Emmanouil D. Karagiannis
A5022677116- RNA Interference and Gene Delivery
- Protease and Inhibitor Mechanisms
- Advanced biosensing and bioanalysis techniques
- Angiogenesis and VEGF in Cancer
- Single-cell and spatial transcriptomics
- Nanoparticle-Based Drug Delivery
- Cancer Genomics and Diagnostics
- Cell Adhesion Molecules Research
- Lipid Membrane Structure and Behavior
- Force Microscopy Techniques and Applications
- Advanced Electron Microscopy Techniques and Applications
- Corneal Surgery and Treatments
- Chemokine receptors and signaling
- CRISPR and Genetic Engineering
- Cancer, Hypoxia, and Metabolism
- Retinal Diseases and Treatments
- Blood Coagulation and Thrombosis Mechanisms
- RNA and protein synthesis mechanisms
- Proteoglycans and glycosaminoglycans research
- Evolution and Genetic Dynamics
- Immunotherapy and Immune Responses
- Pluripotent Stem Cells Research
- Advanced Fluorescence Microscopy Techniques
- Peptidase Inhibition and Analysis
- Cell Image Analysis Techniques
Massachusetts Institute of Technology
2012-2025
McGovern Institute for Brain Research
2015-2025
Metropolitan Hospital
2022
IIT@MIT
2021
Engineering Arts (United States)
2021
Allen Institute
2021
Howard Hughes Medical Institute
2021
Johns Hopkins Medicine
2004-2010
Johns Hopkins University
2004-2010
University of Maryland, Baltimore
2005
Identifying transcript location in cells where specific RNAs occur within a cell or tissue has been limited by technology and imaging capabilities. Expansion microscopy allowed for better visualization of small structures expanding the tissues with polymer- hydrogel-based system. Alon et al. combined expansion long-read situ RNA sequencing, resulting more precise transcripts. This method, termed “ExSeq” was used to detect RNAs, both new transcripts those previously demonstrated localize...
Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, open source computational methods. Using we generated resource 51,926 matched cell images diverse types including lines, xenografts, diagnostic samples with limited...
Abstract A holistic understanding of tissue and organ structure function requires the detection molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous up to 40 antigens transcripts using metal-tagged antibodies but has so far been restricted two-dimensional imaging. Here we report development 3D IMC for multiplexed analysis at single-cell resolution demonstrate utility technology by human breast cancer samples. The resulting...
How cell-to-cell copy number alterations that underpin genomic instability
Abstract Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization them in intact tissues, with precision, is challenging do high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines an innovative label and optimized protocol, support dense tissues for visualization. We validate signal-to-background ratio, uniformity continuity, umExM brain slices, supports imaging proteins at a...
Abstract Lipids are fundamental building blocks of cells and their organelles, yet nanoscale resolution imaging lipids has been largely limited to electron microscopy techniques. We introduce validate a chemical tag that enables lipid membranes be imaged optically at via lipid-optimized form expansion microscopy, which we call membrane (mExM). mExM, novel post-expansion antibody labeling protocol, protein-lipid relationships in organelles such as mitochondria, the endoplasmic reticulum,...
The heterogeneity of breast cancer plays a major role in drug response and resistance has been extensively characterized at the genomic level. Here, single-cell mass cytometry (BCMC) panel is optimized to identify cell phenotypes their oncogenic signalling states biobank patient-derived tumour xenograft (PDTX) models representing diversity human cancer. BCMC identifies 13 cellular (11 2 murine), associated with both subtypes specific features. Pre-treatment phenotypic composition determinant...
Matrix metalloproteinases (MMPs) are a class of extracellular and membrane-bound proteases involved in an array physiological processes, including angiogenesis. We present detailed computational model MMP9 activation inhibition. Our is validated to existing biochemical experimental data. determine kinetic rate constants for the processes by MMP3, MMP10, MMP13, trypsin; inhibition tissue inhibitors (TIMPs) 1 2; deactivation. This approach allows us investigate discrepancies our understanding...
Abstract Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization them in intact tissues, with precision, is challenging do high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines a novel label and optimized protocol, support dense tissues for visualization. We validated signal-to-background ratio, uniformity continuity, umExM brain slices, supported imaging proteins at resolution...
One well documented family of enzymes responsible for the proteolytic processes that occur in extracellular matrix is soluble and membrane-associated metalloproteinases. Here we present first theoretical model biochemical network describing proteolysis collagen I by metalloproteinases 2 (MMP2) membrane type 1 (MT1-MMP) presence tissue inhibitor (TIMP2) a bulk, cell-free, stirred environment. The can serve as tool quantitatively activation MMP2 proenzyme (pro-MMP2), ectodomain shedding...
We introduce a systematic computational methodology based on bioinformatics that has enabled us to identify and classify >120 endogenous peptide inhibitors of endothelial cell proliferation migration. These peptides are derived from members the type IV collagen, thrombospondin, CXC chemokine protein families, as well somatotropin hormones, serpins, various kringle-containing proteins. Their activity in suppressing migration cells vitro provides proof principle for validity this method....
Angiogenesis or neovascularization, the process of new blood vessel formation from preexisting microvasculature, involves interactions among several cell types including parenchymal, endothelial cells, and immune cells. The vessels is tightly regulated by a balance between endogenous proangiogenic antiangiogenic factors to maintain homeostasis in tissue; tumor progression metastasis breast cancer have been shown be angiogenesis-dependent. We previously introduced systematic methodology...
Cell penetrating peptides have demonstrated potential to facilitate the cellular delivery of therapeutic molecules. Here we develop a set 50 cell peptide based formulations with deliver small interfering RNAs intercellularly. The transfection efficacy siRNA containing lipid-like nanoparticles decorated different was evaluated both in vitro and vivo correlated physical chemical properties. In vitro, these particles were internalized primarily through macropinocytosis. When presented bone...
Angiogenesis is the formation of neovasculature from a pre-existing vascular network. Progression solid tumors including lung cancer angiogenesis-dependent. We previously introduced bioinformatics-based methodology to identify endogenous anti-angiogenic peptide sequences, and validated these predictions in vitro human umbilical vein endothelial cell (HUVEC) proliferation migration assays.One family peptides with high activity derived alpha-fibrils type IV collagen. Based on results...