The iAtlas portal serves as an interactive companion to the recently published paper “The Immune Landscape of Cancer”.
About the CRI iAtlas
The Cancer Research Institute (CRI) iAtlas is an interactive web-based platform and set of analytic tools for studying interactions between tumors and the immune microenvironment. These tools allow researchers to explore associations among a variety of immune characterizations as well as with genomic and clinical phenotypes. The initial version of CRI iAtlas is based on an analysis performed by the Cancer Genome Atlas (TCGA) Research Network on the TCGA data set comprising over 10,000 tumor samples and 33 tumor samples (Thorsson et al. Immunity, 2018). In this analysis, each tumor sample was scored for a variety of readouts for immune response, such as immune cell composition, adaptive cell receptor repertoire, neoantigen load, and expression of genes coding for immunomodulatory proteins. The web tool allows researchers to explore these data readouts, and the relation between them in TCGA tumor types and in overarching immune subtypes identified in the study. CRI iAtlas is made possible through a collaboration between the Cancer Research Institute, Sage Bionetworks and the Institute for Systems Biology.
TCGA PanCancerAtlas Immune Response Working Group
The Immune Response Working Group (IRWG) comprised a diverse set of researchers devoted to exploring the relationship between tumors and the immune microenvironment and its impact on patient outcomes. This working group was one of many in the TCGA PanCancer Atlas initiative, each exploring a different aspect of cross-tumor type analysis. Each reported their findings in a series of articles in Cell Press in April 2018.
Highlights of the Thorsson et al. study include the following:
six identified immune subtypes span cancer tissue types and molecular subtypes;
immune subtypes differ by somatic aberrations, microenvironment and survival;
multiple control modalities of molecular networks affect tumor-immune interactions.
These analyses serve as a resource for exploring immunogenicity across cancer types. To learn more or to cite this work, please refer to the publication:
CRI iAtlas Explorer
The main feature of the iAtlas web tool is the iAtlas Explorer, which provides several Analysis Modules to explore and visualize results from the Thorsson et al. Immune Landscape study. Each module presents information organized by theme, with multiple views and interactive controls to enhance and extend the information included in the original paper figures.
Sample Group Overview: This module provides short summaries of your selected groups, and allows you to see how they overlap with other groups.
Tumor Microenvironment: Explore the immune cell proportions in your sample groups.
Immune Feature Trends: This module allows you to see how immune readouts vary across your groups, and how they relate to one another.
Clinical Outcomes: Plot survival curves based on immune characteristics and identify variables associated with outcome.
Immunomodulators: Explore the expression of genes that code for immunomodulating proteins, including checkpoint proteins.
About the Cancer Research Institute
The Cancer Research Institute (CRI), established in 1953, is the world’s leading nonprofit organization dedicated exclusively to transforming cancer patient care by advancing scientific efforts to develop new and effective immune system-based strategies to prevent, diagnose, treat, and eventually cure all cancers. Guided by a world-renowned Scientific Advisory Council that includes three Nobel laureates and 26 members of the National Academy of Sciences, CRI has invested over $350 million in support of research conducted by immunologists and tumor immunologists at the world’s leading medical centers and universities, and has contributed to many of the key scientific advances that demonstrate the potential for immunotherapy to change the face of cancer treatment. Learn more at www.cancerresearch.org.
About Sage Bionetworks
Sage Bionetworks is a nonprofit biomedical research organization, founded in 2009, with a vision to promote innovations in personalized medicine by enabling a community-based approach to scientific inquiries and discoveries. Sage Bionetworks strives to activate patients and to incentivize scientists, funders and researchers to work in fundamentally new ways in order to shape research, accelerate access to knowledge and transform human health. It is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, Washington and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships. More information is available at www.sagebionetworks.org.
About Institute for Systems Biology
The Institute for Systems Biology is a nonprofit biomedical research organization based in Seattle, Washington. It was founded in 2000 by systems biologist Leroy Hood, immunologist Alan Aderem, and protein chemist Ruedi Aebersold. ISB was established on the belief that the conventional models for exploring and funding breakthrough science have not caught up with the real potential of what is possible today. ISB serves as the ultimate environment where scientific collaboration stretches across disciplines and across academic and industrial organizations, where our researchers have the intellectual freedom to challenge the status quo, and where grand visions for breakthroughs in human health inspire a collective drive to achieve the seemingly impossible. Our core values ensure that we always keep our focus on the big ideas that eventually will have the largest impact on human health. ISB is an affiliate of Providence Health & Services. Learn more at www.systemsbiology.org.