Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Moving Spatially Resolved Multiplexed Protein Profiling toward Clinical Oncology.

ABSTRACT: The shift in cancer therapy from broadly cytotoxic agents toward "personalized" treatments that target specific alterations in each patient's tumor requires diagnostic pathology approaches that are quantitative and biospecimen-friendly. Novel multiplexed antibody-based imaging technologies can measure single-cell expression of over 60 proteins in intact tumor sections and hold promise for clinical oncology.

SUBMITTER: Pourmaleki M

PROVIDER: S-EPMC10070169 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Moving Spatially Resolved Multiplexed Protein Profiling toward Clinical Oncology.

Pourmaleki Maryam M Socci Nicholas D ND Hollmann Travis J TJ Mellinghoff Ingo K IK

Cancer discovery 20230401 4

The shift in cancer therapy from broadly cytotoxic agents toward "personalized" treatments that target specific alterations in each patient's tumor requires diagnostic pathology approaches that are quantitative and biospecimen-friendly. Novel multiplexed antibody-based imaging technologies can measure single-cell expression of over 60 proteins in intact tumor sections and hold promise for clinical oncology. ...[more]

PMID: 37009699

Similar Datasets

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.

Project description:Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here, we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 to 1000 distinct RNA species in hundreds of individual cells. Correlation analysis of the ~10(4) to 10(6) pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins.

| S-EPMC4662681 | biostudies-literature

Spatially resolved, highly multiplexed RNA profiling in single cells

Project description:Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 – 1000 unique RNA species in hundreds of individual cells. Correlation analysis of the ~10^4 – 10^6 pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins. A single sample is analyzed

2015-04-09 | E-GEOD-67685 | biostudies-arrayexpress

HIPI: Spatially resolved multiplexed protein expression inferred from H&E WSIs.

Project description:Solid tumors are characterized by complex interactions between the tumor, the immune system and the microenvironment. These interactions and intra-tumor variations have both diagnostic and prognostic significance and implications. However, quantifying the underlying processes in patient samples requires expensive and complicated molecular experiments. In contrast, H&E staining is typically performed as part of the routine standard process, and is very cheap. Here we present HIPI (H&E Image Interpretation and Protein Expression Inference) for predicting cell marker expression from tumor H&E images. We process paired H&E and CyCIF images taken from serial sections of colorectal cancers to train our model. We show that our model accurately predicts the spatial distribution of several important cell markers, on both held-out tumor regions as well as new tumor samples taken from different patients. Moreover, using only the tissue image morphology, HIPI is able to colocalize the interactions between different cell types, further demonstrating its potential clinical significance.

| S-EPMC11476684 | biostudies-literature

Spatially resolved, highly multiplexed RNA profiling in single cells

Project description:Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 – 1000 unique RNA species in hundreds of individual cells. Correlation analysis of the ~10^4 – 10^6 pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins.

2015-04-09 | GSE67685 | GEO

Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome.

Project description:Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 477 mitochondrial proteins with 94% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum (ER). The temporal control of RinID enables pulse-chase labeling of ER proteome in HeLa cells, which reveals substantially higher clearance rate for secreted proteins than ER resident proteins.

| S-EPMC10205723 | biostudies-literature

Wavevector multiplexed atomic quantum memory via spatially-resolved single-photon detection.

Project description:Parallelized quantum information processing requires tailored quantum memories to simultaneously handle multiple photons. The spatial degree of freedom is a promising candidate to facilitate such photonic multiplexing. Using a single-photon resolving camera, we demonstrate a wavevector multiplexed quantum memory based on a cold atomic ensemble. Observation of nonclassical correlations between Raman scattered photons is confirmed by an average value of the second-order correlation function [Formula: see text] in 665 separated modes simultaneously. The proposed protocol utilizing the multimode memory along with the camera will facilitate generation of multi-photon states, which are a necessity in quantum-enhanced sensing technologies and as an input to photonic quantum circuits.

| S-EPMC5732182 | biostudies-literature

Highly Multiplexed Spatially Resolved Proteomic and Transcriptional Profiling of the Glioblastoma Microenvironment Using Archived Formalin-Fixed Paraffin-Embedded Specimens.

Project description:Glioblastoma is a heterogeneous tumor for which effective treatment options are limited and often insufficient. Few studies have examined the intratumoral transcriptional and proteomic heterogeneity of the glioblastoma microenvironment to characterize the spatial distribution of potential molecular and cellular therapeutic immunooncology targets. We applied an integrated multimodal approach comprised of NanoString GeoMx Digital Spatial Profiling, single-cell RNA-seq (scRNA-seq), and expert neuropathologic assessment to characterize archival formalin-fixed paraffin-embedded glioblastoma specimens. Clustering analysis and spatial cluster maps highlighted the intratumoral heterogeneity of each specimen. Mixed cell deconvolution analysis revealed that neoplastic and vascular cells were the prominent cell types throughout each specimen, with macrophages, oligodendrocyte precursors, neurons, astrocytes, and oligodendrocytes present in lower abundance and illustrated the regional distribution of the respective cellular enrichment scores. The spatial resolution of the actionable immunotherapeutic landscape showed that robust B7H3 gene and protein expression was broadly distributed throughout each specimen and identified STING and VISTA as potential targets. Lastly, we uncovered remarkable variability in VEGFA expression and discovered unanticipated associations between VEGFA, endothelial cell markers, hypoxia, and the expression of immunoregulatory genes, indicative of regionally distinct immunosuppressive microdomains. This work provides an early demonstration of the ability of an integrated panel-based spatial biology approach to characterize and quantify the intrinsic molecular heterogeneity of the glioblastoma microenvironment.

| S-EPMC9937641 | biostudies-literature

Highly dispersive multiplexed micromechanical device array for spatially resolved sensing and actuation.

Project description:The powerful resource of parallelizing simple devices for realizing and enhancing complex operations comes with the drawback of multiple connections for addressing and controlling the individual elements. Here we report on a technological platform where several mechanical resonators can be individually probed and electrically actuated by using dispersive multiplexing within a single electrical channel. We demonstrate room temperature control of the individual device vibrational motion and spatially-resolved readouts. As the single elements have proven to be excellent bolometers and individual nodes for reservoir computing, our platform can be directly employed for single-channel addressing of multiple devices, with immediate applications for far-infrared cameras, spatial light modulators and recurrent neural networks operating at room temperature.

| S-EPMC11599719 | biostudies-literature

Spatially resolved and multiplexed MicroRNA quantification from tissue using nanoliter well arrays.

Project description:Spatially resolved gene expression patterns are emerging as a key component of medical studies, including companion diagnostics, but technologies for quantification and multiplexing are limited. We present a method to perform spatially resolved and multiplexed microRNA (miRNA) measurements from formalin-fixed, paraffin-embedded (FFPE) tissue. Using nanoliter well arrays to pixelate the tissue section and photopatterned hydrogels to quantify miRNA, we identified differentially expressed miRNAs in tumors from a genetically engineered mouse model for non-small cell lung cancer (K-rasLSL-G12D/+; p53fl/fl). This technology could be used to quantify heterogeneities in tissue samples and lead to informed, biomarker-based diagnostics.

| S-EPMC7211184 | biostudies-literature

Spatially resolved transcriptomic profiling of ovarian aging in mice.

Project description:Ovarian aging precedes that of any other mammalian organ and is the primary cause of female age-related infertility. The biological mechanisms responsible for ovarian aging remain unclear. Previous studies have been limited by their use of bulk RNA-sequencing, which masks the dynamic and heterogeneous nature of the ovary. In this study, we spatially resolved the transcriptomic landscape of ovaries from young and aged outbred mice. In total, we defined eight main ovarian cell populations, all of which were characterized by significant transcriptomic changes between young and aged samples. Further sub-cluster analysis revealed separate transcriptomes for distinct granulosa cell populations found in young versus aged mice, in addition to an oocyte sub-cluster population completely absent from aged mouse ovaries. This study provides a new perspective on mammalian ovarian aging using spatial transcriptomics to achieve deeper understanding of the localization and cell-population-specific mechanisms underlying age-related fertility decline.

| S-EPMC9391589 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data