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Article: Quantitative Analysis of Autophagy in Single Cells: Differential Response to Amino Acid and Glucose Starvation.

Martin, Katie R / Celano, Stephanie L / Sheldon, Ryan D / Jones, Russell G / MacKeigan, Jeffrey P

bioRxiv : the preprint server for biology

2023

Abstract: Autophagy is a highly conserved, intracellular recycling process by which cytoplasmic contents are degraded in the lysosome. This process occurs at a low level constitutively; however, it is induced robustly in response to stressors, in particular, ... ...

Abstract	Autophagy is a highly conserved, intracellular recycling process by which cytoplasmic contents are degraded in the lysosome. This process occurs at a low level constitutively; however, it is induced robustly in response to stressors, in particular, starvation of critical nutrients such as amino acids and glucose. That said, the relative contribution of these inputs is ambiguous and many starvation medias are poorly defined or devoid of multiple nutrients. Here, we sought to generate a quantitative catalog of autophagy across multiple stages and in single, living cells under normal growth conditions as well as in media starved specifically of amino acids or glucose. We found that autophagy is induced by starvation of amino acids, but not glucose, in U2OS cells, and that MTORC1-mediated ULK1 regulation and autophagy are tightly linked to amino acid levels. While autophagy is engaged immediately during amino acid starvation, a heightened response occurs during a period marked by transcriptional upregulation of autophagy genes during sustained starvation. Finally, we demonstrated that cells immediately return to their initial, low-autophagy state when nutrients are restored, highlighting the dynamic relationship between autophagy and environmental conditions. In addition to sharing our findings here, we provide our data as a high-quality resource for others interested in mathematical modeling or otherwise exploring autophagy in individual cells across a population.
Language	English
Publishing date	2023-12-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.01.569679
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Article: Molecular dynamics simulations provide insights into ULK-101 potency and selectivity toward autophagic kinases ULK1/2.

Vaughan, Robert M / Dickson, Bradley M / Martin, Katie R / MacKeigan, Jeffrey P

bioRxiv : the preprint server for biology

2023

Abstract: Kinase domains are highly conserved within protein kinases in both sequence and structure. Many factors, including phosphorylation, amino acid substitutions or mutations, and small molecule inhibitor binding, influence conformations of the kinase domain ... ...

Abstract	Kinase domains are highly conserved within protein kinases in both sequence and structure. Many factors, including phosphorylation, amino acid substitutions or mutations, and small molecule inhibitor binding, influence conformations of the kinase domain and enzymatic activity. The serine/threonine kinases ULK1 and ULK2 are highly conserved with N- and C-terminal domains, phosphate-binding P-loops, αC-helix, regulatory and catalytic spines, and activation loop DFG and APE motifs. Here, we performed molecular dynamics (MD) simulations to understand better the potency and selectivity of the ULK1/2 small molecule inhibitor, ULK-101. We observed stable bound states for ULK-101 to the adenosine triphosphate (ATP)-binding site of ULK2, coordinated by hydrogen bonding with the hinge backbone and the catalytic lysine sidechain. Notably, ULK-101 occupies a hydrophobic pocket associated with the N-terminus of the αC-helix. Large movements in the P-loop are also associated with ULK-101 inhibitor binding and exit from ULK2. Our data further suggests that ULK-101 could induce a folded P-loop conformation and hydrophobic pocket reflected in its nanomolar potency and kinome selectivity.
Language	English
Publishing date	2023-12-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.01.569261
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Article: Spectrum of germline and somatic mitochondrial DNA variants in Tuberous Sclerosis Complex.

Giannikou, Krinio / Martin, Katie R / Abdel-Azim, Ahmad G / Pamir, Kaila J / Hougard, Thomas R / Bagwe, Shefali / Tang, Yan / MacKeigan, Jeffrey P / Kwiatkowski, David J / Henske, Elizabeth P / Lam, Hilaire C

Frontiers in genetics

2023 Volume 13, Page(s) 917993

Abstract: Tuberous Sclerosis Complex (TSC) is caused by loss of function variants in ... ...

Abstract	Tuberous Sclerosis Complex (TSC) is caused by loss of function variants in either
Language	English
Publishing date	2023-01-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.917993
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Chemical Biology Screening Identifies a Vulnerability to Checkpoint Kinase Inhibitors in TSC2-Deficient Renal Angiomyolipomas.

Vaughan, Robert M / Kordich, Jennifer J / Chan, Chun-Yuan / Sasi, Nanda K / Celano, Stephanie L / Sisson, Kellie A / Van Baren, Megan / Kortus, Matthew G / Aguiar, Dean J / Martin, Katie R / MacKeigan, Jeffrey P

Frontiers in oncology

2022 Volume 12, Page(s) 852859

Abstract: The tuberous sclerosis complex (TSC) is a rare genetic syndrome and multisystem disease resulting in tumor formation in major organs. A molecular hallmark of TSC is a dysregulation of the mammalian target of rapamycin (mTOR) through loss-of-function ... ...

Abstract	The tuberous sclerosis complex (TSC) is a rare genetic syndrome and multisystem disease resulting in tumor formation in major organs. A molecular hallmark of TSC is a dysregulation of the mammalian target of rapamycin (mTOR) through loss-of-function mutations in either tumor suppressor
Language	English
Publishing date	2022-03-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2022.852859
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Article ; Online: Determining the Impact of Metabolic Nutrients on Autophagy.

Guillaume, Jessica D / Celano, Stephanie L / Martin, Katie R / MacKeigan, Jeffrey P

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1862, Page(s) 151–162

Abstract: Tumorigenesis relies on the ability of cancer cells to obtain necessary nutrients and fulfill increased energy demands associated with rapid proliferation. However, as a result of increased metabolite consumption and poor vascularization, most cancer ... ...

Abstract	Tumorigenesis relies on the ability of cancer cells to obtain necessary nutrients and fulfill increased energy demands associated with rapid proliferation. However, as a result of increased metabolite consumption and poor vascularization, most cancer cells must survive in a nutrient poor and high cellular stress microenvironment. Cancer cells undergo metabolic reprogramming to evade cell death and ensure proliferation; in particular, cancer cells utilize the catabolic process of autophagy. Autophagy creates an intracellular pool of metabolites by sequestering cytosolic macromolecules in double-membrane vesicles targeted for lysosomal degradation. During times of environmental stress and nutrient starvation, autophagy is upregulated through the dynamic interactions between two nutrient sensing proteins, AMP activated protein kinase (AMPK) and mechanistic target of rapamycin (mTOR), in cooperation with Unc-51 like autophagy activating kinase 1 (ULK1). In this way, a lack of metabolic nutrients plays a critical role in inducing autophagy, while the products of autophagy also serve as readily available fuel for the cell. In this chapter, we describe methods to visualize and quantify autophagy using a fluorescent sensor of autophagic membranes. Thus, the impact of specific nutrients on autophagy can be measured using live-cell fluorescent microscopy.
MeSH term(s)	Animals ; Autophagosomes/metabolism ; Autophagy/physiology ; Carcinogenesis/pathology ; Cell Culture Techniques/instrumentation ; Cell Culture Techniques/methods ; Cell Line, Tumor ; Culture Media/chemistry ; Green Fluorescent Proteins/chemistry ; Humans ; Intravital Microscopy/instrumentation ; Intravital Microscopy/methods ; Metabolomics/instrumentation ; Metabolomics/methods ; Microscopy, Fluorescence/instrumentation ; Microscopy, Fluorescence/methods ; Microtubule-Associated Proteins/chemistry ; Microtubule-Associated Proteins/metabolism ; Nutrients/analysis ; Nutrients/metabolism ; Single Molecule Imaging/instrumentation ; Single Molecule Imaging/methods ; Single-Cell Analysis/instrumentation ; Single-Cell Analysis/methods
Chemical Substances	Culture Media ; Microtubule-Associated Proteins ; Nutrients ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2018-10-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8769-6_11
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1.

Szymańska, Paulina / Martin, Katie R / MacKeigan, Jeffrey P / Hlavacek, William S / Lipniacki, Tomasz

PloS one

2015 Volume 10, Issue 3, Page(s) e0116550

Abstract: We constructed a mechanistic, computational model for regulation of (macro)autophagy and protein synthesis (at the level of translation). The model was formulated to study the system-level consequences of interactions among the following proteins: two ... ...

Abstract	We constructed a mechanistic, computational model for regulation of (macro)autophagy and protein synthesis (at the level of translation). The model was formulated to study the system-level consequences of interactions among the following proteins: two key components of MTOR complex 1 (MTORC1), namely the protein kinase MTOR (mechanistic target of rapamycin) and the scaffold protein RPTOR; the autophagy-initiating protein kinase ULK1; and the multimeric energy-sensing AMP-activated protein kinase (AMPK). Inputs of the model include intrinsic AMPK kinase activity, which is taken as an adjustable surrogate parameter for cellular energy level or AMP:ATP ratio, and rapamycin dose, which controls MTORC1 activity. Outputs of the model include the phosphorylation level of the translational repressor EIF4EBP1, a substrate of MTORC1, and the phosphorylation level of AMBRA1 (activating molecule in BECN1-regulated autophagy), a substrate of ULK1 critical for autophagosome formation. The model incorporates reciprocal regulation of mTORC1 and ULK1 by AMPK, mutual inhibition of MTORC1 and ULK1, and ULK1-mediated negative feedback regulation of AMPK. Through analysis of the model, we find that these processes may be responsible, depending on conditions, for graded responses to stress inputs, for bistable switching between autophagy and protein synthesis, or relaxation oscillations, comprising alternating periods of autophagy and protein synthesis. A sensitivity analysis indicates that the prediction of oscillatory behavior is robust to changes of the parameter values of the model. The model provides testable predictions about the behavior of the AMPK-MTORC1-ULK1 network, which plays a central role in maintaining cellular energy and nutrient homeostasis.
MeSH term(s)	AMP-Activated Protein Kinases/metabolism ; Adaptor Proteins, Signal Transducing/metabolism ; Autophagy ; Autophagy-Related Protein-1 Homolog ; Cell Cycle Proteins ; Computational Biology/methods ; Gene Expression Regulation ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Mechanistic Target of Rapamycin Complex 1 ; Models, Genetic ; Multiprotein Complexes/metabolism ; Phosphoproteins/metabolism ; Protein Biosynthesis ; Protein-Serine-Threonine Kinases/metabolism ; Sirolimus/pharmacology ; TOR Serine-Threonine Kinases/metabolism
Chemical Substances	AMBRA1 protein, human ; Adaptor Proteins, Signal Transducing ; Cell Cycle Proteins ; EIF4EBP1 protein, human ; Intracellular Signaling Peptides and Proteins ; Multiprotein Complexes ; Phosphoproteins ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; Autophagy-Related Protein-1 Homolog (EC 2.7.11.1) ; Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; ULK1 protein, human (EC 2.7.11.1) ; AMP-Activated Protein Kinases (EC 2.7.11.31) ; Sirolimus (W36ZG6FT64)
Language	English
Publishing date	2015-03-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0116550
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: PI3K-C2α knockdown decreases autophagy and maturation of endocytic vesicles.

Merrill, Nathan M / Schipper, Joshua L / Karnes, Jonathan B / Kauffman, Audra L / Martin, Katie R / MacKeigan, Jeffrey P

PloS one

2017 Volume 12, Issue 9, Page(s) e0184909

Abstract: Phosphoinositide 3-kinase (PI3K) family members are involved in diverse cellular fates including cell growth, proliferation, and survival. While many molecular details are known about the Class I and III PI3Ks, less is known about the Class II PI3Ks. To ... ...

Abstract	Phosphoinositide 3-kinase (PI3K) family members are involved in diverse cellular fates including cell growth, proliferation, and survival. While many molecular details are known about the Class I and III PI3Ks, less is known about the Class II PI3Ks. To explore the function of all eight PI3K isoforms in autophagy, we knock down each gene individually and measure autophagy. We find a significant decrease in autophagy following siRNA-mediated PIK3C2A (encoding the Class 2 PI3K, PI3K-C2α) knockdown. This defective autophagy is rescued by exogenous PI3K-C2α, but not kinase-dead PI3K-C2α. Using confocal microscopy, we probe for markers of endocytosis and autophagy, revealing that PI3K-C2α colocalizes with markers of endocytosis. Though endocytic uptake is intact, as demonstrated by transferrin labeling, PIK3C2A knockdown results in vesicle accumulation at the recycling endosome. We isolate distinct membrane sources and observe that PI3K-C2α interacts with markers of endocytosis and autophagy, notably ATG9. Knockdown of either PIK3C2A or ATG9A/B, but not PI3KC3, results in an accumulation of transferrin-positive clathrin coated vesicles and RAB11-positive vesicles at the recycling endosome. Taken together, these results support a role for PI3K-C2α in the proper maturation of endosomes, and suggest that PI3K-C2α may be a critical node connecting the endocytic and autophagic pathways.
MeSH term(s)	Autophagy ; Biomarkers/metabolism ; Cell Line ; Cell Proliferation ; Endocytosis ; Endosomes/metabolism ; Gene Knockdown Techniques ; Humans ; Phosphatidylinositol 3-Kinases/genetics ; Phosphatidylinositol 3-Kinases/metabolism ; RNA, Small Interfering/metabolism ; Signal Transduction ; Transport Vesicles/metabolism
Chemical Substances	Biomarkers ; RNA, Small Interfering ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; PIK3C2A protein, human (EC 2.7.1.137)
Language	English
Publishing date	2017-09-14
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0184909
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Identification of Kinases Responsible for p53-Dependent Autophagy.

Celano, Stephanie L / Yco, Lisette P / Kortus, Matthew G / Solitro, Abigail R / Gunaydin, Hakan / Scott, Mark / Spooner, Edward / O'Hagan, Ronan C / Fuller, Peter / Martin, Katie R / Shumway, Stuart D / MacKeigan, Jeffrey P

iScience

2019 Volume 15, Page(s) 109–118

Abstract: In cancer, autophagy is upregulated to promote cell survival and tumor growth during times of nutrient stress and can confer resistance to drug treatments. Several major signaling networks control autophagy induction, including the p53 tumor suppressor ... ...

Abstract	In cancer, autophagy is upregulated to promote cell survival and tumor growth during times of nutrient stress and can confer resistance to drug treatments. Several major signaling networks control autophagy induction, including the p53 tumor suppressor pathway. In response to DNA damage and other cellular stresses, p53 is stabilized and activated, while HDM2 binds to and ubiquitinates p53 for proteasome degradation. Thus blocking the HDM2-p53 interaction is a promising therapeutic strategy in cancer; however, the potential survival advantage conferred by autophagy induction may limit therapeutic efficacy. In this study, we leveraged an HDM2 inhibitor to identify kinases required for p53-dependent autophagy. Interestingly, we discovered that p53-dependent autophagy requires several kinases, including the myotonic dystrophy protein kinase-like alpha (MRCKα). MRCKα is a CDC42 effector reported to activate actin-myosin cytoskeletal reorganization. Overall, this study provides evidence linking MRCKα to autophagy and reveals additional insights into the role of kinases in p53-dependent autophagy.
Language	English
Publishing date	2019-04-23
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2019.04.023
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Article ; Online: Mitochondrial morphological features are associated with fission and fusion events.

Westrate, Laura M / Drocco, Jeffrey A / Martin, Katie R / Hlavacek, William S / MacKeigan, Jeffrey P

PloS one

2014 Volume 9, Issue 4, Page(s) e95265

Abstract: Mitochondria are dynamic organelles that undergo constant remodeling through the regulation of two opposing processes, mitochondrial fission and fusion. Although several key regulators and physiological stimuli have been identified to control ... ...

Abstract	Mitochondria are dynamic organelles that undergo constant remodeling through the regulation of two opposing processes, mitochondrial fission and fusion. Although several key regulators and physiological stimuli have been identified to control mitochondrial fission and fusion, the role of mitochondrial morphology in the two processes remains to be determined. To address this knowledge gap, we investigated whether morphological features extracted from time-lapse live-cell images of mitochondria could be used to predict mitochondrial fate. That is, we asked if we could predict whether a mitochondrion is likely to participate in a fission or fusion event based on its current shape and local environment. Using live-cell microscopy, image analysis software, and supervised machine learning, we characterized mitochondrial dynamics with single-organelle resolution to identify features of mitochondria that are predictive of fission and fusion events. A random forest (RF) model was trained to correctly classify mitochondria poised for either fission or fusion based on a series of morphological and positional features for each organelle. Of the features we evaluated, mitochondrial perimeter positively correlated with mitochondria about to undergo a fission event. Similarly mitochondrial solidity (compact shape) positively correlated with mitochondria about to undergo a fusion event. Our results indicate that fission and fusion are positively correlated with mitochondrial morphological features; and therefore, mitochondrial fission and fusion may be influenced by the mechanical properties of mitochondrial membranes.
MeSH term(s)	Bacterial Proteins/metabolism ; Cell Line, Tumor ; GTP Phosphohydrolases/genetics ; Gene Knockdown Techniques ; Humans ; Luminescent Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Dynamics ; Mutation/genetics
Chemical Substances	Bacterial Proteins ; Luminescent Proteins ; yellow fluorescent protein, Bacteria ; GTP Phosphohydrolases (EC 3.6.1.-) ; OPA1 protein, human (EC 3.6.1.-)
Language	English
Publishing date	2014-04-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0095265
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Article ; Online: Integrating virtual and biochemical screening for protein tyrosine phosphatase inhibitor discovery.

Martin, Katie R / Narang, Pooja / Medina-Franco, José L / Meurice, Nathalie / MacKeigan, Jeffrey P

Methods (San Diego, Calif.)

2013 Volume 65, Issue 2, Page(s) 219–228

Abstract: Protein tyrosine phosphatases (PTPs) represent an important class of enzymes that mediate signal transduction and control diverse aspects of cell behavior. The importance of their activity is exemplified by their significant contribution to disease ... ...

Abstract	Protein tyrosine phosphatases (PTPs) represent an important class of enzymes that mediate signal transduction and control diverse aspects of cell behavior. The importance of their activity is exemplified by their significant contribution to disease etiology with over half of all human PTP genes implicated in at least one disease. Small molecule inhibitors targeting individual PTPs are important biological tools, and are needed to fully characterize the function of these enzymes. Moreover, potent and selective PTP inhibitors hold the promise to transform the treatment of many diseases. While numerous methods exist to develop PTP-directed small molecules, we have found that complimentary use of both virtual (in silico) and biochemical (in vitro) screening approaches expedite compound identification and drug development. Here, we summarize methods pertinent to our work and others. Focusing on specific challenges and successes we have experienced, we discuss the considerable caution that must be taken to avoid enrichment of inhibitors that function by non-selective oxidation. We also discuss the utility of using "open" PTP structures to identify active-site directed compounds, a rather unconventional choice for virtual screening. When integrated closely, virtual and biochemical screening can be used in a productive workflow to identify small molecules targeting PTPs.
MeSH term(s)	Biological Assay/instrumentation ; Biological Assay/methods ; Catalytic Domain ; Computer Simulation ; Drug Discovery ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Humans ; Protein Tyrosine Phosphatases/chemistry ; Protein Tyrosine Phosphatases/metabolism ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology
Chemical Substances	Enzyme Inhibitors ; Small Molecule Libraries ; Protein Tyrosine Phosphatases (EC 3.1.3.48)
Language	English
Publishing date	2013-08-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2013.08.013
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