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Book: Molecular and cellular aspects of the serpinopathies and disorders in serpin activity

Silverman, Gary A.

2007

Author's details	ed. Gary A. Silverman
Language	English
Size	XXIX, 639 S. : Ill.
Publisher	World Scientific
Publishing place	Singapore u.a.
Publishing country	Singapore
Document type	Book
HBZ-ID	HT014855720
ISBN	978-981-256-963-9 ; 981-256-963-4
Database	Catalogue ZB MED Medicine, Health

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2007 A 2340	order for loan	Magazin

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Article ; Online: Multiple Genes Core to ERAD, Macroautophagy and Lysosomal Degradation Pathways Participate in the Proteostasis Response in α1-Antitrypsin Deficiency.

Li, Jie / Moretti, Francesca / Hidvegi, Tunda / Sviben, Sanja / Fitzpatrick, James A J / Sundaramoorthi, Hemalatha / Pak, Stephen C / Silverman, Gary A / Knapp, Britta / Filipuzzi, Ireos / Alford, John / Reece-Hoyes, John / Nigsch, Florian / Murphy, Leon O / Nyfeler, Beat / Perlmutter, David H

Cellular and molecular gastroenterology and hepatology

2024 Volume 17, Issue 6, Page(s) 1007–1024

Abstract: Background & aims: In the classic form of α1-antitrypsin deficiency (ATD), the misfolded α1-antitrypsin Z (ATZ) variant accumulates in the endoplasmic reticulum (ER) of liver cells. A gain-of-function proteotoxic mechanism is responsible for chronic ... ...

Abstract	Background & aims: In the classic form of α1-antitrypsin deficiency (ATD), the misfolded α1-antitrypsin Z (ATZ) variant accumulates in the endoplasmic reticulum (ER) of liver cells. A gain-of-function proteotoxic mechanism is responsible for chronic liver disease in a subgroup of homozygotes. Proteostatic response pathways, including conventional endoplasmic reticulum-associated degradation and autophagy, have been proposed as the mechanisms that allow cellular adaptation and presumably protection from the liver disease phenotype. Recent studies have concluded that a distinct lysosomal pathway called endoplasmic reticulum-to-lysosome completely supplants the role of the conventional macroautophagy pathway in degradation of ATZ. Here, we used several state-of-the-art approaches to characterize the proteostatic responses more fully in cellular systems that model ATD. Methods: We used clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing coupled to a cell selection step by fluorescence-activated cell sorter to perform screening for proteostasis genes that regulate ATZ accumulation and combined that with selective genome editing in 2 other model systems. Results: Endoplasmic reticulum-associated degradation genes are key early regulators and multiple autophagy genes, from classic as well as from ER-to-lysosome and other newly described ER-phagy pathways, participate in degradation of ATZ in a manner that is temporally regulated and evolves as ATZ accumulation persists. Time-dependent changes in gene expression are accompanied by specific ultrastructural changes including dilation of the ER, formation of globular inclusions, budding of autophagic vesicles, and alterations in the overall shape and component parts of mitochondria. Conclusions: Macroautophagy is a critical component of the proteostasis response to cellular ATZ accumulation and it becomes more important over time as ATZ synthesis continues unabated. Multiple subtypes of macroautophagy and nonautophagic lysosomal degradative pathways are needed to respond to the high concentrations of misfolded protein that characterizes ATD and these pathways are attractive candidates for genetic variants that predispose to the hepatic phenotype.
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2819778-1
ISSN	2352-345X ; 2352-345X
ISSN (online)	2352-345X
ISSN	2352-345X
DOI	10.1016/j.jcmgh.2024.02.006
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Article ; Online: Variants in autophagy genes MTMR12 and FAM134A are putative modifiers of the hepatic phenotype in α1-antitrypsin deficiency.

Tafaleng, Edgar N / Li, Jie / Wang, Yan / Hidvegi, Tunda / Soto-Gutierrez, Alex / Locke, Adam E / Nicholas, Thomas J / Wang, Yung-Chun / Pak, Stephen / Cho, Michael H / Silverman, Edwin K / Silverman, Gary A / Jin, Sheng Chih / Fox, Ira J / Perlmutter, David H

Hepatology (Baltimore, Md.)

2024

Abstract: Background and aims: In the classical form of α1-antitrypsin deficiency, a misfolded variant α1-antitrypsin Z accumulates in the endoplasmic reticulum of liver cells and causes liver cell injury by gain-of-function proteotoxicity in a sub-group of ... ...

Abstract	Background and aims: In the classical form of α1-antitrypsin deficiency, a misfolded variant α1-antitrypsin Z accumulates in the endoplasmic reticulum of liver cells and causes liver cell injury by gain-of-function proteotoxicity in a sub-group of affected homozygotes but relatively little is known about putative modifiers. Here, we carried out genomic sequencing in a uniquely affected family with an index case of liver failure and 2 homozygous siblings with minimal or no liver disease. Their sequences were compared to sequences in well-characterized cohorts of homozygotes with or without liver disease, and then candidate sequence variants were tested for changes in the kinetics of α1-antitrypsin variant Z degradation in iPS-derived hepatocyte-like cells derived from the affected siblings themselves. Approach and results: Specific variants in autophagy genes MTMR12 and FAM134A could each accelerate the degradation of α1-antitrypsin variant Z in cells from the index patient, but both MTMR12 and FAM134A variants were needed to slow the degradation of α1-antitrypsin variant Z in cells from a protected sib, indicating that inheritance of both variants is needed to mediate the pathogenic effects of hepatic proteotoxicity at the cellular level. Analysis of homozygote cohorts showed that multiple patient-specific variants in proteostasis genes are likely to explain liver disease susceptibility at the population level. Conclusions: These results validate the concept that genetic variation in autophagy function can determine susceptibility to liver disease in α1-antitrypsin deficiency and provide evidence that polygenic mechanisms and multiple patient-specific variants are likely needed for proteotoxic pathology.
Language	English
Publishing date	2024-04-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	604603-4
ISSN	1527-3350 ; 0270-9139
ISSN (online)	1527-3350
ISSN	0270-9139
DOI	10.1097/HEP.0000000000000865
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Article: Longitudinal modeling of human neuronal aging identifies RCAN1-TFEB pathway contributing to neurodegeneration of Huntington's disease.

Lee, Seong Won / Oh, Young Mi / Victor, Matheus B / Strunilin, Ilya / Chen, Shawei / Dahiya, Sonika / Dolle, Roland E / Pak, Stephen C / Silverman, Gary A / Perlmutter, David H / Yoo, Andrew S

Research square

2023

Abstract: Aging is a common risk factor in neurodegenerative disorders and the ability to investigate aging of neurons in an isogenic background would facilitate discovering the interplay between neuronal aging and onset of neurodegeneration. Here, we perform ... ...

Abstract	Aging is a common risk factor in neurodegenerative disorders and the ability to investigate aging of neurons in an isogenic background would facilitate discovering the interplay between neuronal aging and onset of neurodegeneration. Here, we perform direct neuronal reprogramming of longitudinally collected human fibroblasts to reveal genetic pathways altered at different ages. Comparative transcriptome analysis of longitudinally aged striatal medium spiny neurons (MSNs), a primary neuronal subtype affected in Huntington's disease (HD), identified pathways associated with RCAN1, a negative regulator of calcineurin. Notably, RCAN1 undergoes age-dependent increase at the protein level detected in reprogrammed MSNs as well as in human postmortem striatum. In patient-derived MSNs of adult-onset HD (HD-MSNs), counteracting
Language	English
Publishing date	2023-05-09
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-2815300/v1
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Article ; Online: Longitudinal modeling of human neuronal aging reveals the contribution of the RCAN1-TFEB pathway to Huntington's disease neurodegeneration.

Lee, Seong Won / Oh, Young Mi / Victor, Matheus B / Yang, Yan / Chen, Shawei / Strunilin, Ilya / Dahiya, Sonika / Dolle, Roland E / Pak, Stephen C / Silverman, Gary A / Perlmutter, David H / Yoo, Andrew S

Nature aging

2023 Volume 4, Issue 1, Page(s) 95–109

Abstract: Aging is a common risk factor in neurodegenerative disorders. Investigating neuronal aging in an isogenic background stands to facilitate analysis of the interplay between neuronal aging and neurodegeneration. Here we perform direct neuronal ... ...

Abstract	Aging is a common risk factor in neurodegenerative disorders. Investigating neuronal aging in an isogenic background stands to facilitate analysis of the interplay between neuronal aging and neurodegeneration. Here we perform direct neuronal reprogramming of longitudinally collected human fibroblasts to reveal genetic pathways altered at different ages. Comparative transcriptome analysis of longitudinally aged striatal medium spiny neurons (MSNs) in Huntington's disease identified pathways involving RCAN1, a negative regulator of calcineurin. Notably, RCAN1 protein increased with age in reprogrammed MSNs as well as in human postmortem striatum and RCAN1 knockdown rescued patient-derived MSNs of Huntington's disease from degeneration. RCAN1 knockdown enhanced chromatin accessibility of genes involved in longevity and autophagy, mediated through enhanced calcineurin activity, leading to TFEB's nuclear localization by dephosphorylation. Furthermore, G2-115, an analog of glibenclamide with autophagy-enhancing activities, reduced the RCAN1-calcineurin interaction, phenocopying the effect of RCAN1 knockdown. Our results demonstrate that targeting RCAN1 genetically or pharmacologically can increase neuronal resilience in Huntington's disease.
MeSH term(s)	Humans ; Aged ; Calcineurin/genetics ; Huntington Disease/genetics ; Aging/genetics ; Transcription Factors/metabolism ; Corpus Striatum/metabolism ; DNA-Binding Proteins/metabolism ; Muscle Proteins/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism
Chemical Substances	Calcineurin (EC 3.1.3.16) ; Transcription Factors ; RCAN1 protein, human ; DNA-Binding Proteins ; Muscle Proteins ; TFEB protein, human ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
Language	English
Publishing date	2023-12-08
Publishing country	United States
Document type	Journal Article
ISSN	2662-8465
ISSN (online)	2662-8465
DOI	10.1038/s43587-023-00538-3
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Article ; Online: Functional analysis of a novel de novo variant in PPP5C associated with microcephaly, seizures, and developmental delay.

Fielder, Sara M / Rosenfeld, Jill A / Burrage, Lindsay C / Emrick, Lisa / Lalani, Seema / Attali, Ruben / Bembenek, Joshua N / Hoang, Hieu / Baldridge, Dustin / Silverman, Gary A / Schedl, Tim / Pak, Stephen C

Molecular genetics and metabolism

2022 Volume 136, Issue 1, Page(s) 65–73

Abstract: We describe a proband evaluated through the Undiagnosed Diseases Network (UDN) who presented with microcephaly, developmental delay, and refractory epilepsy with a de novo p.Ala47Thr missense variant in the protein phosphatase gene, PPP5C. This gene has ... ...

Abstract	We describe a proband evaluated through the Undiagnosed Diseases Network (UDN) who presented with microcephaly, developmental delay, and refractory epilepsy with a de novo p.Ala47Thr missense variant in the protein phosphatase gene, PPP5C. This gene has not previously been associated with a Mendelian disease, and based on the population database, gnomAD, the gene has a low tolerance for loss-of-function variants (pLI = 1, o/e = 0.07). We functionally evaluated the PPP5C variant in C. elegans by knocking the variant into the orthologous gene, pph-5, at the corresponding residue, Ala48Thr. We employed assays in three different biological processes where pph-5 was known to function through opposing the activity of genes, mec-15 and sep-1. We demonstrated that, in contrast to control animals, the pph-5 Ala48Thr variant suppresses the neurite growth phenotype and the GABA signaling defects of mec-15 mutants, and the embryonic lethality of sep-1 mutants. The Ala48Thr variant did not display dominance and behaved similarly to the reference pph-5 null, indicating that the variant is likely a strong hypomorph or complete loss-of-function. We conclude that pph-5 Ala48Thr is damaging in C. elegans. By extension in the proband, PPP5C p.Ala47Thr is likely damaging, the de novo dominant presentation is consistent with haplo-insufficiency, and the PPP5C variant is likely responsible for one or more of the proband's phenotypes.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/genetics ; Child ; Developmental Disabilities/genetics ; F-Box Proteins/genetics ; Humans ; Microcephaly/genetics ; Mutation, Missense ; Nuclear Proteins/genetics ; Phenotype ; Phosphoprotein Phosphatases/genetics ; Seizures/genetics ; Separase/genetics
Chemical Substances	Caenorhabditis elegans Proteins ; F-Box Proteins ; MEC-15 protein, C elegans ; Nuclear Proteins ; Phosphoprotein Phosphatases (EC 3.1.3.16) ; protein phosphatase 5 (EC 3.1.3.16) ; SEP-1 protein, C elegans (EC 3.4.22.49) ; Separase (EC 3.4.22.49)
Language	English
Publishing date	2022-03-22
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1418518-0
ISSN	1096-7206 ; 1096-7192
ISSN (online)	1096-7206
ISSN	1096-7192
DOI	10.1016/j.ymgme.2022.03.007
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Zs.A 617: Show issues

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Article ; Online: Hepatic fibrosis and carcinogenesis in α1-antitrypsin deficiency: a prototype for chronic tissue damage in gain-of-function disorders.

Perlmutter, David H / Silverman, Gary A

Cold Spring Harbor perspectives in biology

2011 Volume 3, Issue 3

Abstract: In α1-antitrypsin (AT) deficiency, a point mutation renders a hepatic secretory glycoprotein prone to misfolding and polymerization. The mutant protein accumulates in the endoplasmic reticulum of liver cells and causes hepatic fibrosis and hepatocellular ...

Abstract	In α1-antitrypsin (AT) deficiency, a point mutation renders a hepatic secretory glycoprotein prone to misfolding and polymerization. The mutant protein accumulates in the endoplasmic reticulum of liver cells and causes hepatic fibrosis and hepatocellular carcinoma by a gain-of-function mechanism. Genetic and/or environmental modifiers determine whether an affected homozygote is susceptible to hepatic fibrosis/carcinoma. Two types of proteostasis mechanisms for such modifiers have been postulated: variation in the function of intracellular degradative mechanisms and/or variation in the signal transduction pathways that are activated to protect the cell from protein mislocalization and/or aggregation. In recent studies we found that carbamazepine, a drug that has been used safely as an anticonvulsant and mood stabilizer, reduces the hepatic load of mutant AT and hepatic fibrosis in a mouse model by enhancing autophagic disposal of this mutant protein. These results provide evidence that pharmacological manipulation of endogenous proteostasis mechanisms is an appealing strategy for chemoprophylaxis in disorders involving gain-of-function mechanisms.
MeSH term(s)	Animals ; Carcinoma, Hepatocellular/etiology ; Carcinoma, Hepatocellular/pathology ; Humans ; Liver Cirrhosis/etiology ; Liver Cirrhosis/pathology ; Liver Neoplasms/etiology ; Liver Neoplasms/pathology ; Mice ; Mitochondrial Diseases/etiology ; Models, Molecular ; Mutation/genetics ; Proteostasis Deficiencies/complications ; Proteostasis Deficiencies/drug therapy ; Signal Transduction/physiology ; alpha 1-Antitrypsin/genetics ; alpha 1-Antitrypsin Deficiency/complications ; alpha 1-Antitrypsin Deficiency/drug therapy ; alpha 1-Antitrypsin Deficiency/genetics
Chemical Substances	alpha 1-Antitrypsin
Language	English
Publishing date	2011-03-01
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1943-0264
ISSN (online)	1943-0264
DOI	10.1101/cshperspect.a005801
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis.

Shi, Qingya / Pei, Fen / Silverman, Gary A / Pak, Stephen C / Perlmutter, David H / Liu, Bing / Bahar, Ivet

International journal of molecular sciences

2020 Volume 21, Issue 8

Abstract: Autophagy plays an essential role in cell survival/death and functioning. Modulation of autophagy has been recognized as a promising therapeutic strategy against diseases/disorders associated with uncontrolled growth or accumulation of biomolecular ... ...

Abstract	Autophagy plays an essential role in cell survival/death and functioning. Modulation of autophagy has been recognized as a promising therapeutic strategy against diseases/disorders associated with uncontrolled growth or accumulation of biomolecular aggregates, organelles, or cells including those caused by cancer, aging, neurodegeneration, and liver diseases such as α1-antitrypsin deficiency. Numerous pharmacological agents that enhance or suppress autophagy have been discovered. However, their molecular mechanisms of action are far from clear. Here, we collected a set of 225 autophagy modulators and carried out a comprehensive quantitative systems pharmacology (QSP) analysis of their targets using both existing databases and predictions made by our machine learning algorithm. Autophagy modulators include several highly promiscuous drugs (e.g., artenimol and olanzapine acting as activators, fostamatinib as an inhibitor, or melatonin as a dual-modulator) as well as selected drugs that uniquely target specific proteins (~30% of modulators). They are mediated by three layers of regulation: (i) pathways involving core autophagy-related (ATG) proteins such as mTOR, AKT, and AMPK; (ii) upstream signaling events that regulate the activity of ATG pathways such as calcium-, cAMP-, and MAPK-signaling pathways; and (iii) transcription factors regulating the expression of ATG proteins such as TFEB, TFE3, HIF-1, FoxO, and NF-κB. Our results suggest that PKA serves as a linker, bridging various signal transduction events and autophagy. These new insights contribute to a better assessment of the mechanism of action of autophagy modulators as well as their side effects, development of novel polypharmacological strategies, and identification of drug repurposing opportunities.
MeSH term(s)	Autophagy/drug effects ; Autophagy/genetics ; Biomarkers ; Brain/drug effects ; Brain/metabolism ; Computational Biology/methods ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Drug Discovery/methods ; Gene Expression Regulation/drug effects ; Humans ; Liver/drug effects ; Liver/metabolism ; Pharmacology/methods ; Phosphatidylinositol 3-Kinases/metabolism ; Signal Transduction/drug effects ; Structure-Activity Relationship ; TOR Serine-Threonine Kinases/metabolism
Chemical Substances	Biomarkers ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; Cyclic AMP-Dependent Protein Kinases (EC 2.7.11.11)
Language	English
Publishing date	2020-04-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21082855
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Article ; Online: Necrotic cell death: harnessing the Dark side of the Force in mammary gland involution.

Luke, Cliff J / Silverman, Gary A

Nature cell biology

2011 Volume 13, Issue 3, Page(s) 197–199

Abstract: In response to major cellular insults, a massive increase in lysosomal membrane permeability (LMP) leads to necrosis. Data now reveal that this potent lysosomal-mediated necrotic cell-death machinery can also be harnessed for complex physiological ... ...

Abstract	In response to major cellular insults, a massive increase in lysosomal membrane permeability (LMP) leads to necrosis. Data now reveal that this potent lysosomal-mediated necrotic cell-death machinery can also be harnessed for complex physiological processes, such as post-lactation mammary gland involution.
MeSH term(s)	Animals ; Breast/pathology ; Female ; Humans ; Lactation ; Lysosomes/enzymology ; Lysosomes/metabolism ; Mammary Glands, Animal/pathology ; Necrosis ; Permeability ; Signal Transduction ; Weaning
Language	English
Publishing date	2011-03-01
Publishing country	England
Document type	Comment ; News
ZDB-ID	1474722-4
ISSN	1476-4679 ; 1465-7392
ISSN (online)	1476-4679
ISSN	1465-7392
DOI	10.1038/ncb0311-197
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Zs.A 5169: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Expanding the C. elegans toolbox into a toolshed.

Ghazi, Arjumand / Yanowitz, Judith / Silverman, Gary A

Methods (San Diego, Calif.)

2014 Volume 68, Issue 3, Page(s) 379–380

MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Cell Biology
Language	English
Publishing date	2014-07-29
Publishing country	United States
Document type	Editorial ; Introductory Journal Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2014.07.005
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