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Article: Krüppel-like Factor (KLF) family members control expression of genes required for serous cavity and alveolar macrophage identities.

Pestal, Kathleen / Slayden, Leianna C / Barton, Gregory M

bioRxiv : the preprint server for biology

2024

Abstract: Tissue-resident macrophages adopt distinct gene expression profiles and exhibit functional specialization based on their tissue of residence. Recent studies have begun to define the signals and transcription factors that induce these identities. Here we ... ...

Abstract	Tissue-resident macrophages adopt distinct gene expression profiles and exhibit functional specialization based on their tissue of residence. Recent studies have begun to define the signals and transcription factors that induce these identities. Here we describe an unexpected and specific role for the broadly expressed transcription factor Kruppel-like Factor 2 (KLF2) in the development of embryonically derived Large Cavity Macrophages (LCM) in the serous cavities. KLF2 not only directly regulates the transcription of genes previously shown to specify LCM identity, such as retinoic acid receptors and GATA6, but also is required for induction of many other transcripts that define the identity of these cells. We identify a similar role for KLF4 in regulating the identity of alveolar macrophages in the lung. These data demonstrate that broadly expressed transcription factors, such as Group 2 KLFs, can play important roles in the specification of distinct identities of tissue-resident macrophages.
Language	English
Publishing date	2024-03-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.28.582578
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Article ; Online: Regulation of the nucleic acid-sensing Toll-like receptors.

Lind, Nicholas A / Rael, Victoria E / Pestal, Kathleen / Liu, Bo / Barton, Gregory M

Nature reviews. Immunology

2021 Volume 22, Issue 4, Page(s) 224–235

Abstract: Many of the ligands for Toll-like receptors (TLRs) are unique to microorganisms, such that receptor activation unequivocally indicates the presence of something foreign. However, a subset of TLRs recognizes nucleic acids, which are present in both the ... ...

Abstract	Many of the ligands for Toll-like receptors (TLRs) are unique to microorganisms, such that receptor activation unequivocally indicates the presence of something foreign. However, a subset of TLRs recognizes nucleic acids, which are present in both the host and foreign microorganisms. This specificity enables broad recognition by virtue of the ubiquity of nucleic acids but also introduces the possibility of self-recognition and autoinflammatory or autoimmune disease. Defining the regulatory mechanisms required to ensure proper discrimination between foreign and self-nucleic acids by TLRs is an area of intense research. Progress over the past decade has revealed a complex array of regulatory mechanisms that ensure maintenance of this delicate balance. These regulatory mechanisms can be divided into a conceptual framework with four categories: compartmentalization, ligand availability, receptor expression and signal transduction. In this Review, we discuss our current understanding of each of these layers of regulation.
MeSH term(s)	Autoimmune Diseases ; Humans ; Ligands ; Nucleic Acids ; Signal Transduction ; Toll-Like Receptors
Chemical Substances	Ligands ; Nucleic Acids ; Toll-Like Receptors
Language	English
Publishing date	2021-07-16
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2062776-2
ISSN	1474-1741 ; 1474-1733
ISSN (online)	1474-1741
ISSN	1474-1733
DOI	10.1038/s41577-021-00577-0
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Article ; Online: In vitro-transcribed guide RNAs trigger an innate immune response via the RIG-I pathway.

Wienert, Beeke / Shin, Jiyung / Zelin, Elena / Pestal, Kathleen / Corn, Jacob E

PLoS biology

2018 Volume 16, Issue 7, Page(s) e2005840

Abstract: Clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR-associated 9 (Cas9) genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has ...

Abstract	Clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR-associated 9 (Cas9) genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has become relatively easy, editing of therapeutically relevant primary cells and tissues can remain challenging. One recent advancement is the delivery of a Cas9 protein and an in vitro-transcribed (IVT) guide RNA (gRNA) as a precomplexed ribonucleoprotein (RNP). This approach allows editing of primary cells such as T cells and hematopoietic stem cells, but the consequences beyond genome editing of introducing foreign Cas9 RNPs into mammalian cells are not fully understood. Here, we show that the IVT gRNAs commonly used by many laboratories for RNP editing trigger a potent innate immune response that is similar to canonical immune-stimulating ligands. IVT gRNAs are recognized in the cytosol through the retinoic acid-inducible gene I (RIG-I) pathway but not the melanoma differentiation-associated gene 5 (MDA5) pathway, thereby triggering a type I interferon response. Removal of the 5'-triphosphate from gRNAs ameliorates inflammatory signaling and prevents the loss of viability associated with genome editing in hematopoietic stem cells. The potential for Cas9 RNP editing to induce a potent antiviral response indicates that care must be taken when designing therapeutic strategies to edit primary cells.
MeSH term(s)	Cell Line ; Cytosol/metabolism ; DEAD Box Protein 58/metabolism ; Humans ; Immunity, Innate/genetics ; Interferon Type I/metabolism ; Models, Biological ; RNA, Guide, CRISPR-Cas Systems/genetics ; RNA, Guide, CRISPR-Cas Systems/metabolism ; Receptors, Immunologic ; Transcription, Genetic
Chemical Substances	Interferon Type I ; RNA, Guide, CRISPR-Cas Systems ; Receptors, Immunologic ; RIGI protein, human (EC 3.6.1.-) ; DEAD Box Protein 58 (EC 3.6.4.13)
Language	English
Publishing date	2018-07-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.2005840
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Article ; Online: Intracellular Nucleic Acid Detection in Autoimmunity.

Crowl, John T / Gray, Elizabeth E / Pestal, Kathleen / Volkman, Hannah E / Stetson, Daniel B

Annual review of immunology

2017 Volume 35, Page(s) 313–336

Abstract: Protective immune responses to viral infection are initiated by innate immune sensors that survey extracellular and intracellular space for foreign nucleic acids. The existence of these sensors raises fundamental questions about self/nonself ... ...

Abstract	Protective immune responses to viral infection are initiated by innate immune sensors that survey extracellular and intracellular space for foreign nucleic acids. The existence of these sensors raises fundamental questions about self/nonself discrimination because of the abundance of self-DNA and self-RNA that occupy these same compartments. Recent advances have revealed that enzymes that metabolize or modify endogenous nucleic acids are essential for preventing inappropriate activation of the innate antiviral response. In this review, we discuss rare human diseases caused by dysregulated nucleic acid sensing, focusing primarily on intracellular sensors of nucleic acids. We summarize lessons learned from these disorders, we rationalize the existence of these diseases in the context of evolution, and we propose that this framework may also apply to a number of more common autoimmune diseases for which the underlying genetics and mechanisms are not yet fully understood.
MeSH term(s)	Animals ; Autoimmune Diseases of the Nervous System/immunology ; Autoimmunity ; Humans ; Immunity, Innate ; Interferon Type I/metabolism ; Lupus Erythematosus, Systemic/immunology ; Nervous System Malformations/immunology ; Nucleic Acids/immunology ; Toll-Like Receptors/metabolism ; Virus Diseases/immunology
Chemical Substances	Interferon Type I ; Nucleic Acids ; Toll-Like Receptors
Language	English
Publishing date	2017-01-30
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	604953-9
ISSN	1545-3278 ; 0732-0582
ISSN (online)	1545-3278
ISSN	0732-0582
DOI	10.1146/annurev-immunol-051116-052331
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Article ; Online: In vitro-transcribed guide RNAs trigger an innate immune response via the RIG-I pathway.

Beeke Wienert / Jiyung Shin / Elena Zelin / Kathleen Pestal / Jacob E Corn

PLoS Biology, Vol 16, Iss 7, p e

2018 Volume 2005840

Abstract	Clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR-associated 9 (Cas9) genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has become relatively easy, editing of therapeutically relevant primary cells and tissues can remain challenging. One recent advancement is the delivery of a Cas9 protein and an in vitro-transcribed (IVT) guide RNA (gRNA) as a precomplexed ribonucleoprotein (RNP). This approach allows editing of primary cells such as T cells and hematopoietic stem cells, but the consequences beyond genome editing of introducing foreign Cas9 RNPs into mammalian cells are not fully understood. Here, we show that the IVT gRNAs commonly used by many laboratories for RNP editing trigger a potent innate immune response that is similar to canonical immune-stimulating ligands. IVT gRNAs are recognized in the cytosol through the retinoic acid-inducible gene I (RIG-I) pathway but not the melanoma differentiation-associated gene 5 (MDA5) pathway, thereby triggering a type I interferon response. Removal of the 5'-triphosphate from gRNAs ameliorates inflammatory signaling and prevents the loss of viability associated with genome editing in hematopoietic stem cells. The potential for Cas9 RNP editing to induce a potent antiviral response indicates that care must be taken when designing therapeutic strategies to edit primary cells.
Keywords	Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article: Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples.

medRxiv : the preprint server for health sciences

2021

Abstract: Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a ... ...

Abstract	Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI-FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against the gold standard, nasopharyngeal swab specimens. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.
Language	English
Publishing date	2021-01-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.01.10.21249151
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Article ; Online: Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples.

PloS one

2021 Volume 16, Issue 8, Page(s) e0255690

Abstract	Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against nasopharyngeal swab specimens and found saliva methods require further optimization to match this gold standard. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.
MeSH term(s)	Adult ; COVID-19/diagnosis ; COVID-19 Testing/methods ; Female ; Humans ; Male ; Mass Screening/methods ; RNA/genetics ; RNA/isolation & purification ; RNA, Viral/genetics ; RNA, Viral/isolation & purification ; Real-Time Polymerase Chain Reaction/methods ; Robotics/methods ; SARS-CoV-2/genetics ; Saliva/chemistry ; Specimen Handling/methods
Chemical Substances	RNA, Viral ; RNA (63231-63-0)
Language	English
Publishing date	2021-08-05
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.
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0255690
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Article ; Online: Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-organ Development.

Pestal, Kathleen / Funk, Cory C / Snyder, Jessica M / Price, Nathan D / Treuting, Piper M / Stetson, Daniel B

Immunity

2015 Volume 43, Issue 5, Page(s) 933–944

Abstract: Mutations in ADAR, which encodes the ADAR1 RNA-editing enzyme, cause Aicardi-Goutières syndrome (AGS), a severe autoimmune disease associated with an aberrant type I interferon response. How ADAR1 prevents autoimmunity remains incompletely defined. Here, ...

Abstract	Mutations in ADAR, which encodes the ADAR1 RNA-editing enzyme, cause Aicardi-Goutières syndrome (AGS), a severe autoimmune disease associated with an aberrant type I interferon response. How ADAR1 prevents autoimmunity remains incompletely defined. Here, we demonstrate that ADAR1 is a specific and essential negative regulator of the MDA5-MAVS RNA sensing pathway. Moreover, we uncovered a MDA5-MAVS-independent function for ADAR1 in the development of multiple organs. We showed that the p150 isoform of ADAR1 uniquely regulated the MDA5 pathway, whereas both the p150 and p110 isoforms contributed to development. Abrupt deletion of ADAR1 in adult mice revealed that both of these functions were required throughout life. Our findings delineate genetically separable roles for both ADAR1 isoforms in vivo, with implications for the human diseases caused by ADAR mutations.
MeSH term(s)	Adaptor Proteins, Signal Transducing/metabolism ; Adenosine Deaminase/metabolism ; Animals ; Autoimmune Diseases of the Nervous System/metabolism ; Autoimmunity/physiology ; DEAD-box RNA Helicases/metabolism ; HEK293 Cells ; Humans ; Interferon Type I/metabolism ; Interferon-Induced Helicase, IFIH1 ; Mice ; Nervous System Malformations/metabolism ; Protein Isoforms/metabolism ; RNA/metabolism ; RNA Editing/physiology ; RNA-Binding Proteins/metabolism ; Signal Transduction/physiology
Chemical Substances	Adaptor Proteins, Signal Transducing ; IPS-1 protein, mouse ; Interferon Type I ; Protein Isoforms ; RNA-Binding Proteins ; RNA (63231-63-0) ; ADAR1 protein, mouse (EC 3.5.4.4) ; Adenosine Deaminase (EC 3.5.4.4) ; Ifih1 protein, mouse (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13) ; Interferon-Induced Helicase, IFIH1 (EC 3.6.4.13)
Language	English
Publishing date	2015-11-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1217235-2
ISSN	1097-4180 ; 1074-7613
ISSN (online)	1097-4180
ISSN	1074-7613
DOI	10.1016/j.immuni.2015.11.001
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Zs.A 4227: 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: RAE-1 ligands for the NKG2D receptor are regulated by E2F transcription factors, which control cell cycle entry.

Jung, Heiyoun / Hsiung, Benjamin / Pestal, Kathleen / Procyk, Emily / Raulet, David H

The Journal of experimental medicine

2012 Volume 209, Issue 13, Page(s) 2409–2422

Abstract: The NKG2D stimulatory receptor expressed by natural killer cells and T cell subsets recognizes cell surface ligands that are induced on transformed and infected cells and facilitate immune rejection of tumor cells. We demonstrate that expression of ... ...

Abstract	The NKG2D stimulatory receptor expressed by natural killer cells and T cell subsets recognizes cell surface ligands that are induced on transformed and infected cells and facilitate immune rejection of tumor cells. We demonstrate that expression of retinoic acid early inducible gene 1 (RAE-1) family NKG2D ligands in cancer cell lines and proliferating normal cells is coupled directly to cell cycle regulation. Raet1 genes are directly transcriptionally activated by E2F family transcription factors, which play a central role in regulating cell cycle entry. Induction of RAE-1 occurred in primary cell cultures, embryonic brain cells in vivo, and cells in healing skin wounds and, accordingly, wound healing was delayed in mice lacking NKG2D. Transcriptional activation by E2Fs is likely coordinated with posttranscriptional regulation by other stress responses. These findings suggest that cellular proliferation, as occurs in cancer cells but also other pathological conditions, is a key signal tied to immune reactions mediated by NKG2D-bearing lymphocytes.
MeSH term(s)	Animals ; Cell Cycle Checkpoints/immunology ; Cell Cycle Checkpoints/physiology ; Cell Line, Tumor ; Cell Proliferation ; Cells, Cultured ; E2F Transcription Factors/metabolism ; Gene Expression ; Ligands ; Lymphocytes/immunology ; Lymphocytes/metabolism ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; NK Cell Lectin-Like Receptor Subfamily K/deficiency ; NK Cell Lectin-Like Receptor Subfamily K/genetics ; NK Cell Lectin-Like Receptor Subfamily K/metabolism ; Signal Transduction ; Stress, Physiological ; Transcription, Genetic ; Wound Healing/genetics ; Wound Healing/immunology ; Wound Healing/physiology
Chemical Substances	E2F Transcription Factors ; Klrk1 protein, mouse ; Ligands ; Membrane Proteins ; NK Cell Lectin-Like Receptor Subfamily K ; Raet1a protein, mouse
Language	English
Publishing date	2012-11-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	218343-2
ISSN	1540-9538 ; 0022-1007
ISSN (online)	1540-9538
ISSN	0022-1007
DOI	10.1084/jem.20120565
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Ua VI Zs.107: 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: IGI-LuNER: single-well multiplexed RT-qPCR test for SARS-CoV-2.

medRxiv : the preprint server for health sciences

2020

Abstract: Commonly used RT-qPCR-based SARS-CoV-2 diagnostics require 2-3 separate reactions or rely on detection of a single viral target, adding time and cost or risk of false-negative results. Currently, no test combines detection of widely used SARS-CoV-2 E- ... ...

Abstract	Commonly used RT-qPCR-based SARS-CoV-2 diagnostics require 2-3 separate reactions or rely on detection of a single viral target, adding time and cost or risk of false-negative results. Currently, no test combines detection of widely used SARS-CoV-2 E- and N-gene targets and a sample control in a single, multiplexed reaction. We developed the IGI-LuNER RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (NER). This combined, cost-effective test can be performed in 384-well plates with detection sensitivity suitable for clinical reporting, and will aid in future sample pooling efforts, thus improving throughput of SARS-CoV-2 detection.
Language	English
Publishing date	2020-12-11
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.12.10.20247338
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