TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response

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Abstract

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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Author and article information

Contributors

Zexian Zeng:

ORCID: https://orcid.org/0000-0002-3905-3244

Cheryl J Wong

Lin Yang

Nofal Ouardaoui

Dian Li:

ORCID: https://orcid.org/0000-0002-5374-7314

Wubing Zhang

Shengqing Gu

Yi Zhang

Yang Liu

Xiaoqing Wang

Jingxin Fu

Liye Zhou

Boning Zhang

Sarah Kim

Kathleen B Yates

Myles Brown:

ORCID: https://orcid.org/0000-0002-8213-1658

Gordon J Freeman

Ravindra Uppaluri

Robert Manguso

X Shirley Liu:

ORCID: https://orcid.org/0000-0003-4736-7339

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: 07 January 2022

Publication date (Electronic): 17 September 2021

Publication date PMC-release: 17 September 2021

Volume: 50

Issue: D1

Pages: D1391-D1397

Affiliations

Department of Data Science, Dana Farber Cancer Institute , Boston, MA 02215, USA

Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston, MA 02215, USA

Department of Data Science, Dana Farber Cancer Institute , Boston, MA 02215, USA

Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115 USA

Department of Data Science, Dana Farber Cancer Institute , Boston, MA 02215, USA

School of Life Science and Technology, Tongji University , Shanghai, 200060, China

Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA 02215, USA

Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215, USA