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Bao L, Li Y, Hu X, Gong Y, Chen J, Huang P, Tan Z, Ge M, Pan Z. Targeting SIGLEC15 as an emerging immunotherapy for anaplastic thyroid cancer. Int Immunopharmacol 2024; 133:112102. [PMID: 38652971 DOI: 10.1016/j.intimp.2024.112102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Anaplastic thyroid carcinoma (ATC) is the most aggressive subtype of thyroid cancer with few effective therapies. Though immunotherapies such as targeting PD-1/PD-L1 axis have benefited patients with solid tumor, the druggable immune checkpoints are quite limited in ATC. In our study, we focused on the anti-tumor potential of sialic acid-binding Ig-like lectins (Siglecs) in ATC. Through screening by integrating microarray datasets including 216 thyroid-cancer tissues and single-cell RNA-sequencing, SIGLEC family members CD33, SIGLEC1, SIGLEC10 and SIGLEC15 were significantly overexpressed in ATC, among which SIGLEC15 increased highest and mainly expressed on cancer cells. SIGLEC15high ATC cells are characterized by high expression of serine protease PRSS23 and cancer stem cell marker CD44. Compared with SIGLEC15low cancer cells, SIGLEC15high ATC cells exhibited higher interaction frequency with tumor microenvironment cells. Further study showed that SIGLEC15high cancer cells mainly interacted with T cells by immunosuppressive signals such as MIF-TNFRSF14 and CXCL12-CXCR4. Notably, treatment of anti-SIGLEC15 antibody profoundly increased the cytotoxic ability of CD8+ T cells in a co-culture model and zebrafish-derived ATC xenografts. Consistently, administration of anti-SIGLEC15 antibody significantly inhibited tumor growth and prolonged mouse survival in an immunocompetent model of murine ATC, which was associated with increase of M1/M2, natural killer (NK) cells and CD8+ T cells, and decrease of myeloid-derived suppressor cells (MDSCs). SIGLEC15 inhibited T cell activation by reducing NFAT1, NFAT2, and NF-κB signals. Blocking SIGLEC15 increased the secretion of IFN-γ and IL-2 in vitro and in vivo. In conclusion, our finding demonstrates that SIGLEC15 is an emerging and promising target for immunotherapy in ATC.
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Affiliation(s)
- Lisha Bao
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, 310014, Hangzhou, China
| | - Ying Li
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Xiaoping Hu
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, 310014, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, 310014, Hangzhou, China
| | - Yingying Gong
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, 310014, Hangzhou, China
| | - Jinming Chen
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China
| | - Ping Huang
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, 310014, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, 310014, Hangzhou, China
| | - Zhuo Tan
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, 310014, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, 310014, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, 310014, Hangzhou, China
| | - Minghua Ge
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, 310014, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, 310014, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, 310014, Hangzhou, China.
| | - Zongfu Pan
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, 310014, Hangzhou, China; Clinical Research Center for Cancer of Zhejiang Province, 310014, Hangzhou, China.
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Maden SK, Huuki-Myers LA, Kwon SH, Collado-Torres L, Maynard KR, Hicks SC. lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression. bioRxiv 2024:2024.04.04.588105. [PMID: 38617294 PMCID: PMC11014536 DOI: 10.1101/2024.04.04.588105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Relative cell type fraction estimates in bulk RNA-sequencing data are important to control for cell composition differences across heterogenous tissue samples. Current computational tools estimate relative RNA abundances rather than cell type proportions in tissues with varying cell sizes, leading to biased estimates. We present lute, a computational tool to accurately deconvolute cell types with varying sizes. Our software wraps existing deconvolution algorithms in a standardized framework. Using simulated and real datasets, we demonstrate how lute adjusts for differences in cell sizes to improve the accuracy of cell composition. Software is available from https://bioconductor.org/packages/lute.
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Affiliation(s)
- Sean K. Maden
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Louise A. Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Kristen R. Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Michielsen L, Reinders MJT, Mahfouz A. Predicting cell population-specific gene expression from genomic sequence. Front Bioinform 2024; 4:1347276. [PMID: 38501113 PMCID: PMC10944912 DOI: 10.3389/fbinf.2024.1347276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/23/2024] [Indexed: 03/20/2024] Open
Abstract
Most regulatory elements, especially enhancer sequences, are cell population-specific. One could even argue that a distinct set of regulatory elements is what defines a cell population. However, discovering which non-coding regions of the DNA are essential in which context, and as a result, which genes are expressed, is a difficult task. Some computational models tackle this problem by predicting gene expression directly from the genomic sequence. These models are currently limited to predicting bulk measurements and mainly make tissue-specific predictions. Here, we present a model that leverages single-cell RNA-sequencing data to predict gene expression. We show that cell population-specific models outperform tissue-specific models, especially when the expression profile of a cell population and the corresponding tissue are dissimilar. Further, we show that our model can prioritize GWAS variants and learn motifs of transcription factor binding sites. We envision that our model can be useful for delineating cell population-specific regulatory elements.
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Affiliation(s)
- Lieke Michielsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Marcel J. T. Reinders
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Ahmed Mahfouz
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
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Matsushita Y, Liu J, Chu AKY, Ono W, Welch JD, Ono N. Endosteal stem cells at the bone-blood interface: A double-edged sword for rapid bone formation: Bone marrow endosteal stem cells provide a robust source of bone-making osteoblasts both in normal and abnormal bone formation. Bioessays 2024; 46:e2300173. [PMID: 38161246 DOI: 10.1002/bies.202300173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Endosteal stem cells are a subclass of bone marrow skeletal stem cell populations that are particularly important for rapid bone formation occurring in growth and regeneration. These stem cells are strategically located near the bone surface in a specialized microenvironment of the endosteal niche. These stem cells are abundant in young stages but eventually depleted and replaced by other stem cell types residing in a non-endosteal perisinusoidal niche. Single-cell molecular profiling and in vivo cell lineage analyses play key roles in discovering endosteal stem cells. Importantly, endosteal stem cells can transform into bone tumor-making cells when deleterious mutations occur in tumor suppressor genes. The emerging hypothesis is that osteoblast-chondrocyte transitional identities confer a special subset of endosteal stromal cells with stem cell-like properties, which may make them susceptible for tumorigenic transformation. Endosteal stem cells are likely to represent an important therapeutic target of bone diseases caused by aberrant bone formation.
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Affiliation(s)
- Yuki Matsushita
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Jialin Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Angel Ka Yan Chu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Wanida Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Noriaki Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas, USA
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Chen X, Qi Y, Huang Q, Sun C, Zheng Y, Ji L, Shi Y, Cheng X, Li Z, Zheng S, Cao Y, Gu Z, Yu J. Single-cell transcriptome characteristics of testicular terminal epithelium lineages during aging in the Drosophila. Aging Cell 2024; 23:e14057. [PMID: 38044573 DOI: 10.1111/acel.14057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/05/2023] Open
Abstract
Aging is a complex biological process leading to impaired functions, with a variety of hallmarks. In the testis of Drosophila, the terminal epithelium region is involved in spermatid release and maturation, while its functional diversity and regulatory mechanism remain poorly understood. In this study, we performed single-cell RNA-sequencing analysis (scRNA-seq) to characterize the transcriptomes of terminal epithelium in Drosophila testes at 2-, 10 and 40-Days. Terminal epithelium populations were defined with Metallothionein A (MtnA) and subdivided into six novel sub-cell clusters (EP0-EP5), and a series of marker genes were identified based on their expressions. The data revealed the functional characteristics of terminal epithelium populations, such as tight junction, focal adhesion, bacterial invasion, oxidative stress, mitochondrial function, proteasome, apoptosis and metabolism. Interestingly, we also found that disrupting genes for several relevant pathways in terminal epithelium led to male fertility disorders. Moreover, we also discovered a series of age-biased genes and pseudotime trajectory mediated state-biased genes during terminal epithelium aging. Differentially expressed genes during terminal epithelium aging were mainly participated in the regulation of several common signatures, e.g. mitochondria-related events, protein synthesis and degradation, and metabolic processes. We further explored the Drosophila divergence and selection in the functional constraints of age-biased genes during aging, revealing that age-biased genes in epithelial cells of 2 Days group evolved rapidly and were endowed with greater evolutionary advantages. scRNA-seq analysis revealed the diversity of testicular terminal epithelium populations, providing a gene target resource for further systematic research of their functions during aging.
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Affiliation(s)
- Xia Chen
- Department of Obstetrics and Gynecology, Nantong First People's Hospital, Affiliated Hospital 2 of Nantong University; Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Yujuan Qi
- Clinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Qiuru Huang
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China
| | - Chi Sun
- Department of Geriatrics, Affiliated Hospital of Nantong University, Nantong University, Nantong, China
| | - Yanli Zheng
- Department of Obstetrics and Gynecology, Nantong First People's Hospital, Affiliated Hospital 2 of Nantong University; Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Li Ji
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China
| | - Yi Shi
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China
| | - Xinmeng Cheng
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China
| | - Zhenbei Li
- Clinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Sen Zheng
- Clinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Yijuan Cao
- Clinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, China
| | - Zhifeng Gu
- Department of Rheumatology, Affiliated Hospital of Nantong University, Nantong University, Nantong, China
| | - Jun Yu
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China
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Lin Q, Zeng R, Yang J, Xu Z, Jin S, Wei G. Prognostic stratification of sepsis through DNA damage response based RiskScore system: insights from single-cell RNA-sequencing and transcriptomic profiling. Front Immunol 2024; 15:1345321. [PMID: 38404591 PMCID: PMC10884272 DOI: 10.3389/fimmu.2024.1345321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Background A novel risk scoring system, predicated on DNA damage response (DDR), was developed to enhance prognostic predictions and potentially inform the creation of more effective therapeutic protocols for sepsis. Methods To thoroughly delineate the expression profiles of DDR markers within the context of sepsis, an analytical approach utilizing single-cell RNA-sequencing (scRNA-seq) was implemented. Our study utilized single-cell analysis techniques alongside weighted gene co-expression network analysis (WGCNA) to pinpoint the genes that exhibit the most substantial associations with DNA damage response (DDR). Through Cox proportional hazards LASSO regression, we distinguished DDR-associated genes and established a risk model, enabling the stratification of patients into high- and low-risk groups. Subsequently, we carried out an analysis to determine our model's predictive accuracy regarding patient survival. Moreover, we examined the distinct biological characteristics, various signal transduction routes, and immune system responses in sepsis patients, considering different risk categories and outcomes related to survival. Lastly, we conducted experimental validation of the identified genes through in vivo and in vitro assays, employing RT-PCR, ELISA, and flow cytometry. Results Both single-cell RNA sequencing (scRNA-seq) and bulk transcriptomic analyses have demonstrated a strong correlation between DNA damage response (DDR) levels and sepsis prognosis. Specific cell subtypes, including monocytes, megakaryocytes, CD4+ T cells, and neutrophils, have shown elevated DDR activity. Cells with increased DDR scores exhibited more robust and numerous interactions with other cell populations. The weighted gene co-expression network analysis (WGCNA) and single-cell analyses revealed 71 DDR-associated genes. We developed a four-gene risk scoring system using ARL4C, CD247, RPL7, and RPL31, identified through univariate COX, LASSO COX regression, and log-rank (Mantel-Cox) tests. Nomograms, calibration plots, and decision curve analyses (DCA) regarding these specific genes have provided significant clinical benefits for individuals diagnosed with sepsis. The study suggested that individuals categorized as lower-risk demonstrated enhanced infiltration of immune cells, upregulated expression of immune regulators, and a more prolific presence of immune-associated functionalities and pathways. RT-qPCR analyses on a sepsis rat model revealed differential gene expression predominantly in the four targeted genes. Furthermore, ARL4C knockdown in sepsis model in vivo and vitro caused increased inflammatory response and a worse prognosis. Conclusion The delineated DDR expression landscape offers insights into sepsis pathogenesis, whilst our riskScore model, based on a robust four-gene signature, could underpin personalized sepsis treatment strategies.
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Affiliation(s)
| | | | | | | | | | - Guan Wei
- Department of Emergency Surgery, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
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Yamaguchi K, Nakayama J, Yamamoto T, Semba K, Shirota T, Yamamoto Y. Collagen induction of immune cells in the mammary glands during pregnancy. Physiol Genomics 2024; 56:128-135. [PMID: 37955336 DOI: 10.1152/physiolgenomics.00098.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/14/2023] Open
Abstract
The mammary glands are dynamic tissues affected by pregnancy-related hormones during the pregnancy-lactation cycle. Collagen production and its dynamics are essential to the remodeling of the mammary glands. Alterations of the mammary microenvironment and stromal cells during the pregnancy-lactation cycle are important for understanding the physiology of the mammary glands and the development of breast tumors. In this study, we performed an evaluation of collagen dynamics in the mammary fat pad during the pregnancy-lactation cycle. Reanalysis of single-cell RNA-sequencing (scRNA-Seq) data showed the ectopic collagen expression in the immune cells and cell-cell interactions for collagens with single-cell resolution. The scRNA-Seq data showed that type I and type III collagen were produced not only by stromal fibroblasts but also by lymphoid and myeloid cell types in the pregnancy phase. Furthermore, the total cell-cell interaction score for collagen interactions was dramatically increased in the pregnancy tissue. The data presented in this study provide evidence that immune cells contribute, at least in part, to mammary collagen dynamics. Our findings suggest that immune cells, including lymphoid and myeloid cells, might be supportive members of the extracellular matrix orchestration in the pregnancy-lactation cycle of the mammary glands.NEW & NOTEWORTHY Our study evaluated mammary gland collagen dynamics during the pregnancy-lactation cycle using single-cell RNA-sequencing data. We found ectopic collagen expression in immune cells and an increase in collagen interactions during pregnancy. Type I and type III collagen were produced by lymphoid, myeloid, and stromal fibroblast cells during pregnancy. These findings suggest that immune cells, including lymphoid and myeloid cells, play a crucial role in supporting the extracellular matrix in mammary glands during pregnancy-lactation cycles.
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Affiliation(s)
- Karen Yamaguchi
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Tokyo, Japan
| | - Jun Nakayama
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Tomofumi Yamamoto
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Molecular and Cellular Medicine, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Translational Research Center, Fukushima Medical University, Fukushima, Japan
| | - Tatsuo Shirota
- Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Tokyo, Japan
| | - Yusuke Yamamoto
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
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Wohnhaas CT, Baßler K, Watson CK, Shen Y, Leparc GG, Tilp C, Heinemann F, Kind D, Stierstorfer B, Delić D, Brunner T, Gantner F, Schultze JL, Viollet C, Baum P. Monocyte-derived alveolar macrophages are key drivers of smoke-induced lung inflammation and tissue remodeling. Front Immunol 2024; 15:1325090. [PMID: 38348034 PMCID: PMC10859862 DOI: 10.3389/fimmu.2024.1325090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Smoking is a leading risk factor of chronic obstructive pulmonary disease (COPD), that is characterized by chronic lung inflammation, tissue remodeling and emphysema. Although inflammation is critical to COPD pathogenesis, the cellular and molecular basis underlying smoking-induced lung inflammation and pathology remains unclear. Using murine smoke models and single-cell RNA-sequencing, we show that smoking establishes a self-amplifying inflammatory loop characterized by an influx of molecularly heterogeneous neutrophil subsets and excessive recruitment of monocyte-derived alveolar macrophages (MoAM). In contrast to tissue-resident AM, MoAM are absent in homeostasis and characterized by a pro-inflammatory gene signature. Moreover, MoAM represent 46% of AM in emphysematous mice and express markers causally linked to emphysema. We also demonstrate the presence of pro-inflammatory and tissue remodeling associated MoAM orthologs in humans that are significantly increased in emphysematous COPD patients. Inhibition of the IRAK4 kinase depletes a rare inflammatory neutrophil subset, diminishes MoAM recruitment, and alleviates inflammation in the lung of cigarette smoke-exposed mice. This study extends our understanding of the molecular signaling circuits and cellular dynamics in smoking-induced lung inflammation and pathology, highlights the functional consequence of monocyte and neutrophil recruitment, identifies MoAM as key drivers of the inflammatory process, and supports their contribution to pathological tissue remodeling.
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Affiliation(s)
- Christian T. Wohnhaas
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Carolin K. Watson
- Immunology & Respiratory Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Yang Shen
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Germán G. Leparc
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Cornelia Tilp
- Immunology & Respiratory Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Fabian Heinemann
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - David Kind
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Birgit Stierstorfer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Denis Delić
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Mannheim, Germany
| | - Thomas Brunner
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Florian Gantner
- Department of Biology, University of Konstanz, Konstanz, Germany
- Translational Medicine & Clinical Pharmacology, C. H. Boehringer Sohn AG & Co. KG, Biberach, Germany
| | - Joachim L. Schultze
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn, Bonn, Germany
| | - Coralie Viollet
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Patrick Baum
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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9
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Li J, Gui T, Yao L, Guo H, Lin YL, Lu J, Duffy M, Zgonis M, Mauck R, Dyment N, Zhang Y, Scanzello C, Seale P, Qin L. Synovium and infrapatellar fat pad share common mesenchymal progenitors and undergo coordinated changes in osteoarthritis. J Bone Miner Res 2024:zjad009. [PMID: 38477740 DOI: 10.1093/jbmr/zjad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/09/2023] [Accepted: 12/01/2023] [Indexed: 03/14/2024]
Abstract
Osteoarthritis (OA) affects multiple tissues in the knee joint, including the synovium and intra-articular adipose tissue (IAAT) that are attached to each other. However, whether these two tissues share the same progenitor cells and hence function as a single unit in joint homeostasis and diseases is largely unknown. Single-cell transcriptomic profiling of synovium and infrapatellar fat pad (IFP), the largest IAAT, from control and OA mice revealed five mesenchymal clusters and predicted mesenchymal progenitor cells (MPCs) as the common progenitors for other cells: synovial lining fibroblasts (SLFs), myofibroblasts (MFs), and preadipocytes 1 and 2. Histologic examination of joints in reporter mice having Dpp4-CreER and Prg4-CreER that label MPCs and SLFs, respectively, demonstrated that Dpp4+ MPCs reside in the synovial sublining layer and give rise to Prg4+ SLFs and Perilipin+ adipocytes during growth and OA progression. After OA injury, both MPCs and SLFs gave rise to MFs, which remained in the thickened synovium at later stages of OA. In culture, Dpp4+ MPCs possessed mesenchymal progenitor properties, such as proliferation and multilineage differentiation. In contrast, Prg4+ SLFs did not contribute to adipocytes in IFP and Prg4+ cells barely grew in vitro. Taken together, we demonstrate that the synovium and joint fat pad are one integrated functional tissue sharing common mesenchymal progenitors and undergoing coordinated changes during OA progression.
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Affiliation(s)
- Jun Li
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tao Gui
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Bone and Joint Surgery, Institute of Orthopedic Diseases, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, China
| | - Lutian Yao
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Orthopaedics, The First Hospital of China Medical University, Shenyang, Liaoning Province 110112, China
| | - Hanli Guo
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Yu-Lieh Lin
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Jiawei Lu
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Michael Duffy
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Miltiadis Zgonis
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Robert Mauck
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Translational Musculoskeletal Research Center, Corp. Michael J Crescenz, VA Medical Center, Philadelphia PA 19104, United States
| | - Nathaniel Dyment
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Yejia Zhang
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Translational Musculoskeletal Research Center, Corp. Michael J Crescenz, VA Medical Center, Philadelphia PA 19104, United States
- Department of Physical Medicine & Rehabilitation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Carla Scanzello
- Translational Musculoskeletal Research Center, Corp. Michael J Crescenz, VA Medical Center, Philadelphia PA 19104, United States
- Division of Rheumatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Patrick Seale
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Ling Qin
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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10
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Yoshitake R, Mori H, Ha D, Wu X, Wang J, Wang X, Saeki K, Chang G, Shim HJ, Chan Y, Chen S. Molecular features of luminal breast cancer defined through spatial and single-cell transcriptomics. Clin Transl Med 2024; 14:e1548. [PMID: 38282415 PMCID: PMC10823285 DOI: 10.1002/ctm2.1548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 12/28/2023] [Accepted: 01/06/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Intratumour heterogeneity is a hallmark of most solid tumours, including breast cancers. We applied spatial transcriptomics and single-cell RNA-sequencing on patient-derived xenografts (PDXs) to profile spatially resolved cell populations within oestrogen receptor-positive (ER+ ) breast cancer and to elucidate their importance in oestrogen-dependent tumour growth. METHODS Two PDXs of 'ER-high' breast cancers with opposite oestrogen-mediated growth responses were investigated: oestrogen-suppressed GS3 (80-100% ER) and oestrogen-dependent SC31 (40-90% ER) models. The observation was validated via single-cell analyses on an 'ER-low' PDX, GS1 (5% ER). The results from our spatial and single-cell analyses were further supported by a public ER+ breast cancer single-cell dataset and protein-based dual immunohistochemistry (IHC) of SC31 examining important luminal cancer markers (i.e., ER, progesterone receptor and Ki67). The translational implication of our findings was assessed by clinical outcome analyses on publicly available cohorts. RESULTS Our space-gene-function study revealed four spatially distinct compartments within ER+ breast cancers. These compartments showed functional diversity (oestrogen-responsive, proliferative, hypoxia-induced and inflammation-related). The 'proliferative' population, rather than the 'oestrogen-responsive' compartment, was crucial for oestrogen-dependent tumour growth, leading to the acquisition of luminal B-like features. The cells expressing typical oestrogen-responsive genes like PGR were not directly linked to oestrogen-dependent proliferation. Dual IHC analyses demonstrated the distinct contribution of the Ki67+ proliferative cells toward oestrogen-mediated growth and their response to a CDK4/6 inhibitor. The gene signatures derived from the proliferative, hypoxia-induced and inflammation-related compartments were significantly correlated with worse clinical outcomes, while patients with the oestrogen-responsive signature showed better prognoses, suggesting that this compartment would not be directly associated with oestrogen-dependent tumour progression. CONCLUSIONS Our study identified the gene signature in our 'proliferative' compartment as an important determinant of luminal cancer subtypes. This 'proliferative' cell population is a causative feature of luminal B breast cancer, contributing toward its aggressive behaviours.
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Affiliation(s)
- Ryohei Yoshitake
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Hitomi Mori
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
- Department of Surgery and OncologyGraduate School of Medicine, Kyushu UniversityFukuokaJapan
| | - Desiree Ha
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Xiwei Wu
- Integrative Genomics CoreBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Jinhui Wang
- Integrative Genomics CoreBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Xiaoqiang Wang
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Kohei Saeki
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
- Faculty of Veterinary MedicineOkayama University of ScienceImabariEhimeJapan
| | - Gregory Chang
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Hyun Jeong Shim
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Yin Chan
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
| | - Shiuan Chen
- Department of Cancer Biology and Molecular MedicineBeckman Research Institute of City of HopeDuarteCaliforniaUSA
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11
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Ma F, Gharaee-Kermani M, Tsoi LC, Plazyo O, Chaskar P, Harms P, Patrick MT, Xing X, Hile G, Piketty C, Lazzari A, Van Delm W, Maverakis E, Nakamura M, Modlin RL, Kahlenberg JM, Billi AC, Julia V, Krishnaswamy JK, Gudjonsson JE. Single-cell profiling of prurigo nodularis demonstrates immune-stromal crosstalk driving profibrotic responses and reversal with nemolizumab. J Allergy Clin Immunol 2024; 153:146-160. [PMID: 37506977 DOI: 10.1016/j.jaci.2023.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Prurigo nodularis (PN) is a chronic neuroimmune skin disease characterized by bilaterally distributed pruritic hyperkeratotic nodules on extremities and trunk. Neuroimmune dysregulation and chronic scratching are believed to both induce and maintain the characteristic lesions. OBJECTIVES This study sought to provide a comprehensive view of the molecular pathogenesis of PN at the single-cell level to identify and outline key pathologic processes and the cell types involved. Features that distinguish PN skin from the skin of patients with atopic dermatitis were of particular interest. We further aimed to determine the impact of the IL31RA antagonist, nemolizumab, and its specificity at the single-cell level. METHODS Single-cell RNA-sequencing of skin from 15 healthy donors and nonlesional and lesional skin from 6 patients each with PN and atopic dermatitis, combined with spatial-sequencing using the 10x Visium platform. Integration with bulk RNA-sequencing data from patients treated with nemolizumab. RESULTS This study demonstrates that PN is an inflammatory skin disease characterized by both keratinocyte proliferation and activation of profibrotic responses. This study also demonstrates that the COL11A1+ fibroblast subset is a major contributor to fibrosis and is predominantly found in the papillary dermis of PN skin. Activation of fibrotic responses is the main distinguishing feature between PN and atopic dermatitis skin. This study further shows the broad effect of nemolizumab on PN cell types, with a prominent effect driving COL11A1+ fibroblast and keratinocyte responses toward normal. CONCLUSIONS This study provides a high-resolution characterization of the cell types and cellular processes activated in PN skin, establishing PN as a chronic fibrotic inflammatory skin disease. It further demonstrates the broad effect of nemolizumab on pathological processes in PN skin.
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Affiliation(s)
- Feiyang Ma
- Department of Dermatology, University of Michigan, Ann Arbor, Mich
| | | | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Mich; Department of Biostatistics, University of Michigan, Ann Arbor, Mich; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Mich
| | - Olesya Plazyo
- Department of Dermatology, University of Michigan, Ann Arbor, Mich
| | | | - Paul Harms
- Department of Dermatology, University of Michigan, Ann Arbor, Mich; Department of Pathology, University of Michigan, Ann Arbor, Mich
| | | | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Mich
| | - Grace Hile
- Department of Dermatology, University of Michigan, Ann Arbor, Mich
| | | | | | | | - Emanual Maverakis
- Department of Dermatology, University of California-Davis, Sacramento, Calif
| | - Mio Nakamura
- Department of Dermatology, University of Michigan, Ann Arbor, Mich
| | - Robert L Modlin
- Department of Dermatology, University of California-Los Angeles, Calif
| | - J Michelle Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, Mich; Taubman Medical Research Institute, University of Michigan, Ann Arbor, Mich
| | - Allison C Billi
- Department of Dermatology, University of Michigan, Ann Arbor, Mich
| | | | | | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, Mich; Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, Mich; Taubman Medical Research Institute, University of Michigan, Ann Arbor, Mich.
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12
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Jiang H, Liu J, Song Y, Lei J. Quantitative Modeling of Stemness in Single-Cell RNA Sequencing Data: A Nonlinear One-Class Support Vector Machine Method. J Comput Biol 2024; 31:41-57. [PMID: 38010500 DOI: 10.1089/cmb.2022.0484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Intratumoral heterogeneity and the presence of cancer stem cells are challenging issues in cancer therapy. An appropriate quantification of the stemness of individual cells for assessing the potential for self-renewal and differentiation from the cell of origin can define a measurement for quantifying different cell states, which is important in understanding the dynamics of cancer evolution, and might further provide possible targeted therapies aimed at tumor stem cells. Nevertheless, it is usually difficult to quantify the stemness of a cell based on molecular information associated with the cell. In this study, we proposed a stemness definition method with one-class Hadamard kernel support vector machine (OCHSVM) based on single-cell RNA sequencing (scRNA-seq) data. Applications of the proposed OCHSVM stemness are assessed by various data sets, including preimplantation embryo cells, induced pluripotent stem cells, or tumor cells. We further compared the OCHSVM model with state-of-the-art methods CytoTRACE, one-class logistic regression, or one-class SVM methods with different kernels. The computational results demonstrate that the OCHSVM method is more suitable for stemness identification using scRNA-seq data.
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Affiliation(s)
- Hao Jiang
- School of Mathematics, Renmin University of China, Beijing, China
| | - Jingxin Liu
- School of Software, Beihang University, Beijing, China
| | - You Song
- School of Software, Beihang University, Beijing, China
| | - Jinzhi Lei
- School of Mathematical Sciences, Center for Applied Mathematics, Tiangong University, Tianjin, China
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13
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Mu Y, Zheng D, Peng Q, Wang X, Zhang Y, Yin Y, Wang E, Ye F, Wang J. Integration of single-cell and bulk RNA-sequencing to analyze the heterogeneity of hepatocellular carcinoma and establish a prognostic model. Cancer Rep (Hoboken) 2024; 7:e1935. [PMID: 37994394 PMCID: PMC10809200 DOI: 10.1002/cnr2.1935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/18/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The highly heterogeneous nature of hepatocellular carcinoma (HCC) results in different responses and prognoses to the same treatment in patients with similar clinical stages. AIMS Thus, it is imperative to investigate the association between HCC tumor heterogeneity and treatment response and prognosis. METHODS AND RESULTS At first, we downloaded scRNA-seq, bulk RNA-seq, and clinical data from TCGA and GEO databases. We conducted quality control, normalization using SCTransform, dimensionality reduction using PCA, batch effect removal using Harmony, dimensionality reduction using UMAP, and cell annotation-based marker genes on the scRNA-seq data. We recognized tumor cells, identified tumor-related genes (TRGs), and performed cell communication analysis. Next, we developed a prognostic model using univariable Cox, LASSO, and multivariate Cox analyses. The signature was evaluated using survival analysis, ROC curves, C-index, and nomogram. Last, we studied the predictability of the signature in terms of prognosis and immunotherapeutic response for HCC, assessed a variety of drugs for clinical treatment, and used the qRT-PCR analysis to validate the mRNA expression levels of prognostic TRGs. CONCLUSION To conclude, this study expounded upon the influence of tumor cell heterogeneity on the prediction of treatment outcomes and prognosis in HCC. This, in turn, enhances the predictive ability of the TNM staging system and furnishes novel perspectives on the prognostic assessment and therapy of HCC.
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Affiliation(s)
- Yaping Mu
- The School of Integrated Traditional Chinese and Western MedicineSouthwest Medical UniversityLuzhouSichuanChina
| | - Ding Zheng
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Qinghua Peng
- The School of Integrated Traditional Chinese and Western MedicineSouthwest Medical UniversityLuzhouSichuanChina
| | - Xiaodong Wang
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Yurong Zhang
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Yue Yin
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Encheng Wang
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
| | - Fei Ye
- School of Traditional Chinese MedicineBeijing University of Traditional Chinese MedicineBeijingChina
| | - Jing Wang
- The School of Integrated Traditional Chinese and Western MedicineSouthwest Medical UniversityLuzhouSichuanChina
- Department of HepatobiliaryThe Affiliated Traditional Chinese Medicine Hospital of Southwest Medical UniversityLuzhouSichuanChina
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14
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Pan Q, Liu R, Zhang X, Cai L, Li Y, Dong P, Gao J, Liu Y, He L. CXCL14 as a potential marker for immunotherapy response prediction in renal cell carcinoma. Ther Adv Med Oncol 2023; 15:17588359231217966. [PMID: 38152696 PMCID: PMC10752123 DOI: 10.1177/17588359231217966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023] Open
Abstract
Background Epigenetic mechanisms play vital roles in the activation, differentiation, and effector function of immune cells. The breast and kidney-expressed chemokine (CXCL14) mainly contributes to the regulation of immune cells. However, its role in shaping the tumor immune microenvironment (TIME) is yet to be elucidated in renal cell carcinoma (RCC). Objectives This study aimed to elucidate the role of CXCL14 in predicting the efficacy of immunotherapy in patients with RCC. Methods CXCL14 expression and RNA-sequencing, single-cell RNA-sequencing (scRNA-seq), and survival datasets of RCC from public databases were analyzed, and survival was compared between different CXCL14 levels. The correlation between CXCL14 and immune infiltration and human leukocyte antigen (HLA) gene expression was analyzed with TIMER2.0 and gene expression profiling interactive analysis. Institutional scRNA-seq and immunohistochemical staining analyses were used to verify the relationship between CXCL14 expression level and the efficacy of immunotherapy. Results CXCL14 was expressed in fibroblast and malignant cells in RCC, and higher expression was associated with better survival. Enrichment analysis revealed that CXCL14 is involved in immune activation, primarily in antigen procession, antigen presentation, and major histocompatibility complex assemble. CXCL14 expression was positively correlated with T-cell infiltration as well as HLA-related gene expression. Among the RCC cohort receiving nivolumab in Checkmate 025, the patients with CXCL14 high expression had better overall survival than those with CXCL14 low expression after immunotherapy. scRNA-seq revealed a cluster of CXCL14+ fibroblast in immunotherapy responders. Immunohistochemistry analysis verified that the patients with high CXCL14 expression had an increased proportion of high CD8 expression simultaneously. The expression level of CXCL14 was associated with CXCR4 expression in RCC. Conclusion CXCL14 expression is associated with immunotherapy response in RCC. It is a promising biomarker for immunotherapy response prediction and may be an effective epigenetic modulator in combination with immunotherapy approaches.
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Affiliation(s)
- Qiwen Pan
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ruiqi Liu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xinyue Zhang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Lingling Cai
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yilin Li
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Pei Dong
- Department of Urology Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jianming Gao
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yang Liu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou 510060, P. R. China
| | - Liru He
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou 510060, P. R. China
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15
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Hess A, Gentile SD, Ben Saad A, Rahman R, Habboub T, Pratt DS, Mullen AC. Single-cell transcriptomics stratifies organoid models of metabolic dysfunction-associated steatotic liver disease. EMBO J 2023; 42:e113898. [PMID: 37962490 PMCID: PMC10711666 DOI: 10.15252/embj.2023113898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 11/15/2023] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing cause of morbidity with limited treatment options. Thus, accurate in vitro systems to test new therapies are indispensable. While recently, human liver organoid models have emerged to assess steatotic liver disease, a systematic evaluation of their translational potential is still missing. Here, we evaluated human liver organoid models of MASLD, comparatively testing disease induction in three conditions: oleic acid, palmitic acid, and TGF-β1. Through single-cell analyses, we find that all three models induce inflammatory signatures, but only TGF-β1 promotes collagen production, fibrosis, and hepatic stellate cell expansion. In striking contrast, oleic acid ameliorates fibrotic signatures and reduces the hepatic stellate cell population. Linking data from each model to gene expression signatures associated with MASLD disease progression further demonstrates that palmitic acid and TGF-β1 more robustly model inflammation and fibrosis. Our findings highlight the importance of stratifying MASLD organoid models by signatures of clinical disease progression, provide a single-cell reference to benchmark future organoid injury models, and allow us to study evolving steatohepatitis, fibrosis, and HSC susceptibility to injury in a dynamic, multi-lineage human in vitro system.
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Affiliation(s)
- Anja Hess
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Present address:
Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
| | - Stefan D Gentile
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Klarman Cell ObservatoryBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Amel Ben Saad
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Raza‐Ur Rahman
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Tim Habboub
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Daniel S Pratt
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Autoimmune and Cholestatic Liver CenterMassachusetts General HospitalBostonMAUSA
| | - Alan C Mullen
- Division of Gastroenterology, Massachusetts General HospitalHarvard Medical SchoolBostonMAUSA
- Klarman Cell ObservatoryBroad Institute of MIT and HarvardCambridgeMAUSA
- Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonMAUSA
- Harvard Stem Cell InstituteCambridgeMAUSA
- Present address:
University of Massachusetts Chan Medical SchoolWorcesterMAUSA
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16
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Schmøkel SS, Nordentoft I, Lindskrog SV, Lamy P, Knudsen M, Jensen JB, Dyrskjøt L. Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies. Nucleus 2023; 14:2186686. [PMID: 36878883 PMCID: PMC10012951 DOI: 10.1080/19491034.2023.2186686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection: sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed that a combination of IgePal lysis buffer, tissue dissection by sectioning, and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well-described clinical and histopathological information and known clinical outcomes with snRNA-seq.
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Affiliation(s)
- Sofie S Schmøkel
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sia V Lindskrog
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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17
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Shi J, Li J, Wang H, Li X, Wang Q, Zhao C, Cheng L, Han R, Chen P, Guo H, Tang Z, Zhou C, Zhang Z, Wu F. Single-Cell Profiling of Tumor-Associated Neutrophils in Advanced Non-Small Cell Lung Cancer. Lung Cancer (Auckl) 2023; 14:85-99. [PMID: 38025400 PMCID: PMC10676108 DOI: 10.2147/lctt.s430967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023]
Abstract
Purpose Neutrophils act as a non-negligible regulator in the initiation and progression of malignancies, playing bifacial roles in the process. Thus, to understand the heterogeneity of tumor-associated neutrophils (TANs) comprehensively in advanced non-small cell lung cancer (NSCLC) at single-cell resolution is necessary and urgent. Materials and Methods We applied single-cell RNA-sequencing (scRNA-seq) to portray the subtype-specific transcriptome landscape of TANs in advanced NSCLC using nine freshly obtained specimens. The scRNA-seq data were further processed for pseudo-time analysis to depict the developmental trajectory of TANs. Meanwhile, the interplay between TANs and other cell types within tumor microenvironment (TME) was revealed by intercellular interaction analysis. Results Seven distinct TAN subtypes were defined, of which, the N3 cluster was considered inflammatory phenotype expressing genes encoding multiple chemotactic cytokines, and correlated with inferior overall survival, indicating that N3 might be a pro-tumorigenic TAN subtype. N1 and N5 clusters were considered to be well differentiated and mature neutrophils based on CXCR2 expression and pseudo-time patterns, and both accounted for relatively high proportions in lung adenocarcinoma. In addition, genes related to neutrophil differentiation were discovered. We also found that TAN subtypes interacted most closely with macrophages through chemokine signaling pathways within TME. Conclusion Our study refined TAN subtypes and mapped the transcriptome landscape of TANs at single-cell resolution in advanced NSCLC, collectively indicating the heterogeneity of TANs in NSCLC. Neutrophil differentiation- and maturation-related genes were also discovered, which shed light on different functions of TAN subclones in tumor immune escape, and may further provide novel targets for immunotherapy.
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Affiliation(s)
- Jinpeng Shi
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Jiayu Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Haowei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Qi Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Chao Zhao
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Lei Cheng
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Ruoshuang Han
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Peixin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Haoyue Guo
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Zhuoran Tang
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Zhemin Zhang
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Fengying Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, School of Medicine, Tongji University, Shanghai, People’s Republic of China
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Kim CW, Joo SY, Kim B, Kim JY, Jang S, Tzeng SJ, Lee SJ, Kim M, Kim I. Single cell transcriptome analyses reveal the roles of B cells in fructose-induced hypertension. Front Immunol 2023; 14:1279439. [PMID: 38045685 PMCID: PMC10691591 DOI: 10.3389/fimmu.2023.1279439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023] Open
Abstract
Rationale While the immune system plays a crucial role in the development of hypertension, the specific contributions of distinct immune cell populations remain incompletely understood. The emergence of single-cell RNA-sequencing (scRNA-seq) technology enables us to analyze the transcriptomes of individual immune cells and to assess the significance of each immune cell type in hypertension development. Objective We aimed to investigate the hypothesis that B cells play a crucial role in the development of fructose-induced hypertension. Methods and Results Eight-week-old Dahl salt-sensitive (SS) male rats were divided into two groups and given either tap water (TW) or a 20% fructose solution (HFS) for 4 weeks. Systolic blood pressure was measured using the tail-cuff method. ScRNA-seq analysis was performed on lamina propria cells (LPs) and peripheral blood mononuclear cells (PBMCs) obtained from SS rats subjected to either TW or HFS. The HFS treatment induced hypertension in the SS rats. The analysis revealed 27 clusters in LPs and 28 clusters in PBMCs, allowing for the identification and characterization of various immune cell types within each cluster. Specifically, B cells and follicular helper T (Tfh) cells were prominent in LPs, while B cells and M1 macrophages dominated PBMCs in the HFS group. Moreover, the HFS treatment triggered an increase in the number of B cells in both LPs and PBMCs, accompanied by activation of the interferon pathway. Conclusions The significant involvement of B cells in intestinal and PBMC responses indicates their pivotal contribution to the development of hypertension. This finding suggests that targeting B cells could be a potential strategy to mitigate high blood pressure in fructose-induced hypertension. Moreover, the simultaneous increase in follicular B cells and Tfh cells in LPs, along with the upregulation of interferon pathway genes in B cells, underscores a potential autoimmune factor contributing to the pathogenesis of fructose-induced hypertension in the intestine.
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Affiliation(s)
- Cheong-Wun Kim
- Department of Pharmacology, BK21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sung Yong Joo
- Department of Animal Science, Pusan National University, Miryang, Republic of Korea
| | - Boa Kim
- Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jee Young Kim
- Department of Pharmacology, BK21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sungmin Jang
- Department of Pharmacology, BK21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shiang-Jong Tzeng
- Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sang Jin Lee
- Division of Rheumatology, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Myunghoo Kim
- Department of Animal Science, Pusan National University, Miryang, Republic of Korea
| | - Inkyeom Kim
- Department of Pharmacology, BK21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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Qi J, Zhu H, Li Y, Guan X, He Y, Ren G, Guo Q, Liu L, Gu Y, Dong X, Liu Y. Creation of a High-Throughput Microfluidic Platform for Single-Cell Transcriptome Sequencing of Cell-Cell Interactions. Small Methods 2023; 7:e2300730. [PMID: 37712212 DOI: 10.1002/smtd.202300730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/21/2023] [Indexed: 09/16/2023]
Abstract
Cell-cell interaction is one of the major modalities for transmitting information between cells and activating the effects of functional cells. However, the construction of high-throughput analysis technologies from cell omics focusing on the impact of interactions of functional cells on targets has been relatively unexplored. Here, they propose a droplet-based microfluidic platform for cell-cell interaction sequencing (c-c-seq) and screening in vitro to address this challenge. A class of interacting cells is pre-labeled using cell molecular tags, and additional single-cell sequencing reagents are introduced to quickly form functional droplet mixes. Lastly, gene expression analysis is used to deduce the impact of the interaction, while molecular sequence tracing identifies the type of interaction. Research into the active effect between antigen-presenting cells and T cells, one of the most common cell-to-cell interactions, is crucial for the advancement of cancer therapy, particularly T cell receptor-engineered T cell therapy. As it allows for high throughput, this platform is superior to well plates as a research platform for cell-to-cell interactions. When combined with the next generation of sequencing, the platform may be able to more accurately evaluate interactions between epitopes and receptors and verify their functional relevance.
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Affiliation(s)
- Jingyu Qi
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Yijian Li
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangyu Guan
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying He
- Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Guanhua Ren
- China National Institute of Standardization, Beijing, 100191, China
| | - Qiang Guo
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Ying Gu
- BGI Research, Shenzhen, 518083, China
| | - Xuan Dong
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, 518083, China
| | - Ya Liu
- BGI Research, Shenzhen, 518083, China
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Zhao H, Li Y, Sun G, Cheng M, Ding X, Wang K. Single-cell transcriptional gene signature analysis identifies IL-17 signaling pathway as the key pathway in sepsis. Immunobiology 2023; 228:152763. [PMID: 38039751 DOI: 10.1016/j.imbio.2023.152763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/27/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
Sepsis is a multiple dysregulated systemic inflammatory response with high mortality and leads to public concern. This study was designed to identify possible critical pathways associated with sepsis clinical severity and outcome, which offer potential biomarkers and therapeutic targets for sepsis diagnosis and treatment. Single-cell transcriptome profiles of human peripheral blood mononuclear (PBMC) in the healthy control population and sepsis patients were downloaded from the sepsis database GSE167363 and performed quality control before subsequent analysis. The bulk-RNA sequencing of blood samples in the sepsis-associated databases GSE100159 and GSE133822 was also used to confirm the association between critical pathways and sepsis pathology after processing raw data. We found there was a total of 18 distinct clusters in PBMC of sepsis, which was identified by the t-SNE and UMAP dimension reduction analysis. Meanwhile, the main cell types including B, NK, T, and monocyte cells were identified via the cell maker website and the "Single R" package cell-type annotation analysis. Subsequently, GO and KEGG enrichment analysis of differential expression genes in each cluster found that DEGs between healthy control and sepsis patients were significantly enriched in the IL-17 signaling pathway in monocyte, NK, and T cells. Finally, GSE100159 and GSE133822 confirmed IL-17 signaling pathway-associated genes including IL-17R, TRAF6, RELB, TRAF5, CEBPB, JUNB, CXCL1, CXCL3, CXCL8, CXCR1, and CXCR2 were significantly up-regulated in sepsis blood samples compared with the age-matched healthy control population. Taken together, we concluded that the IL-17 signaling pathway serves as a significant potential mechanism of sepsis and provides a promising therapeutic target for sepsis treatment. This research will further deepen our understanding of sepsis development.
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Affiliation(s)
- Huayan Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuanzhe Li
- Department of Pediatrics, Children's Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guiying Sun
- Epidemiology and Statistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ming Cheng
- Medical Information, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xianfei Ding
- General Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Kun Wang
- Department of Anesthesiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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21
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Hsu P, Choi, EJ, Patel, SA, Wong, WH, Olvera, JG, Yao, P, Liu YC, Tsai MS, Wang W, Boland BS, Chang JT. Responsiveness to Vedolizumab Therapy in Ulcerative Colitis is Associated With Alterations in Immune Cell-Cell Communications. Inflamm Bowel Dis 2023; 29:1602-1612. [PMID: 37235748 PMCID: PMC10547234 DOI: 10.1093/ibd/izad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Ulcerative colitis (UC) and Crohn's disease are 2 types of inflammatory bowel disease (IBD), a group of chronic digestive disorders caused by aberrant immune responses to intestinal microbes. Although changes in the composition of immune cell subsets in the context of IBD have been previously described, the interactions and communication among cells are less well understood. Moreover, the precise mechanisms of action underlying many biologic therapies, including the anti-α4β7 integrin antagonist vedolizumab, remain incompletely understood. Our study aimed to explore possible additional mechanisms through which vedolizumab acts. METHODS We performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) on peripheral blood and colon immune cells derived from patients with ulcerative colitis treated with the anti-α4β7 integrin antagonist vedolizumab. We applied a previously published computational approach, NicheNet, to predict immune cell-cell interactions, revealing putative ligand-receptor pairs and key transcriptional changes downstream of these cell-cell communications (CCC). RESULTS We observed decreased proportions of T helper 17 (TH17) cells in UC patients who responded to vedolizumab and therefore focused the study on identifying cell-cell communications and signals of TH17 cells with other immune cells. For example, we observed that colon TH17 cells from vedolizumab nonresponders were predicted to have a greater degree of interactions with classical monocytes compared with responders, whereas colon TH17 cells from vedolizumab responders exhibited more interactions with myeloid dendritic cells compared with nonresponders. CONCLUSIONS Overall, our results indicate that efforts to elucidate cell-cell communications among immune and nonimmune cell types may increase the mechanistic understanding of current and investigational therapies for IBD.
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Affiliation(s)
- Paul Hsu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Eunice J Choi,
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Shefali A Patel,
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - William H Wong,
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Jocelyn G Olvera,
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Priscilla Yao,
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Yi Chia Liu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Matthew S Tsai
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, CA, 92161, USA
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22
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Apostolova P, Kreutmair S, Toffalori C, Punta M, Unger S, Burk AC, Wehr C, Maas-Bauer K, Melchinger W, Haring E, Hoefflin R, Shoumariyeh K, Hupfer V, Lauer EM, Duquesne S, Lowinus T, Gonzalo Núñez N, Alberti C, da Costa Pereira S, Merten CH, Power L, Weiss M, Böke C, Pfeifer D, Marks R, Bertz H, Wäsch R, Ihorst G, Gentner B, Duyster J, Boerries M, Andrieux G, Finke J, Becher B, Vago L, Zeiser R. Phase II trial of hypomethylating agent combined with nivolumab for acute myeloid leukaemia relapse after allogeneic haematopoietic cell transplantation-Immune signature correlates with response. Br J Haematol 2023; 203:264-281. [PMID: 37539479 DOI: 10.1111/bjh.19007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]
Abstract
Acute myeloid leukaemia (AML) relapse after allogeneic haematopoietic cell transplantation (allo-HCT) is often driven by immune-related mechanisms and associated with poor prognosis. Immune checkpoint inhibitors combined with hypomethylating agents (HMA) may restore or enhance the graft-versus-leukaemia effect. Still, data about using this combination regimen after allo-HCT are limited. We conducted a prospective, phase II, open-label, single-arm study in which we treated patients with haematological AML relapse after allo-HCT with HMA plus the anti-PD-1 antibody nivolumab. The response was correlated with DNA-, RNA- and protein-based single-cell technology assessments to identify biomarkers associated with therapeutic efficacy. Sixteen patients received a median number of 2 (range 1-7) nivolumab applications. The overall response rate (CR/PR) at day 42 was 25%, and another 25% of the patients achieved stable disease. The median overall survival was 15.6 months. High-parametric cytometry documented a higher frequency of activated (ICOS+ , HLA-DR+ ), low senescence (KLRG1- , CD57- ) CD8+ effector T cells in responders. We confirmed these findings in a preclinical model. Single-cell transcriptomics revealed a pro-inflammatory rewiring of the expression profile of T and myeloid cells in responders. In summary, the study indicates that the post-allo-HCT HMA/nivolumab combination induces anti-AML immune responses in selected patients and could be considered as a bridging approach to a second allo-HCT. Trial-registration: EudraCT-No. 2017-002194-18.
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Affiliation(s)
- Petya Apostolova
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Kreutmair
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Cristina Toffalori
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Center for OMICS Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Susanne Unger
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ann-Cathrin Burk
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Wehr
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kristina Maas-Bauer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wolfgang Melchinger
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eileen Haring
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rouven Hoefflin
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Khalid Shoumariyeh
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valerie Hupfer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eliza Maria Lauer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Duquesne
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Theresa Lowinus
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Chiara Alberti
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Carla Helena Merten
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Laura Power
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Matthias Weiss
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Caroline Böke
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Reinhard Marks
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hartmut Bertz
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ralph Wäsch
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gabriele Ihorst
- Clinical Trials Unit, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernhard Gentner
- Translational Stem Cell and Leukemia Unit, San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Justus Duyster
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Juergen Finke
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Robert Zeiser
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Signalling Research Centres BIOSS and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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Huang P, Zhou X, Zheng M, Yu Y, Jin G, Zhang S. Regulatory T cells are associated with the tumor immune microenvironment and immunotherapy response in triple-negative breast cancer. Front Immunol 2023; 14:1263537. [PMID: 37767092 PMCID: PMC10521732 DOI: 10.3389/fimmu.2023.1263537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Introduction Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with a high risk of distant metastasis, an extremely poor prognosis, and a high risk of death. Regulatory T cells (Tregs) contribute to the formation of a tumor immunosuppressive microenvironment, which plays an important role in the progression and treatment resistance of TNBC. Methods A public single-cell sequencing dataset demonstrated increased infiltration of Tregs in TNBC tissues relative to normal breast tissue. Weighted gene co-expression network analysis was used to identify Treg infiltration-related modules for METABRIC TNBC samples. Subsequently, we obtained two Treg infiltration-associated clusters of TNBC by applying consensus clustering and further constructed a prognostic model based on this Treg infiltration-associated gene module. The ability of the selected gene in the prognostic model, thymidine kinase-1 (TK1), to promote the progression of TNBC was evaluated in vitro. Results We concluded that two Treg infiltration-associated clusters had different prognoses and sensitivities to drugs commonly used in breast cancer treatment, and multi-omics analysis revealed that the two clusters had different copy number variations of key tumor progression genes. The 7-gene risk score based on TNBC Treg infiltration was a reliable prognostic indicator both in the training and validation cohorts. Moreover, patients with TNBC with high Treg infiltration-related scores lacked the activation of immune activation pathways and exhibited resistance to anti-PD1 immunotherapy. Knocking down TK1 led to impaired proliferation, migration, and invasion of TNBC cells in vitro. In addition, specimens from patients with TNBC with high TK1 expression showed significantly higher Treg infiltration in tumors. Results of spatial transcriptome analysis showed that TK1 positive cells mainly localize in tumor area, and Treg cell infiltration in TNBC tissues was associated with high expression of TK1. Pan-cancer analysis also demonstrated that TK1 is associated with poor prognosis and activation of proliferation pathways in multiple cancers. Discussion We established a prognostic model related to Treg infiltration and this model can be used to establish a clinically relevant classification of TNBC progression. Additionally, our work revealed the underestimable potential of TK1 as a tumor biomarker and immunotherapeutic target.
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Affiliation(s)
- Pengfei Huang
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Xinyue Zhou
- Graduate School, Tianjin Medical University, Tianjin, China
| | - Minying Zheng
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Yongjun Yu
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Gongsheng Jin
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
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Cao F, Qi Y, Wu W, Li X, Yang C. Single-cell and genetic multi-omics analysis combined with experiments confirmed the signature and potential targets of cuproptosis in hepatocellular carcinoma. Front Cell Dev Biol 2023; 11:1240390. [PMID: 37745297 PMCID: PMC10516581 DOI: 10.3389/fcell.2023.1240390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023] Open
Abstract
Background: Cuproptosis, as a recently discovered type of programmed cell death, occupies a very important role in hepatocellular carcinoma (HCC) and provides new methods for immunotherapy; however, the functions of cuproptosis in HCC are still unclear. Methods: We first analyzed the transcriptome data and clinical information of 526 HCC patients using multiple algorithms in R language and extensively described the copy number variation, prognostic and immune infiltration characteristics of cuproptosis related genes (CRGs). Then, the hub CRG related genes associated with prognosis through LASSO and Cox regression analyses and constructed a prognostic prediction model including multiple molecular markers and clinicopathological parameters through training cohorts, then this model was verified by test cohorts. On the basis of the model, the clinicopathological indicators, immune infiltration and tumor microenvironment characteristics of HCC patients were further explored via bioinformation analysis. Then, We further explored the key gene biological function by single-cell analysis, cell viability and transwell experiments. Meantime, we also explored the molecular docking of the hub genes. Results: We have screened 5 hub genes associated with HCC prognosis and constructed a prognosis prediction scoring model. And the model results showed that patients in the high-risk group had poor prognosis and the expression levels of multiple immune markers, including PD-L1, CD276 and CTLA4, were higher than those patients in the low-risk group. We found a significant correlation between risk score and M0 macrophages and memory CD4+ T cells. And the single-cell analysis and molecular experiments showed that BEX1 were higher expressed in HCC tissues and deletion inhibited the proliferation, invasion and migration and EMT pathway of HCC cells. Finally, it was observed that BEX1 could bind to sorafenib to form a stable conformation. Conclusion: The study not only revealed the multiomics characteristics of CRGs in HCC but also constructed a new high-accuracy prognostic prediction model. Meanwhile, BEX1 were also identified as hub genes that can mediate the cuproptosis of hepatocytes as potential therapeutic targets for HCC.
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Affiliation(s)
- Feng Cao
- Department of General, Visceral and Transplantation Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Yong Qi
- Department of General Surgery, The First Hospital of Anhui Medical University, Hefei, China
| | - Wenyong Wu
- Department of General Surgery, The First Hospital of Anhui Medical University, Hefei, China
| | - Xutong Li
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chuang Yang
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
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25
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Ji Z, Lu W, Wu S, Zhang Y, Meng D, Zhang X, Dai X, Chen H, Ma L, Sun Y, Jiang L, Kong X. Single-Cell RNA-Sequencing Reveals Peripheral T Helper Cells Promoting the Development of IgG4-Related Disease by Enhancing B Cell Activation and Differentiation. Int J Mol Sci 2023; 24:13735. [PMID: 37762039 PMCID: PMC10530310 DOI: 10.3390/ijms241813735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Abnormal B cell differentiation plays a critical role in IgG4-related disease (IgG4-RD), but the underlying mechanism remains largely unknown. We investigated the cell landscape from three IgG4-RD retroperitoneal tissues and three control tissues using single-cell RNA-sequencing. Critical cell type or markers were further validated in the peripheral blood from the patients with IgG4-RD and healthy controls via flow cytometry as well as in the IgG4-RD and control tissue via immunofluorescence staining. The increases in B cells, plasma cells, and CD4+ T cells were found in IgG4-RD retroperitoneal tissue. Importantly, among CD4+ T cells, an increase in CD4+CXCR5-PD1hi peripheral T helper (Tph) cells with a high expression of IL-21 and TIGIT was discovered in IgG4-RD tissue, which was further validated in peripheral blood of the patients with IgG4-RD. The Tph cell and TIGIT+ Tph cell proportion were remarkably higher in active IgG4-RD patients and correlated with disease activity. Moreover, TIGIT+CD4+ cells were able to promote B cell differentiation via IL-21. Our study revealed that Tph cells are increased in IgG4-RD and probably play critical roles in B cell differentiation through TIGIT-IL-21 axis. Peripheral Tph cell and TIGIT+Tph cell are potential markers for IgG4-RD disease activity.
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Affiliation(s)
- Zongfei Ji
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Weiqi Lu
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Sifan Wu
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Yong Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Dan Meng
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiao Zhang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Xiaojuan Dai
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Huiyong Chen
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Lili Ma
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ying Sun
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
| | - Lindi Jiang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
- Evidence-Based Medicine Center, Fudan University, Shanghai 200032, China
| | - Xiufang Kong
- Department of Rheumatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai 200032, China; (Z.J.)
- Evidence-Based Medicine Center, Fudan University, Shanghai 200032, China
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Fang Y, Bian C, Li Z, Jin L, Chen C, Miao Y, Huang H, Zeng Z. ScRNA-seq revealed disruption in CD8 + NKG2A + natural killer T cells in patients after liver transplantation and immunosuppressive therapy. Immun Inflamm Dis 2023; 11:e990. [PMID: 37773707 PMCID: PMC10524014 DOI: 10.1002/iid3.990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/21/2023] [Accepted: 08/07/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Liver transplantation (LT) offers a good survival chance for both the patient in short or long term, but still faces many challenges in the treatment of LT, such as the side effects associated with long-term immunosuppression, which is one of the side effects that occurs in most patients. However, the dynamics of the cellular immune system composition over time during immune tolerance to LT after immunosuppressive therapy are not known. METHODS Using single-cell transcriptome sequencing, we analyzed five peripheral blood samples (one normal individual and four patients who underwent LT and received immunosuppressive therapy for 2 months, 1 year, 3 years, and 7 years, respectively) for immune cell composition and gene expression. RESULTS A total of 17,462 peripheral blood mononuclear cells were acquired from a normal individual without LT and patients who underwent LT and received immunosuppressive therapy for 2 months, 1 year, 3 years, and 7 years, respectively. A total of 24 cell clusters were obtained and categorized into four different cell types based on gene expression characteristics as follows: eight clusters of T cells, two clusters of B cells, two clusters of neutrophils, two clusters of monocytes, natural killer cells, and natural killer T (NKT) cells (n = 4), and six other cell clusters. Cell subset analysis, pseudotime analysis, and intercellular communication analysis revealed that the CD8+ NKT cells specifically expressed NKG2A (KLRC1, CD159A), which may be an important cell group for CD8+ NKG2A+ NKT cells in LT, thereby highlighting the heterogeneity and functional diversity in patients who undergo LT. CONCLUSIONS We comprehensively analyzed single-cell RNA sequencing data from a normal individual and patients who underwent LT and elucidated the mechanism underlying the development of immune tolerance in LT. CD8+ NKT cells specifically expressing KLRC1 play a crucial role in LT, and dynamic monitoring of these cells may provide novel avenues for the diagnosis and treatment of LT-related immune rejection.
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Affiliation(s)
- Yuan Fang
- Organ Transplantation Centerthe First Affiliated Hospital of Kunming Medical UniversityKunmingYunnanPR China
| | - CongWen Bian
- Organ Transplantation Centerthe First Affiliated Hospital of Kunming Medical UniversityKunmingYunnanPR China
| | - ZhiTao Li
- Organ Transplantation Centerthe First Affiliated Hospital of Kunming Medical UniversityKunmingYunnanPR China
| | - Li Jin
- Organ Transplantation Centerthe First Affiliated Hospital of Kunming Medical UniversityKunmingYunnanPR China
| | - ChuHong Chen
- Organ Transplantation Centerthe First Affiliated Hospital of Kunming Medical UniversityKunmingYunnanPR China
| | - YingLei Miao
- Yunnan Province Clinical Research Center for Digestive DiseasesYunnanPR China
| | - HanFei Huang
- Organ Transplantation Centerthe First Affiliated Hospital of Kunming Medical UniversityKunmingYunnanPR China
| | - Zhong Zeng
- Organ Transplantation Centerthe First Affiliated Hospital of Kunming Medical UniversityKunmingYunnanPR China
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27
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Lin J, Feng D, Liu J, Yang Y, Wei X, Lin W, Lin Q. Construction of stemness gene score by bulk and single-cell transcriptome to characterize the prognosis of breast cancer. Aging (Albany NY) 2023; 15:8185-8203. [PMID: 37602872 PMCID: PMC10496995 DOI: 10.18632/aging.204963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Breast cancer (BC) is a heterogeneous disease characterized by significant differences in prognosis and therapy response. Numerous prognostic tools have been developed for breast cancer. Usually these tools are based on bulk RNA-sequencing (RNA-Seq) and ignore tumor heterogeneity. Consequently, the goal of this study was to construct a single-cell level tool for predicting the prognosis of BC patients. In this study, we constructed a stemness-risk gene score (SGS) model based on single-sample gene set enrichment analysis (ssGSEA). Patients were divided into two groups based on the median SGS. Patients with a high SGS scores had a significantly worse prognosis than those with a low SGS, and these groups exhibited differences in several tumor characteristics, such as immune infiltration, gene mutations, and copy number variants. Our results indicate that the SGS is a reliable tool for predicting prognosis and response to immunotherapy in BC patients.
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Affiliation(s)
- Jun Lin
- Department of Anesthesiology, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Anesthesiology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
- Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Deyi Feng
- Xiamen University, Xiamen 361100, China
| | - Jie Liu
- Department of Endoscopy, Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, China
| | - Ye Yang
- The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xujin Wei
- The Graduate School of Fujian Medical University, Fuzhou 350001, China
| | - Wenqian Lin
- Department of Anesthesiology, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Anesthesiology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
- Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Qun Lin
- Department of Anesthesiology, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Anesthesiology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
- Anesthesiology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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Ho P, Melms JC, Rogava M, Frangieh CJ, Poźniak J, Shah SB, Walsh Z, Kyrysyuk O, Amin AD, Caprio L, Fullerton BT, Soni RK, Ager CR, Biermann J, Wang Y, Khosravi-Maharlooei M, Zanetti G, Mu M, Fatima H, Moore EK, Vasan N, Bakhoum SF, Reiner SL, Bernatchez C, Sykes M, Mace EM, Wucherpfennig KW, Schadendorf D, Bechter O, Shah P, Schwartz GK, Marine JC, Izar B. The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity. Cancer Cell 2023; 41:1207-1221.e12. [PMID: 37327789 PMCID: PMC10524902 DOI: 10.1016/j.ccell.2023.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023]
Abstract
The cell-autonomous balance of immune-inhibitory and -stimulatory signals is a critical process in cancer immune evasion. Using patient-derived co-cultures, humanized mouse models, and single-cell RNA-sequencing of patient melanomas biopsied before and on immune checkpoint blockade, we find that intact cancer cell-intrinsic expression of CD58 and ligation to CD2 is required for anti-tumor immunity and is predictive of treatment response. Defects in this axis promote immune evasion through diminished T cell activation, impaired intratumoral T cell infiltration and proliferation, and concurrently increased PD-L1 protein stabilization. Through CRISPR-Cas9 and proteomics screens, we identify and validate CMTM6 as critical for CD58 stability and upregulation of PD-L1 upon CD58 loss. Competition between CD58 and PD-L1 for CMTM6 binding determines their rate of endosomal recycling over lysosomal degradation. Overall, we describe an underappreciated yet critical axis of cancer immunity and provide a molecular basis for how cancer cells balance immune inhibitory and stimulatory cues.
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Affiliation(s)
- Patricia Ho
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Chris J Frangieh
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Klarman Cell Observatory, the Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Shivem B Shah
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Zachary Walsh
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Oleksandr Kyrysyuk
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Lindsay Caprio
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Benjamin T Fullerton
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY 10032, USA
| | - Casey R Ager
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Mohsen Khosravi-Maharlooei
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Immunology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Giorgia Zanetti
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Michael Mu
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Hijab Fatima
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Emily K Moore
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Medicine, Division of Rheumatology, Columbia University, New York, NY 10032, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven L Reiner
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Chantale Bernatchez
- Department of Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA; Department of Surgery, Columbia University, New York, NY 10032, USA
| | - Emily M Mace
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, 45147 Essen, Germany
| | | | - Parin Shah
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.
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Liu X, Dai K, Zhang X, Huang G, Lynn H, Rabata A, Liang J, Noble PW, Jiang D. Multiple Fibroblast Subtypes Contribute to Matrix Deposition in Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2023; 69:45-56. [PMID: 36927333 PMCID: PMC10324043 DOI: 10.1165/rcmb.2022-0292oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/16/2023] [Indexed: 03/18/2023] Open
Abstract
Progressive pulmonary fibrosis results from a dysfunctional tissue repair response and is characterized by fibroblast proliferation, activation, and invasion and extracellular matrix accumulation. Lung fibroblast heterogeneity is well recognized. With single-cell RNA sequencing, fibroblast subtypes have been reported by recent studies. However, the roles of fibroblast subtypes in effector functions in lung fibrosis are not well understood. In this study, we incorporated the recently published single-cell RNA-sequencing datasets on murine lung samples of fibrosis models and human lung samples of fibrotic diseases and analyzed fibroblast gene signatures. We identified and confirmed the novel fibroblast subtypes we reported recently across all samples of both mouse models and human lung fibrotic diseases, including idiopathic pulmonary fibrosis, systemic sclerosis-associated interstitial lung disease, and coronavirus disease (COVID-19). Furthermore, we identified specific cell surface proteins for each fibroblast subtype through differential gene expression analysis, which enabled us to isolate primary cells representing distinct fibroblast subtypes by flow cytometry sorting. We compared matrix production, including fibronectin, collagen, and hyaluronan, after profibrotic factor stimulation and assessed the invasive capacity of each fibroblast subtype. Our results suggest that in addition to myofibroblasts, lipofibroblasts and Ebf1+ (Ebf transcription factor 1+) fibroblasts are two important fibroblast subtypes that contribute to matrix deposition and also have enhanced invasive, proliferative, and contraction phenotypes. The histological locations of fibroblast subtypes are identified in healthy and fibrotic lungs by these cell surface proteins. This study provides new insights to inform approaches to targeting lung fibroblast subtypes to promote the development of therapeutics for lung fibrosis.
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Affiliation(s)
- Xue Liu
- Department of Medicine and Women’s Guild Lung Institute and
| | - Kristy Dai
- Department of Medicine and Women’s Guild Lung Institute and
| | - Xuexi Zhang
- Department of Medicine and Women’s Guild Lung Institute and
| | - Guanling Huang
- Department of Medicine and Women’s Guild Lung Institute and
| | - Heather Lynn
- Department of Medicine and Women’s Guild Lung Institute and
| | - Anas Rabata
- Department of Medicine and Women’s Guild Lung Institute and
| | - Jiurong Liang
- Department of Medicine and Women’s Guild Lung Institute and
| | - Paul W. Noble
- Department of Medicine and Women’s Guild Lung Institute and
| | - Dianhua Jiang
- Department of Medicine and Women’s Guild Lung Institute and
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
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30
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Randic T, Magni S, Philippidou D, Margue C, Grzyb K, Preis JR, Wroblewska JP, Nazarov PV, Mittelbronn M, Frauenknecht KBM, Skupin A, Kreis S. Single-cell transcriptomics of NRAS-mutated melanoma transitioning to drug resistance reveals P2RX7 as an indicator of early drug response. Cell Rep 2023; 42:112696. [PMID: 37379213 DOI: 10.1016/j.celrep.2023.112696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/01/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
Treatment options for patients with NRAS-mutant melanoma are limited and lack an efficient targeted drug combination that significantly increases overall and progression-free survival. In addition, targeted therapy success is hampered by the inevitable emergence of drug resistance. A thorough understanding of the molecular processes driving cancer cells' escape mechanisms is crucial to tailor more efficient follow-up therapies. We performed single-cell RNA sequencing of NRAS-mutant melanoma treated with MEK1/2 plus CDK4/6 inhibitors to decipher transcriptional transitions during the development of drug resistance. Cell lines resuming full proliferation (FACs [fast-adapting cells]) and cells that became senescent (SACs [slow-adapting cells]) over prolonged treatment were identified. The early drug response was characterized by transitional states involving increased ion signaling, driven by upregulation of the ATP-gated ion channel P2RX7. P2RX7 activation was associated with improved therapy responses and, in combination with targeted drugs, could contribute to the delayed onset of acquired resistance in NRAS-mutant melanoma.
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Affiliation(s)
- Tijana Randic
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Stefano Magni
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Demetra Philippidou
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Christiane Margue
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Jasmin Renate Preis
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Joanna Patrycja Wroblewska
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg
| | - Petr V Nazarov
- Data Integration and Analysis Unit (DIA), Luxembourg Institute of Health, 1A-B, Rue Thomas Edison, 1445 Strassen, Luxembourg; Department of Cancer Research (DoCR), Luxembourg Institute of Health (LIH), Luxembourg, 6A, Rue Nicolas-Ernest Barblé, 1210 Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg; Department of Cancer Research (DoCR), Luxembourg Institute of Health (LIH), Luxembourg, 6A, Rue Nicolas-Ernest Barblé, 1210 Luxembourg, Luxembourg; National Center of Pathology (NCP), Laboratoire National de Santé (LNS), 3555 Dudelange, Luxembourg
| | - Katrin B M Frauenknecht
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), 3555 Dudelange, Luxembourg; Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg; Department of Cancer Research (DoCR), Luxembourg Institute of Health (LIH), Luxembourg, 6A, Rue Nicolas-Ernest Barblé, 1210 Luxembourg, Luxembourg; Department of Neuroscience, University of California San Diego, 9500 Gillman Drive, La Jolla, CA 92093, USA
| | - Stephanie Kreis
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 6, Avenue du Swing, 4367 Belvaux, Luxembourg.
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31
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Zhao Q, Zheng Y, Zhao D, Zhao L, Geng L, Ma S, Cai Y, Liu C, Yan Y, Belmonte JCI, Wang S, Zhang W, Liu GH, Qu J. Single-cell profiling reveals a potent role of quercetin in promoting hair regeneration. Protein Cell 2023; 14:398-415. [PMID: 37285263 PMCID: PMC10246722 DOI: 10.1093/procel/pwac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/16/2022] [Indexed: 07/21/2023] Open
Abstract
Hair loss affects millions of people at some time in their life, and safe and efficient treatments for hair loss are a significant unmet medical need. We report that topical delivery of quercetin (Que) stimulates resting hair follicles to grow with rapid follicular keratinocyte proliferation and replenishes perifollicular microvasculature in mice. We construct dynamic single-cell transcriptome landscape over the course of hair regrowth and find that Que treatment stimulates the differentiation trajectory in the hair follicles and induces an angiogenic signature in dermal endothelial cells by activating HIF-1α in endothelial cells. Skin administration of a HIF-1α agonist partially recapitulates the pro-angiogenesis and hair-growing effects of Que. Together, these findings provide a molecular understanding for the efficacy of Que in hair regrowth, which underscores the translational potential of targeting the hair follicle niche as a strategy for regenerative medicine, and suggest a route of pharmacological intervention that may promote hair regrowth.
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Affiliation(s)
| | | | | | - Liyun Zhao
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuan Wu Hospital, Capital Medical University, Beijing 100053, China
| | - Lingling Geng
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuan Wu Hospital, Capital Medical University, Beijing 100053, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chengyu Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yupeng Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
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Lyu F, Gao X, Ma M, Xie M, Shang S, Ren X, Liu M, Chen J. Crafting a Personalized Prognostic Model for Malignant Prostate Cancer Patients Using Risk Gene Signatures Discovered through TCGA-PRAD Mining, Machine Learning, and Single-Cell RNA-Sequencing. Diagnostics (Basel) 2023; 13:1997. [PMID: 37370891 DOI: 10.3390/diagnostics13121997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Prostate cancer is a significant clinical issue, particularly for high Gleason score (GS) malignancy patients. Our study aimed to engineer and validate a risk model based on the profiles of high-GS PCa patients for early identification and the prediction of prognosis. METHODS We conducted differential gene expression analysis on patient samples from The Cancer Genome Atlas (TCGA) and enriched our understanding of gene functions. Using the least absolute selection and shrinkage operator (LASSO) regression, we established a risk model and validated it using an independent dataset from the International Cancer Genome Consortium (ICGC). Clinical variables were incorporated into a nomogram to predict overall survival (OS), and machine learning was used to explore the risk factor characteristics' impact on PCa prognosis. Our prognostic model was confirmed using various databases, including single-cell RNA-sequencing datasets (scRNA-seq), the Cancer Cell Line Encyclopedia (CCLE), PCa cell lines, and tumor tissues. RESULTS We identified 83 differentially expressed genes (DEGs). Furthermore, WASIR1, KRTAP5-1, TLX1, KIF4A, and IQGAP3 were determined to be significant risk factors for OS and progression-free survival (PFS). Based on these five risk factors, we developed a risk model and nomogram for predicting OS and PFS, with a C-index of 0.823 (95% CI, 0.766-0.881) and a 10-year area under the curve (AUC) value of 0.788 (95% CI, 0.633-0.943). Additionally, the 3-year AUC was 0.759 when validating using ICGC. KRTAP5-1 and WASIR1 were found to be the most influential prognosis factors when using the optimized machine learning model. Finally, the established model was interrelated with immune cell infiltration, and the signals were found to be differentially expressed in PCa cells when using scRNA-seq datasets and tissues. CONCLUSIONS We engineered an original and novel prognostic model based on five gene signatures through TCGA and machine learning, providing new insights into the risk of scarification and survival prediction for PCa patients in clinical practice.
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Affiliation(s)
- Feng Lyu
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China
| | - Xianshu Gao
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China
| | - Mingwei Ma
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China
| | - Mu Xie
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China
| | - Shiyu Shang
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China
- First Clinical Medical School, Hebei North University, Zhangjiakou 075000, China
| | - Xueying Ren
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China
| | - Mingzhu Liu
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China
| | - Jiayan Chen
- Department of Radiation Oncology, Peking University First Hospital, Beijing 100034, China
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Matsushita Y, Manabe H, Ohyama T, Nakamura S, Nagata M, Ono W, Ono N. Hes1 marks peri-condensation mesenchymal cells that generate both chondrocytes and perichondrial cells in early bone development. J Biol Chem 2023; 299:104805. [PMID: 37172728 PMCID: PMC10267520 DOI: 10.1016/j.jbc.2023.104805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/23/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Bone development starts with condensations of undifferentiated mesenchymal cells that set a framework for future bones within the primordium. In the endochondral pathway, mesenchymal cells inside the condensation differentiate into chondrocytes and perichondrial cells in a SOX9-dependent mechanism. However, the identity of mesenchymal cells outside the condensation and how they participate in developing bones remain undefined. Here we show that mesenchymal cells surrounding the condensation contribute to both cartilage and perichondrium, robustly generating chondrocytes, osteoblasts, and marrow stromal cells in developing bones. Single-cell RNA-seq analysis of Prrx1-cre-marked limb bud mesenchymal cells at E11.5 reveals that Notch effector Hes1 is expressed in a mutually exclusive manner with Sox9 that is expressed in pre-cartilaginous condensations. Analysis of a Notch signaling reporter CBF1:H2B-Venus reveals that peri-condensation mesenchymal cells are active for Notch signaling. In vivo lineage-tracing analysis using Hes1-creER identifies that Hes1+ early mesenchymal cells surrounding the SOX9+ condensation at E10.5 contribute to both cartilage and perichondrium at E13.5, subsequently becoming growth plate chondrocytes, osteoblasts of trabecular and cortical bones, and marrow stromal cells in postnatal bones. In contrast, Hes1+ cells in the perichondrium at E12.5 or E14.5 do not generate chondrocytes within cartilage, contributing to osteoblasts and marrow stromal cells only through the perichondrial route. Therefore, Hes1+ peri-condensation mesenchymal cells give rise to cells of the skeletal lineage through cartilage-dependent and independent pathways, supporting the theory that early mesenchymal cells outside the condensation also play important roles in early bone development.
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Affiliation(s)
- Yuki Matsushita
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas, USA; Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroaki Manabe
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas, USA
| | - Takahiro Ohyama
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shogo Nakamura
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Mizuki Nagata
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas, USA
| | - Wanida Ono
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas, USA
| | - Noriaki Ono
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas, USA.
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Yang J, Tan H, Sun M, Chen R, Jian Z, Song Y, Zhang J, Bian S, Zhang B, Zhang Y, Gao X, Chen Z, Wu B, Ye X, Lv H, Liu Z, Huang L. Single-cell RNA sequencing reveals a mechanism underlying the susceptibility of the left atrial appendage to intracardiac thrombogenesis during atrial fibrillation. Clin Transl Med 2023; 13:e1297. [PMID: 37278111 DOI: 10.1002/ctm2.1297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/21/2023] [Accepted: 05/27/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Atrial fibrillation (AF) is associated with an increased risk of thrombosis of the left atrial appendage (LAA). However, the molecular mechanisms underlying this site-specificity remain poorly understood. Here, we present a comparative single-cell transcriptional profile of paired atrial appendages from patients with AF and illustrate the chamber-specific properties of the main cell types. METHODS Single-cell RNA sequencing analysis of matched atrial appendage samples from three patients with persistent AF was evaluated by 10× genomics. The AF mice model was created using Tbx5 knockout mice. Validation experiments were performed by glutathione S-transferase pull-down assays, coimmunoprecipitation (Co-IP), cleavage assays and shear stress experiments in vitro. RESULTS In LAA, phenotype switching from endothelial cells to fibroblasts and inflammation associated with proinflammatory macrophage infiltration were observed. Importantly, the coagulation cascade is highly enriched in LAA endocardial endothelial cells (EECs), accompanying the up-regulation of a disintegrin and metalloproteinase with thrombospondin motifs 1 (ADAMTS1) and the down-regulation of the tissue factor pathway inhibitor (TFPI) and TFPI2. Similar alterations were verified in an AF mouse model (Tbx5+/- ) and EECs treated with simulated AF shear stress in vitro. Furthermore, we revealed that the cleavage of both TFPI and TFPI2 based on their interaction with ADAMTS1 would lead to loss of anticoagulant activities of EECs. CONCLUSIONS This study highlights the decrease in the anticoagulant status of EECs in LAA as a potential mechanism underlying the propensity for thrombosis, which may aid the development of anticoagulation therapeutic approaches targeting functionally distinct cell subsets or molecules during AF.
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Affiliation(s)
- Jie Yang
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Hu Tan
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Mengjia Sun
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Renzheng Chen
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhao Jian
- Department of Cardiovascular Surgery, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yuanbin Song
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jihang Zhang
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shizhu Bian
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Bo Zhang
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yi Zhang
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xubin Gao
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhen Chen
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Boji Wu
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xiaowei Ye
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Hailin Lv
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhen Liu
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lan Huang
- Institute of Cardiovascular Diseases of PLA, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Cardiology, the Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
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Xu H, Dai Q, Wang X, Jin A, Yang Y, Huang X, Wang X, Gao X, Sun S, Liu Y, Zhu Y, Shen SG, Bian Q, Jiang L. ScRNA-seq links dental fibroblasts heterogeneity with mechanoresponsiveness. J Periodontal Res 2023. [PMID: 37221903 DOI: 10.1111/jre.13139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/31/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND OBJECTIVE Periodontal ligament (PDL) and dental pulp (DP) share a common origin but have distinct biological and mechanical functions. To what extent the mechanoresponsive property of PDL can be attributed to its unique transcriptional profiles of cellular heterogeneity is unclear. This study aims to decipher cellular heterogeneity and distinct mechanoresponsive characteristics of odontogenic soft tissues and their underlying molecular mechanisms. MATERIALS AND METHODS A single-cell comparison of digested human periodontal ligament (PDL) and dental pulp (DP) was performed using scRNA-seq. An in vitro loading model was constructed to measure mechanoresponsive ability. Dual-luciferase assay, overexpression, and shRNA knockdown were used to investigate the molecular mechanism. RESULTS Our results demonstrate striking fibroblast heterogeneity across and within human PDL and DP. We demonstrated that a tissue-specific subset of fibroblasts existed in PDL exhibiting high expression of mechanoresponsive extracellular matrix (ECM) genes, which was verified by an in vitro loading model. ScRNA-seq analysis indicated a particularly enriched regulator in PDL-specific fibroblast subtype, Jun Dimerization Protein 2 (JDP2). Overexpression and knockdown of JDP2 extensively regulated the downstream mechanoresponsive ECM genes in human PDL cells. The force loading model demonstrated that JDP2 responded to tension and that knockdown of JDP2 effectively inhibited the mechanical force-induced ECM remodeling. CONCLUSIONS Our study constructed the PDL and DP ScRNA-seq atlas to demonstrate PDL and DP fibroblast cellular heterogeneity and identify a PDL-specific mechanoresponsive fibroblast subtype and its underlying mechanism.
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Affiliation(s)
- Hongyuan Xu
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Qinggang Dai
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- The 2nd Dental Center, Ninth People's Hospital, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyu Wang
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Anting Jin
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yiling Yang
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Xiangru Huang
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Xijun Wang
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Xin Gao
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Siyuan Sun
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yuanqi Liu
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yanfei Zhu
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Steve Gf Shen
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University School, Shanghai, China
- Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Qian Bian
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lingyong Jiang
- Department of Oral and Cranio-maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
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Zhao X, Zhang H, Han Y, Fang C, Liu J. Navigating the immunometabolic heterogeneity of B cells in murine hepatocellular carcinoma at single cell resolution. Int Immunopharmacol 2023; 120:110257. [PMID: 37182447 DOI: 10.1016/j.intimp.2023.110257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/16/2023]
Abstract
Induction of antitumor immunity is critical for the therapeutic efficacy of hepatocellular carcinoma (HCC) immunotherapy. The cellular metabolic state underpins the effector function of immune cells, yet our understanding of the phenotypic and metabolic heterogeneity of B cells within HCC microenvironment is poorly developed. Herein, we investigated the composition, distribution, phenotype, function and metabolic profiles of B-cell subsets in HCC and adjacent liver tissues from an orthotopic HCC mouse model using single-cell RNA sequencing (scRNA-seq). Our results identified six B-cell clusters, which can be classified into plasma cells and activated and exhausted B cells according to marker expression, functional and temporal distribution. Exhausted B cells exhibited low metabolic activities and impaired effector functions. Activated B and plasma cells showed higher metabolic activity than exhausted B cells, but there were clear differences in their metabolic profiles. In addition, we found that the effector function of exhausted B cells was further diminished in HCC tissues compared with adjacent liver tissues, but their metabolic activity was significantly enhanced. Collectively, we comprehensively characterized the metabolic profile and alterations in B-cell subsets in HCC, which contributes to the understanding of B-cell immunology in HCC and lays the foundation for exploring novel targets in HCC immunotherapy.
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Affiliation(s)
- Xindong Zhao
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China
| | - Huanran Zhang
- Department of Emergency Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China; The Key Laboratory for Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases of Zhejiang Province, Hangzhou City, Zhejiang Province 310003, China
| | - Yiru Han
- Department of Health Care, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China
| | - Chengyu Fang
- Department of Ultrasound Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China
| | - Jingqi Liu
- Department of Ultrasound Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China.
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Horeth E, Bard J, Che M, Wrynn T, Song E, Marzullo B, Burke M, Popat S, Loree T, Zemer J, Tapia J, Frustino J, Kramer J, Sinha S, Romano R. High-Resolution Transcriptomic Landscape of the Human Submandibular Gland. J Dent Res 2023; 102:525-535. [PMID: 36726292 PMCID: PMC10249006 DOI: 10.1177/00220345221147908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Saliva-secreting and transporting cells are part of the complex cellular milieu of the human salivary gland, where they play important roles in normal glandular physiology and diseased states. However, comprehensive molecular characterization, particularly at single-cell resolution, is still incomplete, in part due to difficulty in procuring normal human tissues. Here, we perform an in-depth analysis of male and female adult human submandibular gland (SMG) samples by bulk RNA sequencing (RNA-seq) and examine the molecular underpinnings of the heterogeneous cell populations by single-cell (sc) RNA-seq. Our results from scRNA-seq highlight the remarkable diversity of clusters of epithelial and nonepithelial cells that reside in the SMG that is also faithfully recapitulated by deconvolution of the bulk-RNA data sets. Our analyses reveal complex transcriptomic heterogeneity within both the ductal and acinar subpopulations and identify atypical SMG cell types, such as mucoacinar cells that are unique to humans and ionocytes that have been recently described in the mouse. We use CellChat to explore ligand-receptor interactome predictions that likely mediate crucial cell-cell communications between the various cell clusters. Finally, we apply a trajectory inference method to investigate specific cellular branching points and topology that offers insights into the dynamic and complex differentiation process of the adult SMG. The data sets and the analyses herein comprise an extensive wealth of high-resolution information and a valuable resource for a deeper mechanistic understanding of human SMG biology and pathophysiology.
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Affiliation(s)
- E. Horeth
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - J. Bard
- Genomics and Bioinformatics Core, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - M. Che
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - T. Wrynn
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - E.A.C. Song
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - B. Marzullo
- Genomics and Bioinformatics Core, State University of New York at Buffalo, Buffalo, NY, USA
| | - M.S. Burke
- Erie County Medical Center, Department of Head & Neck/Plastic & Reconstructive Surgery, Buffalo, NY, USA
| | - S. Popat
- Erie County Medical Center, Department of Head & Neck/Plastic & Reconstructive Surgery, Buffalo, NY, USA
| | - T. Loree
- Erie County Medical Center, Department of Head & Neck/Plastic & Reconstructive Surgery, Buffalo, NY, USA
| | - J. Zemer
- Erie County Medical Center Division of Oral Oncology & Maxillofacial Prosthetics, Buffalo, NY, USA
| | - J.L. Tapia
- Department of Oral Diagnostic Sciences, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - J. Frustino
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
- Erie County Medical Center Division of Oral Oncology & Maxillofacial Prosthetics, Buffalo, NY, USA
| | - J.M. Kramer
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
| | - S. Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - R.A. Romano
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
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Puigdevall P, Jerber J, Danecek P, Castellano S, Kilpinen H. Somatic mutations alter the differentiation outcomes of iPSC-derived neurons. Cell Genom 2023; 3:100280. [PMID: 37082143 PMCID: PMC10112289 DOI: 10.1016/j.xgen.2023.100280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 04/22/2023]
Abstract
The use of induced pluripotent stem cells (iPSC) as models for development and human disease has enabled the study of otherwise inaccessible tissues. A remaining challenge in developing reliable models is our limited understanding of the factors driving irregular differentiation of iPSCs, particularly the impact of acquired somatic mutations. We leveraged data from a pooled dopaminergic neuron differentiation experiment of 238 iPSC lines profiled with single-cell RNA and whole-exome sequencing to study how somatic mutations affect differentiation outcomes. We found that deleterious somatic mutations in key developmental genes, notably the BCOR gene, are strongly associated with failure in dopaminergic neuron differentiation and a larger proliferation rate in culture. We further identified broad differences in cell type composition between incorrectly and successfully differentiating lines, as well as significant changes in gene expression contributing to the inhibition of neurogenesis. Our work calls for caution in interpreting differentiation-related phenotypes in disease-modeling experiments.
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Affiliation(s)
- Pau Puigdevall
- UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Haartmaninkatu 8, PO Box 63, Helsinki 00014, Finland
| | - Julie Jerber
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sergi Castellano
- UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Helena Kilpinen
- UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Haartmaninkatu 8, PO Box 63, Helsinki 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1, PO Box 65, Helsinki 00014, Finland
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Hermans F, Hemeryck L, Bueds C, Torres Pereiro M, Hasevoets S, Kobayashi H, Lambrechts D, Lambrichts I, Bronckaers A, Vankelecom H. Organoids from mouse molar and incisor as new tools to study tooth-specific biology and development. Stem Cell Reports 2023; 18:1166-1181. [PMID: 37084723 DOI: 10.1016/j.stemcr.2023.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/23/2023] Open
Abstract
Organoid models provide powerful tools to study tissue biology and development in a dish. Presently, organoids have not yet been developed from mouse tooth. Here, we established tooth organoids (TOs) from early-postnatal mouse molar and incisor, which are long-term expandable, express dental epithelium stem cell (DESC) markers, and recapitulate key properties of the dental epithelium in a tooth-type-specific manner. TOs display in vitro differentiation capacity toward ameloblast-resembling cells, even more pronounced in assembloids in which dental mesenchymal (pulp) stem cells are combined with the organoid DESCs. Single-cell transcriptomics supports this developmental potential and reveals co-differentiation into junctional epithelium- and odontoblast-/cementoblast-like cells in the assembloids. Finally, TOs survive and show ameloblast-resembling differentiation also in vivo. The developed organoid models provide new tools to study mouse tooth-type-specific biology and development and gain deeper molecular and functional insights that may eventually help to achieve future human biological tooth repair and replacement.
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Affiliation(s)
- Florian Hermans
- Department of Morphology, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium; Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, KU Leuven (University of Leuven), 3000 Leuven, Belgium
| | - Lara Hemeryck
- Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, KU Leuven (University of Leuven), 3000 Leuven, Belgium
| | - Celine Bueds
- Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, KU Leuven (University of Leuven), 3000 Leuven, Belgium
| | - Marc Torres Pereiro
- Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, KU Leuven (University of Leuven), 3000 Leuven, Belgium
| | - Steffie Hasevoets
- Department of Morphology, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Hiroto Kobayashi
- Department of Anatomy and Structural Science, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Ivo Lambrichts
- Department of Morphology, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Annelies Bronckaers
- Department of Morphology, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium.
| | - Hugo Vankelecom
- Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, KU Leuven (University of Leuven), 3000 Leuven, Belgium.
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40
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Ren L, Xu B, Xu J, Li J, Jiang J, Ren Y, Liu P. A Machine Learning Model to Predict Survival and Therapeutic Responses in Multiple Myeloma. Int J Mol Sci 2023; 24:ijms24076683. [PMID: 37047654 PMCID: PMC10095137 DOI: 10.3390/ijms24076683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Multiple myeloma (MM) is a highly heterogeneous hematologic tumor. Ubiquitin proteasome pathways (UPP) play a vital role in its initiation and development. We used cox regression analysis and least absolute shrinkage and selector operation (LASSO) to select ubiquitin proteasome pathway associated genes (UPPGs) correlated with the overall survival (OS) of MM patients in a Gene Expression Omnibus (GEO) dataset, and we formed this into ubiquitin proteasome pathway risk score (UPPRS). The association between clinical outcomes and responses triggered by proteasome inhibitors (PIs) and UPPRS were evaluated. MMRF CoMMpass was used for validation. We applied machine learning algorithms to MM clinical and UPPRS in the whole cohort to make a prognostic nomogram. Single-cell data and vitro experiments were performed to unravel the mechanism and functions of UPPRS. UPPRS consisting of 9 genes showed a strong ability to predict OS in MM patients. Additionally, UPPRS can be used to sort out the patients who would gain more benefits from PIs. A machine learning model incorporating UPPRS and International Staging System (ISS) improved survival prediction in both datasets compared to the revisions of ISS. At the single-cell level, high-risk UPPRS myeloma cells exhibited increased cell adhesion. Targeted UPPGs effectively inhibited myeloma cells in vitro. The UPP genes risk score is a helpful tool for risk stratification in MM patients, particularly those treated with PIs.
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Affiliation(s)
- Liang Ren
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bei Xu
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiadai Xu
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jing Li
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jifeng Jiang
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuhong Ren
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Peng Liu
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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41
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Wishart CL, Spiteri AG, Locatelli G, King NJC. Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures. Glia 2023; 71:904-925. [PMID: 36527260 PMCID: PMC10952672 DOI: 10.1002/glia.24314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/06/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
Microglia and bone marrow-derived monocytes are key elements of central nervous system (CNS) inflammation, both capable of enhancing and dampening immune-mediated pathology. However, the study-specific focus on individual cell types, disease models or experimental approaches has limited our ability to infer common and disease-specific responses. This meta-analysis integrates bulk and single-cell transcriptomic datasets of microglia and monocytes from disease models of autoimmunity, neurodegeneration, sterile injury, and infection to build a comprehensive resource connecting myeloid responses across CNS disease. We demonstrate that the bulk microglial and monocyte program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature. Integration of six single-cell RNA-sequencing datasets revealed that these disease-specific signatures are likely driven by differing proportions of unique myeloid subpopulations that were individually expanded in different disease settings. These subsets were functionally-defined as neurodegeneration-associated, inflammatory, interferon-responsive, phagocytic, antigen-presenting, and lipopolysaccharide-responsive cellular states, revealing a core set of myeloid responses at the single-cell level that are conserved across CNS pathology. Showcasing the predictive and practical value of this resource, we performed differential expression analysis on microglia and monocytes across disease and identified Cd81 as a new neuroinflammatory-stable gene that accurately identified microglia and distinguished them from monocyte-derived cells across all experimental models at both the bulk and single-cell level. Together, this resource dissects the influence of disease environment on shared immune response programmes to build a unified perspective of myeloid behavior across CNS pathology.
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Affiliation(s)
- Claire L. Wishart
- Infection, Immunity, Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
- Sydney Cytometry FacilityThe University of Sydney and Centenary InstituteSydneyNew South WalesAustralia
- Ramaciotti Facility for Human Systems BiologyThe University of Sydney and Centenary InstituteSydneyNew South WalesAustralia
- Charles Perkins CentreThe University of SydneySydneyNew South WalesAustralia
| | - Alanna G. Spiteri
- Infection, Immunity, Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
- Sydney Cytometry FacilityThe University of Sydney and Centenary InstituteSydneyNew South WalesAustralia
- Ramaciotti Facility for Human Systems BiologyThe University of Sydney and Centenary InstituteSydneyNew South WalesAustralia
- Charles Perkins CentreThe University of SydneySydneyNew South WalesAustralia
| | - Giuseppe Locatelli
- Theodor Kocher InstituteUniversity of BernBernSwitzerland
- Novartis Institutes for BioMedical ResearchNovartisBaselSwitzerland
| | - Nicholas J. C. King
- Infection, Immunity, Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
- Sydney Cytometry FacilityThe University of Sydney and Centenary InstituteSydneyNew South WalesAustralia
- Ramaciotti Facility for Human Systems BiologyThe University of Sydney and Centenary InstituteSydneyNew South WalesAustralia
- Charles Perkins CentreThe University of SydneySydneyNew South WalesAustralia
- Sydney Institute for Infectious Diseases, Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
- The University of Sydney Nano Institute, Faculty of ScienceThe University of SydneySydneyNew South WalesAustralia
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42
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Itai T, Jia P, Dai Y, Chen J, Chen X, Zhao Z. De novo mutations disturb early brain development more frequently than common variants in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2023; 192:62-70. [PMID: 36863698 DOI: 10.1002/ajmg.b.32932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/08/2022] [Accepted: 01/29/2023] [Indexed: 03/04/2023]
Abstract
Investigating functional, temporal, and cell-type expression features of mutations is important for understanding a complex disease. Here, we collected and analyzed common variants and de novo mutations (DNMs) in schizophrenia (SCZ). We collected 2,636 missense and loss-of-function (LoF) DNMs in 2,263 genes across 3,477 SCZ patients (SCZ-DNMs). We curated three gene lists: (a) SCZ-neuroGenes (159 genes), which are intolerant to LoF and missense DNMs and are neurologically important, (b) SCZ-moduleGenes (52 genes), which were derived from network analyses of SCZ-DNMs, and (c) SCZ-commonGenes (120 genes) from a recent GWAS as reference. To compare temporal gene expression, we used the BrainSpan dataset. We defined a fetal effect score (FES) to quantify the involvement of each gene in prenatal brain development. We further employed the specificity indexes (SIs) to evaluate cell-type expression specificity from single-cell expression data in cerebral cortices of humans and mice. Compared with SCZ-commonGenes, SCZ-neuroGenes and SCZ-moduleGenes were highly expressed in the prenatal stage, had higher FESs, and had higher SIs in fetal replicating cells and undifferentiated cell types. Our results suggested that gene expression patterns in specific cell types in early fetal stages might have impacts on the risk of SCZ during adulthood.
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Affiliation(s)
- Toshiyuki Itai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jingchun Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Xiangning Chen
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA.,Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
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43
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Groves SM, Panchy N, Tyson DR, Harris LA, Quaranta V, Hong T. Involvement of Epithelial-Mesenchymal Transition Genes in Small Cell Lung Cancer Phenotypic Plasticity. Cancers (Basel) 2023; 15:1477. [PMID: 36900269 PMCID: PMC10001072 DOI: 10.3390/cancers15051477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive cancer recalcitrant to treatment, arising predominantly from epithelial pulmonary neuroendocrine (NE) cells. Intratumor heterogeneity plays critical roles in SCLC disease progression, metastasis, and treatment resistance. At least five transcriptional SCLC NE and non-NE cell subtypes were recently defined by gene expression signatures. Transition from NE to non-NE cell states and cooperation between subtypes within a tumor likely contribute to SCLC progression by mechanisms of adaptation to perturbations. Therefore, gene regulatory programs distinguishing SCLC subtypes or promoting transitions are of great interest. Here, we systematically analyze the relationship between SCLC NE/non-NE transition and epithelial to mesenchymal transition (EMT)-a well-studied cellular process contributing to cancer invasiveness and resistance-using multiple transcriptome datasets from SCLC mouse tumor models, human cancer cell lines, and tumor samples. The NE SCLC-A2 subtype maps to the epithelial state. In contrast, SCLC-A and SCLC-N (NE) map to a partial mesenchymal state (M1) that is distinct from the non-NE, partial mesenchymal state (M2). The correspondence between SCLC subtypes and the EMT program paves the way for further work to understand gene regulatory mechanisms of SCLC tumor plasticity with applicability to other cancer types.
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Affiliation(s)
- Sarah M. Groves
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Nicholas Panchy
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Darren R. Tyson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
| | - Leonard A. Harris
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
- Cancer Biology Program, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
- National Institute for Mathematical and Biological Synthesis, Knoxville, TN 37996, USA
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44
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Dharmaratne M, Kulkarni AS, Taherian Fard A, Mar JC. scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data. Gigascience 2023; 12:6999327. [PMID: 36691728 PMCID: PMC9871437 DOI: 10.1093/gigascience/giac126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 08/27/2022] [Accepted: 12/15/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) methods have been advantageous for quantifying cell-to-cell variation by profiling the transcriptomes of individual cells. For scRNA-seq data, variability in gene expression reflects the degree of variation in gene expression from one cell to another. Analyses that focus on cell-cell variability therefore are useful for going beyond changes based on average expression and, instead, identifying genes with homogeneous expression versus those that vary widely from cell to cell. RESULTS We present a novel statistical framework, scShapes, for identifying differential distributions in single-cell RNA-sequencing data using generalized linear models. Most approaches for differential gene expression detect shifts in the mean value. However, as single-cell data are driven by overdispersion and dropouts, moving beyond means and using distributions that can handle excess zeros is critical. scShapes quantifies gene-specific cell-to-cell variability by testing for differences in the expression distribution while flexibly adjusting for covariates if required. We demonstrate that scShapes identifies subtle variations that are independent of altered mean expression and detects biologically relevant genes that were not discovered through standard approaches. CONCLUSIONS This analysis also draws attention to genes that switch distribution shapes from a unimodal distribution to a zero-inflated distribution and raises open questions about the plausible biological mechanisms that may give rise to this, such as transcriptional bursting. Overall, the results from scShapes help to expand our understanding of the role that gene expression plays in the transcriptional regulation of a specific perturbation or cellular phenotype. Our framework scShapes is incorporated into a Bioconductor R package (https://www.bioconductor.org/packages/release/bioc/html/scShapes.html).
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Affiliation(s)
- Malindrie Dharmaratne
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ameya S Kulkarni
- Institute for Aging Research, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA,Department of Medicine, Division of Endocrinology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Atefeh Taherian Fard
- Correspondence address. Atefeh Taherian Fard, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia. E-mail:
| | - Jessica C Mar
- Correspondence address. Jessica C. Mar, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia. E-mail:
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45
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Zhao K, Grayson JM, Khuri N. Multi-Objective Genetic Algorithm for Cluster Analysis of Single-Cell Transcriptomes. J Pers Med 2023; 13. [PMID: 36836417 DOI: 10.3390/jpm13020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Cells are the basic building blocks of human organisms, and the identification of their types and states in transcriptomic data is an important and challenging task. Many of the existing approaches to cell-type prediction are based on clustering methods that optimize only one criterion. In this paper, a multi-objective Genetic Algorithm for cluster analysis is proposed, implemented, and systematically validated on 48 experimental and 60 synthetic datasets. The results demonstrate that the performance and the accuracy of the proposed algorithm are reproducible, stable, and better than those of single-objective clustering methods. Computational run times of multi-objective clustering of large datasets were studied and used in supervised machine learning to accurately predict the execution times of clustering of new single-cell transcriptomes.
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46
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Jimenez DG, Altunbulakli C, Swoboda S, Sobti A, Askmyr D, Ali A, Greiff L, Lindstedt M. Single-cell analysis of myeloid cells in HPV + tonsillar cancer. Front Immunol 2023; 13:1087843. [PMID: 36741389 PMCID: PMC9893928 DOI: 10.3389/fimmu.2022.1087843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
The incidence of human papillomavirus-positive (HPV+) tonsillar cancer has been sharply rising during the last decades. Myeloid cells represent an appropriate therapeutic target due to their proximity to virus-infected tumor cells, and their ability to orchestrate antigen-specific immunity, within the tonsil. However, the interrelationship of steady-state and inflammatory myeloid cell subsets, and their impact on patient survival remains unexplored. Here, we used single-cell RNA-sequencing to map the myeloid compartment in HPV+ tonsillar cancer. We observed an expansion of the myeloid compartment in HPV+ tonsillar cancer, accompanied by interferon-induced cellular responses both in dendritic cells (DCs) and monocyte-macrophages. Our analysis unveiled the existence of four DC lineages, two macrophage polarization processes, and their sequential maturation profiles. Within the DC lineages, we described a balance shift in the frequency of progenitor and mature cDC favoring the cDC1 lineage in detriment of cDC2s. Furthermore, we observed that all DC lineages apart from DC5s matured into a common activated DC transcriptional program involving upregulation of interferon-inducible genes. In turn, the monocyte-macrophage lineage was subjected to early monocyte polarization events, which give rise to either interferon-activated or CXCL-producing macrophages, the latter enriched in advanced tumor stages. We validated the existence of most of the single-cell RNA-seq clusters using 26-plex flow cytometry, and described a positive impact of cDC1 and interferon-activated DCs and macrophages on patient survival using gene signature scoring. The current study contributes to the understanding of myeloid ontogeny and dynamics in HPV-driven tonsillar cancer, and highlights myeloid biomarkers that can be used to assess patient prognosis.
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Affiliation(s)
| | | | - Sabine Swoboda
- Department of ORL, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden,Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Aastha Sobti
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - David Askmyr
- Department of ORL, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden,Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ashfaq Ali
- Department of Immunotechnology, Lund University, Lund, Sweden,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Lennart Greiff
- Department of ORL, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden,Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Malin Lindstedt
- Department of Immunotechnology, Lund University, Lund, Sweden,*Correspondence: Malin Lindstedt,
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47
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Chen Z, Chen D, Song Z, Lv Y, Qi D. Mapping the tumor microenvironment in bladder cancer and exploring the prognostic genes by single-cell RNA sequencing. Front Oncol 2023; 12:1105026. [PMID: 36741702 PMCID: PMC9893503 DOI: 10.3389/fonc.2022.1105026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/29/2022] [Indexed: 01/20/2023] Open
Abstract
Despite substantial advances in the treatment using immune checkpoint inhibitors (ICIs), the clinical expected therapeutic effect on bladder cancer has not been achieved, in which the tumor microenvironment (TME) occupies a notable position. In this research, 10X single-cell RNA-sequencing technology was conducted to analyze seven primary bladder tumor tissues (three non-muscle-invasive bladder cancer (NMIBC) and four muscle-invasive bladder cancer (MIBC)) and seven corresponding normal tissues adjacent to cancer; eight various cell types were identified in the bladder cancer (BC) TME, and a complete TME atlas in bladder cancer was made. Moreover, bladder cancer epithelial cells were further subdivided into 14 subgroups, indicating a high intra-tumoral heterogeneity. Additionally, the differences between NMIBC and MIBC were compared based on differential gene expression heatmap, copy number variation (CNV) distribution heatmap, Gene Ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) network mutual analysis, and the Kaplan-Meier survival prognosis analysis were used to identify six key genes associated with the prognosis of bladder cancer: VEGFA, ANXA1, HSP90B1, PSMA7, PRDX6, and PPP1CB. The dynamic change of the expression distribution of six genes on the pseudo-time axis was further verified by cell pseudo-time analysis.
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48
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Lin YH, Duong HG, Limary AE, Kim ES, Hsu P, Patel SA, Wong WH, Indralingam CS, Liu YC, Yao P, Chiang NR, Vandenburgh SA, Anderson TR, Olvera JG, Ferry A, Takehara KK, Jin W, Tsai MS, Yeo GW, Goldrath AW, Chang JT. Small intestine and colon tissue-resident memory CD8 + T cells exhibit molecular heterogeneity and differential dependence on Eomes. Immunity 2023; 56:207-223.e8. [PMID: 36580919 PMCID: PMC9904390 DOI: 10.1016/j.immuni.2022.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/04/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022]
Abstract
Tissue-resident memory CD8+ T (TRM) cells are a subset of memory T cells that play a critical role in limiting early pathogen spread and controlling infection. TRM cells exhibit differences across tissues, but their potential heterogeneity among distinct anatomic compartments within the small intestine and colon has not been well recognized. Here, by analyzing TRM cells from the lamina propria and epithelial compartments of the small intestine and colon, we showed that intestinal TRM cells exhibited distinctive patterns of cytokine and granzyme expression along with substantial transcriptional, epigenetic, and functional heterogeneity. The T-box transcription factor Eomes, which represses TRM cell formation in some tissues, exhibited unexpected context-specific regulatory roles in supporting the maintenance of established TRM cells in the small intestine, but not in the colon. Taken together, these data provide previously unappreciated insights into the heterogeneity and differential requirements for the formation vs. maintenance of intestinal TRM cells.
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Affiliation(s)
- Yun Hsuan Lin
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Han G Duong
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Abigail E Limary
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eleanor S Kim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Paul Hsu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Shefali A Patel
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - William H Wong
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Yi Chia Liu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Priscilla Yao
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Natalie R Chiang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sara A Vandenburgh
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Taylor R Anderson
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jocelyn G Olvera
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Amir Ferry
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kennidy K Takehara
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Matthew S Tsai
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, CA 92161, USA.
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Nettersheim FS, Ghosheh Y, Winkels H, Kobiyama K, Durant C, Armstrong SS, Brunel S, Roy P, Dileepan T, Jenkins MK, Zajonc DM, Ley K. Single-cell transcriptomes and T cell receptors of vaccine-expanded apolipoprotein B-specific T cells. Front Cardiovasc Med 2023; 9:1076808. [PMID: 36684560 PMCID: PMC9849899 DOI: 10.3389/fcvm.2022.1076808] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023] Open
Abstract
Atherosclerotic cardiovascular diseases are the major cause of death worldwide. CD4 T cells responding to Apolipoprotein B (ApoB), the core protein of most lipoproteins, have been identified as critical disease modulators. In healthy individuals, ApoB-reactive (ApoB+) CD4 T cells are mostly regulatory T cells (Tregs), which exert anti-inflammatory effects. Yet, they may obtain pro-inflammatory features and thus become proatherogenic. Evidence from animal studies suggests that vaccination against certain major histocompatibility complex (MHC) II-binding ApoB peptides induces an expansion of ApoB+ Tregs and thus confers atheroprotection. To date, in-depth phenotyping of vaccine-expanded ApoB+ T cells has not yet been performed. To this end, we vaccinated C57BL/6J mice with the ApoB-peptide P6 (ApoB978-993 TGAYSNASSTESASY) and performed single-cell RNA sequencing of tetramer-sorted P6+ T cells. P6+ cells were clonally expanded (one major, two minor clones) and formed a transcriptional cluster distinct from clusters mainly containing non-expanded P6+ and P6- cells. Transcriptomic profiling revealed that most expanded P6+ cells had a strong Treg signature and highly expressed genes mediating suppressive functions. Yet, some expanded P6+ cells only had a residual Treg signature and expressed genes related to T helper 1 (TH1) cells, which are proatherogenic. Modeling the T cell receptor (TCR) and P6:MHC-II interaction showed that only three amino acid residues in the α and β chain contact the P6 peptide in the MHC-II groove and thus determine the specificity of this TCR to P6. Our data begin to reveal the vaccination-induced response to an ApoB epitope.
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Affiliation(s)
- Felix Sebastian Nettersheim
- La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Cardiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Yanal Ghosheh
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Holger Winkels
- La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Cardiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kouji Kobiyama
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | | | - Simon Brunel
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Payel Roy
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Thamotharampillai Dileepan
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Marc K. Jenkins
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Dirk M. Zajonc
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Klaus Ley
- La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
- Immunology Center of Georgia (IMMCG), Augusta University, Augusta, GA, United States
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50
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Willems A, Panchy N, Hong T. Using Single-Cell RNA Sequencing and MicroRNA Targeting Data to Improve Colorectal Cancer Survival Prediction. Cells 2023; 12. [PMID: 36672162 DOI: 10.3390/cells12020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Colorectal cancer has proven to be difficult to treat as it is the second leading cause of cancer death for both men and women worldwide. Recent work has shown the importance of microRNA (miRNA) in the progression and metastasis of colorectal cancer. Here, we develop a metric based on miRNA-gene target interactions, previously validated to be associated with colorectal cancer. We use this metric with a regularized Cox model to produce a small set of top-performing genes related to colon cancer. We show that using the miRNA metric and a Cox model led to a meaningful improvement in colon cancer survival prediction and correct patient risk stratification. We show that our approach outperforms existing methods and that the top genes identified by our process are implicated in NOTCH3 signaling and general metabolism pathways, which are essential to colon cancer progression.
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