Enhancing immuno-oncology investigations through multidimensional decoding of tumor microenvironment with IOBR 2.0
The use of large transcriptome datasets has greatly improved our understanding of the tumor microenvironment (TME) and helped develop precise immunotherapies. The growing application of multi-omics, single-cell RNA sequencing (scRNA-seq), and spatial transcriptome sequencing has led to many new insights, yet these findings still require clinical validation in large cohorts. To advance multi-omics integration in TME research, we have upgraded the Immuno-Oncology Biological Research (IOBR) package to IOBR 2.0, restructuring and standardizing its analytical workflow. IOBR 2.0 offers six modules for TME analysis based on multi-omics data, including data preprocessing, TME estimation, TME infiltration pattern identification, cellular interaction analysis, genome and TME interaction, and feature visualization, as well as modeling. Additionally, IOBR 2.0 enables constructing gene signatures and reference matrices from scRNA-seq data for TME deconvolution. The user-friendly pipeline provides comprehensive insights into tumor-immune interactions, and a detailed GitBook(https://iobr.github.io/book/) offers a complete manual and analysis guide for each module.
Authors
- Dongqiang Zeng (ORCID: https://orcid.org/0000-0001-9724-8325)
- Rong Hua Guo (ORCID: https://orcid.org/0000-0002-0807-1490)
- Zuqiang Wu (ORCID: https://orcid.org/0009-0005-1853-6860)
- Min Shi (ORCID: https://orcid.org/0000-0003-0113-4089)
- Rongfang Shen (ORCID: https://orcid.org/0000-0003-0308-8856)
- Guangchuang Yu (ORCID: https://orcid.org/0000-0002-6485-8781)
- Wangjun Liao (ORCID: https://orcid.org/0000-0002-1364-8442)
- Wenchao Gu (ORCID: https://orcid.org/0000-0002-1505-9887)
- Peng Luo (ORCID: https://orcid.org/0000-0002-8215-2045)
- Shixiang Wang (ORCID: https://orcid.org/0000-0001-9855-7357)
- Yong-Hong Lai
- Wenjun Qiu
- Xi Xu (ORCID: https://orcid.org/0000-0003-4728-615X)
- Yiran Fang
- Qianqian Mao (ORCID: https://orcid.org/0009-0006-2363-055X)
- Xiatong Huang
- Gaofeng Wang (ORCID: https://orcid.org/0009-0006-4436-5628)
Institutions
- Central South University (CN)
- Johns Hopkins University (US)
- Chiba University (JP)
- Beijing Chao-Yang Hospital, Capital Medical University (CN)
- Zhujiang Hospital (CN)
- Beijing Obstetrics and Gynecology Hospital (CN)
- Beijing Chaoyang Emergency Medical Center (CN)
- Southern Medical University (CN)
- South China University of Technology (CN)
Publication Details
- Journal
- Cell Reports Methods
- Published
- 2024-12-01
- DOI
- https://doi.org/10.1016/j.crmeth.2024.100910
- Citations
- 60
- Primary Topic
- Cancer Genomics and Diagnostics
- Type
- article
- Field-Weighted Citation Impact
- 17.11
Funders
- Guangdong Science and Technology Department
- Guangzhou Science and Technology Program key projects
- Science and Technology Planning Project of Guangdong Province