A5079127441- Cellular transport and secretion
- Lipid Membrane Structure and Behavior
- Advanced Proteomics Techniques and Applications
- Calcium signaling and nucleotide metabolism
- Machine Learning in Bioinformatics
- Alzheimer's disease research and treatments
- Epigenetics and DNA Methylation
- Autophagy in Disease and Therapy
- Advanced Biosensing Techniques and Applications
- Endoplasmic Reticulum Stress and Disease
- COVID-19 diagnosis using AI
- Advanced Breast Cancer Therapies
- DNA Repair Mechanisms
- Radiomics and Machine Learning in Medical Imaging
- Pancreatic function and diabetes
- Phytoplasmas and Hemiptera pathogens
- Ubiquitin and proteasome pathways
- Mass Spectrometry Techniques and Applications
- Cancer-related Molecular Pathways
- Advanced biosensing and bioanalysis techniques
- Immunodeficiency and Autoimmune Disorders
- Microtubule and mitosis dynamics
- Biotin and Related Studies
- RNA Interference and Gene Delivery
- RNA modifications and cancer
University of California, San Francisco
2015-2025
Harvard University
2021-2025
University of California System
2024
Research Network (United States)
2022-2024
Seoul National University
2022
National University
2022
Boston VA Research Institute
2021-2022
UCSF Helen Diller Family Comprehensive Cancer Center
2021
Abstract Degradation and recycling of plasma membrane proteins occurs via the endolysosomal system, wherein endosomes bud into cytosol from subsequently mature degradative lysosomal compartments. While methods have been developed for rapid selective capture lysosomes (Lyso-IP), analogous isolation early endosome intermediates are lacking. Here, we develop an approach early/sorting through affinity endosome-associated protein EEA1 (Endo-IP) provide proteomic lipidomic snapshots EEA1-positive...
Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued proliferation inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1 accessory...
Plasma membrane protein degradation and recycling are regulated by the endolysosomal system, wherein endocytic vesicles bud from plasma into cytoplasm mature endosomes then degradative lysosomes. As such, system plays a critical role in determining abundance of proteins on cell surface influencing cellular identity function. Highly polarized cells, like neurons, rely for axonal dendritic specialization synaptic compartmentalization. The importance this to neuronal function is reflected...
Plasma membrane protein degradation and recycling is regulated by the endolysosomal system, wherein endosomes bud from plasma into cytosol mature degradative lysosomes. As such, system plays a critical role in determining abundance of proteins on cell surface, influencing cellular identity function. Highly polarized cells, like neurons, rely for axonal dendritic specialization synaptic compartmentalization. The importance this to neuronal function reflected prevalence risk variants...
Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued proliferation inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1 accessory...
The development of CRISPR-Cas9 screening techniques coupled with chemical inhibition specific biological processes enables high-throughput investigation into many areas molecular biology. We present a protocol to conduct ubiquitin proteasome system-specific chemical-genetic screens in the human HAP1 cell line. This can be adapted for use other lines, compounds and types treatments, any sgRNA library. For complete details on execution this protocol, please refer Hundley et al. (2021).
Abstract Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued proliferation inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1...
Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued proliferation inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1 accessory...
Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenomics approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued growth inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1 accessory protein...
Human induced cortical-like neurons (iNeurons) with endogenously tagged 3xFLAG-EEA1 and TMEM192-3xHA can be used to isolate endosomes lysosomes, using Endo-IP Lyso-IP, respectively. Here, we present an immunofluorescence protocol assess the extent of colocalization between untagged EEA1 TMEM192 markers endolysosomal system in iNeurons.
We present a protocol collection for "Endo-IP and Lyso-IP Toolkit Endolysosomal Profiling of Human Induced Neurons".
We present a general protocol for Western blotting to detect endolysosomal proteins and negative control markers from other organelles assess whole-cell lysates Endo-IPs Lyso-IPs hESCs iNeurons.
Building off of our previously published EEA1-positive endosome isolation technique (Endo-IP), we describe an approach for capturing endosomes and TMEM192-positive lysosomes (Lyso-IP) from human embyronic stem cells (hESCs) induced cortical-like neurons (iNeurons) providing a relatively rapid means by which to examine the endolysosomal system. This enriches hundreds resident proteins cargo, enables downstream proteomic analysis endoslysomal system, along with other applications.
This is a general protocol for Western blotting to detect proteins or interest from whole-cell lysates derived cell culture systems (HeLa, iNeurons).
Previous studies have developed methods for isolation of lysosomes, mitochondria, and peroxisomes from non-denaturing extracts. Here we describe an approach purification early/sorting endosomes, providing a means by which to examine early aspects the endolysosomal system combine this with lysosome using Lyso-IP. We refer new method as Endo-IP. This allows us proteome lipidome perform electron microscopy imaging endosomes.
TOMAHAQ-based targeted proteomics relies on heavy-labeled reference peptides for multi-plexed quantification of interest within a set samples. The APP amyloid precursor protein is thought to be proteolytically processed the endolysosomal system by β-secretase and ϒ-secretase yield various forms Aβ. To quantitatively track products, we describe protocol design generation synthetic TOMAHAQ analysis. We also include extracellular cytosolic domains.
TOMAHAQ-based targeted proteomics relies on heavy-labeled reference peptides for multi-plexed quantification of interest within a set samples. The APP amyloid precursor protein is thought to be proteolytically processed the endolysosomal system by β-secretase and ϒ-secretase yield various forms Aβ. To quantitatively track products, we describe protocol design generation synthetic TOMAHAQ analysis. We also include extracellular cytosolic domains.
Lyso-IP is a method that allows for the isolation of lysosomes proteomics and metabolomics (dx.doi.org/10.17504/protocols.io.bybjpskn; dx.doi.org/10.17504/protocols.io.bx9hpr36). We have developed an analogous approach purification early/sorting endosomes (Endo-IP). In addition, we found endolysosomal via Endo-IP can be coupled to quantitative workflow obtain snapshots Amyloid Precursor Protein (APP) processing its Aβ products (Park et al. 2022). Here, describe methods cell line construction...
Previous studies have developed methods for isolation of lysosomes, mitochondria, and peroxisomes from non-denaturing extracts. Here we describe an approach purification early/sorting endosomes, providing a means by which to examine early aspects the endolysosomal system combine this with lysosome using Lyso-IP. We refer new method as Endo-IP. This allows us proteome lipidome perform electron microscopy imaging endosomes.
Lyso-IP is a method that allows for the isolation of lysosomes proteomics and metabolomics (dx.doi.org/10.17504/protocols.io.bybjpskn; dx.doi.org/10.17504/protocols.io.bx9hpr36). We have developed an analogous approach purification early/sorting endosomes (Endo-IP). In addition, we found endolysosomal via Endo-IP can be coupled to quantitative workflow obtain snapshots Amyloid Precursor Protein (APP) processing its Aβ products (Park et al. 2022). Here, describe methods cell line construction...
Here we present a general protocol for immunological detection by Western blotting of APP and proteins the endolysosomal system, including EEA1, RAB5, PSEN1, LAMP1, LAMP2, TMEM192, BACE1.