The spatial localization of cells not only impacts cellular associations with other cells but also single cell subcellular organelle localization, interactions, and function. New data highlighting the complexities of multiple organelle coordinated responses to spatial localization will be discussed.

Cancer cells can attain different cellular states—driven by specific transcription factors and associated gene regulatory networks which modulate the tumor microenvironment and engage specific multicellular interactions. In this study, we developed novel experimental and analysis methods to integrate high-resolution, high-plex spatial proteotranscriptomics with live-phase holotomography to comprehensively dissect the cell-intrinsic and -extrinsic mechanisms of deleterious immune remodeling and therapeutic resistance in pancreatic cancer.

The recent explosion of high plex methods to evaluate biomolecules in a spatial context allows for identifying novel relationships and interactions between tumor cells and their microenvironment.  This presentation will describe the use of these methods, to (1) determine biomarkers in prostate cancer biopsies to improve tumor grading; and (2) delineate a mechanism through which renal clear cell carcinoma progresses to a renal sarcomatoid cancer subtype.

To advance our ability to treat cancer patients requires knowledge about critical spatial architecture, including how cancer cells are organized and how they interact with each other and their environment. We present the Cancer Atlas. This atlas was used to discover complex relationships between cell types and their neighborhood within the tumor microenvironment. We explore these atlases to identify novel fundamental biology and potential cancer targets across multiple solid malignancies.

Using highly multiplexed protein measurements, single-cell spatial analysis of the Hodgkin's Lymphoma tumor microenvironment reveals cell phenotypes and spatial arrangements in the tissue that are prognostic. We find that aggregation-dependent ligand receptor expression is a promising biomarker of patient survival, and it does not rely on an expression threshold. We demonstrate a biomarker discovery pipeline, and use it to translate a complex biomarker to multiplex immunofluorescence.

We present spatially resolved joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications and gene expression on the same tissue section. These were applied to mouse brains, to map how epigenetic mechanisms control transcriptional phenotype and cell dynamics in tissue. Linking epigenome to transcriptome allows the uncovering of new insights in spatial epigenetic priming, differentiation, and gene regulation within the tissue architecture.

Emerging genomic technologies that measure spatial information about RNA molecules promise to shed light on cell biology and function. However, most analytical techniques have primarily concentrated on spatial relationships at the multicellular and cellular scale without fully tapping into single-molecule spatial information. To address this gap, my lab introduces Bento, a toolkit designed for discerning spatial relationships at the subcellular scale. Bento incorporates a suite of statistical and machine learning methods within an intuitive Python programming interface, emphasizing the FAIR data management principles. To showcase its capabilities, my lab has utilized Bento to study RNA localization changes in doxorubicin-treated cardiomyocytes profiled with spatial transcriptomics.

This presentation will cover the challenges and opportunities of designing and implementing spatial transcriptomics projects. I will also touch on the ways in which we are thinking about integration of high-plex protein analysis or other tissue based staining modalities into our analytical workflows. The talk will be broad, but I hope to be able to share examples from oncology and inflammation therapeutic areas.

Health disparities are complex and a mixture of factors that need to be accounted for in both our planning, implementation, and execution across all research, especially in single-cell and spatial technologies. Dr. Plummer will discuss how major advances in next-generation sequencing and imaging-based approaches are now leading a revolution in how we measure gene expression in tissue sections while preserving cellular organization. Dr. Plummer will highlight current single-cell and spatial-omics tools and the opportunities and hurdles these technologies face for adoption in a global environment.