A5007409264- Advanced Proteomics Techniques and Applications
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- Ferroptosis and cancer prognosis
- Immune cells in cancer
- Cell Image Analysis Techniques
- RNA modifications and cancer
- Advanced Biosensing Techniques and Applications
- Genomics and Phylogenetic Studies
- Cancer, Lipids, and Metabolism
- Cancer, Hypoxia, and Metabolism
- Metabolomics and Mass Spectrometry Studies
- Glycosylation and Glycoproteins Research
- Glioma Diagnosis and Treatment
- Pluripotent Stem Cells Research
- Congenital heart defects research
- Bioinformatics and Genomic Networks
- Nanoplatforms for cancer theranostics
- Cancer Research and Treatments
- interferon and immune responses
- Cancer Cells and Metastasis
- Photoacoustic and Ultrasonic Imaging
Nanostring Technologies (United States)
2022-2024
Brotman Baty Institute
2023-2024
Abstract The house mouse ( Mus musculus ) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans 1,2 . Mouse gestation lasts only 3 weeks, during which the genome orchestrates astonishing transformation of a single-cell zygote into free-living pup composed more than 500 million cells. Here, establish global framework for exploring mammalian development, we applied optimized combinatorial indexing profile transcriptional states 12.4 nuclei...
Abstract The house mouse, Mus musculus , is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of single cell zygote into free-living pup composed >500 million cells. Towards global framework for exploring mammalian development, we applied combinatorial indexing (sci-*) profile transcriptional states 12.4...
A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation multiple "omes". Here we present the implementation a novel proteogenomic (SPG) assay on GeoMx Digital Spatial Profiler platform with next-generation sequencing readout that enables high-plex digital quantitation proteins (>100-plex) RNA (whole transcriptome, >18,000-plex) from single formalin-fixed paraffin-embedded (FFPE) sample. This...
Abstract Background: Lung adenocarcinoma is one of the leading causes cancer-related mortality. One most frequently occurring mutations in lung cancer KRAS mutations. Recent development chemical inhibitors that specifically target oncogenic variants Ras, particularly commonly mutated KRAS-G12D isoform, represents a significant breakthrough targeted therapeutics. The tissue-level mechanisms underlying cell-autonomous and non-cell-autonomous effects KRas-G12D are poorly understood....
Abstract Background: Tumor progression and therapeutic response are regulated by the tumor microenvironment. Understanding spatial association architecture of molecular characteristics composition immune microenvironment at single-cell subcellular resolution encourages improvements in clinical prognosis immunotherapy benefits. Single-cell Spatial profiling technologies permit study transcriptional activity spatial, level provide abundant, high-resolution information required for...
Abstract A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation multiple “omes”. Here we present the implementation a novel proteogenomic (SPG) assay on GeoMx® Digital Spatial Profiler platform with NGS readout that enables high-plex digital quantitation proteins (> 100-plex) RNA (whole transcriptome, > 18,000-plex) from single FFPE sample. This study highlighted high concordance, R 0.85,...
Abstract The advancement of spatially resolved, multiplex proteomic and transcriptomic technologies has revolutionized redefined the approaches to complex biological questions pertaining tissue heterogeneity, tumor microenvironments, cellular interactions, diversity, therapeutic response. Most spatial yield single analyte or datasets from separate formalin-fixed paraffin-embedded (FFPE) tissues sections. Multiple studies have demonstrated a poor correlation between RNA expression protein...
<p>Supplementary Figure S16: Representative grey scale images of used in the assessment spatial proteogenomic data quality across mouse tissue types. FFPE sections were stained with GeoMx NGS Mouse Protein modules (137-plex), Mm WTA, and antibodies against CD45 (Immune), PanCK (Tumor) Syto13 (nuclear, DNA). Supplementary S17: ROI-to-ROI comparison to single analyte controls. 137-plex WTA. The Pearson’s R was calculated between each ROI from assay all ROIs (A) RNA (B) protein targets...
<p>Supplementary Figure S1: Impact of staining order on protein detection. FFPE cell line, A431CA, was stained with GeoMx Protein assays for nCounter readout and mock RNA probe (Buffer R only). (A) Swarm plots showing the distribution target in relation to SNR. (B) Pearson’s correlation control calculated each test condition. (C) The number targets above detection threshold, SNR ≥ 3. (D) Summary percent decrease detectable condition compared control. Supplementary S2: Assessment...
<div><p>A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation multiple “omes”. Here we present the implementation a novel proteogenomic (SPG) assay on GeoMx Digital Spatial Profiler platform with next-generation sequencing readout that enables high-plex digital quantitation proteins (>100-plex) RNA (whole transcriptome, >18,000-plex) from single formalin-fixed...
<p>Supplementary Figure S1: Impact of staining order on protein detection. FFPE cell line, A431CA, was stained with GeoMx Protein assays for nCounter readout and mock RNA probe (Buffer R only). (A) Swarm plots showing the distribution target in relation to SNR. (B) Pearson’s correlation control calculated each test condition. (C) The number targets above detection threshold, SNR ≥ 3. (D) Summary percent decrease detectable condition compared control. Supplementary S2: Assessment...
<p>Supplementary Figure S10: Representative images of CRC sample used in the assessment spatial proteogenomic data quality. FFPE colorectal cancer (CRC) sections (A) (zoomed (B)) were stained with GeoMx NGS Human Protein modules (147-plex), WTA, and antibodies against CD45 (Immune; left panel) PanCK (Tumor; right panel). Supplementary S11: ROI-to-ROI comparison to single analyte controls. 147-plex human modules, (Tumor) (Immune). The Pearson’s R was calculated between each ROI from...
<p>Supplementary Figure S10: Representative images of CRC sample used in the assessment spatial proteogenomic data quality. FFPE colorectal cancer (CRC) sections (A) (zoomed (B)) were stained with GeoMx NGS Human Protein modules (147-plex), WTA, and antibodies against CD45 (Immune; left panel) PanCK (Tumor; right panel). Supplementary S11: ROI-to-ROI comparison to single analyte controls. 147-plex human modules, (Tumor) (Immune). The Pearson’s R was calculated between each ROI from...
<div>Abstract<p>A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation multiple “omes”. Here we present the implementation a novel proteogenomic (SPG) assay on GeoMx® Digital Spatial Profiler platform with NGS readout that enables high-plex digital quantitation proteins (> 100-plex) RNA (whole transcriptome, > 18,000-plex) from single FFPE sample. This study highlighted high...
<p>Supplementary Figure S16: Representative grey scale images of used in the assessment spatial proteogenomic data quality across mouse tissue types. FFPE sections were stained with GeoMx NGS Mouse Protein modules (137-plex), Mm WTA, and antibodies against CD45 (Immune), PanCK (Tumor) Syto13 (nuclear, DNA). Supplementary S17: ROI-to-ROI comparison to single analyte controls. 137-plex WTA. The Pearson’s R was calculated between each ROI from assay all ROIs (A) RNA (B) protein targets...
<p>Supplementary Methods S1: Protocol for proteogenomic workflow</p>
<p>Supplementary Figure S19: Representative images used in the assessment of spatial proteogenomic data quality on Glioblastoma multiforme Grade 4. (A) Human brain glioblastoma tissue array was stained with GeoMx NGS Protein modules (147-plex), WTA, and antibodies against GFAP (Astrocyte/Tumor; left panel), CD45 (Immune; middle panel) Syto13 (Nuclei; right panel). (B) ROI were segmented into GFAP+ (left CD45+ (middle or (right Supplementary S20: gcGBM GBM. ROIs for (top GBM (bottom...
<p>Supplementary Figure S19: Representative images used in the assessment of spatial proteogenomic data quality on Glioblastoma multiforme Grade 4. (A) Human brain glioblastoma tissue array was stained with GeoMx NGS Protein modules (147-plex), WTA, and antibodies against GFAP (Astrocyte/Tumor; left panel), CD45 (Immune; middle panel) Syto13 (Nuclei; right panel). (B) ROI were segmented into GFAP+ (left CD45+ (middle or (right Supplementary S20: gcGBM GBM. ROIs for (top GBM (bottom...
<p>Supplementary Methods S1: Protocol for proteogenomic workflow</p>
<p>Supplementary Figure S16: Representative grey scale images of used in the assessment spatial proteogenomic data quality across mouse tissue types. FFPE sections were stained with GeoMx NGS Mouse Protein modules (137-plex), Mm WTA, and antibodies against CD45 (Immune), PanCK (Tumor) Syto13 (nuclear, DNA). Supplementary S17: ROI-to-ROI comparison to single analyte controls. 137-plex WTA. The Pearson’s R was calculated between each ROI from assay all ROIs (A) RNA (B) protein targets...
<p>Assessment of SPG performance on human tissue. FFPE colorectal cancer sections were stained with the GeoMx NGS Human Protein modules (147-plex), WTA, and antibodies against PanCK (Tumor) CD45 (Immune). <b>A,</b> Representative image sample used in assessment data quality versus respective RNA control data. Two ROIs showing strong enrichment immune cells (CD45; magenta) tumor (PanCK, green). Concordance between proteogenomic assay single analyte protein...
<p>Supplementary Methods S1: Protocol for proteogenomic workflow</p>
<p>Supplementary Figure S10: Representative images of CRC sample used in the assessment spatial proteogenomic data quality. FFPE colorectal cancer (CRC) sections (A) (zoomed (B)) were stained with GeoMx NGS Human Protein modules (147-plex), WTA, and antibodies against CD45 (Immune; left panel) PanCK (Tumor; right panel). Supplementary S11: ROI-to-ROI comparison to single analyte controls. 147-plex human modules, (Tumor) (Immune). The Pearson’s R was calculated between each ROI from...