TISMO : syngeneic mouse tumor database to model tumor immunity and immunotherapy response
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research..
Syngeneic mouse models are tumors derived from murine cancer cells engrafted on genetically identical mouse strains. They are widely used tools for studying tumor immunity and immunotherapy response in the context of a fully functional murine immune system. Large volumes of syngeneic mouse tumor expression profiles under different immunotherapy treatments have been generated, although a lack of systematic collection and analysis makes data reuse challenging. We present Tumor Immune Syngeneic MOuse (TISMO), a database with an extensive collection of syngeneic mouse model profiles with interactive visualization features. TISMO contains 605 in vitro RNA-seq samples from 49 syngeneic cancer cell lines across 23 cancer types, of which 195 underwent cytokine treatment. TISMO also includes 1518 in vivo RNA-seq samples from 68 syngeneic mouse tumor models across 19 cancer types, of which 832 were from immune checkpoint blockade (ICB) studies. We manually annotated the sample metadata, such as cell line, mouse strain, transplantation site, treatment, and response status, and uniformly processed and quality-controlled the RNA-seq data. Besides data download, TISMO provides interactive web interfaces to investigate whether specific gene expression, pathway enrichment, or immune infiltration level is associated with differential immunotherapy response. TISMO is available at http://tismo.cistrome.org.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:50 |
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| Enthalten in: |
Nucleic acids research - 50(2022), D1 vom: 07. Jan., Seite D1391-D1397 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Zeng, Zexian [VerfasserIn] |
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| Links: |
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| Themen: |
Biomarkers, Pharmacological |
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| Anmerkungen: |
Date Completed 21.02.2022 Date Revised 12.03.2022 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/nar/gkab804 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM330763113 |
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| 520 | |a © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. | ||
| 520 | |a Syngeneic mouse models are tumors derived from murine cancer cells engrafted on genetically identical mouse strains. They are widely used tools for studying tumor immunity and immunotherapy response in the context of a fully functional murine immune system. Large volumes of syngeneic mouse tumor expression profiles under different immunotherapy treatments have been generated, although a lack of systematic collection and analysis makes data reuse challenging. We present Tumor Immune Syngeneic MOuse (TISMO), a database with an extensive collection of syngeneic mouse model profiles with interactive visualization features. TISMO contains 605 in vitro RNA-seq samples from 49 syngeneic cancer cell lines across 23 cancer types, of which 195 underwent cytokine treatment. TISMO also includes 1518 in vivo RNA-seq samples from 68 syngeneic mouse tumor models across 19 cancer types, of which 832 were from immune checkpoint blockade (ICB) studies. We manually annotated the sample metadata, such as cell line, mouse strain, transplantation site, treatment, and response status, and uniformly processed and quality-controlled the RNA-seq data. Besides data download, TISMO provides interactive web interfaces to investigate whether specific gene expression, pathway enrichment, or immune infiltration level is associated with differential immunotherapy response. TISMO is available at http://tismo.cistrome.org | ||
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| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 7 | |a Biomarkers, Pharmacological |2 NLM | |
| 700 | 1 | |a Wong, Cheryl J |e verfasserin |4 aut | |
| 700 | 1 | |a Yang, Lin |e verfasserin |4 aut | |
| 700 | 1 | |a Ouardaoui, Nofal |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Dian |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Wubing |e verfasserin |4 aut | |
| 700 | 1 | |a Gu, Shengqing |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Yi |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Yang |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Xiaoqing |e verfasserin |4 aut | |
| 700 | 1 | |a Fu, Jingxin |e verfasserin |4 aut | |
| 700 | 1 | |a Zhou, Liye |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Boning |e verfasserin |4 aut | |
| 700 | 1 | |a Kim, Sarah |e verfasserin |4 aut | |
| 700 | 1 | |a Yates, Kathleen B |e verfasserin |4 aut | |
| 700 | 1 | |a Brown, Myles |e verfasserin |4 aut | |
| 700 | 1 | |a Freeman, Gordon J |e verfasserin |4 aut | |
| 700 | 1 | |a Uppaluri, Ravindra |e verfasserin |4 aut | |
| 700 | 1 | |a Manguso, Robert |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, X Shirley |e verfasserin |4 aut | |
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