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Piazza S, Bani C, Colombo F, Mercogliano F, Pozzoli C, Martinelli G, Petroni K, Roberto Pilu S, Sonzogni E, Fumagalli M, Sangiovanni E, Restani P, Dell'Agli M, Di Lorenzo C. Pigmented corn as a gluten-free source of polyphenols with anti-inflammatory and antioxidant properties in CaCo-2 cells. Food Res Int 2024; 191:114640. [PMID: 39059931 DOI: 10.1016/j.foodres.2024.114640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 07/28/2024]
Abstract
A high number of varieties from corn (Zea mays L.) have been consumed for long time all over the world, however pigmented varieties are recently gaining renewed attention due to their beneficial effects and polyphenolic content. The natural lack of gluten makes corn suitable for consumption by celiac population, who need to control their inflammatory state through an appropriate gluten-free diet. The biological effects of polyphenols from pigmented corn are poorly investigated in the context of celiac disease. In this work, we analyzed through HPLC-DAD the phenolic composition of two Italian purple and red varieties ("Scagliolo Rosso" and "Rostrato di Rovetta", respectively) comparing their effects in human intestinal epithelial cells (CaCo-2 cells). The possible impact of gastro-intestinal digestion following oral consumption was assessed as well. The phenolic profile showed the presence of phenolic acids in both varieties, while anthocyanins were identified in Scagliolo Rosso only. After simulated digestion, the level of polyphenols did not significantly change and paralleled with an increased scavenging activity. In CaCo-2 cells, stimulated by a proinflammatory cocktail containing gliadin-derived peptides (IL-1β, IFN-γ, digested gliadin), pigmented corn extracts inhibited the release of CXCL-10 and sICAM-1, with mechanisms partially ascribed to NF-κB impairment. At the same concentration (200 μg/mL), ROS production and catalase depletion were reverted through Nrf-2-independent mechanisms. Our data suggest that polyphenols from pigmented corns might help in controlling the inflammatory and oxidative state of people with celiac disease at intestinal level, at concentrations potentially achievable through a gluten-free diet.
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Affiliation(s)
- Stefano Piazza
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Corinne Bani
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Francesca Colombo
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Francesca Mercogliano
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Carola Pozzoli
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Giulia Martinelli
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Katia Petroni
- Department of Biosciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Salvatore Roberto Pilu
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, Università degli Studi di Milano, 20133 Milan, Italy
| | - Elisa Sonzogni
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Marco Fumagalli
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Enrico Sangiovanni
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy.
| | - Patrizia Restani
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Mario Dell'Agli
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
| | - Chiara Di Lorenzo
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti" (DiSFeB), Università degli Studi di Milano, 20133 Milan, Italy
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2
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Trauernicht M, Filipovska T, Rastogi C, van Steensel B. Optimized reporters for multiplexed detection of transcription factor activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605239. [PMID: 39091757 PMCID: PMC11291157 DOI: 10.1101/2024.07.26.605239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
In any given cell type, dozens of transcription factors (TFs) act in concert to control the activity of the genome by binding to specific DNA sequences in regulatory elements. Despite their considerable importance in determining cell identity and their pivotal role in numerous disorders, we currently lack simple tools to directly measure the activity of many TFs in parallel. Massively parallel reporter assays (MPRAs) allow the detection of TF activities in a multiplexed fashion; however, we lack basic understanding to rationally design sensitive reporters for many TFs. Here, we use an MPRA to systematically optimize transcriptional reporters for 86 TFs and evaluate the specificity of all reporters across a wide array of TF perturbation conditions. We thus identified critical TF reporter design features and obtained highly sensitive and specific reporters for 60 TFs, many of which outperform available reporters. The resulting collection of "prime" TF reporters can be used to uncover TF regulatory networks and to illuminate signaling pathways. HIGHLIGHTS Systematic design and optimization of transcriptional reporters for 86 TFsCharacterization of TF-specific reporter design optimization rulesEvaluation of reporter TF-specificity across a wide array of TF perturbationsIdentification of a collection of 60 "prime" TF reporters with optimized performance.
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3
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Hu P, Du Y, Xu Y, Ye P, Xia J. The role of transcription factors in the pathogenesis and therapeutic targeting of vascular diseases. Front Cardiovasc Med 2024; 11:1384294. [PMID: 38745757 PMCID: PMC11091331 DOI: 10.3389/fcvm.2024.1384294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factors (TFs) constitute an essential component of epigenetic regulation. They contribute to the progression of vascular diseases by regulating epigenetic gene expression in several vascular diseases. Recently, numerous regulatory mechanisms related to vascular pathology, ranging from general TFs that are continuously activated to histiocyte-specific TFs that are activated under specific circumstances, have been studied. TFs participate in the progression of vascular-related diseases by epigenetically regulating vascular endothelial cells (VECs) and vascular smooth muscle cells (VSMCs). The Krüppel-like family (KLF) TF family is widely recognized as the foremost regulator of vascular diseases. KLF11 prevents aneurysm progression by inhibiting the apoptosis of VSMCs and enhancing their contractile function. The presence of KLF4, another crucial member, suppresses the progression of atherosclerosis (AS) and pulmonary hypertension by attenuating the formation of VSMCs-derived foam cells, ameliorating endothelial dysfunction, and inducing vasodilatory effects. However, the mechanism underlying the regulation of the progression of vascular-related diseases by TFs has remained elusive. The present study categorized the TFs involved in vascular diseases and their regulatory mechanisms to shed light on the potential pathogenesis of vascular diseases, and provide novel insights into their diagnosis and treatment.
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Affiliation(s)
- Poyi Hu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yifan Du
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Xu
- Institute of Reproduction Health Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Ye
- Central Hospital of Wuhan, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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4
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Trauernicht M, Rastogi C, Manzo S, Bussemaker H, van Steensel B. Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements. Nucleic Acids Res 2023; 51:9690-9702. [PMID: 37650627 PMCID: PMC10570033 DOI: 10.1093/nar/gkad718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/24/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023] Open
Abstract
TP53 is a transcription factor that controls multiple cellular processes, including cell cycle arrest, DNA repair and apoptosis. The relation between TP53 binding site architecture and transcriptional output is still not fully understood. Here, we systematically examined in three different cell lines the effects of binding site affinity and copy number on TP53-dependent transcriptional output, and also probed the impact of spacer length and sequence between adjacent binding sites, and of core promoter identity. Paradoxically, we found that high-affinity TP53 binding sites are less potent than medium-affinity sites. TP53 achieves supra-additive transcriptional activation through optimally spaced adjacent binding sites, suggesting a cooperative mechanism. Optimally spaced adjacent binding sites have a ∼10-bp periodicity, suggesting a role for spatial orientation along the DNA double helix. We leveraged these insights to construct a log-linear model that explains activity from sequence features, and to identify new highly active and sensitive TP53 reporters.
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Affiliation(s)
- Max Trauernicht
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Stefano G Manzo
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Biosciences, University of Milan “La Statale”, 20133 Milan, Italy
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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Deng J, Peng DH, Fenyo D, Yuan H, Lopez A, Levin DS, Meynardie M, Quinteros M, Ranieri M, Sahu S, Lau SCM, Shum E, Velcheti V, Punekar SR, Rekhtman N, Dowling CM, Weerasekara V, Xue Y, Ji H, Siu Y, Jones D, Hata AN, Shimamura T, Poirier JT, Rudin CM, Hattori T, Koide S, Papagiannakopoulos T, Neel BG, Bardeesy N, Wong KK. In vivo metabolomics identifies CD38 as an emergent vulnerability in LKB1 -mutant lung cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537350. [PMID: 37131623 PMCID: PMC10153147 DOI: 10.1101/2023.04.18.537350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
LKB1/STK11 is a serine/threonine kinase that plays a major role in controlling cell metabolism, resulting in potential therapeutic vulnerabilities in LKB1-mutant cancers. Here, we identify the NAD + degrading ectoenzyme, CD38, as a new target in LKB1-mutant NSCLC. Metabolic profiling of genetically engineered mouse models (GEMMs) revealed that LKB1 mutant lung cancers have a striking increase in ADP-ribose, a breakdown product of the critical redox co-factor, NAD + . Surprisingly, compared with other genetic subsets, murine and human LKB1-mutant NSCLC show marked overexpression of the NAD+-catabolizing ectoenzyme, CD38 on the surface of tumor cells. Loss of LKB1 or inactivation of Salt-Inducible Kinases (SIKs)-key downstream effectors of LKB1- induces CD38 transcription induction via a CREB binding site in the CD38 promoter. Treatment with the FDA-approved anti-CD38 antibody, daratumumab, inhibited growth of LKB1-mutant NSCLC xenografts. Together, these results reveal CD38 as a promising therapeutic target in patients with LKB1 mutant lung cancer. SIGNIFICANCE Loss-of-function mutations in the LKB1 tumor suppressor of lung adenocarcinoma patients and are associated with resistance to current treatments. Our study identified CD38 as a potential therapeutic target that is highly overexpressed in this specific subtype of cancer, associated with a shift in NAD homeostasis.
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6
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Solt LA. Emerging insights and challenges for understanding T cell function through the proteome. Front Immunol 2022; 13:1028366. [DOI: 10.3389/fimmu.2022.1028366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
T cells rapidly transition from a quiescent state into active proliferation and effector function upon exposure to cognate antigen. These processes are tightly controlled by signal transduction pathways that influence changes in chromatin remodeling, gene transcription, and metabolism, all of which collectively drive specific T cell memory or effector cell development. Dysregulation of any of these events can mediate disease and the past several years has shown unprecedented novel approaches to understand these events, down to the single-cell level. The massive explosion of sequencing approaches to assess the genome and transcriptome at the single cell level has transformed our understanding of T cell activation, developmental potential, and effector function under normal and various disease states. Despite these advances, there remains a significant dearth of information regarding how these events are translated to the protein level. For example, resolution of protein isoforms and/or specific post-translational modifications mediating T cell function remains obscure. The application of proteomics can change that, enabling significant insights into molecular mechanisms that regulate T cell function. However, unlike genomic approaches that have enabled exquisite visualization of T cell dynamics at the mRNA and chromatin level, proteomic approaches, including those at the single-cell level, has significantly lagged. In this review, we describe recent studies that have enabled a better understanding of how protein synthesis and degradation change during T cell activation and acquisition of effector function. We also highlight technical advances and how these could be applied to T cell biology. Finally, we discuss future needs to expand upon our current knowledge of T cell proteomes and disease.
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7
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Lawton ML, Emili A. Mass Spectrometry-Based Phosphoproteomics and Systems Biology: Approaches to Study T Lymphocyte Activation and Exhaustion. J Mol Biol 2021; 433:167318. [PMID: 34687714 DOI: 10.1016/j.jmb.2021.167318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/04/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
T lymphocytes respond to extracellular cues and recognize and clear foreign bodies. These functions are tightly regulated by receptor-mediated intracellular signal transduction pathways and phosphorylation cascades resulting in rewiring of transcription, cell adhesion, and metabolic pathways, which leads to changes in downstream effector functions including cytokine secretion and target-cell killing. Given that these pathways become dysregulated in chronic diseases such as cancer, auto-immunity, diabetes, and persistent infections, mapping T cell signaling dynamics in normal and pathological states is central to understanding and modulating immune system behavior. Despite recent advances, there remains much to be learned from the study of T cell signaling at a systems level. The application of global phospho-proteomic profiling technology has the potential to provide unprecedented insights into the molecular networks that govern T cell function. These include capturing the spatiotemporal dynamics of the T cell responses as an ensemble of interacting components, rather than a static view at a single point in time. In this review, we describe innovative experimental approaches to study signaling mechanisms in the TCR, co-stimulatory receptors, synthetic signaling molecules such as chimeric antigen receptors, inhibitory receptors, and T cell exhaustion. Technical advances in mass spectrometry and systems biology frameworks are emphasized as these are poised to identify currently unknown functional relationships and dependencies to create causal predictive models that expand from the traditional narrow reductionist lens of singular components in isolation.
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Affiliation(s)
- Matthew L Lawton
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA.
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8
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Herholt A, Sahoo VK, Popovic L, Wehr MC, Rossner MJ. Dissecting intercellular and intracellular signaling networks with barcoded genetic tools. Curr Opin Chem Biol 2021; 66:102091. [PMID: 34644670 DOI: 10.1016/j.cbpa.2021.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/25/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022]
Abstract
The power of next-generation sequencing has stimulated the development of many analysis techniques for transcriptomics and genomics. More recently, the concept of 'molecular barcoding' has broadened the spectrum of sequencing-based applications to dissect different aspects of intracellular and intercellular signaling. In these assay formats, barcode reporters replace standard reporter genes. The virtually infinitive number of expressed barcode sequences allows high levels of multiplexing, hence accelerating experimental progress. Furthermore, reporter barcodes are used to quantitatively monitor a variety of biological events in living cells which has already provided much insight into complex cellular signaling and will further increase our knowledge in the future.
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Affiliation(s)
- Alexander Herholt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Vivek K Sahoo
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Luksa Popovic
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Michael C Wehr
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Moritz J Rossner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany.
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9
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Letiagina AE, Omelina ES, Ivankin AV, Pindyurin AV. MPRAdecoder: Processing of the Raw MPRA Data With a priori Unknown Sequences of the Region of Interest and Associated Barcodes. Front Genet 2021; 12:618189. [PMID: 34046055 PMCID: PMC8148044 DOI: 10.3389/fgene.2021.618189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
Massively parallel reporter assays (MPRAs) enable high-throughput functional evaluation of numerous DNA regulatory elements and/or their mutant variants. The assays are based on the construction of reporter plasmid libraries containing two variable parts, a region of interest (ROI) and a barcode (BC), located outside and within the transcription unit, respectively. Importantly, each plasmid molecule in a such a highly diverse library is characterized by a unique BC-ROI association. The reporter constructs are delivered to target cells and expression of BCs at the transcript level is assayed by RT-PCR followed by next-generation sequencing (NGS). The obtained values are normalized to the abundance of BCs in the plasmid DNA sample. Altogether, this allows evaluating the regulatory potential of the associated ROI sequences. However, depending on the MPRA library construction design, the BC and ROI sequences as well as their associations can be a priori unknown. In such a case, the BC and ROI sequences, their possible mutant variants, and unambiguous BC-ROI associations have to be identified, whereas all uncertain cases have to be excluded from the analysis. Besides the preparation of additional "mapping" samples for NGS, this also requires specific bioinformatics tools. Here, we present a pipeline for processing raw MPRA data obtained by NGS for reporter construct libraries with a priori unknown sequences of BCs and ROIs. The pipeline robustly identifies unambiguous (so-called genuine) BCs and ROIs associated with them, calculates the normalized expression level for each BC and the averaged values for each ROI, and provides a graphical visualization of the processed data.
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Affiliation(s)
- Anna E Letiagina
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniya S Omelina
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anton V Ivankin
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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10
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Tang CC, Castro Andrade CD, O'Meara MJ, Yoon SH, Sato T, Brooks DJ, Bouxsein ML, Martins JDS, Wang J, Gray NS, Misof B, Roschger P, Blouin S, Klaushofer K, Velduis-Vlug A, Vegting Y, Rosen CJ, O'Connell D, Sundberg TB, Xavier RJ, Ung P, Schlessinger A, Kronenberg HM, Berdeaux R, Foretz M, Wein MN. Dual targeting of salt inducible kinases and CSF1R uncouples bone formation and bone resorption. eLife 2021; 10:67772. [PMID: 34160349 PMCID: PMC8238509 DOI: 10.7554/elife.67772] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/16/2021] [Indexed: 12/17/2022] Open
Abstract
Bone formation and resorption are typically coupled, such that the efficacy of anabolic osteoporosis treatments may be limited by bone destruction. The multi-kinase inhibitor YKL-05-099 potently inhibits salt inducible kinases (SIKs) and may represent a promising new class of bone anabolic agents. Here, we report that YKL-05-099 increases bone formation in hypogonadal female mice without increasing bone resorption. Postnatal mice with inducible, global deletion of SIK2 and SIK3 show increased bone mass, increased bone formation, and, distinct from the effects of YKL-05-099, increased bone resorption. No cell-intrinsic role of SIKs in osteoclasts was noted. In addition to blocking SIKs, YKL-05-099 also binds and inhibits CSF1R, the receptor for the osteoclastogenic cytokine M-CSF. Modeling reveals that YKL-05-099 binds to SIK2 and CSF1R in a similar manner. Dual targeting of SIK2/3 and CSF1R induces bone formation without concomitantly increasing bone resorption and thereby may overcome limitations of most current anabolic osteoporosis therapies.
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Affiliation(s)
- Cheng-Chia Tang
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | | | - Maureen J O'Meara
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Sung-Hee Yoon
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Tadatoshi Sato
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Daniel J Brooks
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States,Center for Advanced Orthopaedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
| | - Mary L Bouxsein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States,Center for Advanced Orthopaedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
| | | | - Jinhua Wang
- Dana Farber Cancer Institute, Harvard Medical SchoolBostonUnited States
| | - Nathanael S Gray
- Dana Farber Cancer Institute, Harvard Medical SchoolBostonUnited States
| | - Barbara Misof
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch HospitalViennaAustria
| | - Paul Roschger
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch HospitalViennaAustria
| | - Stephane Blouin
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch HospitalViennaAustria
| | - Klaus Klaushofer
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch HospitalViennaAustria
| | - Annegreet Velduis-Vlug
- Center for Bone Quality, Leiden University Medical CenterLeidenNetherlands,Center for Clinical and Translational Research, Maine Medical Center Research InstituteScarboroughCanada
| | - Yosta Vegting
- Department of Endocrinology and Metabolism, Academic Medical CenterAmsterdamNetherlands
| | - Clifford J Rosen
- Center for Clinical and Translational Research, Maine Medical Center Research InstituteScarboroughCanada
| | | | | | - Ramnik J Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States,Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
| | - Peter Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Henry M Kronenberg
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Rebecca Berdeaux
- Department of Integrative Biology and Pharmacology, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth)HoustonUnited States
| | - Marc Foretz
- Université de Paris, Institut Cochin, CNRSParisFrance
| | - Marc N Wein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States,Broad Institute of MIT and HarvardCambridgeUnited States,Harvard Stem Cell InstituteCambridgeUnited States
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11
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Zhang J, Zhu S, Ma N, Johnston LJ, Wu C, Ma X. Metabolites of microbiota response to tryptophan and intestinal mucosal immunity: A therapeutic target to control intestinal inflammation. Med Res Rev 2020; 41:1061-1088. [PMID: 33174230 DOI: 10.1002/med.21752] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022]
Abstract
In a complex, diverse intestinal environment, commensal microbiota metabolizes excessive dietary tryptophan to produce more bioactive metabolites connecting with kinds of diverse process, such as host physiological defense, homeostasis, excessive immune activation and the progression and outcome of different diseases, such as inflammatory bowel disease, irritable bowel syndrome and others. Although commensal microbiota includes bacteria, fungi, and protozoa and all that, they often have the similar metabolites in tryptophan metabolism process via same or different pathways. These metabolites can work as signal to activate the innate immunity of intestinal mucosa and induce the rapid inflammation response. They are critical in reconstruction of lumen homeostasis as well. This review aims to seek the potential function and mechanism of microbiota-derived tryptophan metabolites as targets to regulate and shape intestinal immune function, which mainly focused on two aspects. First, analyze the character of tryptophan metabolism in bacteria, fungi, and protozoa, and assess the functions of their metabolites (including indole and eight other derivatives, serotonin (5-HT) and d-tryptophan) on regulating the integrity of intestinal epithelium and the immunity of the intestinal mucosa. Second, focus on the mediator and pathway for their recognition, transfer and crosstalk between microbiota-derived tryptophan metabolites and intestinal mucosal immunity. Disruption of intestinal homeostasis has been described in different intestinal inflammatory diseases, available data suggest the remarkable potential of tryptophan-derived aryl hydrocarbon receptor agonists, indole derivatives on lumen equilibrium. These metabolites as preventive and therapeutic interventions have potential to promote proinflammatory or anti-inflammatory responses of the gut.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Animal Husbandry and Veterinary Department, Beijing Vocational College of Agriculture, Beijing, China
| | - Shengwei Zhu
- Institute of Botany, Key laboratory of plant molecular physiology, Chinese Academy of Sciences, Beijing, China
| | - Ning Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lee J Johnston
- West Central Research and Outreach Center, University of Minnesota, Morris, Minnesota, USA
| | - Chaodong Wu
- Department of Nutrition and Food Science, Texas A&M University, College Station, Texas, USA
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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12
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Xu W, Rush JS, Graham DB, Cao Z, Xavier RJ. USP15 Deubiquitinates CARD9 to Downregulate C-Type Lectin Receptor-Mediated Signaling. Immunohorizons 2020; 4:670-678. [PMID: 33093067 DOI: 10.4049/immunohorizons.2000036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/07/2020] [Indexed: 01/01/2023] Open
Abstract
Posttranslational modifications are efficient means to rapidly regulate protein function in response to a stimulus. Although ubiquitination events and the E3 ubiquitin ligases involved are increasingly characterized in many signaling pathways, their regulation by deubiquitinating enzymes remains less understood. The C-type lectin receptor (CLR) signaling adaptor CARD9 was previously reported to be activated via TRIM62-mediated ubiquitination. In this study, we identify the deubiquitinase USP15 as a novel regulator of CARD9, demonstrating that USP15 constitutively associates with CARD9 and removes TRIM62-deposited ubiquitin marks. Furthermore, USP15 knockdown and knockout specifically enhance CARD9-dependent CLR signaling in both mouse and human immune cells. Altogether, our study identifies a novel regulator of innate immune signaling and provides a blueprint for the identification of additional deubiquitinases that are likely to control these processes.
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Affiliation(s)
- Wenting Xu
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114.,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114.,Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China; and
| | - Jason S Rush
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Daniel B Graham
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114.,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114.,Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Zhifang Cao
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; .,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114.,Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; .,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114.,Broad Institute of MIT and Harvard, Cambridge, MA 02142
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13
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Jones EM, Lubock NB, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, Kosuri S. Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. eLife 2020; 9:54895. [PMID: 33084570 PMCID: PMC7707821 DOI: 10.7554/elife.54895] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/16/2020] [Indexed: 01/14/2023] Open
Abstract
The >800 human G protein–coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state- and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here, we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G protein signal transduction. We tested 7800 of 7828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β2AR) at four concentrations of the agonist isoproterenol. We identified residues specifically important for β2AR signaling, mutations in the human population that are potentially loss of function, and residues that modulate basal activity. Using unsupervised learning, we identify residues critical for signaling, including all major structural motifs and molecular interfaces. We also find a previously uncharacterized structural latch spanning the first two extracellular loops that is highly conserved across Class A GPCRs and is conformationally rigid in both the inactive and active states of the receptor. More broadly, by linking deep mutational scanning with engineered transcriptional reporters, we establish a generalizable method for exploring pharmacogenomics, structure and function across broad classes of drug receptors.
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Affiliation(s)
- Eric M Jones
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Nathan B Lubock
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - A J Venkatakrishnan
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Jeffrey Wang
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Alex M Tseng
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Daniel Cancilla
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Megan Satyadi
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ron O Dror
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
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14
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Aminoacyl-tRNA synthetase inhibition activates a pathway that branches from the canonical amino acid response in mammalian cells. Proc Natl Acad Sci U S A 2020; 117:8900-8911. [PMID: 32253314 DOI: 10.1073/pnas.1913788117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Signaling pathways that sense amino acid abundance are integral to tissue homeostasis and cellular defense. Our laboratory has previously shown that halofuginone (HF) inhibits the prolyl-tRNA synthetase catalytic activity of glutamyl-prolyl-tRNA synthetase (EPRS), thereby activating the amino acid response (AAR). We now show that HF treatment selectively inhibits inflammatory responses in diverse cell types and that these therapeutic benefits occur in cells that lack GCN2, the signature effector of the AAR. Depletion of arginine, histidine, or lysine from cultured fibroblast-like synoviocytes recapitulates key aspects of HF treatment, without utilizing GCN2 or mammalian target of rapamycin complex 1 pathway signaling. Like HF, the threonyl-tRNA synthetase inhibitor borrelidin suppresses the induction of tissue remodeling and inflammatory mediators in cytokine-stimulated fibroblast-like synoviocytes without GCN2, but both aminoacyl-tRNA synthetase (aaRS) inhibitors are sensitive to the removal of GCN1. GCN1, an upstream component of the AAR pathway, binds to ribosomes and is required for GCN2 activation. These observations indicate that aaRS inhibitors, like HF, can modulate inflammatory response without the AAR/GCN2 signaling cassette, and that GCN1 has a role that is distinct from its activation of GCN2. We propose that GCN1 participates in a previously unrecognized amino acid sensor pathway that branches from the canonical AAR.
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15
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Dries R, Stryjewska A, Coddens K, Okawa S, Notelaers T, Birkhoff J, Dekker M, Verfaillie CM, Del Sol A, Mulugeta E, Conidi A, Grosveld FG, Huylebroeck D. Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors. Stem Cells 2019; 38:202-217. [PMID: 31675135 PMCID: PMC7027912 DOI: 10.1002/stem.3111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/09/2019] [Indexed: 01/05/2023]
Abstract
Cooperative actions of extrinsic signals and cell‐intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone morphogenetic proteins [BMPs] and Activin/Nodal) exerts cell‐type specific and context‐dependent transcriptional changes, thereby steering cellular transitions throughout embryogenesis. Little is known about coordinated regulation and transcriptional interplay of the TGFβ system. To understand intrafamily transcriptional regulation as part of this system's actions during development, we selected 95 of its components and investigated their mRNA‐expression dynamics, gene‐gene interactions, and single‐cell expression heterogeneity in mouse embryonic stem cells transiting to neural progenitors. Interrogation at 24 hour intervals identified four types of temporal gene transcription profiles that capture all stages, that is, pluripotency, epiblast formation, and neural commitment. Then, between each stage we performed esiRNA‐based perturbation of each individual component and documented the effect on steady‐state mRNA levels of the remaining 94 components. This exposed an intricate system of multilevel regulation whereby the majority of gene‐gene interactions display a marked cell‐stage specific behavior. Furthermore, single‐cell RNA‐profiling at individual stages demonstrated the presence of detailed co‐expression modules and subpopulations showing stable co‐expression modules such as that of the core pluripotency genes at all stages. Our combinatorial experimental approach demonstrates how intrinsically complex transcriptional regulation within a given pathway is during cell fate/state transitions.
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Affiliation(s)
- Ruben Dries
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Agata Stryjewska
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Kathleen Coddens
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Tineke Notelaers
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Judith Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mike Dekker
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque, Foundation for Science, Bilbao, Spain
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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16
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Alpern D, Gardeux V, Russeil J, Mangeat B, Meireles-Filho ACA, Breysse R, Hacker D, Deplancke B. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 2019; 20:71. [PMID: 30999927 PMCID: PMC6474054 DOI: 10.1186/s13059-019-1671-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 03/07/2019] [Indexed: 01/10/2023] Open
Abstract
Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3' cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.
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Affiliation(s)
- Daniel Alpern
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Julie Russeil
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Bastien Mangeat
- Gene Expression Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Antonio C A Meireles-Filho
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Romane Breysse
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - David Hacker
- Protein Expression Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland.
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17
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Early JO, Menon D, Wyse CA, Cervantes-Silva MP, Zaslona Z, Carroll RG, Palsson-McDermott EM, Angiari S, Ryan DG, Corcoran SE, Timmons G, Geiger SS, Fitzpatrick DJ, O'Connell D, Xavier RJ, Hokamp K, O'Neill LAJ, Curtis AM. Circadian clock protein BMAL1 regulates IL-1β in macrophages via NRF2. Proc Natl Acad Sci U S A 2018; 115:E8460-E8468. [PMID: 30127006 PMCID: PMC6130388 DOI: 10.1073/pnas.1800431115] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A variety of innate immune responses and functions are dependent on time of day, and many inflammatory conditions are associated with dysfunctional molecular clocks within immune cells. However, the functional importance of these innate immune clocks has yet to be fully characterized. NRF2 plays a critical role in the innate immune system, limiting inflammation via reactive oxygen species (ROS) suppression and direct repression of the proinflammatory cytokines, IL-1β and IL-6. Here we reveal that the core molecular clock protein, BMAL1, controls the mRNA expression of Nrf2 via direct E-box binding to its promoter to regulate its activity. Deletion of Bmal1 decreased the response of NRF2 to LPS challenge, resulting in a blunted antioxidant response and reduced synthesis of glutathione. ROS accumulation was increased in Bmal1-/- macrophages, facilitating accumulation of the hypoxic response protein, HIF-1α. Increased ROS and HIF-1α levels, as well as decreased activity of NRF2 in cells lacking BMAL1, resulted in increased production of the proinflammatory cytokine, IL-1β. The excessive prooxidant and proinflammatory phenotype of Bmal1-/- macrophages was rescued by genetic and pharmacological activation of NRF2, or through addition of antioxidants. Our findings uncover a clear role for the molecular clock in regulating NRF2 in innate immune cells to control the inflammatory response. These findings provide insights into the pathology of inflammatory conditions, in which the molecular clock, oxidative stress, and IL-1β are known to play a role.
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Affiliation(s)
- James O Early
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
- Department of Molecular and Cellular Therapeutics, Tissue Engineering Regenerative Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Deepthi Menon
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Cathy A Wyse
- Department of Molecular and Cellular Therapeutics, Tissue Engineering Regenerative Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Mariana P Cervantes-Silva
- Department of Molecular and Cellular Therapeutics, Tissue Engineering Regenerative Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Zbigniew Zaslona
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Richard G Carroll
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
- Department of Molecular and Cellular Therapeutics, Tissue Engineering Regenerative Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Eva M Palsson-McDermott
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Stefano Angiari
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Dylan G Ryan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Sarah E Corcoran
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - George Timmons
- Department of Molecular and Cellular Therapeutics, Tissue Engineering Regenerative Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Sarah S Geiger
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Darren J Fitzpatrick
- Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Daniel O'Connell
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
| | - Ramnik J Xavier
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
| | - Karsten Hokamp
- Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Annie M Curtis
- Department of Molecular and Cellular Therapeutics, Tissue Engineering Regenerative Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland;
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18
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Hegde M, Strand C, Hanna RE, Doench JG. Uncoupling of sgRNAs from their associated barcodes during PCR amplification of combinatorial CRISPR screens. PLoS One 2018; 13:e0197547. [PMID: 29799876 PMCID: PMC5969736 DOI: 10.1371/journal.pone.0197547] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/03/2018] [Indexed: 12/26/2022] Open
Abstract
Many implementations of pooled screens in mammalian cells rely on linking an element of interest to a barcode, with the latter subsequently quantitated by next generation sequencing. However, substantial uncoupling between these paired elements during lentiviral production has been reported, especially as the distance between elements increases. We detail that PCR amplification is another major source of uncoupling, and becomes more pronounced with increased amounts of DNA template molecules and PCR cycles. To lessen uncoupling in systems that use paired elements for detection, we recommend minimizing the distance between elements, using low and equal template DNA inputs for plasmid and genomic DNA during PCR, and minimizing the number of PCR cycles. We also present a vector design for conducting combinatorial CRISPR screens that enables accurate barcode-based detection with a single short sequencing read and minimal uncoupling.
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Affiliation(s)
- Mudra Hegde
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christine Strand
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ruth E. Hanna
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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19
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Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ. Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. Cell Host Microbe 2018; 22:25-37.e6. [PMID: 28704649 DOI: 10.1016/j.chom.2017.06.007] [Citation(s) in RCA: 501] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/12/2017] [Accepted: 06/16/2017] [Indexed: 12/16/2022]
Abstract
Host factors in the intestine help select for bacteria that promote health. Certain commensals can utilize mucins as an energy source, thus promoting their colonization. However, health conditions such as inflammatory bowel disease (IBD) are associated with a reduced mucus layer, potentially leading to dysbiosis associated with this disease. We characterize the capability of commensal species to cleave and transport mucin-associated monosaccharides and identify several Clostridiales members that utilize intestinal mucins. One such mucin utilizer, Peptostreptococcus russellii, reduces susceptibility to epithelial injury in mice. Several Peptostreptococcus species contain a gene cluster enabling production of the tryptophan metabolite indoleacrylic acid (IA), which promotes intestinal epithelial barrier function and mitigates inflammatory responses. Furthermore, metagenomic analysis of human stool samples reveals that the genetic capability of microbes to utilize mucins and metabolize tryptophan is diminished in IBD patients. Our data suggest that stimulating IA production could promote anti-inflammatory responses and have therapeutic benefits.
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Affiliation(s)
- Marta Wlodarska
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Chengwei Luo
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Raivo Kolde
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eva d'Hennezel
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John W Annand
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Cortney E Heim
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Esther K Schmitt
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Abdifatah S Omar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth A Creasey
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ashley L Garner
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sina Mohammadi
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Sahar Abubucker
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Timothy D Arthur
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric A Franzosa
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Leon O Murphy
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Henry J Haiser
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey A Porter
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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20
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Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease. Proc Natl Acad Sci U S A 2017; 114:11392-11397. [PMID: 29073062 DOI: 10.1073/pnas.1705748114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Advances in human genetics have dramatically expanded our understanding of complex heritable diseases. Genome-wide association studies have identified an allelic series of CARD9 variants associated with increased risk of or protection from inflammatory bowel disease (IBD). The predisposing variant of CARD9 is associated with increased NF-κB-mediated cytokine production. Conversely, the protective variant lacks a functional C-terminal domain and is unable to recruit the E3 ubiquitin ligase TRIM62. Here, we used biochemical insights into CARD9 variant proteins to create a blueprint for IBD therapeutics and recapitulated the mechanism of the CARD9 protective variant using small molecules. We developed a multiplexed bead-based technology to screen compounds for disruption of the CARD9-TRIM62 interaction. We identified compounds that directly and selectively bind CARD9, disrupt TRIM62 recruitment, inhibit TRIM62-mediated ubiquitinylation of CARD9, and demonstrate cellular activity and selectivity in CARD9-dependent pathways. Taken together, small molecules targeting CARD9 illustrate a path toward improved IBD therapeutics.
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21
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Johannessen L, Sundberg TB, O'Connell DJ, Kolde R, Berstler J, Billings KJ, Khor B, Seashore-Ludlow B, Fassl A, Russell CN, Latorre IJ, Jiang B, Graham DB, Perez JR, Sicinski P, Phillips AJ, Schreiber SL, Gray NS, Shamji AF, Xavier RJ. Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells. Nat Chem Biol 2017; 13:1102-1108. [PMID: 28805801 DOI: 10.1038/nchembio.2458] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/17/2017] [Indexed: 12/27/2022]
Abstract
Enhancing production of the anti-inflammatory cytokine interleukin-10 (IL-10) is a promising strategy to suppress pathogenic inflammation. To identify new mechanisms regulating IL-10 production, we conducted a phenotypic screen for small molecules that enhance IL-10 secretion from activated dendritic cells. Mechanism-of-action studies using a prioritized hit from the screen, BRD6989, identified the Mediator-associated kinase CDK8, and its paralog CDK19, as negative regulators of IL-10 production during innate immune activation. The ability of BRD6989 to upregulate IL-10 is recapitulated by multiple, structurally differentiated CDK8 and CDK19 inhibitors and requires an intact cyclin C-CDK8 complex. Using a highly parallel pathway reporter assay, we identified a role for enhanced AP-1 activity in IL-10 potentiation following CDK8 and CDK19 inhibition, an effect associated with reduced phosphorylation of a negative regulatory site on c-Jun. These findings identify a function for CDK8 and CDK19 in regulating innate immune activation and suggest that these kinases may warrant consideration as therapeutic targets for inflammatory disorders.
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Affiliation(s)
- Liv Johannessen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Thomas B Sundberg
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Daniel J O'Connell
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Raivo Kolde
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James Berstler
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Katelyn J Billings
- Department of Chemistry, Yale University, New Haven, Connecticut, USA.,Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Bernard Khor
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Caitlin N Russell
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Isabel J Latorre
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Baishan Jiang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniel B Graham
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jose R Perez
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew J Phillips
- Center for the Development of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Stuart L Schreiber
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alykhan F Shamji
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
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22
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Bundled reporter gene assays. Nat Methods 2016. [DOI: 10.1038/nmeth.3906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Chaudhari HG, Staller MV. Scaling-Up Signaling Pathway Analysis. Cell Syst 2016; 2:295-6. [PMID: 27228346 DOI: 10.1016/j.cels.2016.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A new technique for simultaneously measuring the activities of many signaling pathways unravels interconnected signaling networks.
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Affiliation(s)
- Hemangi G Chaudhari
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Max V Staller
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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