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Article ; Online: Single-cell meta-analyses reveal responses of tumor-reactive CXCL13

Liu, Baolin / Zhang, Yuanyuan / Wang, Dongfang / Hu, Xueda / Zhang, Zemin

Nature cancer

2022 Volume 3, Issue 9, Page(s) 1123–1136

Abstract: Immune-checkpoint blockade (ICB) therapies represent a paradigm shift in the treatment of human cancers; however, it remains incompletely understood how tumor-reactive T cells respond to ICB across tumor types. Here, we demonstrate that measuring CXCL13 ... ...

Abstract	Immune-checkpoint blockade (ICB) therapies represent a paradigm shift in the treatment of human cancers; however, it remains incompletely understood how tumor-reactive T cells respond to ICB across tumor types. Here, we demonstrate that measuring CXCL13 expression could effectively identify both precursor and terminally differentiated tumor-reactive CD8
MeSH term(s)	CD8-Positive T-Lymphocytes/pathology ; Chemokine CXCL13 ; Humans ; Immune Checkpoint Inhibitors/pharmacology ; Immunotherapy ; Neoplasms/drug therapy ; Single-Cell Analysis ; Tumor Microenvironment
Chemical Substances	CXCL13 protein, human ; Chemokine CXCL13 ; Immune Checkpoint Inhibitors
Language	English
Publishing date	2022-09-22
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't
ISSN	2662-1347
ISSN (online)	2662-1347
DOI	10.1038/s43018-022-00433-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Understanding the Genetic Mechanisms of Cancer Drug Resistance Using Genomic Approaches.

Hu, Xueda / Zhang, Zemin

Trends in genetics : TIG

2016 Volume 32, Issue 2, Page(s) 127–137

Abstract: A major obstacle in precision cancer medicine is the inevitable resistance to targeted therapies. Tremendous effort and progress has been made over the past few years to understand the biochemical and genetic mechanisms underlying drug resistance, with ... ...

Abstract	A major obstacle in precision cancer medicine is the inevitable resistance to targeted therapies. Tremendous effort and progress has been made over the past few years to understand the biochemical and genetic mechanisms underlying drug resistance, with the goal to eventually overcome such daunting challenges. Diverse mechanisms, such as secondary mutations, oncogene bypass, and epigenetic alterations, can all lead to drug resistance, and the number of known involved genes is growing rapidly, thus providing many possibilities to overcome resistance. The finding of these mechanisms and genes invariably requires the application of genomic and functional genomic approaches to tumors or cancer models. In this review, we briefly highlight the major drug-resistance mechanisms known today, and then focus primarily on the technological approaches leading to the advancement of this field.
MeSH term(s)	Animals ; Drug Resistance, Neoplasm/drug effects ; Drug Resistance, Neoplasm/genetics ; Genomics/methods ; Humans
Language	English
Publishing date	2016-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	619240-3
ISSN	1362-4555 ; 0168-9525 ; 0168-9479
ISSN (online)	1362-4555
ISSN	0168-9525 ; 0168-9479
DOI	10.1016/j.tig.2015.11.003
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Zs.A 2272: Show issues

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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Deciphering Immune Landscape Remodeling Unravels the Underlying Mechanism for Synchronized Muscle and Bone Aging.

Yin, Pengbin / Chen, Ming / Rao, Man / Lin, Yuan / Zhang, Mingming / Xu, Ren / Hu, Xueda / Chen, Ruijing / Chai, Wei / Huang, Xiang / Yu, Haikuan / Yao, Yao / Zhao, Yali / Li, Yi / Zhang, Licheng / Tang, Peifu

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

2023 Volume 11, Issue 5, Page(s) e2304084

Abstract: Evidence from numerous studies has revealed the synchronous progression of aging in bone and muscle; however, little is known about the underlying mechanisms. To this end, human muscles and bones are harvested and the aging-associated transcriptional ... ...

Abstract	Evidence from numerous studies has revealed the synchronous progression of aging in bone and muscle; however, little is known about the underlying mechanisms. To this end, human muscles and bones are harvested and the aging-associated transcriptional dynamics of two tissues in parallel using single-cell RNA sequencing are surveyed. A subset of lipid-associated macrophages (triggering receptor expressed on myeloid cells 2, TREM2
MeSH term(s)	Humans ; Aged ; Muscles ; Bone and Bones ; Cell Differentiation ; Aging ; Molecular Chaperones
Chemical Substances	BAG6 protein, human ; Molecular Chaperones
Language	English
Publishing date	2023-12-13
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2808093-2
ISSN	2198-3844 ; 2198-3844
ISSN (online)	2198-3844
ISSN	2198-3844
DOI	10.1002/advs.202304084
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Article ; Online: Deep single-cell RNA sequencing data of individual T cells from treatment-naïve colorectal cancer patients.

Zhang, Yuanyuan / Zheng, Liangtao / Zhang, Lei / Hu, Xueda / Ren, Xianwen / Zhang, Zemin

Scientific data

2019 Volume 6, Issue 1, Page(s) 131

Abstract: T cells, as a crucial compartment of the tumour microenvironment, play vital roles in cancer immunotherapy. However, the basic properties of tumour-infiltrating T cells (TILs) such as the functional state, migratory capability and clonal expansion remain ...

Abstract	T cells, as a crucial compartment of the tumour microenvironment, play vital roles in cancer immunotherapy. However, the basic properties of tumour-infiltrating T cells (TILs) such as the functional state, migratory capability and clonal expansion remain elusive. Here, using Smart-seq2 protocol, we have generated a RNA sequencing dataset of 11,138 T cells isolated from peripheral blood, adjacent normal and tumour tissues of 12 colorectal cancer (CRC) patients, including 4 with microsatellite instability (MSI). The dataset contained an expression profile of 10,805 T cells, as well as the full-length T cell receptor (TCR) sequences of 9,878 cells after quality control. To facilitate data mining of our T cell dataset, we developed a web-based application to deliver systematic interrogations and customizable functionalities ( http://crctcell.cancer-pku.cn/ ). Functioning with our dataset, the web tool enables the characterization of TILs based on both transcriptome and assembled TCR sequences at the single cell level, which will help unleash the potential value of our CRC T cell data resource.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/immunology ; Female ; Humans ; Internet ; Male ; Microsatellite Instability ; Middle Aged ; RNA-Seq ; Receptors, Antigen, T-Cell/genetics ; Single-Cell Analysis ; Software ; T-Lymphocytes/cytology ; Transcriptome
Chemical Substances	Receptors, Antigen, T-Cell
Language	English
Publishing date	2019-07-24
Publishing country	England
Document type	Dataset ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-019-0131-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: GE-mini: a mobile APP for large-scale gene expression visualization.

Tang, Zefang / Li, Chenwei / Zhang, Karena / Yang, Mingyu / Hu, Xueda

Bioinformatics (Oxford, England)

2017 Volume 33, Issue 6, Page(s) 941–943

Abstract: Summary: The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) projects produced large-scale RNA sequencing data, which provides an opportunity for performing integrated expression analysis for all genes across tens of thousands of tumor ... ...

Abstract	Summary: The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) projects produced large-scale RNA sequencing data, which provides an opportunity for performing integrated expression analysis for all genes across tens of thousands of tumor and normal tissue specimens. Rapid access to and easy visualization of such valuable data could facilitate research in a wide biological area. Here, we present the GE-mini APP for smart phones, a mobile visualization tool for integrated gene expression data based on both TCGA and GTEx. This gene-centric expression viewer provides a convenient method for displaying expression profiles of all available tumor and tissue types, while allowing drilling down to detailed views for specific tissue types. Availability and implementation: Both the iOS and Android APPs are freely available to all non-commercial users in App Store and Google Play. The QR codes of App store and Google play are also provided for scanning and download. The GE-mini web server is also available at http://gemini.cancer-pku.cn/ . Contacts: tangzefang@pku.edu.cn or huxueda@pku.edu.cn. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Gene Expression Regulation, Neoplastic ; Humans ; Mobile Applications ; Neoplasms/genetics ; Sequence Analysis, RNA/methods
Language	English
Publishing date	2017--15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btw775
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Zs.A 2374: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Immune phenotypic linkage between colorectal cancer and liver metastasis.

Liu, Yedan / Zhang, Qiming / Xing, Baocai / Luo, Nan / Gao, Ranran / Yu, Kezhuo / Hu, Xueda / Bu, Zhaode / Peng, Jirun / Ren, Xianwen / Zhang, Zemin

Cancer cell

2022 Volume 40, Issue 4, Page(s) 424–437.e5

Abstract: The tumor microenvironment (TME) is connected to immunotherapy responses, but it remains unclear how cancer cells and host tissues differentially influence the immune composition within TME. Here, we performed single-cell analyses for autologous samples ... ...

Abstract	The tumor microenvironment (TME) is connected to immunotherapy responses, but it remains unclear how cancer cells and host tissues differentially influence the immune composition within TME. Here, we performed single-cell analyses for autologous samples from liver metastasized colorectal cancer to disentangle factors shaping TME. By aligning CD45
MeSH term(s)	CD8-Positive T-Lymphocytes ; Colorectal Neoplasms/pathology ; Humans ; Immunotherapy ; Liver Neoplasms/genetics ; Tumor Microenvironment
Language	English
Publishing date	2022-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078448-X
ISSN	1878-3686 ; 1535-6108
ISSN (online)	1878-3686
ISSN	1535-6108
DOI	10.1016/j.ccell.2022.02.013
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Zs.A 5650: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 104: Show issues

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Article ; Online: Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment.

Kang, Boxi / Camps, Jordi / Fan, Biao / Jiang, Hongpeng / Ibrahim, Mahmoud M / Hu, Xueda / Qin, Shishang / Kirchhoff, Dennis / Chiang, Derek Y / Wang, Shan / Ye, Yingjiang / Shen, Zhanlong / Bu, Zhaode / Zhang, Zemin / Roider, Helge G

Genome biology

2022 Volume 23, Issue 1, Page(s) 265

Abstract: Background: The tumor microenvironment (TME) has been shown to strongly influence treatment outcome for cancer patients in various indications and to influence the overall survival. However, the cells forming the TME in gastric cancer have not been ... ...

Abstract	Background: The tumor microenvironment (TME) has been shown to strongly influence treatment outcome for cancer patients in various indications and to influence the overall survival. However, the cells forming the TME in gastric cancer have not been extensively characterized. Results: We combine bulk and single-cell RNA sequencing from tumors and matched normal tissue of 24 treatment-naïve GC patients to better understand which cell types and transcriptional programs are associated with malignant transformation of the stomach. Clustering 96,623 cells of non-epithelial origin reveals 81 well-defined TME cell types. We find that activated fibroblasts and endothelial cells are most prominently overrepresented in tumors. Intercellular network reconstruction and survival analysis of an independent cohort imply the importance of these cell types together with immunosuppressive myeloid cell subsets and regulatory T cells in establishing an immunosuppressive microenvironment that correlates with worsened prognosis and lack of response in anti-PD1-treated patients. In contrast, we find a subset of IFNγ activated T cells and HLA-II expressing macrophages that are linked to treatment response and increased overall survival. Conclusions: Our gastric cancer single-cell TME compendium together with the matched bulk transcriptome data provides a unique resource for the identification of new potential biomarkers for patient stratification. This study helps further to elucidate the mechanism of gastric cancer and provides insights for therapy.
MeSH term(s)	Humans ; Stomach Neoplasms/genetics ; Endothelial Cells ; Tumor Microenvironment ; Gene Expression Profiling ; Transcriptome ; Single-Cell Analysis
Language	English
Publishing date	2022-12-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-022-02828-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dynamics of peripheral T cell clones during PD-1 blockade in non-small cell lung cancer.

Zhang, Fan / Bai, Hua / Gao, Ranran / Fei, Kailun / Duan, Jianchun / Zhang, Zemin / Wang, Jie / Hu, Xueda

Cancer immunology, immunotherapy : CII

2020 Volume 69, Issue 12, Page(s) 2599–2611

Abstract: Understanding of the functional states and clonal dynamics of T cells after immune checkpoint blockade (ICB) is valuable for improving these therapeutic strategies. Here we performed Smart-seq2 single-cell RNA sequencing (scRNA-seq) analysis on 3,110 ... ...

Abstract	Understanding of the functional states and clonal dynamics of T cells after immune checkpoint blockade (ICB) is valuable for improving these therapeutic strategies. Here we performed Smart-seq2 single-cell RNA sequencing (scRNA-seq) analysis on 3,110 peripheral T cells of non-small cell lung cancer (NSCLC) patients before and after the initiation of programmed cell death protein 1 (PD-1) blockade. We identified individual peripheral T cell clones based on the full-length T cell receptor (TCR) sequences and monitored their dynamics during immunotherapy. We found a higher cytotoxic activity in the tumor-related CD4
MeSH term(s)	Aged ; Antineoplastic Agents, Immunological/pharmacology ; Antineoplastic Agents, Immunological/therapeutic use ; CD4-Positive T-Lymphocytes/drug effects ; CD4-Positive T-Lymphocytes/immunology ; CD4-Positive T-Lymphocytes/metabolism ; CD8-Positive T-Lymphocytes/drug effects ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/metabolism ; Carcinoma, Non-Small-Cell Lung/blood ; Carcinoma, Non-Small-Cell Lung/diagnosis ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Carcinoma, Non-Small-Cell Lung/immunology ; Clinical Trials, Phase III as Topic ; Disease Progression ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Lung/diagnostic imaging ; Lung/pathology ; Lung Neoplasms/blood ; Lung Neoplasms/diagnosis ; Lung Neoplasms/drug therapy ; Lung Neoplasms/immunology ; Male ; Middle Aged ; Multicenter Studies as Topic ; Nivolumab/pharmacology ; Nivolumab/therapeutic use ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Programmed Cell Death 1 Receptor/immunology ; Programmed Cell Death 1 Receptor/metabolism ; RNA-Seq ; Randomized Controlled Trials as Topic ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell/metabolism ; Single-Cell Analysis ; T-Lymphocyte Subsets/drug effects ; T-Lymphocyte Subsets/immunology ; T-Lymphocyte Subsets/metabolism
Chemical Substances	Antineoplastic Agents, Immunological ; PDCD1 protein, human ; Programmed Cell Death 1 Receptor ; Receptors, Antigen, T-Cell ; Nivolumab (31YO63LBSN)
Language	English
Publishing date	2020-06-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	195342-4
ISSN	1432-0851 ; 0340-7004
ISSN (online)	1432-0851
ISSN	0340-7004
DOI	10.1007/s00262-020-02642-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 1237: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article: GE-mini: a mobile APP for large-scale gene expression visualization

Tang, Zefang / Li, Chenwei / Zhang, Karena / Yang, Mingyu / Hu, Xueda

Bioinformatics. 2017 Mar. 15, v. 33, no. 6

2017

Abstract	Summary: The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) projects produced large-scale RNA sequencing data, which provides an opportunity for performing integrated expression analysis for all genes across tens of thousands of tumor and normal tissue specimens. Rapid access to and easy visualization of such valuable data could facilitate research in a wide biological area. Here, we present the GE-mini APP for smart phones, a mobile visualization tool for integrated gene expression data based on both TCGA and GTEx. This gene-centric expression viewer provides a convenient method for displaying expression profiles of all available tumor and tissue types, while allowing drilling down to detailed views for specific tissue types. Availability and Implementation: Both the iOS and Android APPs are freely available to all non-commercial users in App Store and Google Play. The QR codes of App store and Google play are also provided for scanning and download. The GE-mini web server is also available at http://gemini.cancer-pku.cn/. Contacts: tangzefang@pku.edu.cn or huxueda@pku.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
Keywords	Internet ; bioinformatics ; drilling ; gene expression ; genes ; mobile telephones ; neoplasms ; sequence analysis
Language	English
Dates of publication	2017-0315
Size	p. 941-943.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	1468345-3
ISSN	1460-2059 ; 1367-4803
ISSN (online)	1460-2059
ISSN	1367-4803
DOI	10.1093/bioinformatics/btw775
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Temporal single-cell tracing reveals clonal revival and expansion of precursor exhausted T cells during anti-PD-1 therapy in lung cancer.

Liu, Baolin / Hu, Xueda / Feng, Kaichao / Gao, Ranran / Xue, Zhiqiang / Zhang, Sujie / Zhang, Yuanyuan / Corse, Emily / Hu, Yi / Han, Weidong / Zhang, Zemin

Nature cancer

2021 Volume 3, Issue 1, Page(s) 108–121

Abstract: Anti-PD-1 treatment has shown unprecedented clinical success in the treatment of non-small-cell lung cancer (NSCLC), but the underlying mechanisms remain incompletely understood. Here, we performed temporal single-cell RNA and paired T-cell receptor ... ...

Abstract	Anti-PD-1 treatment has shown unprecedented clinical success in the treatment of non-small-cell lung cancer (NSCLC), but the underlying mechanisms remain incompletely understood. Here, we performed temporal single-cell RNA and paired T-cell receptor sequencing on 47 tumor biopsies from 36 patients with NSCLC following PD-1-based therapies. We observed increased levels of precursor exhausted T (Texp) cells in responsive tumors after treatment, characterized by low expression of coinhibitory molecules and high expression of GZMK. By contrast, nonresponsive tumors failed to accumulate Texp cells. Our data suggested that Texp cells were unlikely to be derived from the reinvigoration of terminally exhausted cells; instead, they were accumulated by (1) local expansion and (2) replenishment by peripheral T cells with both new and pre-existing clonotypes, a phenomenon we named clonal revival. Our study provides insights into mechanisms underlying PD-1-based therapies, implicating clonal revival and expansion of Texp cells as steps to improve NSCLC treatment.
MeSH term(s)	Carcinoma, Non-Small-Cell Lung/drug therapy ; Humans ; Lung Neoplasms/drug therapy ; Programmed Cell Death 1 Receptor ; Receptors, Antigen, T-Cell/genetics ; T-Lymphocytes/metabolism
Chemical Substances	Programmed Cell Death 1 Receptor ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2021-12-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2662-1347
ISSN (online)	2662-1347
DOI	10.1038/s43018-021-00292-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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