chuangqi Wang
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Fan Zhang
- Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
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Nirmal AJ, Sorger PK. SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. JOURNAL OF OPEN SOURCE SOFTWARE 2024; 9:6604. [PMID: 38873023 PMCID: PMC11173324 DOI: 10.21105/joss.06604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors ("Catching up with Multiplexed Tissue Imaging," 2022). A critical aspect of such "tissue profiling" is quantifying the spatial relationships among cells at different scales from the interaction of neighboring cells to recurrent communities of cells of multiple types. This often involves statistical analysis of 107 or more cells in which up to 100 biomolecules (commonly proteins) have been measured. While software tools currently cater to the analysis of spatial transcriptomics data (Liu et al., 2022), there remains a need for toolkits explicitly tailored to the complexities of multiplexed imaging data including the need to seamlessly integrate image visualization with data analysis and exploration. We introduce SCIMAP, a Python package specifically crafted to address these challenges. With SCIMAP, users can efficiently preprocess, analyze, and visualize large datasets, facilitating the exploration of spatial relationships and their statistical significance. SCIMAP's modular design enables the integration of new algorithms, enhancing its capabilities for spatial analysis.
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Affiliation(s)
- Ajit J Nirmal
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, United States of America
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Peter K Sorger
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, United States of America
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, United States of America
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Edner NM, Houghton LP, Ntavli E, Rees-Spear C, Petersone L, Wang C, Fabri A, Elfaki Y, Rueda Gonzalez A, Brown R, Kisand K, Peterson P, McCoy LE, Walker LSK. TIGIT +Tfh show poor B-helper function and negatively correlate with SARS-CoV-2 antibody titre. Front Immunol 2024; 15:1395684. [PMID: 38868776 PMCID: PMC11167088 DOI: 10.3389/fimmu.2024.1395684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/15/2024] [Indexed: 06/14/2024] Open
Abstract
Circulating follicular helper T cells (cTfh) can show phenotypic alterations in disease settings, including in the context of tissue-damaging autoimmune or anti-viral responses. Using severe COVID-19 as a paradigm of immune dysregulation, we have explored how cTfh phenotype relates to the titre and quality of antibody responses. Severe disease was associated with higher titres of neutralising S1 IgG and evidence of increased T cell activation. ICOS, CD38 and HLA-DR expressing cTfh correlated with serum S1 IgG titres and neutralising strength, and interestingly expression of TIGIT by cTfh showed a negative correlation. TIGIT+cTfh expressed increased IFNγ and decreased IL-17 compared to their TIGIT-cTfh counterparts, and showed reduced capacity to help B cells in vitro. Additionally, TIGIT+cTfh expressed lower levels of CD40L than TIGIT-cTfh, providing a potential explanation for their poor B-helper function. These data identify phenotypic changes in polyclonal cTfh that correlate with specific antibody responses and reveal TIGIT as a marker of cTfh with altered function.
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Affiliation(s)
- Natalie M. Edner
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Luke P. Houghton
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Elisavet Ntavli
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Chloe Rees-Spear
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Lina Petersone
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Chunjing Wang
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Astrid Fabri
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Yassin Elfaki
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Andrea Rueda Gonzalez
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Rachel Brown
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
- Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Laura E. McCoy
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Lucy S. K. Walker
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
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68
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Chen C, Lee S, Zyner KG, Fernando M, Nemeruck V, Wong E, Marshall LL, Wark JR, Aryamanesh N, Tam PPL, Graham ME, Gonzalez-Cordero A, Yang P. Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation. Cell Rep 2024; 43:114219. [PMID: 38748874 DOI: 10.1016/j.celrep.2024.114219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Defining the molecular networks orchestrating human brain formation is crucial for understanding neurodevelopment and neurological disorders. Challenges in acquiring early brain tissue have incentivized the use of three-dimensional human pluripotent stem cell (hPSC)-derived neural organoids to recapitulate neurodevelopment. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the exit of pluripotency and neural differentiation toward human cerebral organoids (hCOs). These data reveal key phospho-signaling events and their convergence on transcriptional factors to regulate hCO formation. Comparative analysis with developing human and mouse embryos demonstrates the fidelity of our hCOs in modeling embryonic brain development. Finally, we demonstrate that biochemical modulation of AKT signaling can control hCO differentiation. Together, our data provide a comprehensive resource to study molecular controls in human embryonic brain development and provide a guide for the future development of hCO differentiation protocols.
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Affiliation(s)
- Carissa Chen
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Scott Lee
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Katherine G Zyner
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Nemeruck
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Emilie Wong
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Lee L Marshall
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jesse R Wark
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark E Graham
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Pengyi Yang
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
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69
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Torres A, Michea MA, Végvári Á, Arce M, Pérez V, Alcota M, Morales A, Vernal R, Budini M, Zubarev RA, González FE. A multi-platform analysis of human gingival crevicular fluid reveals ferroptosis as a relevant regulated cell death mechanism during the clinical progression of periodontitis. Int J Oral Sci 2024; 16:43. [PMID: 38802345 PMCID: PMC11130186 DOI: 10.1038/s41368-024-00306-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Ferroptosis is implicated in the pathogenesis of numerous chronic-inflammatory diseases, yet its association with progressive periodontitis remains unexplored. To investigate the involvement and significance of ferroptosis in periodontitis progression, we assessed sixteen periodontitis-diagnosed patients. Disease progression was clinically monitored over twelve weeks via weekly clinical evaluations and gingival crevicular fluid (GCF) collection was performed for further analyses. Clinical metrics, proteomic data, in silico methods, and bioinformatics tools were combined to identify protein profiles linked to periodontitis progression and to explore their potential connection with ferroptosis. Subsequent western blot analyses validated key findings. Finally, a single-cell RNA sequencing (scRNA-seq) dataset (GSE164241) for gingival tissues was analyzed to elucidate cellular dynamics during periodontitis progression. Periodontitis progression was identified as occurring at a faster rate than traditionally thought. GCF samples from progressing and non-progressing periodontal sites showed quantitative and qualitatively distinct proteomic profiles. In addition, specific biological processes and molecular functions during progressive periodontitis were revealed and a set of hub proteins, including SNCA, CA1, HBB, SLC4A1, and ANK1 was strongly associated with the clinical progression status of periodontitis. Moreover, we found specific proteins - drivers or suppressors - associated with ferroptosis (SNCA, FTH1, HSPB1, CD44, and GCLC), revealing the co-occurrence of this specific type of regulated cell death during the clinical progression of periodontitis. Additionally, the integration of quantitative proteomic data with scRNA-seq analysis suggested the susceptibility of fibroblasts to ferroptosis. Our analyses reveal proteins and processes linked to ferroptosis for the first time in periodontal patients, which offer new insights into the molecular mechanisms of progressive periodontal disease. These findings may lead to novel diagnostic and therapeutic strategies.
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Affiliation(s)
- Alfredo Torres
- Laboratory of Experimental Immunology & Cancer, Faculty of Dentistry, University of Chile, Santiago, Chile
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - M Angélica Michea
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Marion Arce
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Valentina Pérez
- Laboratory of Experimental Immunology & Cancer, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Marcela Alcota
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Alicia Morales
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Rolando Vernal
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile
- Periodontal Biology Laboratory, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - Mauricio Budini
- Laboratory of Cellular and Molecular Pathology, Institute for Research in Dental Sciences, Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Roman A Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fermín E González
- Laboratory of Experimental Immunology & Cancer, Faculty of Dentistry, University of Chile, Santiago, Chile.
- Department of Conservative Dentistry, Faculty of Dentistry, University of Chile, Santiago, Chile.
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70
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Onubogu U, Gatenbee CD, Prabhakaran S, Wolfe KL, Oakes B, Salatino R, Vaubel R, Szentirmai O, Anderson AR, Janiszewska M. Spatial analysis of recurrent glioblastoma reveals perivascular niche organization. JCI Insight 2024; 9:e179853. [PMID: 38805346 DOI: 10.1172/jci.insight.179853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
Tumor evolution is driven by genetic variation; however, it is the tumor microenvironment (TME) that provides the selective pressure contributing to evolution in cancer. Despite high histopathological heterogeneity within glioblastoma (GBM), the most aggressive brain tumor, the interactions between the genetically distinct GBM cells and the surrounding TME are not fully understood. To address this, we analyzed matched primary and recurrent GBM archival tumor tissues with imaging-based techniques aimed to simultaneously evaluate tumor tissues for the presence of hypoxic, angiogenic, and inflammatory niches, extracellular matrix (ECM) organization, TERT promoter mutational status, and several oncogenic amplifications on the same slide and location. We found that the relationships between genetic and TME diversity are different in primary and matched recurrent tumors. Interestingly, the texture of the ECM, identified by label-free reflectance imaging, was predictive of single-cell genetic traits present in the tissue. Moreover, reflectance of ECM revealed structured organization of the perivascular niche in recurrent GBM, enriched in immunosuppressive macrophages. Single-cell spatial transcriptomics further confirmed the presence of the niche-specific macrophage populations and identified interactions between endothelial cells, perivascular fibroblasts, and immunosuppressive macrophages. Our results underscore the importance of GBM tissue organization in tumor evolution and highlight genetic and spatial dependencies.
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Affiliation(s)
- Ugoma Onubogu
- The Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Chandler D Gatenbee
- Department of Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Sandhya Prabhakaran
- Department of Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Kelsey L Wolfe
- The Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Benjamin Oakes
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Roberto Salatino
- The Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Rachael Vaubel
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Oszkar Szentirmai
- Center for Neurological Surgery and Neuroscience, Cleveland Clinic Martin Health, Port St. Lucie, Florida, USA
| | - Alexander Ra Anderson
- Department of Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Michalina Janiszewska
- The Skaggs Graduate School of Chemical and Biological Science, The Scripps Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
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71
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Guo Q, Yuan M, Zhang L, Deng M. scPLAN: a hierarchical computational framework for single transcriptomics data annotation, integration and cell-type label refinement. Brief Bioinform 2024; 25:bbae305. [PMID: 38935069 PMCID: PMC11209730 DOI: 10.1093/bib/bbae305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/22/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
MOTIVATION In the past decade, single-cell RNA sequencing (scRNA-seq) has emerged as a pivotal method for transcriptomic profiling in biomedical research. Precise cell-type identification is crucial for subsequent analysis of single-cell data. And the integration and refinement of annotated data are essential for building comprehensive databases. However, prevailing annotation techniques often overlook the hierarchical organization of cell types, resulting in inconsistent annotations. Meanwhile, most existing integration approaches fail to integrate datasets with different annotation depths and none of them can enhance the labels of outdated data with lower annotation resolutions using more intricately annotated datasets or novel biological findings. RESULTS Here, we introduce scPLAN, a hierarchical computational framework designed for scRNA-seq data analysis. scPLAN excels in annotating unlabeled scRNA-seq data using a reference dataset structured along a hierarchical cell-type tree. It identifies potential novel cell types in a systematic, layer-by-layer manner. Additionally, scPLAN effectively integrates annotated scRNA-seq datasets with varying levels of annotation depth, ensuring consistent refinement of cell-type labels across datasets with lower resolutions. Through extensive annotation and novel cell detection experiments, scPLAN has demonstrated its efficacy. Two case studies have been conducted to showcase how scPLAN integrates datasets with diverse cell-type label resolutions and refine their cell-type labels. AVAILABILITY https://github.com/michaelGuo1204/scPLAN.
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Affiliation(s)
- Qirui Guo
- Center for Quantitative Biology, Peking University, Yiheyuan Road, 100871, Beijing, China
| | - Musu Yuan
- Center for Quantitative Biology, Peking University, Yiheyuan Road, 100871, Beijing, China
| | - Lei Zhang
- Center for Quantitative Biology, Peking University, Yiheyuan Road, 100871, Beijing, China
- Beijing International Center for Mathematical Research, Peking University, Yiheyuan Road, 100871, Beijing, China
- Center for Machine Learning Research, Peking University, Yiheyuan Road, 100871, Beijing, China
| | - Minghua Deng
- Center for Quantitative Biology, Peking University, Yiheyuan Road, 100871, Beijing, China
- School of Mathematical Sciences, Peking University, Yiheyuan Road, 100871, Beijing, China
- Center for Statistical Science, Peking University, Yiheyuan Road, 100871, Beijing, China
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72
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Becker TJ, Enkhmandakh B, Bayarsaihan D. Single-cell RNA analysis of chromodomain-encoding genes in mesenchymal stromal cells of the mouse dental pulp. J Cell Biochem 2024. [PMID: 38779967 DOI: 10.1002/jcb.30608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
The chromodomain helicase DNA-binding (CHD) and chromobox (CBX) families of proteins play crucial roles in cell fate decisions, differentiation, and cell proliferation in a broad variety of tissues and cell types. CHD proteins are ATP-dependent epigenetic enzymes actively engaged in transcriptional regulation, DNA replication, and DNA damage repair, whereas CBX proteins are transcriptional repressors mainly involved in the formation of heterochromatin. The pleiotropic effects of CHD and CBX proteins are largely dependent on their versatility to interact with other key components of the epigenetic and transcriptional machinery. Although the function and regulatory modes of CHD and CBX factors are well established in many cell types, little is known about their roles during osteogenic differentiation. A single-cell RNA-sequencing analysis of the mouse incisor dental pulp revealed distinct spatiotemporal expression patterns of CHD- and CBX-encoding genes within different clusters of mesenchymal stromal cells (MSCs) representing various stages of osteogenic differentiation. Additionally, genes encoding interaction partners of CHD and CBX proteins, such as subunits of the trithorax-COMPASS and polycomb chromatin remodeling complexes, exhibited differential co-expression behaviors within MSC subpopulations. Thus, CHD- and CBX-encoding genes show partially overlapping but distinct expression patterns in MSCs, suggesting their differential roles in osteogenic cell fate decisions.
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Affiliation(s)
- Timothy James Becker
- Department of Computer Science, Connecticut College, New London, Connecticut, USA
| | - Badam Enkhmandakh
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Dashzeveg Bayarsaihan
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, Connecticut, USA
- Institute for System Genomics, University of Connecticut, Storrs, Connecticut, USA
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73
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Glass DR, Mayer-Blackwell K, Ramchurren N, Parks KR, Duran GE, Wright AK, Bastidas Torres AN, Islas L, Kim YH, Fling SP, Khodadoust MS, Newell EW. Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma. Cell Rep Med 2024; 5:101527. [PMID: 38670099 PMCID: PMC11148639 DOI: 10.1016/j.xcrm.2024.101527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/17/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
Cutaneous T cell lymphomas (CTCLs) are skin cancers with poor survival rates and limited treatments. While immunotherapies have shown some efficacy, the immunological consequences of administering immune-activating agents to CTCL patients have not been systematically characterized. We apply a suite of high-dimensional technologies to investigate the local, cellular, and systemic responses in CTCL patients receiving either mono- or combination anti-PD-1 plus interferon-gamma (IFN-γ) therapy. Neoplastic T cells display no evidence of activation after immunotherapy. IFN-γ induces muted endogenous immunological responses, while anti-PD-1 elicits broader changes, including increased abundance of CLA+CD39+ T cells. We develop an unbiased multi-omic profiling approach enabling discovery of immune modules stratifying patients. We identify an enrichment of activated regulatory CLA+CD39+ T cells in non-responders and activated cytotoxic CLA+CD39+ T cells in leukemic patients. Our results provide insights into the effects of immunotherapy in CTCL patients and a generalizable framework for multi-omic analysis of clinical trials.
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Affiliation(s)
- David R Glass
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nirasha Ramchurren
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - K Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - George E Duran
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna K Wright
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Laura Islas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Youn H Kim
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven P Fling
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Michael S Khodadoust
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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74
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Xia G, Zhu S, Liu Y, Pan J, Wang X, Shen C, Du A, Xu C. Transcriptomic profiling and regulatory pathways of cardiac resident macrophages in aging. Cell Mol Life Sci 2024; 81:220. [PMID: 38763956 PMCID: PMC11102896 DOI: 10.1007/s00018-024-05235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/21/2024]
Abstract
Cardiovascular diseases are an array of age-related disorders, and accumulating evidence suggests a link between cardiac resident macrophages (CRMs) and the age-related disorders. However, how does CRMs alter with aging remains elusive. In the present study, aged mice (20 months old) have been employed to check for their cardiac structural and functional alterations, and the changes in the proportion of CRM subsets as well, followed by sorting of CRMs, including C-C Motif Chemokine Receptor 2 (CCR2)+ and CCR2- CRMs, which were subjected to Smart-Seq. Integrated analysis of the Smart-Seq data with three publicly available single-cell RNA-seq datasets revealed that inflammatory genes were drastic upregulated for both CCR2+ and CCR2- CRMs with aging, but genes germane to wound healing were downregulated for CCR2- CRMs, suggesting the differential functions of these two subsets. More importantly, inflammatory genes involved in damage sensing, complement cascades, and phagocytosis were largely upregulated in CCR2- CRMs, implying the imbalance of inflammatory response upon aging. Our work provides a comprehensive framework and transcriptional resource for assessing the impact of aging on CRMs with a potential for further understanding cardiac aging.
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Affiliation(s)
- Guofang Xia
- Department of Cardiology, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai, China
| | - Simeng Zhu
- Department of Cardiology, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai, China
| | - Yujia Liu
- Department of Neurology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingwei Pan
- Department of Cardiology, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiaoqing Wang
- Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital (SAMSPH), Chengdu, China
| | - Chengxing Shen
- Department of Cardiology, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai, China.
| | - Ailian Du
- Department of Neurology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Congfeng Xu
- Department of Cardiology, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai, China.
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75
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Chen WB, Zhang MF, Yang F, Hua JL. Applications of single-cell RNA sequencing in spermatogenesis and molecular evolution. Zool Res 2024; 45:575-585. [PMID: 38766742 PMCID: PMC11188606 DOI: 10.24272/j.issn.2095-8137.2024.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/08/2024] [Indexed: 05/22/2024] Open
Abstract
Spermatogenic cell heterogeneity is determined by the complex process of spermatogenesis differentiation. However, effectively revealing the regulatory mechanisms underlying mammalian spermatogenic cell development and differentiation via traditional methods is difficult. Advances in technology have led to the emergence of many single-cell transcriptome sequencing protocols, which have partially addressed these challenges. In this review, we detail the principles of 10x Genomics technology and summarize the methods for downstream analysis of single-cell transcriptome sequencing data. Furthermore, we explore the role of single-cell transcriptome sequencing in revealing the heterogeneity of testicular ecological niche cells, delineating the establishment and disruption of testicular immune homeostasis during human spermatogenesis, investigating abnormal spermatogenesis in humans, and, ultimately, elucidating the molecular evolution of mammalian spermatogenesis.
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Affiliation(s)
- Wen-Bo Chen
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Meng-Fei Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Fan Yang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Jin-Lian Hua
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A & F University, Yangling, Shaanxi 712100, China. E-mail:
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76
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Lin W, Li Q, Liu L, Wang Q, Zhang D, Wang F, Xu R, Fan Y, Xing M, Zhou C, Yuan Q. Early infiltrating NKT lymphocytes attenuate bone regeneration through secretion of CXCL2. SCIENCE ADVANCES 2024; 10:eadl6343. [PMID: 38758783 PMCID: PMC11100573 DOI: 10.1126/sciadv.adl6343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Trauma rapidly mobilizes the immune response of surrounding tissues and activates regeneration program. Manipulating immune response to promote tissue regeneration shows a broad application prospect. However, the understanding of bone healing dynamics at cellular level remains limited. Here, we characterize the landscape of immune cells after alveolar bone injury and reveal a pivotal role of infiltrating natural killer T (NKT) cells. We observe a rapid increase in NKT cells after injury, which inhibit osteogenic differentiation of mesenchymal stem cells (MSCs) and impair alveolar bone healing. Cxcl2 is up-regulated in NKT cells after injury. Systemic administration of CXCL2-neutralizing antibody or genetic deletion of Cxcl2 improves the bone healing process. In addition, we fabricate a gelatin-based porous hydrogel to deliver NK1.1 depletion antibody, which successfully promotes alveolar bone healing. In summary, our study highlights the importance of NKT cells in the early stage of bone healing and provides a potential therapeutic strategy for accelerating bone regeneration.
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Affiliation(s)
- Weimin Lin
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Qiwen Li
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Linfeng Liu
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Qian Wang
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Danting Zhang
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Feiyu Wang
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Ruoshi Xu
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Yi Fan
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Malcolm Xing
- Department of Mechanical Engineering, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Chenchen Zhou
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases and National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, 610041 Chengdu, Sichuan, China
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77
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Dittrich M, Bernhardt L, Penfold CA, Boroviak TE, Drummer C, Behr R, Müller T, Haaf T. Age-related and species-specific methylation changes in the protein-coding marmoset sperm epigenome. Aging Cell 2024:e14200. [PMID: 38757354 DOI: 10.1111/acel.14200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/10/2024] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
The sperm epigenome is thought to affect the developmental programming of the resulting embryo, influencing health and disease in later life. Age-related methylation changes in the sperm of old fathers may mediate the increased risks for reproductive and offspring medical problems. The impact of paternal age on sperm methylation has been extensively studied in humans and, to a lesser extent, in rodents and cattle. Here, we performed a comparative analysis of paternal age effects on protein-coding genes in the human and marmoset sperm methylomes. The marmoset has gained growing importance as a non-human primate model of aging and age-related diseases. Using reduced representation bisulfite sequencing, we identified age-related differentially methylated transcription start site (ageTSS) regions in 204 marmoset and 27 human genes. The direction of methylation changes was the opposite, increasing with age in marmosets and decreasing in humans. None of the identified ageTSS was differentially methylated in both species. Although the average methylation levels of all TSS regions were highly correlated between marmosets and humans, with the majority of TSS being hypomethylated in sperm, more than 300 protein-coding genes were endowed with species-specifically (hypo)methylated TSS. Several genes of the glycosphingolipid (GSL) biosynthesis pathway, which plays a role in embryonic stem cell differentiation and regulation of development, were hypomethylated (<5%) in human and fully methylated (>95%) in marmoset sperm. The expression levels and patterns of defined sets of GSL genes differed considerably between human and marmoset pre-implantation embryo stages and blastocyst tissues, respectively.
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Affiliation(s)
- Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Laura Bernhardt
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Christopher A Penfold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Thorsten E Boroviak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Charis Drummer
- Platform Degenerative Diseases, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Göttingen, Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Göttingen, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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78
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Roth DM, Piña JO, Raju R, Iben J, Faucz FR, Makareeva E, Leikin S, Graf D, D'Souza RN. Tendon-associated gene expression precedes osteogenesis in mid-palatal suture establishment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.590129. [PMID: 38798531 PMCID: PMC11118303 DOI: 10.1101/2024.05.11.590129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Orthodontic maxillary expansion relies on intrinsic mid-palatal suture mechanobiology to induce guided osteogenesis, yet establishment of the mid-palatal suture within the continuous secondary palate and causes of maxillary insufficiency remain poorly understood. In contrast, advances in cranial suture research hold promise to improve surgical repair of prematurely fused cranial sutures in craniosynostosis to potentially restore the obliterated signaling environment and ensure continual success of the intervention. We hypothesized that mid-palatal suture establishment is governed by shared principles with calvarial sutures and involves functional linkage between expanding primary ossification centres with the midline mesenchyme. We characterized establishment of the mid-palatal suture from late embryonic to early postnatal timepoints. Suture establishment was visualized using histological techniques and multimodal transcriptomics. We identified that mid-palatal suture formation depends on a spatiotemporally controlled signalling milieu in which tendon-associated genes play a significant role. We mapped relationships between extracellular matrix-encoding gene expression, tenocyte markers, and novel suture patency candidate genes. We identified similar expression patterns in FaceBase-deposited scRNA-seq datasets from cranial sutures. These findings demonstrate shared biological principles for suture establishment, providing further avenues for future development and understanding of maxillofacial interventions.
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Affiliation(s)
- Daniela M Roth
- Section on Craniofacial Genetic Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Jeremie Oliver Piña
- Section on Craniofacial Genetic Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Resmi Raju
- Section on Craniofacial Genetic Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - James Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Fabio R Faucz
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elena Makareeva
- Section on Physical Biochemistry, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sergey Leikin
- Section on Physical Biochemistry, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Daniel Graf
- Department of Dentistry, University of Alberta, Edmonton, AB, Canada
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Canada
| | - Rena N D'Souza
- Section on Craniofacial Genetic Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
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79
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Zhang X, Lan R, Liu Y, Pillarisetty VG, Li D, Zhao CL, Sarkar SA, Liu W, Hanna I, Gupta M, Hajdu C, Melamed J, Shusterman M, Widmer J, Allendorf J, Liu YZ. Enhanced Complement Expression in the Tumor Microenvironment Following Neoadjuvant Therapy: Implications for Immunomodulation and Survival in Pancreatic Ductal Adenocarcinoma. RESEARCH SQUARE 2024:rs.3.rs-4104258. [PMID: 38798691 PMCID: PMC11118688 DOI: 10.21203/rs.3.rs-4104258/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background Neoadjuvant therapy (NAT) is increasingly being used for pancreatic ductal adenocarcinoma (PDAC) treatment. However, its specific effects on carcinoma cells and the tumor microenvironment (TME) are not fully understood. This study aims to investigate how NAT differentially impacts PDAC's carcinoma cells and TME. Methods Spatial transcriptomics was used to compare gene expression profiles in carcinoma cells and the TME between 23 NAT-treated and 13 NAT-naïve PDAC patients, correlating with their clinicopathologic features. Analysis of an online single-nucleus RNA sequencing (snRNA-seq) dataset was performed for validation of the specific cell types responsible for NAT-induced gene expression alterations. Results NAT not only induces apoptosis and inhibits proliferation in carcinoma cells but also significantly remodels the TME. Notably, NAT induces a coordinated upregulation of multiple key complement genes (C3, C1S, C1R, C4B and C7) in the TME, making the complement pathway one of the most significantly affected pathways by NAT. Patients with higher TME complement expression following NAT exhibit improved overall survival. These patients also exhibit increased immunomodulatory and neurotrophic cancer-associated fibroblasts (CAFs); more CD4+ T cells, monocytes, and mast cells; and reduced immune exhaustion gene expression. snRNA-seq analysis demonstrates C3 complement was specifically upregulated in CAFs but not in other stroma cell types. Conclusions NAT can enhance complement production and signaling within the TME, which is associated with reduced immunosuppression in PDAC. These findings suggest that local complement dynamics could serve as a novel biomarker for prognosis, evaluating treatment response and resistance, and guiding therapeutic strategies in NAT-treated PDAC patients.
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Affiliation(s)
- Xiaofei Zhang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
- Department of Pathology and Laboratory Medicine, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - Ruoxin Lan
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA
| | - Yongjun Liu
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Venu G Pillarisetty
- Department of Surgery, University of Washington School of Medicine, Seattle, WA
| | - Danting Li
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA
| | - Chaohui L Zhao
- Department of Pathology and Laboratory Medicine, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - Suparna A. Sarkar
- Department of Pathology and Laboratory Medicine, New York University Grossman School of Medicine, New York, NY
| | - Weiguo Liu
- Department of Pathology and Laboratory Medicine, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - Iman Hanna
- Department of Pathology and Laboratory Medicine, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - Mala Gupta
- Department of Pathology and Laboratory Medicine, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - Cristina Hajdu
- Department of Pathology and Laboratory Medicine, New York University Grossman School of Medicine, New York, NY
| | - Jonathan Melamed
- Department of Pathology and Laboratory Medicine, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - Michael Shusterman
- Department of Oncology, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - Jessica Widmer
- Department of Gastroenterology, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - John Allendorf
- Department of Surgery, New York University Grossman Long Island School of Medicine, Long Island, NY
| | - Yao-Zhong Liu
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA
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80
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Middleton L, Melas I, Vasavda C, Raies A, Rozemberczki B, Dhindsa RS, Dhindsa JS, Weido B, Wang Q, Harper AR, Edwards G, Petrovski S, Vitsios D. Phenome-wide identification of therapeutic genetic targets, leveraging knowledge graphs, graph neural networks, and UK Biobank data. SCIENCE ADVANCES 2024; 10:eadj1424. [PMID: 38718126 PMCID: PMC11078195 DOI: 10.1126/sciadv.adj1424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 04/04/2024] [Indexed: 05/12/2024]
Abstract
The ongoing expansion of human genomic datasets propels therapeutic target identification; however, extracting gene-disease associations from gene annotations remains challenging. Here, we introduce Mantis-ML 2.0, a framework integrating AstraZeneca's Biological Insights Knowledge Graph and numerous tabular datasets, to assess gene-disease probabilities throughout the phenome. We use graph neural networks, capturing the graph's holistic structure, and train them on hundreds of balanced datasets via a robust semi-supervised learning framework to provide gene-disease probabilities across the human exome. Mantis-ML 2.0 incorporates natural language processing to automate disease-relevant feature selection for thousands of diseases. The enhanced models demonstrate a 6.9% average classification power boost, achieving a median receiver operating characteristic (ROC) area under curve (AUC) score of 0.90 across 5220 diseases from Human Phenotype Ontology, OpenTargets, and Genomics England. Notably, Mantis-ML 2.0 prioritizes associations from an independent UK Biobank phenome-wide association study (PheWAS), providing a stronger form of triaging and mitigating against underpowered PheWAS associations. Results are exposed through an interactive web resource.
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Affiliation(s)
- Lawrence Middleton
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ioannis Melas
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Chirag Vasavda
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA 02451, USA
| | - Arwa Raies
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Benedek Rozemberczki
- Biological Insights Knowledge Graph (BIKG), Research D&A, R&D IT, AstraZeneca, Cambridge, UK
| | - Ryan S. Dhindsa
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA 02451, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Justin S. Dhindsa
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Blake Weido
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, MA 02451, USA
| | - Andrew R. Harper
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Gavin Edwards
- Biological Insights Knowledge Graph (BIKG), Research D&A, R&D IT, AstraZeneca, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
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81
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Xu Z, Liu F, Ding Y, Pan T, Wu YH, Liu J, Bado IL, Zhang W, Wu L, Gao Y, Hao X, Yu L, Edwards DG, Chan HL, Aguirre S, Dieffenbach MW, Chen E, Shen Y, Hoffman D, Dominguez LB, Rivas CH, Chen X, Wang H, Gugala Z, Satcher RL, Zhang XHF. Unbiased metastatic niche-labeling identifies estrogen receptor-positive macrophages as a barrier of T cell infiltration during bone colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593016. [PMID: 38765966 PMCID: PMC11100675 DOI: 10.1101/2024.05.07.593016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Microenvironment niches determine cellular fates of metastatic cancer cells. However, robust and unbiased approaches to identify niche components and their molecular profiles are lacking. We established Sortase A-Based Microenvironment Niche Tagging (SAMENT), which selectively labels cells encountered by cancer cells during metastatic colonization. SAMENT was applied to multiple cancer models colonizing the same organ and the same cancer to different organs. Common metastatic niche features include macrophage enrichment and T cell depletion. Macrophage niches are phenotypically diverse between different organs. In bone, macrophages express the estrogen receptor alpha (ERα) and exhibit active ERα signaling in male and female hosts. Conditional knockout of Esr1 in macrophages significantly retarded bone colonization by allowing T cell infiltration. ERα expression was also discovered in human bone metastases of both genders. Collectively, we identified a unique population of ERα+ macrophages in the metastatic niche and functionally tied ERα signaling in macrophages to T cell exclusion during metastatic colonization. HIGHLIGHTS SAMENT is a robust metastatic niche-labeling approach amenable to single-cell omics.Metastatic niches are typically enriched with macrophages and depleted of T cells.Direct interaction with cancer cells induces ERα expression in niche macrophages. Knockout of Esr1 in macrophages allows T cell infiltration and retards bone colonization.
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82
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Lotfollahi M, Yuhan Hao, Theis FJ, Satija R. The future of rapid and automated single-cell data analysis using reference mapping. Cell 2024; 187:2343-2358. [PMID: 38729109 PMCID: PMC11184658 DOI: 10.1016/j.cell.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 05/12/2024]
Abstract
As the number of single-cell datasets continues to grow rapidly, workflows that map new data to well-curated reference atlases offer enormous promise for the biological community. In this perspective, we discuss key computational challenges and opportunities for single-cell reference-mapping algorithms. We discuss how mapping algorithms will enable the integration of diverse datasets across disease states, molecular modalities, genetic perturbations, and diverse species and will eventually replace manual and laborious unsupervised clustering pipelines.
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Affiliation(s)
- Mohammad Lotfollahi
- Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Mathematics, Technical University of Munich, Garching, Germany.
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York Genome Center, New York, NY, USA.
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83
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Ellis LV, Bywaters JD, Chen J. Endothelial deletion of p53 generates transitional endothelial cells and improves lung development during neonatal hyperoxia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593014. [PMID: 38766251 PMCID: PMC11100739 DOI: 10.1101/2024.05.07.593014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Bronchopulmonary dysplasia (BPD), a prevalent and chronic lung disease affecting premature newborns, results in vascular rarefaction and alveolar simplification. Although the vasculature has been recognized as a main player in this disease, the recently found capillary heterogeneity and cellular dynamics of endothelial subpopulations in BPD remain unclear. Here, we show Cap2 cells are damaged during neonatal hyperoxic injury, leading to their replacement by Cap1 cells which, in turn, significantly decline. Single-cell RNA-seq identifies the activation of numerous p53 target genes in endothelial cells, including Cdkn1a (p21). While global deletion of p53 results in worsened vasculature, endothelial-specific deletion of p53 reverses the vascular phenotype and improves alveolar simplification during hyperoxia. This recovery is associated with the emergence of a transitional EC state, enriched for oxidative stress response genes and growth factors. These findings implicate the p53 pathway in EC type transition during injury-repair and highlights the endothelial contributions to BPD.
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Affiliation(s)
- Lisandra Vila Ellis
- Department of Cell & Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jonathan D Bywaters
- Department of Cell & Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jichao Chen
- Department of Pulmonary Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Department of Pediatrics, Perinatal Institute Division of Pulmonary Biology, University of Cincinnati and Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
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84
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Pilley SE, Awad D, Latumalea D, Esparza E, Zhang L, Shi X, Unfried M, Wang S, Mulondo R, Kashyap SB, Moaddeli D, Sajjakulnukit P, Sutton D, Wong H, Coakley AJ, Garcia G, Higuchi-Sanabria R, Liu S, Yu B, Tu WB, Kennedy BK, Lyssiotis CA, Mullen PJ. A metabolic atlas of mouse aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592445. [PMID: 38746230 PMCID: PMC11092783 DOI: 10.1101/2024.05.04.592445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Humans are living longer, but this is accompanied by an increased incidence of age-related chronic diseases. Many of these diseases are influenced by age-associated metabolic dysregulation, but how metabolism changes in multiple organs during aging in males and females is not known. Answering this could reveal new mechanisms of aging and age-targeted therapeutics. In this study, we describe how metabolism changes in 12 organs in male and female mice at 5 different ages. Organs show distinct patterns of metabolic aging that are affected by sex differently. Hydroxyproline shows the most consistent change across the dataset, decreasing with age in 11 out of 12 organs investigated. We also developed a metabolic aging clock that predicts biological age and identified alpha-ketoglutarate, previously shown to extend lifespan in mice, as a key predictor of age. Our results reveal fundamental insights into the aging process and identify new therapeutic targets to maintain organ health.
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85
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Chen CC, Buchheit KM, Lee PY, Brodeur KE, Sohail A, Cho L, Baloh CH, Balestrieri B, Derakhshan T, Feng C, Boyce JA, Dwyer DF, Laidlaw TM. IL-4Rα signaling promotes barrier-altering oncostatin M and IL-6 production in aspirin-exacerbated respiratory disease. J Allergy Clin Immunol 2024:S0091-6749(24)00453-6. [PMID: 38704098 DOI: 10.1016/j.jaci.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/02/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Aspirin-exacerbated respiratory disease (AERD) is a severe disease involving dysregulated type 2 inflammation. However, the role other inflammatory pathways play in AERD is poorly understood. OBJECTIVE We sought to broadly define the inflammatory milieu of the upper respiratory tract in AERD and to determine the effects of IL-4Rα inhibition on mediators of nasal inflammation. METHODS Twenty-two AERD patients treated with dupilumab for 3 months were followed over 3 visits and compared to 10 healthy controls. Nasal fluid was assessed for 45 cytokines and chemokines using Olink Target 48. Blood neutrophils and cultured human mast cells, monocytes/macrophages, and nasal fibroblasts were assessed for response to IL-4/13 stimulation in vitro. RESULTS Of the nasal fluid cytokines measured, nearly one third were higher in AERD patients compared to healthy controls, including IL-6 and the IL-6 family-related cytokine oncostatin M (OSM), both of which correlated with nasal albumin levels, a marker of epithelial barrier dysregulation. Dupilumab significantly decreased many nasal mediators, including OSM and IL-6. IL-4 stimulation induced OSM production from mast cells and macrophages but not from neutrophils, and OSM and IL-13 stimulation induced IL-6 production from nasal fibroblasts. CONCLUSION In addition to type 2 inflammation, innate and IL-6-related cytokines are also elevated in the respiratory tract in AERD. Both OSM and IL-6 are locally produced in nasal polyps and likely promote pathology by negatively affecting epithelial barrier function. IL-4Rα blockade, although seemingly directed at type 2 inflammation, also decreases mediators of innate inflammation and epithelial dysregulation, which may contribute to dupilumab's therapeutic efficacy in AERD.
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Affiliation(s)
- Chongjia C Chen
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass.
| | - Kathleen M Buchheit
- Department of Medicine, Harvard Medical School, and the Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Pui Y Lee
- Division of Immunology, Boston Children's Hospital, Boston, Mass
| | - Kailey E Brodeur
- Division of Immunology, Boston Children's Hospital, Boston, Mass
| | - Aaqib Sohail
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Laura Cho
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Carolyn H Baloh
- Department of Medicine, Harvard Medical School, and the Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Barbara Balestrieri
- Department of Medicine, Harvard Medical School, and the Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Tahereh Derakhshan
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Chunli Feng
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Joshua A Boyce
- Department of Medicine, Harvard Medical School, and the Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Daniel F Dwyer
- Department of Medicine, Harvard Medical School, and the Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Tanya M Laidlaw
- Department of Medicine, Harvard Medical School, and the Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
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86
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Giansanti V, Giannese F, Botrugno OA, Gandolfi G, Balestrieri C, Antoniotti M, Tonon G, Cittaro D. Scalable integration of multiomic single-cell data using generative adversarial networks. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae300. [PMID: 38696763 DOI: 10.1093/bioinformatics/btae300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 05/04/2024]
Abstract
MOTIVATION Single-cell profiling has become a common practice to investigate the complexity of tissues, organs, and organisms. Recent technological advances are expanding our capabilities to profile various molecular layers beyond the transcriptome such as, but not limited to, the genome, the epigenome, and the proteome. Depending on the experimental procedure, these data can be obtained from separate assays or the very same cells. Yet, integration of more than two assays is currently not supported by the majority of the computational frameworks avaiable. RESULTS We here propose a Multi-Omic data integration framework based on Wasserstein Generative Adversarial Networks suitable for the analysis of paired or unpaired data with a high number of modalities (>2). At the core of our strategy is a single network trained on all modalities together, limiting the computational burden when many molecular layers are evaluated. AVAILABILITY AND IMPLEMENTATION Source code of our framework is available at https://github.com/vgiansanti/MOWGAN.
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Affiliation(s)
- Valentina Giansanti
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, 20125, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Francesca Giannese
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Oronza A Botrugno
- Functional Genomics of Cancer Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Università Vita-Salute San Raffaele, Milan, 20132, Italy
| | - Giorgia Gandolfi
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Chiara Balestrieri
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Marco Antoniotti
- Department of Informatics, Systems and Communication, Università degli Studi di Milano-Bicocca, Milan, 20125, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre-B4, Università degli Studi di Milano-Bicocca, Milan, 20125, Italy
- Istituto di Bioimmagini e Fisiologia Molecolare, Consiglio Nazionale delle Ricerche (CNR), Milan, 20090, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Functional Genomics of Cancer Unit, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Università Vita-Salute San Raffaele, Milan, 20132, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
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87
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Rice G, Farrelly O, Huang S, Kuri P, Curtis E, Ohman L, Li N, Lengner C, Lee V, Rompolas P. Sox9 marks limbal stem cells and is required for asymmetric cell fate switch in the corneal epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588195. [PMID: 38645161 PMCID: PMC11030424 DOI: 10.1101/2024.04.08.588195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Adult tissues with high cellular turnover require a balance between stem cell renewal and differentiation, yet the mechanisms underlying this equilibrium are unclear. The cornea exhibits a polarized lateral flow of progenitors from the peripheral stem cell niche to the center; attributed to differences in cellular fate. To identify genes that are critical for regulating the asymmetric fates of limbal stem cells and their transient amplified progeny in the central cornea, we utilized an in vivo cell cycle reporter to isolate proliferating basal cells across the anterior ocular surface epithelium and performed single-cell transcriptional analysis. This strategy greatly increased the resolution and revealed distinct basal cell identities with unique expression profiles of structural genes and transcription factors. We focused on Sox9; a transcription factor implicated in stem cell regulation across various organs. Sox9 was found to be differentially expressed between limbal stem cells and their progeny in the central corneal. Lineage tracing analysis confirmed that Sox9 marks long-lived limbal stem cells and conditional deletion led to abnormal differentiation and squamous metaplasia in the central cornea. These data suggest a requirement for Sox9 for the switch to asymmetric fate and commitment toward differentiation, as transient cells exit the limbal niche. By inhibiting terminal differentiation of corneal progenitors and forcing them into perpetual symmetric divisions, we replicated the Sox9 loss-of-function phenotype. Our findings reveal an essential role for Sox9 for the spatial regulation of asymmetric fate in the corneal epithelium that is required to sustain tissue homeostasis.
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88
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Ali HR, West RB. Spatial Biology of Breast Cancer. Cold Spring Harb Perspect Med 2024; 14:a041335. [PMID: 38110242 PMCID: PMC11065165 DOI: 10.1101/cshperspect.a041335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Spatial findings have shaped on our understanding of breast cancer. In this review, we discuss how spatial methods, including spatial transcriptomics and proteomics and the resultant understanding of spatial relationships, have contributed to concepts regarding cancer progression and treatment. In addition to discussing traditional approaches, we examine how emerging multiplex imaging technologies have contributed to the field and how they might influence future research.
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Affiliation(s)
- H Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Robert B West
- Department of Pathology, Stanford University Medical Center, Stanford, California 94305, USA
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89
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Marx V. scRNA-seq: oh, the joys. Nat Methods 2024; 21:750-753. [PMID: 38654084 DOI: 10.1038/s41592-024-02263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
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90
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Callebaut A, Guyer P, Derua R, Buitinga M, Manganaro A, Yi X, Sodré FMC, Vig S, Suleiman M, Marchetti P, Eizirik DL, Kent SC, Mathieu C, James EA, Overbergh L. CD4+ T Cells From Individuals With Type 1 Diabetes Respond to a Novel Class of Deamidated Peptides Formed in Pancreatic Islets. Diabetes 2024; 73:728-742. [PMID: 38387030 PMCID: PMC11043062 DOI: 10.2337/db23-0588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
The β-cell plays a crucial role in the pathogenesis of type 1 diabetes, in part through the posttranslational modification of self-proteins by biochemical processes such as deamidation. These neoantigens are potential triggers for breaking immune tolerance. We report the detection by LC-MS/MS of 16 novel Gln and 27 novel Asn deamidations in 14 disease-related proteins within inflammatory cytokine-stressed human islets of Langerhans. T-cell clones responsive against one Gln- and three Asn-deamidated peptides could be isolated from peripheral blood of individuals with type 1 diabetes. Ex vivo HLA class II tetramer staining detected higher T-cell frequencies in individuals with the disease compared with control individuals. Furthermore, there was a positive correlation between the frequencies of T cells specific for deamidated peptides, insulin antibody levels at diagnosis, and duration of disease. These results highlight that stressed human islets are prone to enzymatic and biochemical deamidation and suggest that both Gln- and Asn-deamidated peptides can promote the activation and expansion of autoreactive CD4+ T cells. These findings add to the growing evidence that posttranslational modifications undermine tolerance and may open the road for the development of new diagnostic and therapeutic applications for individuals living with type 1 diabetes. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Aïsha Callebaut
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA
| | - Perrin Guyer
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA
| | - Rita Derua
- Laboratory of Protein Phosphorylation and Proteomics, KU Leuven, Leuven, Belgium
| | - Mijke Buitinga
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Anthony Manganaro
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Xiaoyan Yi
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Saurabh Vig
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Decio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Sally C. Kent
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Chantal Mathieu
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Eddie A. James
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA
| | - Lut Overbergh
- Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
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91
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Moreno JA, Dudchenko O, Feigin CY, Mereby SA, Chen Z, Ramos R, Almet AA, Sen H, Brack BJ, Johnson MR, Li S, Wang W, Gaska JM, Ploss A, Weisz D, Omer AD, Yao W, Colaric Z, Kaur P, Leger JS, Nie Q, Mena A, Flanagan JP, Keller G, Sanger T, Ostrow B, Plikus MV, Kvon EZ, Aiden EL, Mallarino R. Emx2 underlies the development and evolution of marsupial gliding membranes. Nature 2024; 629:127-135. [PMID: 38658750 PMCID: PMC11062917 DOI: 10.1038/s41586-024-07305-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium-an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.
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Affiliation(s)
- Jorge A Moreno
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Environment and Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Sarah A Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zhuoxin Chen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Harsha Sen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin J Brack
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew R Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sha Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Lewis Sigler Center for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jenna M Gaska
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Yao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Parwinder Kaur
- The University of Western Australia, Crawley, Western Australia, Australia
| | - Judy St Leger
- Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | | | | | - Greta Keller
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Thomas Sanger
- Department of Biology, Loyola University, Chicago, IL, USA
| | - Bruce Ostrow
- Department of Biology, Grand Valley State University, Allendale, MI, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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92
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Ji Y, Zhang Z, Zhao X, Li Z, Hu X, Zhang M, Pan X, Wang X, Chen W. IL-1α facilitates GSH synthesis to counteract oxidative stress in oral squamous cell carcinoma under glucose-deprivation. Cancer Lett 2024; 589:216833. [PMID: 38548217 DOI: 10.1016/j.canlet.2024.216833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/08/2024]
Abstract
Understanding the intrinsic mechanisms underpinning cancer metabolism and therapeutic resistance is of central importance for effective nutrition-starvation therapies. Here, we report that Interleukin 1A (IL1A) mRNA and IL-1α protein facilitate glutathione (GSH) synthesis to counteract oxidative stress and resistance against nutrition-starvation therapy in oral squamous cell carcinoma (OSCC). The expression of IL1A mRNA was elevated in the case of OSCC associated with unfavorable clinical outcomes. Both IL1A mRNA and IL-1α protein expression were increased under glucose-deprivation in vitro and in vivo. The transcription of IL1A mRNA was regulated in an NRF2-dependent manner in OSCC cell lines under glucose-deprivation. Moreover, the IL-1α conferred resistance to oxidative stress via GSH synthesis in OSCC cell lines. The intratumoral administration of siRNAs against IL1A mRNA markedly reversed GSH production and sensitized OSCC cells to Anlotinib in HN6 xenograft models. Overall, the current study demonstrates novel evidence that the autocrine IL-1α favors endogenous anti-oxidative process and confers therapeutic resistance to nutrition-starvation in OSCCs.
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Affiliation(s)
- Yikang Ji
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China
| | - Zhen Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China
| | - Xinran Zhao
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China
| | - Zhiyin Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China
| | - Xin Hu
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China
| | - Mi Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China
| | - Xinhua Pan
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China
| | - Xu Wang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China.
| | - Wantao Chen
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, China.
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93
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Niepoth N, Merritt JR, Uminski M, Lei E, Esquibies VS, Bando IB, Hernandez K, Gebhardt C, Wacker SA, Lutzu S, Poudel A, Soma KK, Rudolph S, Bendesky A. Evolution of a novel adrenal cell type that promotes parental care. Nature 2024; 629:1082-1090. [PMID: 38750354 DOI: 10.1038/s41586-024-07423-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Cell types with specialized functions fundamentally regulate animal behaviour, and yet the genetic mechanisms that underlie the emergence of novel cell types and their consequences for behaviour are not well understood1. Here we show that the monogamous oldfield mouse (Peromyscus polionotus) has recently evolved a novel cell type in the adrenal gland that expresses the enzyme AKR1C18, which converts progesterone into 20α-hydroxyprogesterone. We then demonstrate that 20α-hydroxyprogesterone is more abundant in oldfield mice, where it induces monogamous-typical parental behaviours, than in the closely related promiscuous deer mice (Peromyscus maniculatus). Using quantitative trait locus mapping in a cross between these species, we ultimately find interspecific genetic variation that drives expression of the nuclear protein GADD45A and the glycoprotein tenascin N, which contribute to the emergence and function of this cell type in oldfield mice. Our results provide an example by which the recent evolution of a new cell type in a gland outside the brain contributes to the evolution of social behaviour.
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Affiliation(s)
- Natalie Niepoth
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Jennifer R Merritt
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Michelle Uminski
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Emily Lei
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Victoria S Esquibies
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Ina B Bando
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Kimberly Hernandez
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Christoph Gebhardt
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Sarah A Wacker
- Department of Chemistry and Biochemistry, Manhattan College, New York, NY, USA
| | - Stefano Lutzu
- Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, New York, NY, USA
| | - Asmita Poudel
- Department of Psychology, University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kiran K Soma
- Department of Psychology, University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephanie Rudolph
- Department of Neuroscience, Albert Einstein College of Medicine, New York, NY, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, New York, NY, USA
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.
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94
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Fujiwara N, Kimura G, Nakagawa H. Emerging Roles of Spatial Transcriptomics in Liver Research. Semin Liver Dis 2024. [PMID: 38574750 DOI: 10.1055/a-2299-7880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Spatial transcriptomics, leveraging sequencing- and imaging-based techniques, has emerged as a groundbreaking technology for mapping gene expression within the complex architectures of tissues. This approach provides an in-depth understanding of cellular and molecular dynamics across various states of healthy and diseased livers. Through the integration of sophisticated bioinformatics strategies, it enables detailed exploration of cellular heterogeneity, transitions in cell states, and intricate cell-cell interactions with remarkable precision. In liver research, spatial transcriptomics has been particularly revelatory, identifying distinct zonated functions of hepatocytes that are crucial for understanding the metabolic and detoxification processes of the liver. Moreover, this technology has unveiled new insights into the pathogenesis of liver diseases, such as the role of lipid-associated macrophages in steatosis and endothelial cell signals in liver regeneration and repair. In the domain of liver cancer, spatial transcriptomics has proven instrumental in delineating intratumor heterogeneity, identifying supportive microenvironmental niches and revealing the complex interplay between tumor cells and the immune system as well as susceptibility to immune checkpoint inhibitors. In conclusion, spatial transcriptomics represents a significant advance in hepatology, promising to enhance our understanding and treatment of liver diseases.
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Affiliation(s)
- Naoto Fujiwara
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Genki Kimura
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Mie University, Mie, Japan
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95
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Kang ZY, Huang QY, Zhen NX, Xuan NX, Zhou QC, Zhao J, Cui W, Zhang ZC, Tian BP. Heterogeneity of immune cells and their communications unveiled by transcriptome profiling in acute inflammatory lung injury. Front Immunol 2024; 15:1382449. [PMID: 38745657 PMCID: PMC11092984 DOI: 10.3389/fimmu.2024.1382449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/03/2024] [Indexed: 05/16/2024] Open
Abstract
Background Acute Respiratory Distress Syndrome (ARDS) or its earlier stage Acute lung injury (ALI), is a worldwide health concern that jeopardizes human well-being. Currently, the treatment strategies to mitigate the incidence and mortality of ARDS are severely restricted. This limitation can be attributed, at least in part, to the substantial variations in immunity observed in individuals with this syndrome. Methods Bulk and single cell RNA sequencing from ALI mice and single cell RNA sequencing from ARDS patients were analyzed. We utilized the Seurat program package in R and cellmarker 2.0 to cluster and annotate the data. The differential, enrichment, protein interaction, and cell-cell communication analysis were conducted. Results The mice with ALI caused by pulmonary and extrapulmonary factors demonstrated differential expression including Clec4e, Retnlg, S100a9, Coro1a, and Lars2. We have determined that inflammatory factors have a greater significance in extrapulmonary ALI, while multiple pathways collaborate in the development of pulmonary ALI. Clustering analysis revealed significant heterogeneity in the relative abundance of immune cells in different ALI models. The autocrine action of neutrophils plays a crucial role in pulmonary ALI. Additionally, there was a significant increase in signaling intensity between B cells and M1 macrophages, NKT cells and M1 macrophages in extrapulmonary ALI. The CXCL, CSF3 and MIF, TGFβ signaling pathways play a vital role in pulmonary and extrapulmonary ALI, respectively. Moreover, the analysis of human single-cell revealed DCs signaling to monocytes and neutrophils in COVID-19-associated ARDS is stronger compared to sepsis-related ARDS. In sepsis-related ARDS, CD8+ T and Th cells exhibit more prominent signaling to B-cell nucleated DCs. Meanwhile, both MIF and CXCL signaling pathways are specific to sepsis-related ARDS. Conclusion This study has identified specific gene signatures and signaling pathways in animal models and human samples that facilitate the interaction between immune cells, which could be targeted therapeutically in ARDS patients of various etiologies.
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Affiliation(s)
- Zhi-ying Kang
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qian-yu Huang
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ning-xin Zhen
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Nan-xia Xuan
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qi-chao Zhou
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Wei Cui
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhao-cai Zhang
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bao-ping Tian
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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96
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Moon S, Zhao F, Uddin MN, Tucker CJ, Karmaus PWF, Fessler MB. Flotillin-2 dampens T cell antigen-sensitivity and functionality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591344. [PMID: 38746431 PMCID: PMC11092481 DOI: 10.1101/2024.04.26.591344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
T cell receptor (TCR) engagement triggers T cell responses, yet how TCR-mediated activation is regulated at the plasma membrane remains unclear. Here, we report that deleting the membrane scaffolding protein Flotillin-2 (Flot2) increases T cell antigen sensitivity, resulting in enhanced TCR signaling and effector function to weak TCR stimulation. T cell-specific Flot2-deficient mice exhibited reduced tumor growth and enhanced immunity to infection. Flot2-null CD4 + T cells exhibited increased T helper 1 polarization, proliferation, Nur77 induction, and phosphorylation of ZAP70 and LCK upon weak TCR stimulation, indicating a sensitized TCR-triggering threshold. Single cell-RNA sequencing suggested that Flot2 - null CD4 + T cells follow a similar route of activation as wild-type CD4 + T cells but exhibit higher occupancy of a discrete activation state under weak TCR stimulation. Given prior reports that TCR clustering influences sensitivity of T cells to stimuli, we evaluated TCR distribution with super-resolution microscopy. Flot2 ablation increased the number of surface TCR nanoclusters on naïve CD4 + T cells. Collectively, we posit that Flot2 modulates T cell functionality to weak TCR stimulation, at least in part, by regulating surface TCR clustering. Our findings have implications for improving T cell reactivity in diseases with poor antigenicity, such as cancer and chronic infections.
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Zhang W, Yu R, Xu Z, Li J, Gao W, Jiang M, Dai Q. scCompressSA: dual-channel self-attention based deep autoencoder model for single-cell clustering by compressing gene-gene interactions. BMC Genomics 2024; 25:423. [PMID: 38684946 PMCID: PMC11059774 DOI: 10.1186/s12864-024-10286-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Single-cell clustering has played an important role in exploring the molecular mechanisms about cell differentiation and human diseases. Due to highly-stochastic transcriptomics data, accurate detection of cell types is still challenged, especially for RNA-sequencing data from human beings. In this case, deep neural networks have been increasingly employed to mine cell type specific patterns and have outperformed statistic approaches in cell clustering. RESULTS Using cross-correlation to capture gene-gene interactions, this study proposes the scCompressSA method to integrate topological patterns from scRNA-seq data, with support of self-attention (SA) based coefficient compression (CC) block. This SA-based CC block is able to extract and employ static gene-gene interactions from scRNA-seq data. This proposed scCompressSA method has enhanced clustering accuracy in multiple benchmark scRNA-seq datasets by integrating topological and temporal features. CONCLUSION Static gene-gene interactions have been extracted as temporal features to boost clustering performance in single-cell clustering For the scCompressSA method, dual-channel SA based CC block is able to integrate topological features and has exhibited extraordinary detection accuracy compared with previous clustering approaches that only employ temporal patterns.
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Affiliation(s)
- Wei Zhang
- Zhejiang Sci-Tech University, Second Street 928, Hangzhou, Zhejiang, 310018, China
| | - Ruochen Yu
- Zhejiang Sci-Tech University, Second Street 928, Hangzhou, Zhejiang, 310018, China
| | - Zeqi Xu
- Zhejiang Sci-Tech University, Second Street 928, Hangzhou, Zhejiang, 310018, China
| | - Junnan Li
- Zhejiang Sci-Tech University, Second Street 928, Hangzhou, Zhejiang, 310018, China
| | - Wenhao Gao
- Zhejiang Sci-Tech University, Second Street 928, Hangzhou, Zhejiang, 310018, China
| | - Mingfeng Jiang
- Zhejiang Sci-Tech University, Second Street 928, Hangzhou, Zhejiang, 310018, China.
| | - Qi Dai
- Zhejiang Sci-Tech University, Second Street 928, Hangzhou, Zhejiang, 310018, China.
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Silver SV, Tucker KJ, Vickman RE, Lanman NA, Semmes OJ, Alvarez NS, Popovics P. PROSTATE CELL HETEROGENEITY AND CXCL17 UPREGULATION IN MOUSE STEROID HORMONE IMBALANCE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590980. [PMID: 38712029 PMCID: PMC11071464 DOI: 10.1101/2024.04.24.590980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Benign prostatic hyperplasia (BPH) is a prevalent age-related condition often characterized by debilitating urinary symptoms. Its etiology is believed to stem from hormonal imbalance, particularly an elevated estradiol-to-testosterone ratio and chronic inflammation. Our previous studies using a mouse steroid hormone imbalance model identified a specific increase in macrophages that migrate and accumulate in the prostate lumen where they differentiate into lipid-laden foam cells in mice implanted with testosterone and estradiol pellets, but not in sham animals. The current study focused on further characterizing the cellular heterogeneity of the prostate in this model as well as identifying the specific transcriptomic signature of the recruited foam cells. Moreover, we aimed to identify the epithelia-derived signals that drive macrophage infiltration and luminal translocation. Male C57BL/6J mice were implanted with slow-release testosterone and estradiol pellets (T+E2) and harvested the ventral prostates two weeks later for scRNA-seq analysis, or performed sham surgery. We identified Ear2+ and Cd72+ macrophages that were elevated in response to steroid hormone imbalance, whereas a Mrc1+ resident macrophage population did not change. In addition, an Spp1+ foam cell cluster was almost exclusively found in T+E2 mice. Further markers of foam cells were also identified, including Gpnmb and Trem2, and GPNMB was confirmed as a novel histological marker with immunohistochemistry. Foam cells were also shown to express known pathological factors Vegf, Tgfb1, Ccl6, Cxcl16 and Mmp12. Intriguingly, a screen for chemokines identified the upregulation of epithelial-derived Cxcl17, a known monocyte attractant, in T+E2 prostates suggesting that it might be responsible for the elevated macrophage number as well as their translocation to the lumen. Our study identified macrophage subsets that respond to steroid hormone imbalance as well as further confirmed a potential pathological role of luminal foam cells in the prostate. These results underscore a pathological role of the identified prostate foam cells and suggests CXCL17-mediated macrophage migration as a critical initiating event.
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Affiliation(s)
- Samara V. Silver
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA
| | - Kayah J. Tucker
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA
| | - Renee E Vickman
- Department of Surgery, Endeavor Health, an Academic Affiliate of the University of Chicago Pritzker School of Medicine, Evanston, IL, USA
| | - Nadia A. Lanman
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - O John Semmes
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA
| | - Nehemiah S. Alvarez
- Department of Surgery, Endeavor Health, an Academic Affiliate of the University of Chicago Pritzker School of Medicine, Evanston, IL, USA
| | - Petra Popovics
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA
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99
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Guo Y, Lu W, Zhang Z, Liu H, Zhang A, Zhang T, Wu Y, Li X, Yang S, Cui Q, Li Z. A novel pyroptosis-related gene signature exhibits distinct immune cells infiltration landscape in Wilms' tumor. BMC Pediatr 2024; 24:279. [PMID: 38678251 PMCID: PMC11055250 DOI: 10.1186/s12887-024-04731-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/31/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Wilms' tumor (WT) is the most common renal tumor in childhood. Pyroptosis, a type of inflammation-characterized and immune-related programmed cell death, has been extensively studied in multiple tumors. In the current study, we aim to construct a pyroptosis-related gene signature for predicting the prognosis of Wilms' tumor. METHODS We acquired RNA-seq data from TARGET kidney tumor projects for constructing a gene signature, and snRNA-seq data from GEO database for validating signature-constructing genes. Pyroptosis-related genes (PRGs) were collected from three online databases. We constructed the gene signature by Lasso Cox regression and then established a nomogram. Underlying mechanisms by which gene signature is related to overall survival states of patients were explored by immune cell infiltration analysis, differential expression analysis, and functional enrichment analysis. RESULTS A pyroptosis-related gene signature was constructed with 14 PRGs, which has a moderate to high predicting capacity with 1-, 3-, and 5-year area under the curve (AUC) values of 0.78, 0.80, and 0.83, respectively. A prognosis-predicting nomogram was established by gender, stage, and risk score. Tumor-infiltrating immune cells were quantified by seven algorithms, and the expression of CD8( +) T cells, B cells, Th2 cells, dendritic cells, and type 2 macrophages are positively or negatively correlated with risk score. Two single nuclear RNA-seq samples of different histology were harnessed for validation. The distribution of signature genes was identified in various cell types. CONCLUSIONS We have established a pyroptosis-related 14-gene signature in WT. Moreover, the inherent roles of immune cells (CD8( +) T cells, B cells, Th2 cells, dendritic cells, and type 2 macrophages), functions of differentially expressed genes (tissue/organ development and intercellular communication), and status of signaling pathways (proteoglycans in cancer, signaling pathways regulating pluripotent of stem cells, and Wnt signaling pathway) have been elucidated, which might be employed as therapeutic targets in the future.
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Affiliation(s)
- Yujun Guo
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China
| | - Wenjun Lu
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310024, China
- Laboratory of Systems Immunology, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Ze'nan Zhang
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China
| | - Hengchen Liu
- Department of Colorectal Surgery and Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, Zhejiang, 310022, China
| | - Aodan Zhang
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China
- Department of Pediatric Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.246 Xuefu Road, Harbin, Heilongjiang, 150000, China
| | - Tingting Zhang
- Psychology and Health Management Center, Harbin Medical University, No.157 Baojian Road, Harbin, Heilongjiang, 150081, China
| | - Yang Wu
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China
- Department of Pediatric Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.246 Xuefu Road, Harbin, Heilongjiang, 150000, China
| | - Xiangqi Li
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China
- Department of Pediatric Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.246 Xuefu Road, Harbin, Heilongjiang, 150000, China
| | - Shulong Yang
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China
- Department of Pediatric Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.246 Xuefu Road, Harbin, Heilongjiang, 150000, China
| | - Qingbo Cui
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China.
- Department of Pediatric Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.246 Xuefu Road, Harbin, Heilongjiang, 150000, China.
| | - Zhaozhu Li
- Department of Pediatric Surgery, The Sixth Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.998 Aiying Street, Harbin, Heilongjiang, 150027, China.
- Department of Pediatric Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, No.246 Xuefu Road, Harbin, Heilongjiang, 150000, China.
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100
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Cao T, Zhang W, Wang Q, Wang C, Ma W, Zhang C, Ge M, Tian M, Yu J, Jiao A, Wang L, Liu M, Wang P, Guo Z, Zhou Y, Chen S, Yin W, Yi J, Guo H, Han H, Zhang B, Wu K, Fan D, Wang X, Nie Y, Lu Y, Zhao X. Cancer SLC6A6-mediated taurine uptake transactivates immune checkpoint genes and induces exhaustion in CD8 + T cells. Cell 2024; 187:2288-2304.e27. [PMID: 38565142 DOI: 10.1016/j.cell.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/12/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Taurine is used to bolster immunity, but its effects on antitumor immunity are unclear. Here, we report that cancer-related taurine consumption causes T cell exhaustion and tumor progression. The taurine transporter SLC6A6 is correlated with aggressiveness and poor outcomes in multiple cancers. SLC6A6-mediated taurine uptake promotes the malignant behaviors of tumor cells but also increases the survival and effector function of CD8+ T cells. Tumor cells outcompete CD8+ T cells for taurine by overexpressing SLC6A6, which induces T cell death and malfunction, thereby fueling tumor progression. Mechanistically, taurine deficiency in CD8+ T cells increases ER stress, promoting ATF4 transcription in a PERK-JAK1-STAT3 signaling-dependent manner. Increased ATF4 transactivates multiple immune checkpoint genes and induces T cell exhaustion. In gastric cancer, we identify a chemotherapy-induced SP1-SLC6A6 regulatory axis. Our findings suggest that tumoral-SLC6A6-mediated taurine deficiency promotes immune evasion and that taurine supplementation reinvigorates exhausted CD8+ T cells and increases the efficacy of cancer therapies.
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Affiliation(s)
- Tianyu Cao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wenyao Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Qi Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China; College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Chen Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China; College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Wanqi Ma
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Cangang Zhang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Minghui Ge
- Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu 210042, China
| | - Miaomiao Tian
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jia Yu
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Liang Wang
- Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Manjiao Liu
- Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu 210042, China
| | - Pei Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zhiyu Guo
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Yun Zhou
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Shuyi Chen
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wen Yin
- Department of Blood Transfusion, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jing Yi
- Department of Blood Transfusion, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Hao Guo
- Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu 210042, China
| | - Hua Han
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Kaichun Wu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Daiming Fan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xin Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710038, China.
| | - Yongzhan Nie
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Yuanyuan Lu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Xiaodi Zhao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
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