Spatial biology is an ever-evolving discipline focusing on improving our understanding of biological processes within the context of spatial organization, such as how cells are arranged within tissues or how specific biomarkers are distributed within these cells. The field of spatial analysis has grown exponentially over the last few years, especially within oncology research, being applied to study the relationships between the tumor and the ecosystem that belies the complex and ever shape-shifting tumor microenvironment (TME).
Such technological advances have created unprecedented opportunities to allow a detailed characterization of specific cell phenotypes, defined by co- or lack of expression of multiple markers, that may help in predicting clinical responses and mechanisms of resistance to cancer therapy. Indeed, walking into this year’s AACR2024 you couldn’t fail to recognize the myriad of vendors and different technologies available to study spatial biology. With over 200 submitted abstracts using such techniques to address aspects of tumor biology, therapy resistance and novel biomarker development, it’s clear that with this momentum we’re going to see more spatial methods in clinical trials.
With that in mind, Aviv Regev, Head, Executive Vice President, Genentech and early adopter as to the importance of spatial context of tumors, discussed during one of the plenary sessions how insights from skin cells have helped researchers study melanoma progression and develop possible treatment strategies, especially for tumors refractory to immunotherapy. Using a combination of spatial analyses and single-cell RNA sequencing (scRNA-Seq) she revealed that malignant cells comprising immune “cold” niches have a distinct gene expression signature that can predict immune cell exclusion. Regev and colleagues found that while tumors with more “cold” niches did not respond as well to immunotherapy over those with “hot” niches, they were more likely to respond to inhibitors of the cyclin dependent kinases 4 and 6 (CDK4/6), suggesting a potential therapeutic vulnerability. Importantly, such data highlight the need to potentially combine the advantages of targeted therapy and immunotherapy and enhance the immune response of “cold” more effectively.
MD Anderson Cancer Center has also been leading the way with integrating spatial biology into their research workflows and early trials, most recently creating spatial maps of a given tissue at single-cell resolution with the resulting maps providing unique biological insights into the cancer microenvironment. During this year’s conference, Ansam Sinjab, a research scientist in Professor Kadara’s lab of Translational Molecular Pathology, discussed charting the evolution of lung pre-cancer development and progression using high-resolution single-cell and spatial atlases of lung premalignancy to better characterize the evolution from pre-malignant lesions (PMLs) to fully formed lung adenocarcinoma (LUAD). https://aacrjournals.org/cancerres/article/84/6_Supplement/3893/740388/Abstract-3893-A-multimodal-spatial-omics-atlas-of. The group combined spatial omics (transcriptomic and proteomic using various vendors) and scRNA-Seq analysis to map molecular profiles, cell states and interactions of matched samples from LUAD, PMLs and normal tissues adjacent to lesions taken from up to 17 patients. Analysis on more than half a million single cells, revealed that loss of alveolar differentiation and development of alveolar intermediate cells were the key features in the progression of PMLs to LUAD. They also noted heterogeneity in abundance and spatial organization of key immune subsets, such as regulatory T cells and B cells, as well as differences in the composition of tertiary lymphoid structures between adjacent normal cells, PMLs and LUAD. This study provided a deeper understanding that could point to targets for the early detection and perhaps early therapy intervention of lung cancer.
While techniques such as immunohistochemistry (IHC) and in situ hybridization (ISH) have been in routine use for more than 50 years, albeit with limited success as to their degree of multiplexing due to the number of dyes that can be differentiated, a frequent term at this year’s conference was “Spatial Omics”- Essentially the integration of both spatial proteomic and transcriptomic information to study spatial relationships and functional states.
During our Spotlight Theatre talk and subsequent poster presentation (https://aacrjournals.org/cancerres/article/84/6_Supplement/94/739330/Abstract-94-Interrogation-of-STING-induced), Courtney Todorov, one of our senior scientists within our spatial group as part of Pharma Services at NeoGenomics, discussed our proprietary updated integrated MultiOmyx™-RNAscope™ assay. The ability to co-detect same slide RNA and protein can enable critical information such as the source of secreted proteins (e.g. cytokines) or cell-type specific transcript levels. As highlighted in Courtney’s talk, this integrated approach was shown to spatially correlate the distribution of cytokine RNA expression in immune cell subsets within the tumor microenvironment. Similar workflows were also highlighted by Lunaphore (now part of Bio-Techne), wherein they incorporated RNAscope™ and sequential immunofluorescence (seqIF™) protocols to achieve same-slide co-detection of RNA and protein targets. The combined workflow was automated on their COMET™ platform for staining and imaging. This integrated multiomics protocol allowed for up to three RNAscope™ detection cycles combined with twelve seqIF™ cycles, for a final 12-plex RNA + 24-plex protein panel (https://aacrjournals.org/cancerres/article/84/6_Supplement/3797/735935/Abstract-3797-Unveiling-the-spatial-dynamics-of).
One novel approach to spatial techniques highlighted during the conference was 3D spatial biology. Indeed, in a prequel commentary to the annual AACR meeting, Linghua Wang, MD Anderson noted that “the transition from 2D to 3D spatial profiling marks a revolutionary era in cancer research, offering unprecedented potential to enhance cancer diagnosis and treatment”. This commentary also outlined the experimental and computational advancements and challenges in 3D spatial molecular profiling, underscoring the innovation needed in imaging tools, software, artificial intelligence, and machine learning to overcome implementation hurdles and harness the full potential of 3D analysis in the field (https://aacrjournals.org/cancerdiscovery/article-abstract/14/4/625/741976/The-3D-Revolution-in-Cancer-Discovery). Leveraging innovative 3D spatial techniques from Alpenglow Biosciences, Laura Dillon, Vice President of Translational Medicine & Bioinformatics at Incendia Therapeutics, discussed at both talks and poster sessions research to characterize immune exclusion in the TME using 2D and 3D spatial technologies to quantify the heterogeneous nature of immune infiltration and collagen structures (https://aacrjournals.org/cancerres/article/84/6_Supplement/2309/737312/Abstract-2309-3D-spatial-quantification-of).
This year, with nine poster presentations and as mentioned an Exhibitor Spotlight Theatre talk, we at NeoGenomics had a very productive and busy meeting. Many of our poster presentations included research addressing the TME in a variety of tumor indications using MultiOmyx™, our end to end spatial multiplexed immunofluorescence (IF) technology solution, enabling visualization and characterization of multiple biomarkers (up to 60 protein biomarkers) on a single FFPE tissue section coupled to proprietary AI-driven image algorithms. For more information on all our AACR 2024 abstracts and poster presentations, please visit https://neogenomics.com/newsroom/literature.
AACR 2024 undoubtedly showcased that improvements in many of the spatial technologies, particularly in single cell resolution, “multi-omic” approaches may finally lead to decoding the holy grail of solid tumors, the TME ecosystem. That aside, the data that we have today clearly demonstrates that spatial arrangements of the TME perform better in predicting e.g. immunotherapy response compared to existing methods that include PD‐L1 expression, TMB and bulk gene expression profiling and in my mind, it’s spatial biology that will likely become a major contributor to the advancement of personalized medicine within oncology applications.
I hope everyone had a great and inspiring conference and again if you missed any of our posters and talks please feel free to click on the links provided and visit our website for more information. www.neogenomics.com
About NeoGenomics, Inc.
NeoGenomics, Inc. specializes in cancer genetics testing and information services, providing one of the most comprehensive oncology-focused testing menus in the world to help physicians diagnose and treat cancer. NeoGenomics is committed to connecting patients with life altering therapies and trials. We believe that, together, with our partners, we can help patients with cancer today and the next person diagnosed tomorrow. In carrying out these commitments, NeoGenomics adheres to all applicable state and federal data protection laws, provides transparency and choice to patients regarding the handling and use of their data through expressed authorizations and our Notice of Privacy Practices, and has invested in leading technologies to ensure the data we maintain is secured at all times.