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Article ; Online: Cellular and molecular alterations in a human hepatocellular in vitro model of nonalcoholic fatty liver disease development and stratification.

Willett, Rose A / Tryndyak, Volodymyr P / Beland, Frederick A / Pogribny, Igor P

Journal of environmental science and health. Part C, Toxicology and carcinogenesis

2024 Volume 42, Issue 1, Page(s) 74–92

Abstract: The rapidly increasing incidence of nonalcoholic fatty liver disease (NAFLD) is a growing health crisis worldwide. If not detected early, NAFLD progression can lead to irreversible pathological states, including liver fibrosis and cirrhosis. ... ...

Abstract	The rapidly increasing incidence of nonalcoholic fatty liver disease (NAFLD) is a growing health crisis worldwide. If not detected early, NAFLD progression can lead to irreversible pathological states, including liver fibrosis and cirrhosis. Using
MeSH term(s)	Humans ; Non-alcoholic Fatty Liver Disease/genetics ; Non-alcoholic Fatty Liver Disease/metabolism ; Non-alcoholic Fatty Liver Disease/pathology ; Carcinoma, Hepatocellular ; Liver Neoplasms/genetics ; Liver Neoplasms/pathology ; Liver Cirrhosis/genetics ; Liver Cirrhosis/metabolism ; Liver Cirrhosis/pathology ; Fatty Acids, Nonesterified/metabolism
Chemical Substances	Fatty Acids, Nonesterified
Language	English
Publishing date	2024-01-19
Publishing country	United States
Document type	Journal Article
ISSN	2689-6591
ISSN (online)	2689-6591
DOI	10.1080/26896583.2023.2293493
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Article ; Online: TMEM55B links autophagy flux, lysosomal repair, and TFE3 activation in response to oxidative stress.

Jeong, Eutteum / Willett, Rose / Rissone, Alberto / La Spina, Martina / Puertollano, Rosa

Nature communications

2024 Volume 15, Issue 1, Page(s) 93

Abstract: Lysosomes have emerged as critical regulators of cellular homeostasis. Here we show that the lysosomal protein TMEM55B contributes to restore cellular homeostasis in response to oxidative stress by three different mechanisms: (1) TMEM55B mediates NEDD4- ... ...

Abstract	Lysosomes have emerged as critical regulators of cellular homeostasis. Here we show that the lysosomal protein TMEM55B contributes to restore cellular homeostasis in response to oxidative stress by three different mechanisms: (1) TMEM55B mediates NEDD4-dependent PLEKHM1 ubiquitination, causing PLEKHM1 proteasomal degradation and halting autophagosome/lysosome fusion; (2) TMEM55B promotes recruitment of components of the ESCRT machinery to lysosomal membranes to stimulate lysosomal repair; and (3) TMEM55B sequesters the FLCN/FNIP complex to facilitate translocation of the transcription factor TFE3 to the nucleus, allowing expression of transcriptional programs that enable cellular adaptation to stress. Knockout of tmem55 genes in zebrafish embryos increases their susceptibility to oxidative stress, causing early death of tmem55-KO animals in response to arsenite toxicity. Altogether, our work identifies a role for TMEM55B as a molecular sensor that coordinates autophagosome degradation, lysosomal repair, and activation of stress responses.
MeSH term(s)	Animals ; Zebrafish/genetics ; Zebrafish/metabolism ; Autophagy/genetics ; Lysosomes/metabolism ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Oxidative Stress
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44316-6
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Article ; Online: Effect of an obesogenic high-fat and high-sucrose diet on hepatic gene expression signatures in male Collaborative Cross mice.

Tryndyak, Volodymyr P / Willett, Rose A / Nagumalli, Suresh K / Li, Dan / Avigan, Mark I / Beland, Frederick A / Rusyn, Ivan / Pogribny, Igor P

American journal of physiology. Gastrointestinal and liver physiology

2023 Volume 324, Issue 3, Page(s) G232–G243

Abstract: Nonalcoholic fatty liver disease (NAFLD), the most prevalent chronic liver disease, is characterized by substantial variations in case-level severity. In this study, we used a genetically diverse Collaborative Cross (CC) mouse population model to analyze ...

Abstract	Nonalcoholic fatty liver disease (NAFLD), the most prevalent chronic liver disease, is characterized by substantial variations in case-level severity. In this study, we used a genetically diverse Collaborative Cross (CC) mouse population model to analyze the global transcriptome and clarify the molecular mechanisms involved in hepatic fat accumulation that determine the level and severity of NAFLD. Twenty-four strains of male CC mice were maintained on a high-fat/high-sucrose (HF/HS) diet for 12 wk, and their hepatic gene expression profiles were determined by next-generation RNA sequencing. We found that the development of the nonalcoholic fatty liver (NAFL) phenotype in CC mice coincided with significant changes in the expression of hepatic genes at the population level, evidenced by the presence of 724 differentially expressed genes involved in lipid and carbohydrate metabolism, cell morphology, vitamin and mineral metabolism, energy production, and DNA replication, recombination, and repair. Importantly, expression of 68 of these genes strongly correlated with the extent of hepatic lipid accumulation in the overall population of HF/HS diet-fed male CC mice. Results of partial least squares (PLS) modeling showed that these derived hepatic gene expression signatures help to identify the individual mouse strains that are highly susceptible to the development of NAFLD induced by an HF/HS diet. These findings imply that gene expression profiling, combined with a PLS modeling approach, may be a useful tool to predict NAFLD severity in genetically diverse patient populations.
MeSH term(s)	Male ; Humans ; Mice ; Animals ; Non-alcoholic Fatty Liver Disease/metabolism ; Transcriptome ; Collaborative Cross Mice/genetics ; Sucrose/metabolism ; Liver/metabolism ; Diet, High-Fat ; Lipids ; Mice, Inbred C57BL ; Lipid Metabolism
Chemical Substances	Sucrose (57-50-1) ; Lipids
Language	English
Publishing date	2023-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	603840-2
ISSN	1522-1547 ; 0193-1857
ISSN (online)	1522-1547
ISSN	0193-1857
DOI	10.1152/ajpgi.00225.2022
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Article ; Online: Non-alcoholic fatty liver disease-associated DNA methylation and gene expression alterations in the livers of Collaborative Cross mice fed an obesogenic high-fat and high-sucrose diet.

Tryndyak, Volodymyr P / Willett, Rose A / Avigan, Mark I / Sanyal, Arun J / Beland, Frederick A / Rusyn, Ivan / Pogribny, Igor P

Epigenetics

2022 Volume 17, Issue 11, Page(s) 1462–1476

Abstract: Non-alcoholic fatty liver disease (NAFLD) is a highly prevalent chronic liver disease, and patient susceptibility to its onset and progression is influenced by several factors. In this study, we investigated whether altered hepatic DNA methylation in ... ...

Abstract	Non-alcoholic fatty liver disease (NAFLD) is a highly prevalent chronic liver disease, and patient susceptibility to its onset and progression is influenced by several factors. In this study, we investigated whether altered hepatic DNA methylation in liver tissue correlates with the degree of severity of NAFLD-like liver injury induced by a high-fat and high-sucrose (HF/HS) diet in Collaborative Cross (CC) mice. Using genome-wide targeted bisulphite DNA methylation next-generation sequencing, we found that mice with different non-alcoholic fatty liver (NAFL) phenotypes could be distinguished by changes in hepatic DNA methylation profiles. Specifically, NAFL-prone male CC042 mice exhibited more prominent DNA methylation changes compared with male CC011 mice and female CC011 and CC042 mice that developed only a mild NAFL phenotype. Moreover, these mouse strains demonstrated different patterns of DNA methylation. While the HF/HS diet induced both DNA hypomethylation and DNA hypermethylation changes in all the mouse strains, the NAFL-prone male CC042 mice demonstrated a global predominance of DNA hypermethylation, whereas a more pronounced DNA hypomethylation pattern developed in the mild-NAFL phenotypic mice. In a targeted analysis of selected genes that contain differentially methylated regions (DMRs), we identified NAFL phenotype-associated differences in DNA methylation and gene expression of the
MeSH term(s)	Humans ; Male ; Female ; Mice ; Animals ; Non-alcoholic Fatty Liver Disease/genetics ; Non-alcoholic Fatty Liver Disease/metabolism ; DNA Methylation ; Collaborative Cross Mice/genetics ; Sucrose/metabolism ; Liver/metabolism ; Diet ; DNA/metabolism ; Gene Expression ; Diet, High-Fat/adverse effects
Chemical Substances	Sucrose (57-50-1) ; DNA (9007-49-2)
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ISSN	1559-2308
ISSN (online)	1559-2308
DOI	10.1080/15592294.2022.2043590
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Article: Lipidomic profiling of the hepatic esterified fatty acid composition in diet-induced nonalcoholic fatty liver disease in genetically diverse Collaborative Cross mice

Nagumalli, Suresh K. / Willett, Rose A. / de Conti, Aline / Tryndyak, Volodymyr P. / Avigan, Mark I. / da Costa, Gonçalo Gamboa / Beland, Frederick A. / Rusyn, Ivan / Pogribny, Igor P.

Journal of nutritional biochemistry. 2022 June 20,

2022

Abstract: Nonalcoholic fatty liver disease (NAFLD), one of the most common forms of chronic liver disease, is characterized by the excessive accumulation of lipid species in hepatocytes. Recent studies have indicated that in addition to the total lipid quantities, ...

Abstract	Nonalcoholic fatty liver disease (NAFLD), one of the most common forms of chronic liver disease, is characterized by the excessive accumulation of lipid species in hepatocytes. Recent studies have indicated that in addition to the total lipid quantities, changes in lipid composition are a determining factor in hepatic lipotoxicity. Using ultra-high performance liquid chromatography coupled with electrospray tandem mass spectrometry, we analyzed the esterified fatty acid composition in 24 strains of male and female Collaborative Cross (CC) mice fed a high fat/high sucrose (HF/HS) diet for 12 weeks. Changes in lipid composition were found in all strains after the HF/HS diet, most notably characterized by increases in monounsaturated fatty acids (MUFA) and decreases in polyunsaturated fatty acids (PUFA). Similar changes in MUFA and PUFA were observed in a choline- and folate-deficient (CFD) mouse model of NAFLD, as well as in hepatocytes treated in vitro with free fatty acids. Analysis of fatty acid composition revealed that alterations were accompanied by an increase in the estimated activity of MUFA generating SCD1 enzyme and an estimated decrease in the activity of PUFA generating FADS1 and FADS2 enzymes. PUFA/MUFA ratios were inversely correlated with lipid accumulation in male and female CC mice fed the HF/HS diet and with morphological markers of hepatic injury in CFD diet-fed mouse model of NAFLD. These results demonstrate that different models of NAFLD are characterized by similar changes in the esterified fatty acid composition and that alterations in PUFA/MUFA ratios may serve as a diagnostic marker for NAFLD severity.
Keywords	diet ; enzymes ; esterification ; fatty acid composition ; fatty liver ; females ; hepatocytes ; lipidomics ; lipotoxicity ; males ; mice ; sucrose ; tandem mass spectrometry ; ultra-performance liquid chromatography
Language	English
Dates of publication	2022-0620
Publishing place	Elsevier Inc.
Document type	Article
Note	Pre-press version
ZDB-ID	1014929-6
ISSN	1873-4847 ; 0955-2863
ISSN (online)	1873-4847
ISSN	0955-2863
DOI	10.1016/j.jnutbio.2022.109108
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Expression of functional Myc-tagged conserved oligomeric Golgi (COG) subcomplexes in mammalian cells.

Willett, Rose A / Kudlyk, Tetyana A / Lupashin, Vladimir V

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

2015 Volume 1270, Page(s) 167–177

Abstract: Docking and fusion of transport carriers in eukaryotic cells are regulated by a family of multi-subunit tethering complexes (MTC) that sequentially and/or simultaneously interact with other components of vesicle fusion machinery, such as SNAREs, Rabs, ... ...

Abstract	Docking and fusion of transport carriers in eukaryotic cells are regulated by a family of multi-subunit tethering complexes (MTC) that sequentially and/or simultaneously interact with other components of vesicle fusion machinery, such as SNAREs, Rabs, coiled-coil tethers, and vesicle coat components. Probing for interactions of multi-protein complexes has relied heavily on the method of exogenously expressing individual proteins and then determining their interaction stringency. An obvious pitfall of this method is that the protein interactions are not occurring in their native multi-subunit state. Here, we describe an assay where we express all eight subunits of the conserved oligomeric Golgi (COG) complex that contain the same triple-Myc epitope tag and then an assay for the (sub) complex's interaction with known protein partners. The expression of all eight proteins allows for the assembled complex to interact with partner proteins, and by having the same tag on all eight COG subunits, we are able to very accurately quantify the interaction with each subunit. The use of this assay has highlighted a very important level of specificity of interactions between COG subcomplexes and their intracellular partners.
MeSH term(s)	Animals ; Blotting, Western ; Cell Line ; Gene Expression ; Golgi Apparatus/metabolism ; Humans ; Immunoprecipitation ; Plasmids/genetics ; Protein Binding ; Protein Multimerization ; Protein Transport ; Proto-Oncogene Proteins c-myc/genetics ; Recombinant Fusion Proteins/chemistry ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Transfection ; Vesicular Transport Proteins/chemistry ; Vesicular Transport Proteins/genetics ; Vesicular Transport Proteins/metabolism
Chemical Substances	Proto-Oncogene Proteins c-myc ; Recombinant Fusion Proteins ; Vesicular Transport Proteins
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-2309-0_13
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Article ; Online: Lipidomic profiling of the hepatic esterified fatty acid composition in diet-induced nonalcoholic fatty liver disease in genetically diverse Collaborative Cross mice.

Nagumalli, Suresh K / Willett, Rose A / de Conti, Aline / Tryndyak, Volodymyr P / Avigan, Mark I / da Costa, Gonçalo Gamboa / Beland, Frederick A / Rusyn, Ivan / Pogribny, Igor P

The Journal of nutritional biochemistry

2022 Volume 109, Page(s) 109108

Abstract: Non-alcoholic fatty liver disease (NAFLD), one of the most common forms of chronic liver disease, is characterized by the excessive accumulation of lipid species in hepatocytes. Recent studies have indicated that in addition to the total lipid quantities, ...

Abstract	Non-alcoholic fatty liver disease (NAFLD), one of the most common forms of chronic liver disease, is characterized by the excessive accumulation of lipid species in hepatocytes. Recent studies have indicated that in addition to the total lipid quantities, changes in lipid composition are a determining factor in hepatic lipotoxicity. Using ultra-high performance liquid chromatography coupled with electrospray tandem mass spectrometry, we analyzed the esterified fatty acid composition in 24 strains of male and female Collaborative Cross (CC) mice fed a high fat/high sucrose (HF/HS) diet for 12 weeks. Changes in lipid composition were found in all strains after the HF/HS diet, most notably characterized by increases in monounsaturated fatty acids (MUFA) and decreases in polyunsaturated fatty acids (PUFA). Similar changes in MUFA and PUFA were observed in a choline- and folate-deficient (CFD) mouse model of NAFLD, as well as in hepatocytes treated in vitro with free fatty acids. Analysis of fatty acid composition revealed that alterations were accompanied by an increase in the estimated activity of MUFA generating SCD1 enzyme and an estimated decrease in the activity of PUFA generating FADS1 and FADS2 enzymes. PUFA/MUFA ratios were inversely correlated with lipid accumulation in male and female CC mice fed the HF/HS diet and with morphological markers of hepatic injury in CFD diet-fed mouse model of NAFLD. These results demonstrate that different models of NAFLD are characterized by similar changes in the esterified fatty acid composition and that alterations in PUFA/MUFA ratios may serve as a diagnostic marker for NAFLD severity.
MeSH term(s)	Animals ; Choline ; Collaborative Cross Mice ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Fatty Acids ; Fatty Acids, Monounsaturated ; Fatty Acids, Nonesterified ; Fatty Acids, Unsaturated ; Female ; Folic Acid ; Lipidomics ; Liver ; Male ; Mice ; Non-alcoholic Fatty Liver Disease/etiology ; Sucrose
Chemical Substances	Fatty Acids ; Fatty Acids, Monounsaturated ; Fatty Acids, Nonesterified ; Fatty Acids, Unsaturated ; Sucrose (57-50-1) ; Folic Acid (935E97BOY8) ; Choline (N91BDP6H0X)
Language	English
Publishing date	2022-07-17
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1014929-6
ISSN	1873-4847 ; 0955-2863
ISSN (online)	1873-4847
ISSN	0955-2863
DOI	10.1016/j.jnutbio.2022.109108
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Article: Multipronged interaction of the COG complex with intracellular membranes.

Willett, Rose / Pokrovskaya, Irina / Kudlyk, Tetyana / Lupashin, Vladimir

Cellular logistics

2014 Volume 4, Issue 1, Page(s) e27888

Abstract: The conserved oligomeric Golgi complex is a peripheral membrane protein complex that orchestrates the tethering and fusion of intra-Golgi transport carriers with Golgi membranes. In this study we have investigated the membrane attachment of the COG ... ...

Abstract	The conserved oligomeric Golgi complex is a peripheral membrane protein complex that orchestrates the tethering and fusion of intra-Golgi transport carriers with Golgi membranes. In this study we have investigated the membrane attachment of the COG complex and it's on/off dynamic on Golgi membranes. Several complimentary approaches including knock-sideways depletion, FRAP, and FLIP revealed that assembled COG complex is not diffusing from Golgi periphery in live HeLa cells. Moreover, COG subunits remained membrane-associated even in COG4 and COG7 depleted cells when Golgi architecture was severely affected. Overexpression of myc-tagged COG sub-complexes revealed that different membrane-associated COG partners including β-COP, p115 and SNARE STX5 preferentially bind to different COG assemblies, indicating that COG subunits interact with Golgi membranes in a multipronged fashion.
Language	English
Publishing date	2014-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2682440-1
ISSN	2159-2799 ; 2159-2780
ISSN (online)	2159-2799
ISSN	2159-2780
DOI	10.4161/cl.27888
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Article ; Online: TFEB regulates lysosomal positioning by modulating TMEM55B expression and JIP4 recruitment to lysosomes.

Willett, Rose / Martina, José A / Zewe, James P / Wills, Rachel / Hammond, Gerald R V / Puertollano, Rosa

Nature communications

2017 Volume 8, Issue 1, Page(s) 1580

Abstract: Lysosomal distribution is linked to the role of lysosomes in many cellular functions, including autophagosome degradation, cholesterol homeostasis, antigen presentation, and cell invasion. Alterations in lysosomal positioning contribute to different ... ...

Abstract	Lysosomal distribution is linked to the role of lysosomes in many cellular functions, including autophagosome degradation, cholesterol homeostasis, antigen presentation, and cell invasion. Alterations in lysosomal positioning contribute to different human pathologies, such as cancer, neurodegeneration, and lysosomal storage diseases. Here we report the identification of a novel mechanism of lysosomal trafficking regulation. We found that the lysosomal transmembrane protein TMEM55B recruits JIP4 to the lysosomal surface, inducing dynein-dependent transport of lysosomes toward the microtubules minus-end. TMEM55B overexpression causes lysosomes to collapse into the cell center, whereas depletion of either TMEM55B or JIP4 results in dispersion toward the cell periphery. TMEM55B levels are transcriptionally upregulated following TFEB and TFE3 activation by starvation or cholesterol-induced lysosomal stress. TMEM55B or JIP4 depletion abolishes starvation-induced retrograde lysosomal transport and prevents autophagosome-lysosome fusion. Overall our data suggest that the TFEB/TMEM55B/JIP4 pathway coordinates lysosome movement in response to a variety of stress conditions.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; COS Cells ; Cell Line, Tumor ; Chlorocebus aethiops ; Gene Expression Regulation ; HeLa Cells ; Humans ; Lysosomal Membrane Proteins/metabolism ; Lysosomes/metabolism ; Microtubules/physiology ; Phosphoinositide Phosphatases/genetics ; Phosphoinositide Phosphatases/metabolism ; Protein Transport/genetics ; Protein Transport/physiology ; RNA Interference ; RNA, Small Interfering/genetics ; Vesicular Transport Proteins/genetics ; Vesicular Transport Proteins/metabolism
Chemical Substances	Adaptor Proteins, Signal Transducing ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Lysosomal Membrane Proteins ; RNA, Small Interfering ; SPAG9 protein, human ; TFE3 protein, human ; TFEB protein, human ; Vesicular Transport Proteins ; Phosphoinositide Phosphatases (EC 3.1.3.36) ; PIP4P1 protein, human (EC 3.1.3.78)
Language	English
Publishing date	2017-11-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-017-01871-z
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Article ; Online: Fluorescent microscopy as a tool to elucidate dysfunction and mislocalization of Golgi glycosyltransferases in COG complex depleted mammalian cells.

Willett, Rose A / Pokrovskaya, Irina D / Lupashin, Vladimir V

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

2013 Volume 1022, Page(s) 61–72

Abstract: Staining of molecules such as proteins and glycoconjugates allows for an analysis of their localization within the cell and provides insight into their functional status. Glycosyltransferases, a class of enzymes which are responsible for glycosylating ... ...

Abstract	Staining of molecules such as proteins and glycoconjugates allows for an analysis of their localization within the cell and provides insight into their functional status. Glycosyltransferases, a class of enzymes which are responsible for glycosylating host proteins, are mostly localized to the Golgi apparatus, and their localization is maintained in part by a protein vesicular tethering complex, the conserved oligomeric Golgi (COG) complex. Here we detail a combination of fluorescent lectin and immuno-staining in cells depleted of COG complex subunits to examine the status of Golgi glycosyltransferases. The combination of these techniques allows for a detailed characterization of the changes in function and localization of Golgi glycosyltransferases with respect to transient COG subunit depletion.
MeSH term(s)	Adaptor Proteins, Vesicular Transport/genetics ; Fluorescent Antibody Technique/methods ; Glycosyltransferases/analysis ; Glycosyltransferases/metabolism ; Golgi Apparatus/enzymology ; Golgi Apparatus/metabolism ; Golgi Apparatus/ultrastructure ; HeLa Cells ; Humans ; Microscopy, Fluorescence/methods ; RNA Interference ; RNA, Small Interfering/genetics ; Staining and Labeling/methods
Chemical Substances	Adaptor Proteins, Vesicular Transport ; RNA, Small Interfering ; Glycosyltransferases (EC 2.4.-)
Language	English
Publishing date	2013-06-28
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-465-4_6
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