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Article ; Online: JMnorm: a novel joint multi-feature normalization method for integrative and comparative epigenomics.

Xiang, Guanjue / Guo, Yuchun / Bumcrot, David / Sigova, Alla

2024 Volume 52, Issue 2, Page(s) e11

Abstract: Combinatorial patterns of epigenetic features reflect transcriptional states and functions of genomic regions. While many epigenetic features have correlated relationships, most existing data normalization approaches analyze each feature independently. ... ...

Abstract	Combinatorial patterns of epigenetic features reflect transcriptional states and functions of genomic regions. While many epigenetic features have correlated relationships, most existing data normalization approaches analyze each feature independently. Such strategies may distort relationships between functionally correlated epigenetic features and hinder biological interpretation. We present a novel approach named JMnorm that simultaneously normalizes multiple epigenetic features across cell types, species, and experimental conditions by leveraging information from partially correlated epigenetic features. We demonstrate that JMnorm-normalized data can better preserve cross-epigenetic-feature correlations across different cell types and enhance consistency between biological replicates than data normalized by other methods. Additionally, we show that JMnorm-normalized data can consistently improve the performance of various downstream analyses, which include candidate cis-regulatory element clustering, cross-cell-type gene expression prediction, detection of transcription factor binding and changes upon perturbations. These findings suggest that JMnorm effectively minimizes technical noise while preserving true biologically significant relationships between epigenetic datasets. We anticipate that JMnorm will enhance integrative and comparative epigenomics.
MeSH term(s)	Epigenesis, Genetic ; Epigenomics/methods ; Genome ; Genomics/methods ; Protein Binding ; Computational Biology/methods
Language	English
Publishing date	2024-01-12
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad1146
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Article ; Online: Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration.

Ramaswami, Gokul / Yuva-Aydemir, Yeliz / Akerberg, Brynn / Matthews, Bryan / Williams, Jenna / Golczer, Gabriel / Huang, Jiaqi / Al Abdullatif, Ali / Huh, Dann / Burkly, Linda C / Engle, Sandra J / Grossman, Iris / Sehgal, Alfica / Sigova, Alla A / Fremeau, Robert T / Liu, Yuting / Bumcrot, David

Scientific reports

2024 Volume 14, Issue 1, Page(s) 2153

Abstract: Microglia are the resident immune cells in the brain that play a key role in driving neuroinflammation, a hallmark of neurodegenerative disorders. Inducible microglia-like cells have been developed as an in vitro platform for molecular and therapeutic ... ...

Abstract	Microglia are the resident immune cells in the brain that play a key role in driving neuroinflammation, a hallmark of neurodegenerative disorders. Inducible microglia-like cells have been developed as an in vitro platform for molecular and therapeutic hypothesis generation and testing. However, there has been no systematic assessment of similarity of these cells to primary human microglia along with their responsiveness to external cues expected of primary cells in the brain. In this study, we performed transcriptional characterization of commercially available human inducible pluripotent stem cell (iPSC)-derived microglia-like (iMGL) cells by bulk and single cell RNA sequencing to assess their similarity with primary human microglia. To evaluate their stimulation responsiveness, iMGL cells were treated with Liver X Receptor (LXR) pathway agonists and their transcriptional responses characterized by bulk and single cell RNA sequencing. Bulk transcriptome analyses demonstrate that iMGL cells have a similar overall expression profile to freshly isolated human primary microglia and express many key microglial transcription factors and functional and disease-associated genes. Notably, at the single-cell level, iMGL cells exhibit distinct transcriptional subpopulations, representing both homeostatic and activated states present in normal and diseased primary microglia. Treatment of iMGL cells with LXR pathway agonists induces robust transcriptional changes in lipid metabolism and cell cycle at the bulk level. At the single cell level, we observe heterogeneity in responses between cell subpopulations in homeostatic and activated states and deconvolute bulk expression changes into their corresponding single cell states. In summary, our results demonstrate that iMGL cells exhibit a complex transcriptional profile and responsiveness, reminiscent of in vivo microglia, and thus represent a promising model system for therapeutic development in neurodegeneration.
MeSH term(s)	Humans ; Microglia/metabolism ; Induced Pluripotent Stem Cells ; Pluripotent Stem Cells ; Transcription Factors/metabolism ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2024-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-52311-0
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Article ; Online: Author Correction: Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration.

Scientific reports

2024 Volume 14, Issue 1, Page(s) 9346

Language	English
Publishing date	2024-04-23
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-60234-z
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Article ; Online: Discovery and Targeting of the Signaling Controls of

Schwartz, Brian E / Rajagopal, Vaishnavi / Smith, Cynthia / Cohick, Evan / Whissell, Gavin / Gamboa, Mario / Pai, Rutuja / Sigova, Alla / Grossman, Iris / Bumcrot, David / Sasidharan, Kavitha / Romeo, Stefano / Sehgal, Alfica / Pingitore, Piero

Cells

2020 Volume 9, Issue 10

Abstract: Non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) are emerging worldwide epidemics, projected to become the leading cause of liver transplants. The strongest genetic risk factor for NAFLD/NASH susceptibility and ... ...

Abstract	Non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) are emerging worldwide epidemics, projected to become the leading cause of liver transplants. The strongest genetic risk factor for NAFLD/NASH susceptibility and progression is a single-nucleotide polymorphism (SNP) in the patatin-like phospholipase domain-containing 3 gene (
MeSH term(s)	Animals ; Humans ; Male ; Mice ; Non-alcoholic Fatty Liver Disease/genetics ; Phospholipases A2, Calcium-Independent/metabolism ; Signal Transduction ; Transfection
Chemical Substances	PNPLA3 protein, mouse (EC 3.1.1.3) ; Phospholipases A2, Calcium-Independent (EC 3.1.1.4)
Language	English
Publishing date	2020-10-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells9102247
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Article ; Online: Delivery and Specificity of CRISPR-Cas9 Genome Editing Technologies for Human Gene Therapy.

Gori, Jennifer L / Hsu, Patrick D / Maeder, Morgan L / Shen, Shen / Welstead, G Grant / Bumcrot, David

Human gene therapy

2015 Volume 26, Issue 7, Page(s) 443–451

Abstract: Genome editing using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated 9 (Cas9) technology is revolutionizing the study of gene function and likely will give rise to an entire new class of therapeutics for a wide ... ...

Abstract	Genome editing using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated 9 (Cas9) technology is revolutionizing the study of gene function and likely will give rise to an entire new class of therapeutics for a wide range of diseases. Achieving this goal requires not only characterization of the technology for efficacy and specificity but also optimization of its delivery to the target cells for each disease indication. In this review we survey the various methods by which the CRISPR-Cas9 components have been delivered to cells and highlight some of the more clinically relevant approaches. Additionally, we discuss the methods available for assessing the specificity of Cas9 editing; an important safety consideration for development of the technology.
MeSH term(s)	Bacterial Proteins ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Endonucleases ; Genetic Therapy/trends ; Humans
Chemical Substances	Bacterial Proteins ; Cas9 endonuclease Streptococcus pyogenes (EC 3.1.-) ; Endonucleases (EC 3.1.-)
Language	English
Publishing date	2015-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1028152-6
ISSN	1557-7422 ; 1043-0342
ISSN (online)	1557-7422
ISSN	1043-0342
DOI	10.1089/hum.2015.074
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Article ; Online: Tissue-specific gene silencing monitored in circulating RNA.

Sehgal, Alfica / Chen, Qingmin / Gibbings, Derrick / Sah, Dinah W Y / Bumcrot, David

RNA (New York, N.Y.)

2013 Volume 20, Issue 2, Page(s) 143–149

Abstract: Pharmacologic target gene modulation is the primary objective for RNA antagonist strategies and gene therapy. Here we show that mRNAs encoding tissue-specific gene transcripts can be detected in biological fluids and that RNAi-mediated target gene ... ...

Abstract	Pharmacologic target gene modulation is the primary objective for RNA antagonist strategies and gene therapy. Here we show that mRNAs encoding tissue-specific gene transcripts can be detected in biological fluids and that RNAi-mediated target gene silencing in the liver and brain results in quantitative reductions in serum and cerebrospinal fluid mRNA levels, respectively. Further, administration of an anti-miRNA oligonucleotide resulted in decreased levels of the miRNA in circulation. Moreover, ectopic expression of an adenoviral transgene in the liver was quantified based on measurement of serum mRNA levels. This noninvasive method for monitoring tissue-specific RNA modulation could greatly advance the clinical development of RNA-based therapeutics.
MeSH term(s)	Aged ; Animals ; Biomarkers, Tumor/blood ; Biomarkers, Tumor/genetics ; Gene Expression ; Gene Knockdown Techniques ; Glypicans/genetics ; Humans ; Liver/metabolism ; Macaca fascicularis ; Male ; Organ Specificity ; RNA Interference ; RNA, Messenger/blood ; RNA, Messenger/genetics ; RNA, Small Interfering/genetics ; Rats ; Rats, Sprague-Dawley ; Species Specificity ; alpha-Fetoproteins/genetics
Chemical Substances	Biomarkers, Tumor ; GPC3 protein, human ; Glypicans ; RNA, Messenger ; RNA, Small Interfering ; alpha-Fetoproteins
Language	English
Publishing date	2013-12-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.042507.113
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Zs.A 4777: Show issues

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Article ; Online: Continuous intranigral infusion is not associated with observable behavioral deficits or marked pathology: a preclinical safety study.

Grondin, Richard / Ai, Yi / Hardy, Peter A / Butt, Mark T / Nelson, Brian D / Lemmon, Jack D / Bumcrot, David / Gash, Don M / Gerhardt, Greg A / Zhang, Zhiming

Journal of neurosurgery

2016 Volume 126, Issue 4, Page(s) 1253–1262

Abstract: OBJECTIVE A better understanding of the effects of chronically delivering compounds to the substantia nigra and nearby areas is important for the development of new therapeutic approaches to treat alpha-synucleinopathies, like Parkinson's disease. ... ...

Abstract	OBJECTIVE A better understanding of the effects of chronically delivering compounds to the substantia nigra and nearby areas is important for the development of new therapeutic approaches to treat alpha-synucleinopathies, like Parkinson's disease. Whether chronic intranigral delivery of an infusate could be achieved without causing motor dysfunction or marked pathology remains unclear. The authors evaluated the tolerability of continuously delivering an infusate directly into the rhesus monkey substantia nigra via a programmable pump coupled to a novel intraparenchymal needle-tip catheter surgically implanted using MRI-guided techniques. METHODS The MRI contrast agent gadopentetate dimeglumine (Magnevist, 5 mM) was used to noninvasively evaluate catheter patency and infusion volume associated with 2 flow rates sequentially tested in each of 3 animals: 0.1 µl/min for 14 days into the right substantia nigra and 0.1 µl/min for 7 days plus 0.2 µl/min for an additional 7 days into the left substantia nigra. Flow rate tolerability was assessed via clinical observations and a microscopic examination of the striatum and midbrain regions. RESULTS Evaluation of postsurgical MRI indicated that all 6 catheters remained patent throughout the study and that the volume of distribution achieved in the left midbrain region at a rate of up to 0.2 µl/min (2052 ± 168 mm
MeSH term(s)	Animals ; Catheters, Indwelling ; Contrast Media ; Feasibility Studies ; Female ; Gadolinium DTPA ; Infusion Pumps ; Macaca mulatta ; Magnetic Resonance Imaging ; Models, Animal ; Patient Safety ; Substantia Nigra/diagnostic imaging ; Substantia Nigra/pathology
Chemical Substances	Contrast Media ; Gadolinium DTPA (K2I13DR72L)
Language	English
Publishing date	2016-05-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	3089-2
ISSN	1933-0693 ; 0022-3085
ISSN (online)	1933-0693
ISSN	0022-3085
DOI	10.3171/2016.2.JNS152295
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Article ; Online: An RNAi therapeutic targeting Tmprss6 decreases iron overload in Hfe(-/-) mice and ameliorates anemia and iron overload in murine β-thalassemia intermedia.

Schmidt, Paul J / Toudjarska, Iva / Sendamarai, Anoop K / Racie, Tim / Milstein, Stuart / Bettencourt, Brian R / Hettinger, Julia / Bumcrot, David / Fleming, Mark D

Blood

2012 Volume 121, Issue 7, Page(s) 1200–1208

Abstract: Mutations in HFE lead to hereditary hemochromatosis (HH) because of inappropriately high iron uptake from the diet resulting from decreased hepatic expression of the iron-regulatory hormone hepcidin. -thalassemia is a congenital anemia caused by partial ... ...

Abstract	Mutations in HFE lead to hereditary hemochromatosis (HH) because of inappropriately high iron uptake from the diet resulting from decreased hepatic expression of the iron-regulatory hormone hepcidin. -thalassemia is a congenital anemia caused by partial or complete loss of -globin synthesis causing ineffective erythropoiesis, anemia, decreased hepcidin production, and secondary iron overload. Tmprss6 is postulated to regulate hepcidin production by cleaving Hemojuvelin (Hjv), a key modulator of hepcidin expression, from the hepatocyte surface. On this basis, we hypothesized that treatment of mouse models of HH (Hfe(-/-)) and -thalassemia intermedia (Hbb(th3/+)) with Tmprss6 siRNA formulated in lipid nanoparticles (LNPs) that are preferentially taken up by the liver would increase hepcidin expression and lessen the iron loading in both models. In the present study, we demonstrate that LNP-Tmprss6 siRNA treatment of Hfe(-/-) and Hbb(th3/+) mice induces hepcidin and diminishes tissue and serum iron levels. Furthermore, LNP-Tmprss6 siRNA treatment of Hbb(th3/+) mice substantially improved the anemia by altering RBC survival and ineffective erythropoiesis. Our results indicate that pharmacologic manipulation of Tmprss6 with RNAi therapeutics isa practical approach to treating iron overload diseases associated with diminished hepcidin expression and may have efficacy in modifying disease-associated morbidities of -thalassemia intermedia.
MeSH term(s)	Anemia/genetics ; Anemia/metabolism ; Anemia/therapy ; Animals ; Antimicrobial Cationic Peptides/genetics ; Antimicrobial Cationic Peptides/metabolism ; Base Sequence ; Disease Models, Animal ; Erythrocyte Aging ; Erythropoiesis ; Female ; Hemochromatosis/genetics ; Hemochromatosis/metabolism ; Hemochromatosis/therapy ; Hemochromatosis Protein ; Hepcidins ; Histocompatibility Antigens Class I/genetics ; Iron Overload/genetics ; Iron Overload/metabolism ; Iron Overload/therapy ; Membrane Proteins/antagonists & inhibitors ; Membrane Proteins/deficiency ; Membrane Proteins/genetics ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Nanoparticles ; RNA Interference ; RNA, Small Interfering/administration & dosage ; RNA, Small Interfering/genetics ; RNA, Small Interfering/therapeutic use ; Serine Endopeptidases/genetics ; beta-Thalassemia/genetics ; beta-Thalassemia/metabolism ; beta-Thalassemia/therapy
Chemical Substances	Antimicrobial Cationic Peptides ; Hamp protein, mouse ; Hemochromatosis Protein ; Hepcidins ; Hfe protein, mouse ; Histocompatibility Antigens Class I ; Membrane Proteins ; RNA, Small Interfering ; Serine Endopeptidases (EC 3.4.21.-) ; matriptase 2 (EC 3.4.21.-)
Language	English
Publishing date	2012-12-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80069-7
ISSN	1528-0020 ; 0006-4971
ISSN (online)	1528-0020
ISSN	0006-4971
DOI	10.1182/blood-2012-09-453977
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Uh III Zs.140: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Alpha-synuclein suppression by targeted small interfering RNA in the primate substantia nigra.

McCormack, Alison L / Mak, Sally K / Henderson, Jaimie M / Bumcrot, David / Farrer, Matthew J / Di Monte, Donato A

PloS one

2010 Volume 5, Issue 8, Page(s) e12122

Abstract: The protein alpha-synuclein is involved in the pathogenesis of Parkinson's disease and other neurodegenerative disorders. Its toxic potential appears to be enhanced by increased protein expression, providing a compelling rationale for therapeutic ... ...

Abstract	The protein alpha-synuclein is involved in the pathogenesis of Parkinson's disease and other neurodegenerative disorders. Its toxic potential appears to be enhanced by increased protein expression, providing a compelling rationale for therapeutic strategies aimed at reducing neuronal alpha-synuclein burden. Here, feasibility and safety of alpha-synuclein suppression were evaluated by treating monkeys with small interfering RNA (siRNA) directed against alpha-synuclein. The siRNA molecule was chemically modified to prevent degradation by exo- and endonucleases and directly infused into the left substantia nigra. Results compared levels of alpha-synuclein mRNA and protein in the infused (left) vs. untreated (right) hemisphere and revealed a significant 40-50% suppression of alpha-synuclein expression. These findings could not be attributable to non-specific effects of siRNA infusion since treatment of a separate set of animals with luciferase-targeting siRNA produced no changes in alpha-synuclein. Infusion with alpha-synuclein siRNA, while lowering alpha-synuclein expression, had no overt adverse consequences. In particular, it did not cause tissue inflammation and did not change (i) the number and phenotype of nigral dopaminergic neurons, and (ii) the concentrations of striatal dopamine and its metabolites. The data represent the first evidence of successful anti-alpha-synuclein intervention in the primate substantia nigra and support further development of RNA interference-based therapeutics.
MeSH term(s)	Animals ; Base Sequence ; Dopamine/metabolism ; Female ; Gene Expression Regulation/genetics ; Gene Knockdown Techniques/methods ; Male ; RNA, Small Interfering/genetics ; Saimiri ; Substantia Nigra/metabolism ; alpha-Synuclein/deficiency ; alpha-Synuclein/genetics
Chemical Substances	RNA, Small Interfering ; alpha-Synuclein ; Dopamine (VTD58H1Z2X)
Language	English
Publishing date	2010-08-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0012122
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Article: Sonic hedgehog: making the gradient.

Bumcrot, D A / McMahon, A P

Chemistry & biology

1996 Volume 3, Issue 1, Page(s) 13–16

Abstract: The amino-terminal peptide of Sonic hedgehog is a cell-tethered molecule, which nevertheless seems to provide a developmental signal that acts at a distance and has different effects depending on its concentration. Recent structural data suggest that ... ...

Abstract	The amino-terminal peptide of Sonic hedgehog is a cell-tethered molecule, which nevertheless seems to provide a developmental signal that acts at a distance and has different effects depending on its concentration. Recent structural data suggest that zinc-dependent proteolysis may somehow be involved in Sonic hedgehog's function.
MeSH term(s)	Hedgehog Proteins ; Hydrolysis ; Proteins/chemistry ; Proteins/metabolism ; Signal Transduction ; Trans-Activators ; Zinc/metabolism
Chemical Substances	Hedgehog Proteins ; Proteins ; Trans-Activators ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	1996-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	917827-2
ISSN	1879-1301 ; 1074-5521
ISSN (online)	1879-1301
ISSN	1074-5521
DOI	10.1016/s1074-5521(96)90077-0
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