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Tumor Profiling

Learning the molecular pixels in a tumor

Cellular heterogeneity and perturbation of spatial relationships have been implicated in various physiological and pathological conditions. Cancer migration and metastasis are often led by a subset of aggressive cells, which emerge elusively, with genotypic and phenotypic plasticity in their repertoire. Yet, there is still a knowledge gap in the spatial determinants due to the challenge of integrating single-cell, multi-omic and spatial analysis on the same sample.

To capitalize clinically on new insights gleaned from preliminary single-cell + spatial biology studies, there is an urgency for technologies that democratize and disseminate these methods within the cancer research community. In this project, our focus is on creating multiomic spatial profiling workflows for tumor tissue sections using our open-space MFP technology, using its capability of simultaneous deposition (tag) and lysis (bag) of cells in tissues.

Current Projects

Tag & Bag

Tag & Bag aims to implement spatial barcoding approaches in concert with lysis using microfluidic delivery of oligo barcoding tags. By leveraging improved mass transfer and reaction rates conferred by HFCs and user-defined microscale localization, our aim is to selectively tag ROIs on tissue sections and performing multiplexed assays on unprocessed tissues.

Cell 2 Spec

Cell 2 Spec aims to implement selective local lysis (SpatiaLyse) on live cells and tissue sections to enable interfacing with mass spectrometry (MS). Using viscous shear, and detergent solubilization coupled with controlled enzymatic lysis, we aim to perform MS-sample prep spatially using the MFP.

Our Workflows

GeneScape

The integrated workflow-GeneScape-is used to evaluate heterogeneity in a metastatic mammary carcinoma, showing distinct single nucleotide variants and copy number variations in different tumor tissue regions, suggesting the polyclonal origin of the metastasis as well as development driven by multiple location-specific drivers. Adapted from Voithenberg & Kashyap et. al., Small (2021).

ProteinScape

We present a workflow for the localized extraction and protein analysis of regions of interest from frozen tissues, enabling the evaluation of tumor heterogeneity at the protein level. From Fomitcheva Khartchenko, et al., PLoS One (2021).

quIC

Here, we introduce a quantitative micro-immunochemistry assay that enables the acquisition of dynamic information, via a metric of the evolution of the immunohistochemistry signal during tissue staining, for the quantification of relative antigen density on tissue surfaces. From Kashyap & Fomitcheva Khartchenko et. al., Nat Biomed Eng (2019).

RNA-ISH

Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliver ISH-probes locally to regions of a few hundred micrometers over time periods of tens of minutes. From Voithenberg et al., NAR (2020).

Related Publications

Space in cancer biology: its role and implications

Trends in Cancer

Mapping spatial genetic landscapes in tissue sections through microscale integration of sampling methodology into genomic workflows

Small

A compact and versatile microfluidic probe for local processing of tissue sections and biological specimens

Review of Scientific Instruments

Quantification of tumor heterogeneity: from data acquisition to metric generation

Trends in Biotechnology

Spatially resolved genetic analysis of tissue sections enabled by microscale flow confinement retrieval and isotachophoretic purification

Angewandte Chemie International Edition

Micro-immunohistochemistry using a microfluidic probe

Lab on a Chip

Spatial protein heterogeneity analysis in frozen tissues to evaluate tumor heterogeneity

PLOS One

Tissue lithography: microscale dewaxing to enable retrospective studies on formalin-fixed paraffin-embedded (FFPE) tissue sections